bluuebunny/crossref_metadata_2025 huggingface dataset:
Food security in Southern African cities
Authors: Crush Jonathan , Hovorka Alice , Tevera Daniel
Published: June 2011

Several decades of research on ‘urban agriculture’ have led to markedly different conclusions about the actual and potential role of household food production in African cities. In the context of rapid urbanization, urban agriculture is, once again, being advocated as a means to mitigate the growing food insecurity of the urban poor. This article examines the contemporary importance of household food production in poor urban communities in 11 different Southern African Development Community (SADC) cities. It shows that urban food production is not particularly significant in most communities and that many more households rely on supermarkets and the informal sector to access food. Even fewer households derive income from the sale of produce. This picture varies considerably, however, from city to city, for reasons that require further research and explanation.
Neoliberalism is dead, long live neoliberalism? Neostructuralism and the international aid regime of the 2000s
Authors: Murray Warwick E. , Overton John D.
Published: June 2011

In the 2000s a new aid regime evolved. This promised to move beyond the former neoliberal approach in a number of ways. It would involve greater consultation between donors and recipients, shift the focus from economic growth to broader factors, including poverty, and hand back the responsibility for this to the nation-state. This approach bears strong resemblance to the rise of neostructuralism, a development paradigm that has become highly influential in Latin America. In this article we trace the shifts in the aid regime and ask to what extent the contemporary regime can be defined a postneoliberal paradigm.
Technological innovation, global justice and politics of development
Authors: Papaioannou Theo
Published: June 2011

The importance of innovation in human development is undeniable. Since the 1780s, successive scientific and technological revolutions have introduced new products and services with tremendous impact on well-being and general welfare. Yet innovation has not been available to all individuals and their societies. There are still countries in the developing world which lack proper access to fundamental innovations such as medicines, electricity, information and communication technologies (ICTs) and so on. Unequal generation and diffusion of innovation constitutes a major problem of global justice. However, neither innovation theory nor the theory of global justice provides solutions. On the one hand, innovation theory has so far refused to engage with questions of fairness and justice in the generation and diffusion of new technologies. On the other hand, emerging approaches to global justice have been almost indifferent to the prominence of new technologies in the fight against poverty and inequality. The aim of this article is to bridge the gulf between the literatures of technological innovation and global justice. It will be argued that technological innovation can satisfy minimum requirements of global justice only through successful public action and campaigning against unjust innovation diffusion. This implies that politics of development should support redistributive systems and global social movements against current Intellectual Property Rights (IPR) regimes, providing alternative incentives for successful generation and application of new knowledge.
Evaluating sport-for-development
Authors: Levermore Roger
Published: June 2011

This is the second in a series of three articles that considers the relationship between sport and furthering international development assistance. The first highlighted a significant growth in this relationship, yet evaluation of sport-for-development was criticized for being insufficient. This article therefore details the current level of evaluation of sport-for-development and highlights the approaches used whilst contextualizing it against the evaluation debate in development studies. The picture that emerges is that considerable evaluation is being conducted, particularly of programmes that have won plaudits. They tend to employ a positivist logical framework either by itself or as part of a blended methodology with some instances of participatory methods also. Concerns expressed about these approaches in the general development literature are traced in sport-for-development evaluation.
Shifting between third and first person points of view in EFL narratives
Authors: Shokouhi Hossein , Daram Mahmood , Sabah Somayeh
Published: June 2011

This article reports on the difference between points of view in narrating a short story. The EFL learners taking part in the control group were required to recount the events from the third person perspective and the subjects in the experimental group from the first person perspective. The methodological frame of the study was based on Koven’s (2002) ‘content analysis’ of codification of various speaker role inhabitances, published in the Journal of Pragmatics. The results demonstrate that the first person narrators’ recall performance and the length of their stories are closer to the original version of the story than those of the other group, which indicates a specific ‘orientation’ towards the sequence of events. This was seen in the patterning of clauses as well as in authorial and interlocutory double voicing speech in the first person narrators, which may be justified by the enhancement of two components essential to literary engagement: namely, ‘aesthetic reading’ and ‘personal response’ as parts of ‘critical focalization’.
Concept mapping in the humanities to facilitate reflection: Externalizing the relationship between public and personal learning
Authors: Kandiko Camille , Hay David , Weller Saranne
Published: June 2011

This article discusses how mapping techniques were used in university teaching in a humanities subject. The use of concept mapping was expanded as a pedagogical tool, with a focus on reflective learning processes. Data were collected through a longitudinal study of concept mapping in a university-level Classics course. This was used to explore how mapping can be applied in the discursive context of the humanities in relation to teaching, learning and assessment. A theory was developed of how to facilitate the externalization of the relationship between public and personal reflection through combining social and psychological aspects of learning. The article concludes with suggestions for how this can be applied as a learning and assessment tool to assist the writing and reflection process in the humanities. This situates broader developments in educational theory and research in the unique character of learning and teaching in Classics.
Prevalence of Deep Venous Incompetence and Microvascular Abnormalities in Patients With Diabetes Mellitus
Authors: Mani Raj , Yarde Starla , Edmonds Michael
Published: June 2011

