bluuebunny/crossref_metadata_2025 huggingface dataset:
Resolving Water Conflicts in Mining Areas of Ghana Through Public Participation A Communication Perspective
Authors: Singh Nandita , Koku J.E. , Balfors Berit
Published: September 2008

Mining as a sector is vital to a country's economic growth but the impact of the activities on environment can be an important cause of concern. In Wassa West district of Ghana, mining as an industry has been promoted in the recent past, but with significant impact on environmental aspects, especially water, leading to conflicts between the local communities and the mining companies. The practical theory of ‘Trinity of Voice’ (TOV) has been proposed for understanding the community-related intricacies underlying multi-stakeholder decision-making processes and proposing a futuristic course of action for effective public participation in the same. This article attempts to understand the causes underlying the mining-related water conflicts in Ghana using the TOV theory. Using this theory, the article proposes a practical framework for enhanced effective participation of members from local host communities that in turn can enable resolving the existing conflicts and preventing the same in future.
ALK-Positive Anaplastic Large Cell Lymphoma in a Patient With Chronic Lymphocytic Leukemia
Authors: Ting Liu  , Mai He  , Carlson Diane L. , Hedvat Cyrus , Teruya-Feldstein Julie
Published: September 2008

This article reports the case of a 59-year-old patient with an 8-year history of chronic lymphocytic leukemia (CLL), prostate carcinoma, and squamous cell carcinoma who developed an ALK-positive anaplastic large cell lymphoma (ALCL). Lymph node and bone marrow biopsies showed 2 distinct morphologic populations: ( a) the CLL component showing a diffuse monomorphous infiltrate of small lymphocytes with the typical immunophenotype showing positive CD20, CD5, CD23, and κ light chain restriction and ( b) the ALCL component showing large anaplastic pleomorphic cells positive for CD30, CD45, ALK, CD45Ro, CD4, and vimentin. Polymerase chain reaction performed on the lymph node for immunoglobulin heavy chain and T-cell receptor γ and β showed gene rearrangements after macrodissection of morphologically distinct populations, indicating confirmed genetically distinct populations. Despite intensive chemotherapy, the patient died. This case represents the rare occurrence of an ALK-positive ALCL developing in a patient with CLL.
Studies on Shelf Life of ``Lateblue'' Highbush Blueberries
Authors: Chiabrando V. , Giacalone G.
Published: September 2008

There is a considerable scope to mantain the quality and extend shelf-life of perishable and soft fruits such as strawberries, raspberries, and blueberries by developing and evolving packaging strategies. In this work a study on the packaging of blueberries in plastic film for short-to-medium term storage was carried out. Blueberries cv Lateblue were hand-picked from a commercial plantation and packaged in different barrier films. Four commercially available films were used as packaging materials: two micro-perforated (0.3 mm and 1 mm in diameter), a non-perforated and a macro-perforated (6 mm in diameter). All the samples were stored at 4 °C for 15 days. The benefits of small packages (consumer packs), were evaluated through chemical (total soluble solid content (TSS), titratable acidity and pH), visual (color intensity, surface shine, firmness by touch, intensity of odor, and overall appearance) and sensory (crispness, sweet taste, acidic taste, total flavor, and overall appreciation) evaluation. The berries packaged in micro-perforated (1 mm in diameter) and non-perforated film maintained better quality attributes (high TSS content and titratble acidity) throughout the cold storage. The non-perforated film maintained also berry crispness and a good intensity of flavor. Non and micro-perforated packaging films gave the best results and appeared to be a feasible practice in order to ensure good quality during medium-term storage of blueberries. Moreover nonperforated film treatment was the only treatment that reduced in little or no significant pathogen-induced decay during cold storage.
Quality and Volatile Emission Changes of `Mondial Gala' Apples during On-tree Maturation and Postharvest Storage in Air or Controlled Atmosphere
Authors: Graell J. , Lopez M.L. , Fuentes T. , Echeverría G. , Lara I.
Published: September 2008

Starch index (SI), color, firmness, titratable acidity (TA), soluble solids content (SSC), ethylene production, and aroma volatile emission were recorded weekly during on-tree maturation of `Mondial Gala' apples. Fruit were harvested on commercial date and held for 3.5 and 6.5 months in regular atmosphere (RA) or in three controlled atmospheres (CA) (2% O2 :2% CO2, 1% O2 : 1 % CO2 and 1% O2 :3% CO2). After each storage period plus 0 and 7 days at 20 °C, color, firmness, TA, SSC, aroma volatile emission, acetaldehyde and ethanol concentrations, and sensory acceptability were evaluated. At orchard, changes in SI, SSC, background color, and aroma volatile emission were almost concomitant or slightly previous to the increase in ethylene production. During storage, all three CA conditions, regardless of storage period, led to better preservation of standard quality. CA-stored fruit also received higher acceptability scores, although aroma volatile emission was decreased in response to these storage conditions. At the end of long storage (plus shelf life period), fruit stored in 1 :1 atmosphere showed a good retention of firmness and TA in comparison to the rest of CA-fruit. Fruit stored under all considered CA conditions showed similar aroma volatile emission after 3.5 or 6.5 months of storage. Storage period had no apparent influence on the aroma volatile emission of CA-stored apples, with the exception of fruit stored in 2:2 atmosphere immediately upon removal from storage. No significant differences in sensory acceptability were found either for fruit stored under different CA conditions during 3.5 months immediately after transfer to 20 °C. In contrast, fruit stored in either 1 : 1 or 2: 2 atmospheres during 6.5 months were better accepted by consumers than those stored in 1 : 3 atmosphere upon removal from cold storage. However, these differences disappeared after 7 days of shelf-life at 20 °C.
Pork Fat Composition of Male Hybrids from Lithuanian Indigenous Wattle Pigs and Wild Boar Intercross
Authors: Razmaitė V. , Kerzienė S. , Šiukščius A.
Published: September 2008

