bluuebunny/crossref_metadata_2025 huggingface dataset:
More on language mode
Authors: Dunn Alexandra L. , Fox Tree Jean E.
Published: August 2012

Language mode theory proposes that language activation can span from a monolingual mode (predominant activation of one language) to bilingual mode (both languages activated). While some argue that linguistic performance is influenced by the language mode the bilingual speaker is in, others have found that language mode activation has no affect on performance. We show that changes in language mode can influence bilinguals’ language processing. Spanish–English bilinguals with both languages active (bilingual mode) took longer to reject non-words than Spanish–English bilinguals with one language active (monolingual English mode) and English monolinguals. In addition, reaction times for non-words were longer the more Spanish weighted the bilinguals were, with a linear relationship between non-word reaction times and bilingual dominance. Results can be best described by extending the Bilingual Model of Lexical Access of speech perception to reading.
Investigating the impact of attitude on first language attrition and second language acquisition from a Dynamic Systems Theory perspective
Authors: Cherciov Mirela
Published: August 2012

The factor attitude is generally considered to be among the most influential for first language (L1) attrition. Nevertheless, empirical validations have proven difficult to establish. While some studies could not find clear links between measures of attitude and L1 attrition (Hulsen, 2000; Yağmur, 1997), others showed that attitudes generated from exceptional life events strongly influenced attrition (Schmid, 2002) and that pragmatic vs. ideological motivation to emigrate and ensuing attitudes were clearly linked to L1 attrition (Ben-Rafael & Schmid, 2007). A closer examination of these studies yields a noteworthy pattern: those studies that relied on questionnaires (Hulsen, 2000, Yağmur, 1997) seemed to find no straight correlations between attitude and L1 performance, while the studies that used interviews (Ben-Rafael & Schmid, 2007; Schmid, 2002) established a clearer link between the two. The present study explores the impact of attitude – as measured through both questionnaires and interviews – on L1 attrition and second language (L2) proficiency. The quantitative analysis revealed partially significant results, thus suggesting that the factor attitude would have a limited impact on L1 attrition. Individual qualitative analyses, on the other hand, revealed important links between attitudes and the migrants’ language proficiency profiles. The article argues for a combination of methodological approaches in the study of L1 attrition and underlines the idea that individual-level analyses are well suited to capture the non-linearity of attitude and its impact on L1 attrition. These conclusions fit well with a Dynamic Systems Theory perspective in relation to the constant flux of attitude perceptions and their unpredictable role in attrition (de Bot, Lowie & Verspoor, 2007).
Between mass society and revolutionary praxis: The contradictions of Guy Debord’s Society of the Spectacle
Authors: Kaplan Richard L
Published: August 2012

In 1967, Guy Debord published his landmark analysis of the spectacle. Building on Marx’s theory of alienation, the spectacle describes our passive, quasi-visual relation to the social world. The individual, divorced from the collective praxis that constructs our social world, is reduced to consuming corporate-supplied entrancing narratives. This article explicates and assesses Debord’s theory. Its most serious defect is Debord’s rejection of the necessary intermediation of social life by culture and communication. Furthermore, his analysis subscribes to the trope of mass society, which sees the populace as culturally denuded, divorced from community and subject to the imposition of false needs. Against this alienated world, Debord pits the ideal of a collective revolutionary subject that freely creates society. However, both terms – alienated masses and revolutionary collective – are implicitly dependent upon liberal individualism, which abstracts individuals from the cultural traditions and social relations in which they are embedded.
Vocabularies of gambling justification among Finnish and French players
Authors: Majamäki Maija H , Pöysti Virve K
Published: August 2012

Psychological studies have tended to understand gambling motives as preconceived and individualistic. However, from a sociological point of view motives can only be conceived after the act has taken place, forming vocabularies of justifying one’s action to make it rational in the eyes of others. Motives cannot be taken at face value but as expressions of what is thought to be culturally acceptable. Using group interview data, this comparative study between Finnish and French gamblers asks how gambling is justified in these two cultural contexts. Different vocabularies of justification were found. While the French emphasised the dream of winning large sums of money, the Finns highlighted personal development. The results confirm that cultural aspects should be considered more in gambling research as the vocabularies of justifying gambling are connected to the cultural and institutional context in question.
Genre and the cultural politics of territory: The live experience of free improvisation
Authors: Atton Chris
Published: August 2012

This article is concerned with the relationship between performers and audiences in the live performance of popular music, a relationship that is examined through the concept of genre culture and a microsociological study of improvised music as a territory for behaviour. Normative practices of musical performance and audience behaviour are generally understood to be regulated within the ‘social order’ of live performance situations. By contrast, and taking the live performance of freely improvised music as a case study, the article explores how disruptive interactions between performers and audiences might be considered not merely as challenges to the norms of a genre culture, but as constituents of that culture. Rather than conceptualising a genre in all cases as the negotiated outcome of sets of aesthetic and social practices and expectations, the article argues that this model of genre construction is less adequate for a consideration of more marginal and less stable music-making such as free improvisation.
Responding to the post-9/11 challenges facing ‘post secular societies’: Critical reflections on Habermas’s dialogic solutions
Authors: McGhee Derek
Published: August 2012