The involvement of venous disease in the diabetic neuropathic foot is widely accepted. This article reports the result of prevalence of venous incompetence, impaired calf vein hemodynamics, and loss of microvascular control in the skin over the dorsum of the foot in an effort to document whether increased retrograde pressure caused by venous incompetence or loss of sympathetic regulation of the microcirculation is present in the diabetic patient who is at risk of foot disease. It was found that 64% and 70.7% of diabetic patients had deep venous incompetence in their right and left legs, respectively, which was statistically significantly greater than what was found in a previous report on the general population ( P < .05); 42.7% and 49.3% of patients had a reduced venous refilling time in the right and left legs, respectively, and 30.7% and 33.3% of patients had loss of the arteriovenous response in the right and left legs. Some previous reports have suggested evidence of hemodynamic and morphological changes in patients with diabetic foot disease. The outstanding contribution of this report is the finding of venous incompetence in patients with diabetes but not foot disease. Because some 15% of the population with diabetes develop foot complications, the reported observations offer hope of alleviating symptoms if not preventing ulcers.
Squamous Cell Carcinoma Developing in a Diabetic Foot Ulcer
Authors: Panda S. , Khanna Seema , Singh S.K. , Gupta S.K.
Published: June 2011

Documented cases of malignant transformation of foot ulcer in a diabetic patient in medical literature are very few. This study presents 2 interesting cases of long-standing diabetic foot ulcer, which were subsequently diagnosed to have squamous cell carcinoma on histopathological examination.
The Mediating Force of “Face”
Authors: Francis Clare A.
Published: June 2011

This research shows employees have views on supervisor “face,” defined in terms of moral character and social status. Employee perceptions of supervisor face were examined as a mediator in the relationships between perceived organizational support and work outcomes in a survey of 278 hospital employees and their supervisors. Work outcomes were based on supervisor ratings of employee extra-role behavior and employee in-role behavior. Findings indicated partial mediation by perceptions of supervisor “face.” The evidence shows supervisor moral character and social status influenced work outcomes. Implications of the findings are discussed.
What Attitudes are Moral Attitudes? The Case of Attitude Heritability
Authors: Brandt Mark J. , Wetherell Geoffrey A.
Published: June 2011

Variation in the extent an attitude is imbued with moral conviction is a strong predictor of a variety of consequential social judgments; however, the extant literature has not explained variation in moral conviction. The authors predict that some attitudes may be experienced as moral because they are heritable, promoting group survival and firmly rooting people in these attitudes. To test this hypothesis, the authors surveyed two community samples and a student sample (total N = 456) regarding the extent participants perceived 20 attitudes as moral attitudes, and compared these ratings to established estimates of attitude heritability. Across all three studies, attitudes with greater previously established heritability estimates were more likely to be experienced as moral, even when controlling for a variety of measures of attitude strength and the extent to which an attitude is associated with one’s religious beliefs.
Human memory B cells originate from three distinct germinal center-dependent and -independent maturation pathways
Authors: Berkowska Magdalena A. , Driessen Gertjan J. A. , Bikos Vasilis , Grosserichter-Wagener Christina , Stamatopoulos Kostas , Cerutti Andrea , He Bing , Biermann Katharina , Lange Johan F. , van der Burg Mirjam , van Dongen Jacques J. M. , van Zelm Menno C.
Published: June 2011

Multiple distinct memory B-cell subsets have been identified in humans, but it remains unclear how their phenotypic diversity corresponds to the type of responses from which they originate. Especially, the contribution of germinal center-independent responses in humans remains controversial. We defined 6 memory B-cell subsets based on their antigen-experienced phenotype and differential expression of CD27 and IgH isotypes. Molecular characterization of their replication history, Ig somatic hypermutation, and class-switch profiles demonstrated their origin from 3 different pathways. CD27−IgG+ and CD27+IgM+ B cells are derived from primary germinal center reactions, and CD27+IgA+ and CD27+IgG+ B cells are from consecutive germinal center responses (pathway 1). In contrast, natural effector and CD27−IgA+ memory B cells have limited proliferation and are also present in CD40L-deficient patients, reflecting a germinal center-independent origin. Natural effector cells at least in part originate from systemic responses in the splenic marginal zone (pathway 2). CD27−IgA+ cells share low replication history and dominant Igλ and IgA2 use with gut lamina propria IgA+ B cells, suggesting their common origin from local germinal center-independent responses (pathway 3). Our findings shed light on human germinal center-dependent and -independent B-cell memory formation and provide new opportunities to study these processes in immunologic diseases.
Mapping quantitative trait loci (QTL) in sheep. IV. Analysis of lactation persistency and extended lactation traits in sheep
Authors: Jonas Elisabeth , Thomson Peter C , Hall Evelyn JS , McGill David , Lam Mary K , Raadsma Herman W
Published: June 2011