The aim of this study was to compare the fatty acid composition of lipids from hybrids of Lithuanian indigenous wattle pigs × wild boar (WB) intercross. A total of 39 entire and castrated males from 1/4 and 1/2 WB genotype were included into the study. The fatness of carcasses from ½ WB genotype ( p<0.01) and castrated males ( p<0.01) was higher than that from 1/4 WB genotype and entire boars. 1/2 WB hybrids had higher content of C17 : 0 ( p<0.01), C17 : 1 and C18 : 3n - 3 fatty acids ( p<0.05) and higher PUFA:SFA ratio ( p<0.05) but lower content of C16:0 fatty acid of intramuscular fat than 1/4 WB hybrids. In subcutaneous tissue 1/2 WB hybrids had higher proportion of C17:0 ( p<0.001), C17:1 ( p<0.05), C18 : 3n - 3 ( p<0.05) but lower proportion of C16 : 1 ( p<0.05). Entire boars had lower content of C16:0 ( p<0.01), C18:1 ( p<0.05), C20 :1 ( p<0.05), and the total MUFA ( p<0.05) but higher content of C18 : 2n - 6 ( p<0.05) and the total PUFA ( p<0.01), PUFA:SFA ratio ( p<0.01) than castrates. Significant Pearson's correlations of the intramuscular fat content from both genotypes with MUFA were positive, but those with PUFA and PUFA : SFA ratio were negative. High positive correlation of IMF with SFA was found only in 1/4 WB genotype. PUFA and PUFA: SFA ratio also showed negative correlation with backfat thickness in both genotypes. The correlation coefficients within entire boar and castrate groups were lower than within genetic groups.
Patterns of continuity and disruption
Authors: Kalmus Veronika , Vihalemm Triin
Published: September 2008

This article analyzes inter-generational continuity and cultural reproduction in three transitional countries: Estonia, Latvia and the Czech Republic. We compare the levels of internalization of factor structures of self-identification and values among young people and older generations. We focus specifically on a comparison of young people representing the two main ethno-linguistic groups in Estonia and Latvia: ethnic Estonians, or Latvians, and Russians. The data are derived from representative population surveys carried out in the three countries in November 2005 and spring 2006. In general, we observed greater inter-generational continuity in the Czech Republic, compared with Estonia and Latvia. Cultural reproduction among the ethnic minorities in both Baltic countries has been most vulnerable to transitional changes: Russian youngsters differ from their parents to a greater extent than do young Estonians and Latvians from theirs.
Researching in Partnership
Authors: Tew Jerry
Published: September 2008

Involving service users as full partners in qualitative research requires a reappraisal of many aspects of methodology and practice. This article reflects on a research project which explored the impact upon mental health service users of having been compulsorily admitted to hospital. All interviews were conducted by service user researchers who also played a key role in devising research questions and evaluating results. Building on theoretical understandings of standpoint knowledge and power relations, the article reflects on how well partnership was achieved, and on the contribution made by service users at each stage of the research. It concludes that, while the process of collaboration was generally positive for both service user and academic researchers, imbalances of power could skew relationships and impact adversely on the potential value of the research. It is hoped that this will contribute to current debates as to how best to take forward service user involvement in social work and mental health research.
Adventures in Re-searching the Features of Social Work Supervision in Hong Kong
Authors: Tsui Ming-sum
Published: September 2008

The study examines the features and process of social work supervision in Hong Kong. A successful client outcome is the main objective, but supervisors perceive supervision as a rational and systematic process, whereas supervisees expect emotional support and teamwork. The supervisory relationship is both personal and professional. Tension is reduced by the traditional Chinese cultural values of reciprocity: qing, yuan, and 'face'. The strategy of using supervisory authority is 'consensus by consultation and consent' — which reduces conflict and gains acceptance. The journey of this study charts the interactions among my personal, professional, and academic identities. In order to conduct the research, I have to be more 'academic'. However, without my professional experience, I could not interpret the information in a meaningful manner. When I reviewed the data on the effects of traditional Chinese values, my personal self was reminded that I am also Chinese and that I share these beliefs.
Working Hard to Resist a 'Bad Mother' Label
Authors: Kielty Sandra
Published: September 2008