There is much to be commended in Habermas’s suggestions for the relaxation of the constraints on public liberalism and the idealized norms of deliberative democratic debate in his proposals for the introduction of new institutional spaces that will facilitate the engagement between what he calls ‘religious’ and ‘secular’ citizens in his writings on ‘post-secular’ societies. The article examines the parallels between Habermas’s proposed democratic innovations, which will facilitate the introduction of ‘situated knowledges’ through proposing what I.M. Young would call ‘communicative leveling’, within the context of criticisms of secularism, public realism and the critiques of the idealized norms of deliberative democracy. However, it will be suggested here that there is also a certain convergence between Habermas’s theoretical interventions and the ‘instrumental engagement’ of governments with minority religious communities in the post-9/11 context.
Zigging and zooming all over the place: Young children’s meaning making and movement in the museum
Authors: Hackett Abigail
Published: August 2012

This article draws attention to the walking and running of young children as a key element of their multimodal communicative practices. In addition, the article argues that the walking and running of young children can be seen as a place-making activity, acknowledging the power of young children to create meaning in their world. Drawing on ethnographic data from ongoing research with young children and their families in museums, I present some examples of ways in which young children move during museum visits as a powerful, intentional and communicative practice. Focusing on young children’s perspectives of the museum as a place of primary importance enables us to understand the walking and running of young children in the context of their communicative practices in an embodied, emplaced and experienced world.
Carry mi ackee go a Jamaican market
Authors: Phillips Margaret E , Scott Andrea D , Sutherland Claire E , Gerla Marisa P , Gilzene Annette M
Published: August 2012

Jamaica’s national fruit, the ackee, in its various stages of development and use, serves as the metaphor to reveal key elements of this island nation’s national culture and, by extension, its business and organizational environment. Four stages of the ackee are employed: (1) the TREE, which, in its seeding and growth, exhibits an intrinsic resilience reflected in the country’s ability to overcome adverse environmental conditions; (2) the CLOSED FRUIT, which is poisonous, but, like this developing nation, has a transitional toxicity; (3) the OPEN/RIPE FRUIT, exhibiting its multifaceted diversity by being externally colorful, functionally resourceful, and dependently cooperative, representative of Jamaica’s ethnic diversity, its industriousness and ingenuity, and its affinity for foreign counterpoints, respectively; and, (4) the COOKED FRUIT, which, in the experience of the traditional communal ackee and saltfish breakfast, fosters a ritualistic identity that promotes social cohesion, engenders pride, and reinforces shared identification as Jamaicans.
The Implications of Fictional Media for Political Beliefs
Authors: Mulligan Kenneth , Habel Philip
Published: August 2012

Most research on media effects in political science deals with the news media or political campaigns. Although some recent work looks at the effects of soft news on beliefs and opinions, little attention has been paid to the potential consequences of media that are fictional. Although viewers typically watch fiction for entertainment, the themes, plots, and dialogue may nevertheless influence their thoughts about politics. This article examines the effects of fiction on political beliefs. We do this in the context of an experimental design, where subjects in the treatment group watched the outlandish movie, Wag the Dog. The results show that those who watched the film were more likely to believe in a far-fetched conspiracy, namely that the U.S. government has and will fabricate a war for political gain. The findings stretch the boundaries of fictional influence by focusing on extreme, conspiratorial beliefs. We suggest that political science and communications scholars should focus greater attention on the implications of fiction for beliefs and attitudes, as the consequences can be perverse.
Cancer-Specific Concerns and Physical Activity Among Recently Diagnosed Breast and Prostate Cancer Survivors
Authors: Ottenbacher Allison , Sloane Richard , Snyder Denise C. , Kraus William , Sprod Lisa , Demark-Wahnefried Wendy
Published: August 2012

Background. Cancer treatment -related side effects may have a negative impact on quality of life among cancer survivors and may limit participation in physical activity (PA). Hypothesis. Cancer-specific concerns will be reduced throughout a 10-month diet and exercise intervention among recently diagnosed cancer survivors. Additionally, participants reporting greater levels of PA will also report fewer cancer-specific concerns. Study design. This study is an exploratory analysis of 452 recently diagnosed, early-stage breast and prostate cancer survivors who participated in the FRESH START diet and exercise trial. Data were collected at baseline and 1-year follow-up. Results. At baseline, chief concerns among prostate cancer survivors included ability to have an erection (mean score [standard deviation] = 1.0 [1.3]) and urinary frequency (2.5 [1.4]), whereas among breast cancer survivors, eminent concerns were not feeling sexually attractive (2.0 [1.3]) and worry about cancer in other members of their family (2.1 [1.3]). At 1 year, there was a significant improvement in cancer-specific concerns on breast cancer-specific concerns (P < .01) but not on prostate cancer-specific concerns. At baseline, women who were self-conscious about their dress had higher levels of PA, whereas men reporting issues with incontinence reported lesser increases in PA in response to the intervention. Conclusion. Cancer-specific concerns diminish over time, especially among breast cancer survivors. Among prostate cancer survivors, incontinence is a significant barrier that hinders benefit from PA interventions. Thus, there is a need either for medical interventions to ameliorate incontinence or for behavioral interventions to address this issue among survivors.
The Roles of Implicit Memory Bias, Depression, and Metacognitions in Men and Women With Coronary Artery Disease
Authors: Khodarahimi Siamak , Rasti Ali
Published: August 2012

The purpose of this research was to examine the role of implicit memory bias, depression, and metacognitions in coronary artery disease (CAD) and the relationships between implicit memory bias, depression, and metacognitions based on gender, age, and educational status. Participants were 30 patients with CAD and controls who were selected through a purposive sampling method in Iran. A demographic questionnaire, the Meta-Worry Questionnaire-30; the Beck’s Depression Inventory–II; and the Word Stem Completion Software were used in this study. Resulting data demonstrated that patients with CAD had significant higher levels of depression, metacognitive worry, and negative-mood-inducing words than individuals in the control group. Also, individuals in the control group had significant higher performance on neutral-mood-inducing words than patients with CAD. Depression and metacognitive variables were significantly related to negative- and neutral-mood-inducing words in the total sample. Findings did not support significant relationships of age and educational level to depression, metacognition, and the implicit memory bias in males and females.
Correlates of Hepatitis B Virus and HIV Knowledge Among Gay and Bisexual Homeless Young Adults in Hollywood
Authors: Nyamathi Adeline , Salem Benissa , Reback Cathy J. , Shoptaw Steven , Branson Catherine M. , Idemundia Faith E. , Kennedy Barbara , Khalilifard Farinaz , Marfisee Mary , Liu Yihang
Published: August 2012

Homeless gay and bisexual (G/B) young men have multiple risk factors that increase their risk of contracting hepatitis B virus (HBV) and human immunodeficiency virus (HIV). This study used baseline information from structured instruments to assess correlates of knowledge to HIV and HBV infection from 267 young (18-39 year old) G/B active methamphetamine, cocaine, and crack-using homeless men enrolled in a longitudinal trial. The study is designed to reduce drug use and improve knowledge of hepatitis and HIV/AIDS in a community center in Hollywood, California. Regression modeling revealed that previous hepatitis education delivered to G/B men was associated with higher levels of HIV/AIDS and hepatitis knowledge. Moreover, higher HIV/AIDS knowledge was associated with combining sex and drinking alcohol. Associations with hepatitis B knowledge was found among G/B men who were engaging in sex while under the influence of marijuana, who were receiving support from non–drug users, and who had been homeless in the last 4 months. Although being informed about HIV/AIDS and hepatitis did not preclude risky sexual and drug use behavior, knowledge about the dangers of concurrent sex with substance use is important. As higher levels of knowledge of hepatitis was associated with more moderate drug use, early access to testing and teaching harm reduction strategies remain critical to reduce exposure and infection of HBV and HIV in this population.
Harnessing gemcitabine metabolism: a step towards personalized medicine for pancreatic cancer
Authors: Saif Muhammad Wasif , Lee Yoomi , Kim Richard
Published: August 2012

Pancreatic cancer is a lethal malignancy with a 5-year survival rate of only 6%. Surgical resection remains the only cure, yet even after resection the 5-year survival is only 20% due to a high recurrence rate. Thus, a high proportion of patients with this disease will ultimately require systemic chemotherapy for advanced pancreatic cancer (APC). While the advent of personalized medicine has resulted in significant advances in the management of many cancer types, the standard of care for pancreatic cancer remains gemcitabine based, with very few exceptions. This article first aims to provide an overview of the benefits and limitations of gemcitabine alone, gemcitabine combinations, and different modes of administration of gemcitabine in APC. It then discusses research, suggesting that pharmacogenomic differences in enzymes that affect gemcitabine transport and metabolism can predict benefit from this drug in pancreatic cancer. Finally, the article outlines novel therapies and combinations that exploit these interindividual variations in gemcitabine metabolism to improve the efficacy of this drug in the management of APC.
Significance of C-reactive protein in osteoarthritis and total knee arthroplasty outcomes
Authors: Smith Jessica W. , Martins Thomas B. , Gopez Evelyn , Johnson Troy , Hill Harry R. , Rosenberg Thomas D.
Published: August 2012

Background:

The relationship between systemic inflammatory processes to total knee arthroplasty (TKA) outcomes remains unclear. This study investigates the relationship between serum high-sensitivity C-reactive protein (hs-CRP) and functional outcomes post-TKA.

Methods:

A total of 31 patients with osteoarthritis (OA) who underwent TKA were enrolled in the study; 15 with hs-CRP ≤1.0 mg/l (low hs-CRP group) and 16 subjects with hs-CRP ≥4.0 mg/l (high hs-CRP group). During surgery, synovium and bone sections were sequestered, formalin-fixed, and paraffin embedded for slide preparation. Tissue sections were stained with hematoxylin and eosin and analyzed using a light microscope. A total of 12 cytokines were measured in synovial fluid samples from the knee joint at time of surgery and analyzed using the Luminex Multi-Analyte Profiling System. Relationships between cytokines and hs-CRP were assessed using Spearman correlation coefficients. Student’s t-tests were used to compare Short Form health outcomes survey (SF-12) health outcomes between high and low hs-CRP, and presurgical and postsurgical visits.