Drawing upon interview data from a study investigating the experiences of 20 non-resident mothers in the UK, this article explores the narratives of two participants, one who volunteered to become the non-resident parent and one who lost residence against her will. The central focus of the article is concerned with participants' discursive management of their atypical situation. Specific attention is paid to the different ways in which these women presented their situations and how they positioned themselves in relation to dominant cultural scripts surrounding motherhood. It is argued that non-resident mothers are at risk of isolation as a consequence of social stigma and this may pose barriers to their taking a full and active part in the lives of their children. Suggestions are made whereby social workers might play a useful role in facilitating and supporting non-resident mothers within their locality. The issues raised have relevance for other western jurisdictions operating within a framework of gender-neutral family policy because, the number of non-resident mothers can be expected to rise in line with high family breakdown and divorce rates.
Natural Orifice Management of Anastomotic Leaks After Minimally Invasive Esophagogastrectomy
Authors: Nguyen Ninh T. , Mailey Brian A. , Hinojosa Marcelo W. , Ken Chang
Published: September 2008

A leak after an esophagectomy can lead to significant morbidity and mortality. The treatment options for postoperative leaks include reoperation with pleural drainage and placement of T-tube drainage catheter to control the gastrointestinal leak or complete gastrointestinal diversion, depending on the extent of the leak and tissue viability of the gastric conduit. Both these options require an invasive reoperation. In selected cases, endoscopic deployment of a covered esophageal stent may be an effective minimally invasive option in the management of an esophageal leak. This report describes the indications and techniques for management of an esophageal leak using the natural orifice for drainage of a mediastinal abscess and deployment of an esophageal stent.
'Restricting choices and limiting independence': social and economic impact of multiple sclerosis upon households by level of disability
Authors: Green G. , Todd J.
Published: September 2008

Objective: To examine the relationship between the social and economic impact of multiple sclerosis (MS) and levels of MS-related disability upon households in the following domains: household composition, housing modification, employment, standard of living, children, intimate and close relationships, and social life.

Methods: A national sample of people with MS (pwMS) ( n = 920), consisting of members of the MS Society and those accessing the MS Society website, completed a cross-sectional survey to generate quantitative and qualitative data.

Results: Over three-quarters of the sample reported that MS had impacted on at least some areas of daily life. The reported impact increased significantly in a linear fashion in each domain with increasing disability, as measured by an activities of daily living index, although there was a discernible 'levelling off' in terms of impact in some domains among those at the higher levels of disability and dependency. Analysis of the qualitative data suggests that this impact can be conceptualized as a gradual process of 'restricting choices' and 'limiting independence' for both pwMS and their households.

Discussion: MS restricts social and economic opportunities for pwMS and those who they live with. These findings extend the literature to households to illustrate the impact of MS not only on pwMS but also on their partners, children and other family members.
'Normal, but...': living with type 2 diabetes in Bangkok, Thailand
Authors: Naemiratch Bhensri , Manderson Lenore
Published: September 2008

Objectives: To explore how people in Bangkok, Thailand make sense of the challenges associated with living with type 2 diabetes.

Methods: Ethnographic research was conducted for a period of 18 months, and included participant observation, documentary analysis, and interviews with health providers, family members and 33 adults with type 2 diabetes. Interviews and analyses were iterative, with longitudinal data drawing attention to shifts in meaning in relation to identity construction and the relevance of this to disease management.

Results: People drew on cultural notions of social harmony and bodily imperfection, and ideas of the nature of diabetes as 'invisible' while blood sugar levels were controlled, to reconstruct their identity once diagnosed with diabetes. By maintaining their status as 'normal, but...', people could minimize disruptions in their everyday lives and in relation to others, due to both practices of management and their social effects. Their use of a qualification to their health status ( but) explicitly acknowledged certain behavioural and dietary modifications that were necessary to manage their diabetes, but also emphasized their role in self-management.

Discussion: The diabetes qualification ('normal, but...') acted as a bridge between health and illness, enabling people to separate their physical health status, perceived as being particularly flawed by having diabetes, from their 'normal' social self. The sustained idea of the normality of the embodied and socially embedded self implied that the disease was under control, ensuring its minimal intrusion into social relationships and practical living.
Gastro-oesophageal acid-related disease, co-morbidity and medical care cost
Authors: Jayadevappa Ravishankar , Chhatre Sumedha , Weiner Mark
Published: September 2008

Objective: To analyse the incremental medical care cost of gastro-oesophageal acid-related disease (GERD), and its interactive effects with other diagnoses.

Methods: A retrospective cohort study was conducted. Six hundred GERD patients were randomly selected and 600 non-GERD patients were selected, matched by age, gender, prescription pharmaceutical benefits and insurance status. Information on demographics, direct medical care cost (DMC) (inpatient, ambulatory and pharmaceuticals) and health service utilization was obtained from a large, not-for-profit managed-care organization across 3 years (1996—1998). DMCs were compared between GERD and non-GERD groups using the bootstrap method. Random coefficient log linear regression models were used to analyse incremental cost and assess its association with other diagnoses.