Results:

Mean ± standard deviation (SD) baseline and 1-year hs-CRP values for the low hs-CRP group were 0.55 ± 0.23 mg/l and 1.22 ± 1.32 mg/l, respectively ( n = 15; p = 0.051) and for the high hs-CRP group were 7.86 ± 5.98 mg/l and 14.11 ± 38.9 mg/l, respectively ( n = 13; p = 0.54). Lymphocytes were present in 10 synovium and one bone sample (all but one from high hs-CRP group). Interleukin (IL)-5 and IL-10 were significantly correlated with hs-CRP ( p = 0.0137 and p = 0.0029, respectively). The low hs-CRP group exhibited significant improvement in the physical component of SF-12 at 6 and 12 months compared with baseline, whereas the high hs-CRP group exhibited significant improvement only at 6 months. Body mass index (BMI) had a significant positive correlation with presurgical hs-CRP.

Conclusions:

The results of this study provide support for inflammatory mechanisms contributing to the OA progression, with hs-CRP being a possible predictive variable, combined with BMI and other comorbidities, of post-TKA function.
Centering Race in a Framework for Leadership Preparation
Authors: Gooden Mark A. , Dantley Michael
Published: August 2012

This article argues that a framework of educational leadership must be so designed as to specifically speak to the transitioning demographics in schools in the United States. Particularly salient is a framework that addresses the issue of race within a broader context of social justice. The article outlines five ingredients of such a framework, including self-reflection, a grounding in a critical theoretical construction, a prophetic and pragmatic edge, praxis, and the inclusion of race language. Furthermore, the article outlines pragmatic ways in which educational leadership preparation programs can address the failures of the dominant system to embrace and struggle with the American issue of race in education. The impact of racism and the efficacy of the blending of self-reflection, introspection, as well as intellectual work are discussed as viable vehicles to deal with the matters of race in preparing prospective school leaders. The article concludes with the presentation of a proposed curriculum module, a project undertaken by the University Council for Educational Administration, to assist leadership preparation programs in addressing, through innovative instruction, the notions of privilege and race in their programs.
Promoting the Utilization of Educational Leadership Research in Preparation, Practice, and Policy
Authors: Young Michelle D. , Rorrer Andrea K.
Published: August 2012

Within this article, the authors explore the disconnect between research production, dissemination, and utilization, particularly within the field of educational leadership in the United States. Their exploration begins with an examination of the macro-level contexts within which such activities currently take place. They then turn to an examination of the relative value placed on educational research and its utilization as well as the threats that emerge when high-quality research is not (perceived as) accessible or aligned with perceived needs. Through their explorations, the authors identify significant challenges to research utilization, challenges they argue can be understood, addressed, and overcome.
Misplaced Confidences
Authors: Brandimarte Laura , Acquisti Alessandro , Loewenstein George
Published: August 2012

We test the hypothesis that increasing individuals’ perceived control over the release and access of private information—even information that allows them to be personally identified––will increase their willingness to disclose sensitive information. If their willingness to divulge increases sufficiently, such an increase in control can, paradoxically, end up leaving them more vulnerable. Our findings highlight how, if people respond in a sufficiently offsetting fashion, technologies designed to protect them can end up exacerbating the risks they face.
A3669G polymorphism of glucocorticoid receptor is a susceptibility allele for primary myelofibrosis and contributes to phenotypic diversity and blast transformation
Authors: Poletto Valentina , Rosti Vittorio , Villani Laura , Catarsi Paolo , Carolei Adriana , Campanelli Rita , Massa Margherita , Martinetti Myriam , Viarengo Gianluca , Malovini Alberto , Migliaccio Anna Rita , Barosi Giovanni
Published: August 2012

The frequency of A3669G single nucleotide polymorphism (SNP) of human glucocorticoid receptor has been reported increased in polycythemia vera. We investigated the frequency of A3669G SNP and its impact on disease phenotype and progression in 499 patients with primary myelofibrosis (PMF). The distribution of the A3669G allele differed between PMF patients and 2 healthy control populations (odds ratio, 1.6 and 1.8). The variant allele at the homozygous state (G/G) was associated with higher white blood cell count, larger spleen index, and higher frequency of circulating CD34+ cells at diagnosis. The latter association remained significant after correction for the JAK2V617F genotype. In patients JAK2V617F mutated, the G/G genotype was associated with shorter overall survival (77.6 months vs 298 months, P = .049) and blast transformation (BT)–free survival (76.7 months vs 261 months; P = .018). The latter association remained significant after correction for the known BT risk factors, such as age, sex, white blood cell count, percentage of blasts, IPSS prognostic score, and homozygosity for JAK2V617F (hazard ratio = 3.3; P = .006). In conclusion, the glucocorticoid receptor A3669G is a susceptibility allele for PMF: it contributes to confer the phenotype of excess myeloproliferation, and it cooperates with the JAK2V617F mutation in determining BT.
GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions
Authors: Ko Junsu , Park Hahnbeom , Seok Chaok
Published: August 2012

Background

Protein structures can be reliably predicted by template-based modeling (TBM) when experimental structures of homologous proteins are available. However, it is challenging to obtain structures more accurate than the single best templates by either combining information from multiple templates or by modeling regions that vary among templates or are not covered by any templates.

Results

We introduce GalaxyTBM, a new TBM method in which the more reliable core region is modeled first from multiple templates and less reliable, variable local regions, such as loops or termini, are then detected and re-modeled by anab initiomethod. This TBM method is based on “Seok-server,” which was tested in CASP9 and assessed to be amongst the top TBM servers. The accuracy of the initial core modeling is enhanced by focusing on more conserved regions in the multiple-template selection and multiple sequence alignment stages. Additional improvement is achieved byab initiomodeling of up to 3 unreliable local regions in the fixed framework of the core structure. Overall, GalaxyTBM reproduced the performance of Seok-server, with GalaxyTBM and Seok-server resulting in average GDT-TS of 68.1 and 68.4, respectively, when tested on 68 single-domain CASP9 TBM targets. For application to multi-domain proteins, GalaxyTBM must be combined with domain-splitting methods.

Conclusion

Application of GalaxyTBM to CASP9 targets demonstrates that accurate protein structure prediction is possible by use of a multiple-template-based approach, andab initiomodeling of variable regions can further enhance the model quality.
The genomic basis for the evolution of a novel form of cellular reproduction in the bacterium Epulopiscium
Authors: Miller David A , Suen Garret , Clements Kendall D , Angert Esther R
Published: August 2012

Background

Epulopiscium sp. type B, a large intestinal bacterial symbiont of the surgeonfish Naso tonganus, does not reproduce by binary fission. Instead, it forms multiple intracellular offspring using a process with morphological features similar to the survival strategy of endospore formation in other Firmicutes. We hypothesize that intracellular offspring formation in Epulopiscium evolved from endospore formation and these two developmental programs share molecular mechanisms that are responsible for the observed morphological similarities.

Results

To test this, we sequenced the genome of Epulopiscium sp. type B to draft quality. Comparative analysis with the complete genome of its close, endospore-forming relative, Cellulosilyticum lentocellum, identified homologs of well-known sporulation genes characterized in Bacillus subtilis. Of the 147 highly conserved B. subtilis sporulation genes used in this analysis, we found 57 homologs in the Epulopiscium genome and 87 homologs in the C. lentocellum genome.

Conclusions

Genes coding for components of the central regulatory network which govern the expression of forespore and mother-cell-specific sporulation genes and the machinery used for engulfment appear best conserved. Low conservation of genes expressed late in endospore formation, particularly those that confer resistance properties and encode germinant receptors, suggest that Epulopiscium has lost the ability to form a mature spore. Our findings provide a framework for understanding the evolution of a novel form of cellular reproduction.
MicroRNAs in metamorphic and non-metamorphic transitions in hemimetabolan insect metamorphosis
Authors: Rubio Mercedes , de Horna Anibal , Belles Xavier
Published: August 2012

Background

Previous work showed that miRNAs play key roles in the regulation of metamorphosis in the hemimetabolan species Blattella germanica. To gain insight about which miRNAs might be important, we have constructed two miRNA libraries, one of the penultimate, pre-metamorphic nymphal instar (N5) and the other of the last, metamorphic nymphal instar (N6).

Results

High throughput sequencing gave 61 canonical miRNAs present in the N5 and N6 libraries, although at different proportions in each. Comparison of both libraries led to the identification of three and 37 miRNAs significantly more expressed in N5 and N6 respectively. Twelve of these 40 miRNAs were then investigated further by qRT-PCR and results indicated that miR-252-3p was well expressed in N5 but not in N6, whereas let-7-5p, miR-100-5p and miR-125-5p showed the reverse pattern. 20-Hydroxyecdysone (20E) tended to stimulate miRNA expression, whereas juvenile hormone (JH) inhibited the 20E stimulatory effect. Expression of let-7, miR-100 and miR-125 was increased by 20E, which has also been observed in D. melanogaster. The only miRNA that was inhibited by 20E was miR-252-3p. The involvement of let-7, miR-100 and miR-125 in metamorphosis has been demonstrated in other insects. Depletion of miR-252-3p caused growth and developmental delays, which suggests that this miRNA is involved in regulating these processes prior to metamorphosis.

Conclusions

The comparative analysis of miRNA libraries from pre-metamorphic (N5) and metamorphic stages (N6) of B. germanica proved to be a useful tool to identify miRNAs with roles in hemimetabolan metamorphosis. Three miRNAs emerged as important factors in the metamorphic stage (N6): let-7-5p, miR-100-5p and miR-125-5p, whereas miR-252-3p appears to be important in the pre-metamorphic stage (N5).
AtlasT4SS: A curated database for type IV secretion systems
Authors: Souza Rangel C , del Rosario Quispe Saji Guadalupe , Costa Maiana OC , Netto Diogo S , Lima Nicholas CB , Klein Cecília C , Vasconcelos Ana Tereza R , Nicolás Marisa F
Published: August 2012

Background

The type IV secretion system (T4SS) can be classified as a large family of macromolecule transporter systems, divided into three recognized sub-families, according to the well-known functions. The major sub-family is the conjugation system, which allows transfer of genetic material, such as a nucleoprotein, via cell contact among bacteria. Also, the conjugation system can transfer genetic material from bacteria to eukaryotic cells; such is the case with the T-DNA transfer of Agrobacterium tumefaciens to host plant cells. The system of effector protein transport constitutes the second sub-family, and the third one corresponds to the DNA uptake/release system. Genome analyses have revealed numerous T4SS in Bacteria and Archaea. The purpose of this work was to organize, classify, and integrate the T4SS data into a single database, called AtlasT4SS - the first public database devoted exclusively to this prokaryotic secretion system.