Results: The mean annual DMC for the GERD group was $4906, as compared to $2054 for the non-GERD group. The increase in the DMC in the GERD group was attributable to increased co-morbidity. Age and gender had no effect on total cost for the GERD population. Among costs of services, the GERD group had a 2.00-fold higher cost associated with outpatient services, a 1.70-fold higher cost associated with inpatient services, and a 2.70-fold higher cost associated with pharmacy.

Conclusions: GERD is a chronic disease often associated with other diagnoses that significantly affect total DMC. Although the direct cost of treating GERD is low, patients with GERD had significantly higher total medical care cost than those without GERD. The addition of one more disease to a person's existing group of diseases has an important long-term health cost impact.
Incomplete restoration of Mpl expression in the mpl−/− mouse produces partial correction of the stem cell–repopulating defect and paradoxical thrombocytosis
Authors: Lannutti Brian J. , Epp Angela , Roy Jacqueline , Chen Junmei , Josephson Neil C.
Published: September 2008

Expression of Mpl is restricted to hematopoietic cells in the megakaryocyte lineage and to undifferentiated progenitors, where it initiates critical cell survival and proliferation signals after stimulation by its ligand, thrombopoietin (TPO). As a result, a deficiency in Mpl function in patients with congenital amegakaryocytic thrombocytopenia (CAMT) and in mpl−/− mice produces profound thrombocytopenia and a severe stem cell–repopulating defect. Gene therapy has the potential to correct the hematopoietic defects of CAMT by ectopic gene expression that restores normal Mpl receptor activity. We rescued the mpl−/− mouse with a transgenic vector expressing mpl from the promoter elements of the 2-kb region of DNA just proximal to the natural gene start site. Transgene rescued mice exhibit thrombocytosis but only partial correction of the stem cell defect. Furthermore, they show very low-level expression of Mpl on platelets and megakaryocytes, and the transgene-rescued megakaryocytes exhibit diminished TPO-dependent kinase phosphorylation and reduced platelet production in bone marrow chimeras. Thrombocytosis is an unexpected consequence of reduced Mpl expression and activity. However, impaired TPO homeostasis in the transgene-rescued mice produces elevated plasma TPO levels, which serves as an unchecked stimulus to drive the observed excessive megakaryocytopoiesis.
Embryonic desiccation resistance in Aedes aegypti: presumptive role of the chitinized Serosal Cuticle
Authors: Rezende Gustavo Lazzaro , Martins Ademir Jesus , Gentile Carla , Farnesi Luana Cristina , Pelajo-Machado Marcelo , Peixoto Alexandre Afrânio , Valle Denise
Published: September 2008

Background

One of the major problems concerning dengue transmission is that embryos of its main vector, the mosquitoAedes aegypti, resist desiccation, surviving several months under dry conditions. The serosal cuticle (SC) contributes to mosquito egg desiccation resistance, but the kinetics of SC secretion during embryogenesis is unknown. It has been argued that mosquito SC contains chitin as one of its components, however conclusive evidence is still missing.

Results

We observed an abrupt acquisition of desiccation resistance duringAe. aegyptiembryogenesis associated with serosal cuticle secretion, occurring at complete germ band extension, between 11 and 13 hours after egglaying. After SC formation embryos are viable on dry for at least several days. The presence of chitin as one of the SC constituents was confirmed through Calcofluor and WGA labeling and chitin quantitation. TheAe. aegyptiChitin Synthase A gene (AaCHS1) possesses two alternatively spliced variants,AaCHS1aandAaCHS1b, differentially expressed duringAe. aegyptiembryonic development. It was verified that at the moment of serosal cuticle formation,AaCHS1ais the sole variant specifically expressed.

Conclusion

In addition to the peritrophic matrix and exoskeleton, these findings confirm chitin is also present in the mosquito serosal cuticle. They also point to the role of the chitinized SC in the desiccation resistance ofAe. aegyptieggs.AaCHS1aexpression would be responsible for SC chitin synthesis. With this embryological approach we expect to shed new light regarding this important physiological process related to theAe. aegyptilife cycle.
Microarray analysis of toxicogenomic effects of Ortho-phenylphenol in Staphylococcus aureus
Authors: Jang Hyeung-Jin , Nde Chantal , Toghrol Freshteh , Bentley William E
Published: September 2008

Background

Staphylococcus aureus (S. aureus), is responsible for many infectious diseases, ranging from benign skin infections to life-threatening endocarditis and toxic shock syndrome. Ortho-phenylphenol (OPP) is an antimicrobial agent and an active ingredient of EPA-registered disinfectants with wide human exposure in various agricultural, hospital and veterinary disinfectant products. Despite many uses, an understanding of a cellular response to OPP and it's mechanism of action, targeted genes, and the connectivity between targeted genes and the rest of cell metabolism remains obscure.