Description

The AtlasT4SS is a manual curated database that describes a large number of proteins related to the type IV secretion system reported so far in Gram-negative and Gram-positive bacteria, as well as in Archaea. The database was created using the RDBMS MySQL and the Catalyst Framework based in the Perl programming language and using the Model-View-Controller (MVC) design pattern for Web. The current version holds a comprehensive collection of 1,617 T4SS proteins from 58 Bacteria (49 Gram-negative and 9 Gram-Positive), one Archaea and 11 plasmids. By applying the bi-directional best hit (BBH) relationship in pairwise genome comparison, it was possible to obtain a core set of 134 clusters of orthologous genes encoding T4SS proteins.

Conclusions

In our database we present one way of classifying orthologous groups of T4SSs in a hierarchical classification scheme with three levels. The first level comprises four classes that are based on the organization of genetic determinants, shared homologies, and evolutionary relationships: (i) F-T4SS, (ii) P-T4SS, (iii) I-T4SS, and (iv) GI-T4SS. The second level designates a specific well-known protein families otherwise an uncharacterized protein family. Finally, in the third level, each protein of an ortholog cluster is classified according to its involvement in a specific cellular process. AtlasT4SS database is open access and is available at http://www.t4ss.lncc.br.
Identification of the dehydrin gene family from grapevine species and analysis of their responsiveness to various forms of abiotic and biotic stress
Authors: Yang Yazhou , He Mingyang , Zhu Ziguo , Li Shuxiu , Xu Yan , Zhang Chaohong , Singer Stacy D , Wang Yuejin
Published: August 2012

Background

Dehydrins (DHNs) protect plant cells from desiccation damage during environmental stress, and also participate in host resistance to various pathogens. In this study, we aimed to identify and characterize the DHN gene families from Vitis vinifera and wild V. yeshanensis, which is tolerant to both drought and cold, and moderately resistant to powdery mildew.

Results

Four DHN genes were identified in both V. vinifera and V. yeshanensis, which shared a high sequence identity between the two species but little homology between the genes themselves. These genes were designated DHN1, DHN2, DHN3 and DHN4. All four of the DHN proteins were highly hydrophilic and were predicted to be intrinsically disordered, but they differed in their isoelectric points, kinase selectivities and number of functional motifs. Also, the expression profiles of each gene differed appreciably from one another. Grapevine DHN1 was not expressed in vegetative tissues under normal growth conditions, but was induced by drought, cold, heat, embryogenesis, as well as the application of abscisic acid (ABA), salicylic acid (SA), and methyl jasmonate (MeJA). It was expressed earlier in V. yeshanensis under drought conditions than in V. vinifera, and also exhibited a second round of up-regulation in V. yeshanensis following inoculation with Erysiphe necator, which was not apparent in V. vinifera. Like DHN1, DHN2 was induced by cold, heat, embryogenesis and ABA; however, it exhibited no responsiveness to drought, E. necator infection, SA or MeJA, and was also expressed constitutively in vegetative tissues under normal growth conditions. Conversely, DHN3 was only expressed during seed development at extremely low levels, and DHN4 was expressed specifically during late embryogenesis. Neither DHN3 nor DHN4 exhibited responsiveness to any of the treatments carried out in this study. Interestingly, the presence of particular cis-elements within the promoter regions of each gene was positively correlated with their expression profiles.

Conclusions

The grapevine DHN family comprises four divergent members. While it is likely that their functions overlap to some extent, it seems that DHN1 provides the main stress-responsive function. In addition, our results suggest a close relationship between expression patterns, physicochemical properties, and cis-regulatory elements in the promoter regions of the DHN genes.
Virus-induced gene-silencing in wheat spikes and grains and its application in functional analysis of HMW-GS-encoding genes
Authors: Ma Meng , Yan Yan , Huang Li , Chen Mingshun , Zhao Huixian
Published: August 2012

Background

The Barley stripe mosaic virus (BSMV)-based vector has been developed and used for gene silencing in barley and wheat seedlings to assess gene functions in pathogen- or insect-resistance, but conditions for gene silencing in spikes and grains have not been evaluated. In this study, we explored the feasibility of using BSMV for gene silencing in wheat spikes or grains.

Results

Apparent photobleaching on the spikes infected with BSMV:PDS at heading stage was observed after13 days post inoculation (dpi), and persisted until 30dpi, while the spikes inoculated with BSMV:00 remained green during the same period. Grains of BSMV:PDS infected spikes also exhibited photobleaching. Molecular analysis indicated that photobleached spikes or grains resulted from the reduction of endogenous PDS transcript abundances, suggesting that BSMV:PDS was able to induce PDS silencing in wheat spikes and grains. Inoculation onto wheat spikes from heading to flowering stage was optimal for efficient silencing of PDS in wheat spikes. Furthermore, we used the BSMV-based system to reduce the transcript level of 1Bx14, a gene encoding for High-molecular-weight glutenin subunit 1Bx14 (HMW-GS 1Bx14), by 97 % in the grains of the BSMV:1Bx14 infected spikes at 15dpi, compared with that in BSMV:00 infected spikes, and the reduction persisted until at least 25 dpi. The amount of the HMW-GS 1Bx14 was also detectably decreased. The percentage of glutenin macropolymeric proteins in total proteins was significantly reduced in the grains of 1Bx14-silenced plants as compared with that in the grains of BSMV:00 infected control plants, indicating that HMW-GS 1Bx14 is one of major components participating in the formation of glutenin macropolymers in wheat grains.

Conclusion

This is one of the first reports of successful application of BSMV-based virus-induced-gene-silencing (VIGS) for gene knockdown in wheat spikes and grains and its application in functional analysis of the 1Bx14 gene. The established BSMV-VIGS system will be very useful in future research on functional analysis of genes contributing to grain quality and the metabolic networks in developing seeds of wheat.
Incorporating published univariable associations in diagnostic and prognostic modeling
Authors: A Debray Thomas P , Koffijberg Hendrik , Lu Difei , Vergouwe Yvonne , Steyerberg Ewout W , M Moons Karel G
Published: August 2012

Background

Diagnostic and prognostic literature is overwhelmed with studies reporting univariable predictor-outcome associations. Currently, methods to incorporate such information in the construction of a prediction model are underdeveloped and unfamiliar to many researchers.

Methods

This article aims to improve upon an adaptation method originally proposed by Greenland (1987) and Steyerberg (2000) to incorporate previously published univariable associations in the construction of a novel prediction model. The proposed method improves upon the variance estimation component by reconfiguring the adaptation process in established theory and making it more robust. Different variants of the proposed method were tested in a simulation study, where performance was measured by comparing estimated associations with their predefined values according to the Mean Squared Error and coverage of the 90% confidence intervals.

Results

Results demonstrate that performance of estimated multivariable associations considerably improves for small datasets where external evidence is included. Although the error of estimated associations decreases with increasing amount of individual participant data, it does not disappear completely, even in very large datasets.

Conclusions

The proposed method to aggregate previously published univariable associations with individual participant data in the construction of a novel prediction models outperforms established approaches and is especially worthwhile when relatively limited individual participant data are available.
Total protein, albumin and low-molecular-weight protein excretion in HIV-positive patients
Authors: Campbell Lucy J , Dew Tracy , Salota Rashim , Cheserem Emily , Hamzah Lisa , Ibrahim Fowzia , Sarafidis Pantelis A , Moniz Caje F , Hendry Bruce M , Poulton Mary , Sherwood Roy A , Post Frank A
Published: August 2012

Background

Chronic kidney disease is common in HIV positive patients and renal tubular dysfunction has been reported in those receiving combination antiretroviral therapy (cART). Tenofovir (TFV) in particular has been linked to severe renal tubular disease as well as proximal tubular dysfunction. Markedly elevated urinary concentrations of retinal-binding protein (RBP) have been reported in patients with severe renal tubular disease, and low-molecular-weight proteins (LMWP) such as RBP may be useful in clinical practice to assess renal tubular function in patients receiving TFV. We analysed 3 LMWP as well as protein and albumin in the urine of a sample of HIV positive patients.

Methods

In a cross-sectional fashion, total protein, albumin, RBP, cystatin C, and neutrophil gelatinase-associated lipocalin (NGAL) were quantified in random urine samples of 317 HIV positive outpatients and expressed as the ratio-to-creatinine (RBPCR, CCR and NGALCR). Exposure to cART was categorised as none, cART without TFV, and cART containing TFV and a non-nucleoside reverse-transcriptase-inhibitor (TFV/NNRTI) or TFV and a protease-inhibitor (TFV/PI).

Results

Proteinuria was present in 10.4 % and microalbuminuria in 16.7 % of patients. Albumin accounted for approximately 10 % of total urinary protein. RBPCR was within the reference range in 95 % of patients while NGALCR was elevated in 67 % of patients. No overall differences in urine protein, albumin, and LMWP levels were observed among patients stratified by cART exposure, although a greater proportion of patients exposed to TFV/PI had RBPCR >38.8 μg/mmol (343 μg/g) (p = 0.003). In multivariate analyses, black ethnicity (OR 0.43, 95 % CI 0.24, 0.77) and eGFR <75 mL/min/1.73 m2 (OR 3.54, 95 % CI 1.61, 7.80) were independently associated with upper quartile (UQ) RBPCR. RBPCR correlated well to CCR (r2 = 0.71), but not to NGALCR, PCR or ACR.