Results

Herein, we performed a genome-wide transcriptome analysis of the cellular responses of S. aureus when exposed to 0.82 mM of OPP for 20 and 60 min. Our data indicated that OPP downregulated the biosynthesis of many amino acids, which are required for protein synthesis. In particular, the genes encoding the enzymes of the diaminopimelate (DAP) pathway which results in lysine biosynthesis were significantly downregualted. Intriguingly, we revealed that the transcription of genes encoding ribosomal proteins was upregulated by OPP and at the same time, the genes encoding iron acquisition and transport were downregulated. The genes encoding virulence factors were upregulated and genes encoding phospholipids were downregulated upon 20 min exposure to OPP.

Conclusion

By using microarray analysis that enables us to simultaneously and globally examine the complete transcriptome during cellular responses, we have revealed novel information regarding the mode of action of OPP on Staphylococcus: OPP inhibits anabolism of many amino acids and highly downregulates the genes that encode the enzymes involved in the DAP pathway. Lysine and DAP are essential for building up the peptidoglycan cell wall. It was concluded that the mode of action of OPP is similar to the mechanism of action of some antibiotics. The discovery of this phenomenon provides useful information that will benefit further antimicrobial research on S. aureus.
Novel genome polymorphisms in BCG vaccine strains and impact on efficacy
Authors: Leung Andrea S , Tran Vanessa , Wu Zuowei , Yu Xuping , Alexander David C , Gao George Fu , Zhu Baoli , Liu Jun
Published: September 2008

Bacille Calmette-Guérin (BCG) is an attenuated strain ofMycobacterium boviscurrently used as a vaccine against tuberculosis. Global distribution and propagation of BCG has contributed to thein vitroevolution of the vaccine strain and is thought to partially account for the different outcomes of BCG vaccine trials. Previous efforts by several molecular techniques effectively identified large sequence polymorphisms among BCG daughter strains, but lacked the resolution to identify smaller changes. In this study, we have used a NimbleGen tiling array for whole genome comparison of 13 BCG strains. Using this approach, in tandem with DNA resequencing, we have identified six novel large sequence polymorphisms including four deletions and two duplications in specific BCG strains. Moreover, we have uncovered various polymorphisms in thephoP-phoRlocus. Importantly, these polymorphisms affect genes encoding established virulence factors including cell wall complex lipids, ESX secretion systems, and the PhoP-PhoR two-component system. Our study demonstrates that major virulence factors are different among BCG strains, which provide molecular mechanisms for important vaccine phenotypes including adverse effect profile, tuberculin reactivity and protective efficacy. These findings have important implications for the development of a new generation of vaccines.
BOV – a web-based BLAST output visualization tool
Authors: Gollapudi Rajesh , Revanna Kashi Vishwanath , Hemmerich Chris , Schaack Sarah , Dong Qunfeng
Published: September 2008

Background

The BLAST program is one of the most widely used sequence similarity search tools for genomic research, even by those biologists lacking extensive bioinformatics training. As the availability of sequence data increases, more researchers are downloading the BLAST program for local installation and performing larger and more complex tasks, including batch queries. In order to manage and interpret the results of batch queries, a host of software packages have been developed to assist with data management and post-processing. Among these programs, there is almost a complete lack of visualization tools to provide graphic representation of complex BLAST pair-wise alignments. We have developed a web-based program, B LAST O utput V isualization Tool (BOV), that allows users to interactively visualize the matching regions of query and database hit sequences, thereby allowing the user to quickly and easily dissect complex matching patterns.

Results

Users can upload the standard BLAST output in pair-wise alignment format as input to the web server (including batch queries generated installing and running the stand-alone BLAST program on a local server). The program extracts the alignment coordinates of matching regions between the query and the corresponding database hit sequence. The coordinates are used to plot each matching region as colored lines or trapezoids. Using the straightforward control panels throughout the web site, each plotted matching region can be easily explored in detail by, for example, highlighting the region of interest or examining the raw pair-wise sequence alignment. Tutorials are provided at the website to guide users step-by-step through the functional features of BOV.

Conclusion

BOV provides a user-friendly web interface to visualize the standard BLAST output for investigating wide-ranging genomic problems, including single query and batch query datasets. In particular, this software is valuable to users interested in identifying regions of co-linearity, duplication, translocation, and inversion among sequences. A web server hosting BOV is accessible via http://bioportal.cgb.indiana.edu/cgi-bin/BOV/index.cgi and the software is freely available for local installations.
Transcriptomic analysis of the exit from dormancy of Aspergillus fumigatus conidia
Authors: Lamarre Claude , Sokol Sergueï , Debeaupuis Jean-Paul , Henry Christine , Lacroix Céline , Glaser Philippe , Coppée Jean-Yves , François Jean-Marie , Latgé Jean-Paul
Published: September 2008

Background

Establishment of aspergillosis is depending upon the exit from dormancy and germination of the conidia of Aspergillus fumigatus in the lung. To gain an understanding of the molecular mechanisms underlying the early steps of conidial germination, we undertook a transcriptomic analysis using macroarrays constructed with PCR fragments from > 3,000 genes (around one third of the annotated A. fumigatus genome).

Results

Major results of this analysis are the following: (i) conidia stored pre-packaged mRNAs transcripts (27% of genes have transcripts in the resting conidia; (ii) incubation at 37°C in a nutritive medium induced up- and down-regulation of genes: 19% of the total number of genes deposited on the array were up-regulated whereas 22% of the genes with pre-packaged mRNA in the resting conidia were down-regulated; (iii) most modifications were seen during the first 30 min of germination whereas very little modification of gene expression occurred during the following hour; (iv) one-year old conidia and one-week old conidia behaved similarly at transcriptional level.

Conclusion

Transcriptomic data indicate that the exit from dormancy is associated with a shift from a fermentative metabolism to a respiratory metabolism as well as a trend toward immediate protein synthesis.
A combination of LongSAGE with Solexa sequencing is well suited to explore the depth and the complexity of transcriptome
Authors: Hanriot Lucie , Keime Céline , Gay Nadine , Faure Claudine , Dossat Carole , Wincker Patrick , Scoté-Blachon Céline , Peyron Christelle , Gandrillon Olivier
Published: September 2008

Background

"Open" transcriptome analysis methods allow to study gene expression without a priori knowledge of the transcript sequences. As of now, SAGE (Serial Analysis of Gene Expression), LongSAGE and MPSS (Massively Parallel Signature Sequencing) are the mostly used methods for "open" transcriptome analysis. Both LongSAGE and MPSS rely on the isolation of 21 pb tag sequences from each transcript. In contrast to LongSAGE, the high throughput sequencing method used in MPSS enables the rapid sequencing of very large libraries containing several millions of tags, allowing deep transcriptome analysis. However, a bias in the complexity of the transcriptome representation obtained by MPSS was recently uncovered.

Results

In order to make a deep analysis of mouse hypothalamus transcriptome avoiding the limitation introduced by MPSS, we combined LongSAGE with the Solexa sequencing technology and obtained a library of more than 11 millions of tags. We then compared it to a LongSAGE library of mouse hypothalamus sequenced with the Sanger method.

Conclusion

We found that Solexa sequencing technology combined with LongSAGE is perfectly suited for deep transcriptome analysis. In contrast to MPSS, it gives a complex representation of transcriptome as reliable as a LongSAGE library sequenced by the Sanger method.
Batch Blast Extractor: an automated blastx parser application
Authors: Pirooznia Mehdi , Perkins Edward J , Deng Youping
Published: September 2008

Motivation

BLAST programs are very efficient in finding similarities for sequences. However for large datasets such as ESTs, manual extraction of the information from the batch BLAST output is needed. This can be time consuming, insufficient, and inaccurate. Therefore implementation of a parser application would be extremely useful in extracting information from BLAST outputs.

Results

We have developed a java application, Batch Blast Extractor, with a user friendly graphical interface to extract information from BLAST output. The application generates a tab delimited text file that can be easily imported into any statistical package such as Excel or SPSS for further analysis. For each BLAST hit, the program obtains and saves the essential features from the BLAST output file that would allow further analysis. The program was written in Java and therefore is OS independent. It works on both Windows and Linux OS with java 1.4 and higher. It is freely available from: http://mcbc.usm.edu/BatchBlastExtractor/
ILOOP – a web application for two-channel microarray interwoven loop design
Authors: Pirooznia Mehdi , Gong Ping , Yang Jack Y , Yang Mary Qu , Perkins Edward J , Deng Youping
Published: September 2008

Microarray technology is widely applied to address complex scientific questions. However, there remain fundamental issues on how to design experiments to ensure that the resulting data enables robust statistical analysis. Interwoven loop design has several advantages over other designs. However it suffers in the complexity of design. We have implemented an online web application which allows users to find optimal loop designs for two-color microarray experiments. Given a number of conditions (such as treatments or time points) and replicates, the application will find the best possible design of the experiment and output experimental parameters. It is freely available fromhttp://mcbc.usm.edu/iloop.
Approaches to reduce false positives and false negatives in the analysis of microarray data: applications in type 1 diabetes research
Authors: Wu Jian , Lenchik Nataliya I , Gerling Ivan C
Published: September 2008

Background

As studies of molecular biology system attempt to achieve a comprehensive understanding of a particular system, Type 1 errors may be a significant problem. However, few investigators are inclined to accept the increase in Type 2 errors (false positives) that may result when less stringent statistical cut-off values are used. To address this dilemma, we developed an analysis strategy that used a stringent statistical analysis to create a list of differentially expressed genes that served as "bait" to "fish out" other genes with similar patterns of expression.

Results

Comparing two strains of mice (NOD and C57Bl/6), we identified 93 genes with statistically significant differences in their patterns of expression. Hierarchical clustering identified an additional 39 genes with similar patterns of expression differences between the two strains. Pathway analysis was then employed: 1) identify the central genes and define biological processes that may be regulated by the genes identified, and 2) identify genes on the lists that could not be connected to each other in pathways (potential false positives). For networks created by both gene lists, the most connected (central) genes were interferon gamma (IFN-γ) and tumor necrosis factor alpha (TNF-α). These two cytokines are relevant to the biological differences between the two strains of mice. Furthermore, the network created by the list of 39 genes also suggested other biological differences between the strains.