Conclusions

In HIV positive patients, proteinuria was predominantly of tubular origin and microalbuminuria was common. RBPCR in patients without overt renal tubular disease was generally within the reference range, including those receiving TFV. RBP therefore appears a promising biomarker for monitoring renal tubular function in patients receiving TFV and for distinguishing patients with normal tubular function or mild tubular dysfunction from those with severe renal tubular disease or Fanconi syndrome.
Arsenic exposure through drinking water increases the risk of liver and cardiovascular diseases in the population of West Bengal, India
Authors: Das Nandana , Paul Somnath , Chatterjee Debmita , Banerjee Nilanjana , Majumder Niladri S , Sarma Nilendu , Sau Tanmoy J , Basu Santanu , Banerjee Saptarshi , Majumder Papiya , Bandyopadhyay Apurba K , States J Christopher , Giri Ashok K
Published: August 2012

Background

Arsenic is a natural drinking water contaminant affecting 26 million people in West Bengal, India. Chronic arsenic exposure causes cancer, cardiovascular disease, liver disease, neuropathies and ocular diseases. The aims of the present study were to assess bioindicators of hepatocellular injury as indicated by the levels of liver enzymes, to determine the auto immune status, as indicated by the amounts of anti-nuclear antibodies (ANA) and anti-dsDNA antibodies in their serum, and to predict cardiovascular risk in the arsenic exposed population.

Methods

Effect of chronic arsenic exposure on liver was determined by liver function tests. Autoimmune status was measured by measuring ANA and anti-dsDNA in serum. Inflammatory cytokines associated with increased cardiovascular disease risk, IL6, IL8 and MCP-1 were determined.

Results

Our results indicated that serum levels of bilirubin, alanine transaminase, aspartate transaminase, alkaline phosphatase and ANA were increased in the arsenic exposed population. Serum levels of IL6 and IL8 also increased in the arsenic exposed group.

Conclusions

Chronic arsenic exposure causes liver injury, increases the serum levels of autoimmune markers and imparts increased cardiovascular risk.
Occurrence of maxillary sinus abnormalities detected by cone beam CT in asymptomatic patients
Authors: Rege Inara Carneiro Costa , Sousa Thiago Oliveira , Leles Cláudio Rodrigues , Mendonça Elismauro Francisco
Published: August 2012

Background

Although cone beam computed tomography (CBCT) images of the maxillofacial region allow the inspection of the entire volume of the maxillary sinus (MS), identifying anatomic variations and abnormalities in the image volume, this is frequently neglected by oral radiologists when interpreting images of areas at a distance from the dentoalveolar region, such as the full anatomical aspect of the MS. The aim of this study was to investigate maxillary sinus abnormalities in asymptomatic patients by using CBCT.

Methods

1113 CBCT were evaluated by two examiners and identification of abnormalities, the presence of periapical lesions and proximity to the lower sinus wall were recorded. Data were analyzed using descriptive statistics, chi-square tests and Kappa statistics.

Results

Abnormalities were diagnosed in 68.2% of cases (kappa = 0.83). There was a significant difference between genders (p < 0.001) and there was no difference in age groups. Mucosal thickening was the most prevalent abnormality (66%), followed by retention cysts (10.1%) and opacification (7.8%). No association was observed between the proximity of periapical lesions and the presence and type of inflammatory abnormalities (p = 0.124).

Conclusions

Abnormalities in maxillary sinus emphasizes how important it is for the dentomaxillofacial radiologist to undertake an interpretation of the whole volume of CBCT images.
Apolipoprotein C-I is an APOE genotype-dependent suppressor of glial activation
Authors: Cudaback Eiron , Li Xianwu , Yang Yue , Yoo Thomas , Montine Kathleen S , Craft Suzanne , Montine Thomas J , Keene Christopher Dirk
Published: August 2012

Background

Inheritance of the human ϵ4 allele of the apolipoprotein (apo) E gene (APOE) significantly increases the risk of developing Alzheimer’s disease (AD), in addition to adversely influencing clinical outcomes of other neurologic diseases. While apoE isoforms differentially interact with amyloid β (Aβ), a pleiotropic neurotoxin key to AD etiology, more recent work has focused on immune regulation in AD pathogenesis and on the mechanisms of innate immunomodulatory effects associated with inheritance of different APOE alleles. APOE genotype modulates expression of proximal genes including APOC1, which encodes a small apolipoprotein that is associated with Aβ plaques. Here we tested the hypothesis that APOE-genotype dependent innate immunomodulation may be mediated in part by apoC-I.

Methods

ApoC-I concentration in cerebrospinal fluid from control subjects of differing APOE genotypes was quantified by ELISA. Real-time PCR and ELISA were used to analyze apoC-I mRNA and protein expression, respectively, in liver, serum, cerebral cortex, and cultured primary astrocytes derived from mice with targeted replacement of murine APOE for human APOE ϵ3 or ϵ4. ApoC-I direct modulation of innate immune activity was investigated in cultured murine primary microglia and astrocytes, as well as human differentiated macrophages, using specific toll-like receptor agonists LPS and PIC as well as Aβ.

Results

ApoC-I levels varied with APOE genotype in humans and in APOE targeted replacement mice, with ϵ4 carriers showing significantly less apoC-I in both species. ApoC-I potently reduced pro-inflammatory cytokine secretion from primary murine microglia and astrocytes, and human macrophages, stimulated with LPS, PIC, or Aβ.

Conclusions

ApoC-I is immunosuppressive. Our results illuminate a novel potential mechanism for APOE genotype risk for AD; one in which patients with an ϵ4 allele have decreased expression of apoC-I resulting in increased innate immune activity.