Conclusion

Taken together, these data demonstrate how stringent statistical analysis, combined with hierarchical clustering and pathway analysis may offer deeper insight into the biological processes reflected from a set of expression array data. This approach allows us to 'recapture" false negative genes that otherwise would have been missed by the statistical analysis.
Use artificial neural network to align biological ontologies
Authors: Huang Jingshan , Dang Jiangbo , Huhns Michael N , Zheng W Jim
Published: September 2008

Background

Being formal, declarative knowledge representation models, ontologies help to address the problem of imprecise terminologies in biological and biomedical research. However, ontologies constructed under the auspices of the Open Biomedical Ontologies (OBO) group have exhibited a great deal of variety, because different parties can design ontologies according to their own conceptual views of the world. It is therefore becoming critical to align ontologies from different parties. During automated/semi-automated alignment across biological ontologies, different semantic aspects, i.e., concept name, concept properties, and concept relationships, contribute in different degrees to alignment results. Therefore, a vector of weights must be assigned to these semantic aspects. It is not trivial to determine what those weights should be, and current methodologies depend a lot on human heuristics.

Results

In this paper, we take an artificial neural network approach to learn and adjust these weights, and thereby support a new ontology alignment algorithm, customized for biological ontologies, with the purpose of avoiding some disadvantages in both rule-based and learning-based aligning algorithms. This approach has been evaluated by aligning two real-world biological ontologies, whose features include huge file size, very few instances, concept names in numerical strings, and others.

Conclusion

The promising experiment results verify our proposed hypothesis, i.e., three weights for semantic aspects learned from a subset of concepts are representative of all concepts in the same ontology. Therefore, our method represents a large leap forward towards automating biological ontology alignment.
A stable iterative method for refining discriminative gene clusters
Authors: Xu Min , Zhu Mengxia , Zhang Louxin
Published: September 2008

Background

Microarray technology is often used to identify the genes that are differentially expressed between two biological conditions. On the other hand, since microarray datasets contain a small number of samples and a large number of genes, it is usually desirable to identify small gene subsets with distinct pattern between sample classes. Such gene subsets are highly discriminative in phenotype classification because of their tightly coupling features. Unfortunately, such identified classifiers usually tend to have poor generalization properties on the test samples due to overfitting problem.

Results

We propose a novel approach combining both supervised learning with unsupervised learning techniques to generate increasingly discriminative gene clusters in an iterative manner. Our experiments on both simulated and real datasets show that our method can produce a series of robust gene clusters with good classification performance compared with existing approaches.

Conclusion

This backward approach for refining a series of highly discriminative gene clusters for classification purpose proves to be very consistent and stable when applied to various types of training samples.
A Poisson mixture model to identify changes in RNA polymerase II binding quantity using high-throughput sequencing technology
Authors: Feng Weixing , Liu Yunlong , Wu Jiejun , Nephew Kenneth P , Huang Tim HM , Li Lang
Published: September 2008

We present a mixture model-based analysis for identifying differences in the distribution of RNA polymerase II (Pol II) in transcribed regions, measured using ChIP-seq (chromatin immunoprecipitation following massively parallel sequencing technology). The statistical model assumes that the number of Pol II-targeted sequences contained within each genomic region follows a Poisson distribution. A Poisson mixture model was then developed to distinguish Pol II binding changes in transcribed region using an empirical approach and an expectation-maximization (EM) algorithm developed for estimation and inference. In order to achieve a global maximum in the M-step, a particle swarm optimization (PSO) was implemented. We applied this model to Pol II binding data generated from hormone-dependent MCF7 breast cancer cells and antiestrogen-resistant MCF7 breast cancer cells before and after treatment with 17β-estradiol (E2). We determined that in the hormone-dependent cells, ~9.9% (2527) genes showed significant changes in Pol II binding after E2 treatment. However, only ~0.7% (172) genes displayed significant Pol II binding changes in E2-treated antiestrogen-resistant cells. These results show that a Poisson mixture model can be used to analyze ChIP-seq data.
Selecting subsets of newly extracted features from PCA and PLS in microarray data analysis
Authors: Li Guo-Zheng , Bu Hua-Long , Yang Mary Qu , Zeng Xue-Qiang , Yang Jack Y
Published: September 2008

Background

Dimension reduction is a critical issue in the analysis of microarray data, because the high dimensionality of gene expression microarray data set hurts generalization performance of classifiers. It consists of two types of methods, i.e. feature selection and feature extraction. Principle component analysis (PCA) and partial least squares (PLS) are two frequently used feature extraction methods, and in the previous works, the top several components of PCA or PLS are selected for modeling according to the descending order of eigenvalues. While in this paper, we prove that not all the top features are useful, but features should be selected from all the components by feature selection methods.

Results

We demonstrate a framework for selecting feature subsets from all the newly extracted components, leading to reduced classification error rates on the gene expression microarray data. Here we have considered both an unsupervised method PCA and a supervised method PLS for extracting new components, genetic algorithms for feature selection, and support vector machines and k nearest neighbor for classification. Experimental results illustrate that our proposed framework is effective to select feature subsets and to reduce classification error rates.

Conclusion

Not only the top features newly extracted by PCA or PLS are important, therefore, feature selection should be performed to select subsets from new features to improve generalization performance of classifiers.
Gene selection algorithm by combining reliefF and mRMR
Authors: Zhang Yi , Ding Chris , Li Tao
Published: September 2008

Background

Gene expression data usually contains a large number of genes, but a small number of samples. Feature selection for gene expression data aims at finding a set of genes that best discriminate biological samples of different types. In this paper, we present a two-stage selection algorithm by combining ReliefF and mRMR: In the first stage, ReliefF is applied to find a candidate gene set; In the second stage, mRMR method is applied to directly and explicitly reduce redundancy for selecting a compact yet effective gene subset from the candidate set.

Results

We perform comprehensive experiments to compare the mRMR-ReliefF selection algorithm with ReliefF, mRMR and other feature selection methods using two classifiers as SVM and Naive Bayes, on seven different datasets. And we also provide all source codes and datasets for sharing with others.

Conclusion

The experimental results show that the mRMR-ReliefF gene selection algorithm is very effective.
Allele distribution and genetic diversity of VNTR loci in Salmonella entericaserotype Enteritidis isolates from different sources
Authors: Cho Seongbeom , Whittam Thomas S , Boxrud David J , Bartkus Joanne M , Saeed A Mahdi
Published: September 2008

Background

Salmonella enterica serotype Enteritidis (S. Enteritidis) is a zoonotic pathogen, which can be found in many sources including animals and the environment. However, little is known about the molecular relatedness among S. Enteritidis isolates from different sources. We have applied multiple-locus variable number tandem repeat analysis (MLVA) to study the genetic diversity of S. Enteritidis isolates from human and non-human sources.

Results

We identified 38 unique MLVA types using nine VNTR loci markers for discrimination between 145 S. Enteritidis isolates from different sources including humans (n = 41), chickens (n = 45), and eggs (n = 40). There were 20 distinct MLVA types identified from human isolates, 17 distinct MLVA types from chicken isolates, and 5 from egg isolates. We compared allele distribution and frequency for each VNTR marker and measured allelic polymorphism within each VNTR locus of S. Enteritidis isolates from the sources using Nei's diversity index (D). Differences in allele distribution and frequency were detected in most loci of study isolates. Different genetic diversity for certain loci was identified in isolates from different sources. The average of genetic diversity (D) was lower in egg isolates (0.16) compared to human (0.41) and chicken (0.30). However, for loci SE3, SE7, and SE9, human isolates showed significantly higher diversity than both chicken and egg isolates. Whereas for loci SE5 and SE10, chicken isolates had significantly higher diversity than both human and egg isolates. Minimum-spanning tree (MST) comprised one major cluster, a minor cluster, and four clonal expansions. MLVA application enabled a cluster analysis by the MST of the S. Enteritidis isolates by sources, which allows a great insight into the genetic relatedness and the possible flow of these organisms between different reservoirs and humans.

Conclusion

Differences in allele distribution and genetic diversity of VNTR loci in S. Enteritidis isolates from different sources were found. Polymorphism in most of the VNTR loci was more frequent among human S. Enteritidis isolates than isolates from chickens or eggs. Therefore, VNTR profiles of S. Enteritidis isolates from a specific source should be further evaluated as potential markers in epidemiologic investigations to trace S. Enteritidis to their probable source.
A new picture of cell wall protein dynamics in elongating cells of Arabidopsis thaliana: Confirmed actors and newcomers
Authors: Irshad Muhammad , Canut Hervé , Borderies Gisèle , Pont-Lezica Rafael , Jamet Elisabeth
Published: September 2008

Background

Cell elongation in plants requires addition and re-arrangements of cell wall components. Even if some protein families have been shown to play roles in these events, a global picture of proteins present in cell walls of elongating cells is still missing. A proteomic study was performed on etiolated hypocotyls of Arabidopsis used as model of cells undergoing elongation followed by growth arrest within a short time.

Results

Two developmental stages (active growth and after growth arrest) were compared. A new strategy consisting of high performance cation exchange chromatography and mono-dimensional electrophoresis was established for separation of cell wall proteins. This work allowed identification of 137 predicted secreted proteins, among which 51 had not been identified previously. Apart from expected proteins known to be involved in cell wall extension such as xyloglucan endotransglucosylase-hydrolases, expansins, polygalacturonases, pectin methylesterases and peroxidases, new proteins were identified such as proteases, proteins related to lipid metabolism and proteins of unknown function.

Conclusion

This work highlights the CWP dynamics that takes place between the two developmental stages. The presence of proteins known to be related to cell wall extension after growth arrest showed that these proteins may play other roles in cell walls. Finally, putative regulatory mechanisms of protein biological activity are discussed from this global view of cell wall proteins.