Background

In sheep dairy production, total lactation performance, and length of lactation of lactation are of economic significance. A more persistent lactation has been associated with improved udder health. An extended lactation is defined by a longer period of milkability. This study is the first investigation to examine the presence of quantitative trait loci (QTL) for extended lactation and lactation persistency in sheep.

Methods

An (Awassi × Merino) × Merino single-sire backcross family with 172 ewes was used to map QTL for lactation persistency and extended lactation traits on a framework map of 189 loci across all autosomes. The Wood model was fitted to data from multiple lactations to estimate parameters of ovine lactation curves, and these estimates were used to derive measures of lactation persistency and extended lactation traits of milk, protein, fat, lactose, useful yield, and somatic cell score. These derived traits were subjected to QTL analyses using maximum likelihood estimation and regression analysis.

Results

Overall, one highly significant (LOD > 3.0), four significant (2.0 < LOD < 3.0) and five suggestive (1.7 < LOD < 2.0) QTL were detected across all traits in common by both mapping methods. One additional suggestive QTL was identified using maximum likelihood estimation, and four suggestive (0.01 < P < 0.05) and two significant (P < 0.01) QTL using the regression approach only. All detected QTL had effect sizes in the range of 0.48 to 0.64 SD, corresponding to QTL heritabilities of 3.1 to 8.9%. The comparison of the detected QTL with results in cattle showed conserved linkage regions. Most of the QTL identified for lactation persistency and extended lactation did not coincide. This suggests that persistency and extended lactation for the same as well as different milk yield and component traits are not controlled by the same genes.

Conclusion

This study identified ten novel QTL for lactation persistency and extended lactation in sheep, but results suggest that lactation persistency and extended lactation do not have a major gene in common. These results provide a basis for further validation in extended families and other breeds as well as targeting regions for genome-wide association mapping using high-density SNP arrays.
PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome
Authors: Zhang Jiajie , Mamlouk Amir Madany , Martinetz Thomas , Chang Suhua , Wang Jing , Hilgenfeld Rolf
Published: June 2011

Background

Results of phylogenetic analysis are often visualized as phylogenetic trees. Such a tree can typically only include up to a few hundred sequences. When more than a few thousand sequences are to be included, analyzing the phylogenetic relationships among them becomes a challenging task. The recent frequent outbreaks of influenza A viruses have resulted in the rapid accumulation of corresponding genome sequences. Currently, there are more than 7500 influenza A virus genomes in the database. There are no efficient ways of representing this huge data set as a whole, thus preventing a further understanding of the diversity of the influenza A virus genome.

Results

Here we present a new algorithm, "PhyloMap", which combines ordination, vector quantization, and phylogenetic tree construction to give an elegant representation of a large sequence data set. The use of PhyloMap on influenza A virus genome sequences reveals the phylogenetic relationships of the internal genes that cannot be seen when only a subset of sequences are analyzed.

Conclusions

The application of PhyloMap to influenza A virus genome data shows that it is a robust algorithm for analyzing large sequence data sets. It utilizes the entire data set, minimizes bias, and provides intuitive visualization. PhyloMap is implemented in JAVA, and the source code is freely available at http://www.biochem.uni-luebeck.de/public/software/phylomap.html
NORMA-Gene: A simple and robust method for qPCR normalization based on target gene data
Authors: Heckmann Lars-Henrik , Sørensen Peter B , Krogh Paul Henning , Sørensen Jesper G
Published: June 2011

Background

Normalization of target gene expression, measured by real-time quantitative PCR (qPCR), is a requirement for reducing experimental bias and thereby improving data quality. The currently used normalization approach is based on using one or more reference genes. Yet, this approach extends the experimental work load and suffers from assumptions that may be difficult to meet and to validate.

Results

We developed a data driven normalization algorithm (NORMA-Gene). An analysis of the performance of NORMA-Gene compared to reference gene normalization on artificially generated data-sets showed that the NORMA-Gene normalization yielded more precise results under a large range of parameters tested. Furthermore, when tested on three very different real qPCR data-sets NORMA-Gene was shown to be best at reducing variance due to experimental bias in all three data-sets compared to normalization based on the use of reference gene(s).

Conclusions

Here we present the NORMA-Gene algorithm that is applicable to all biological and biomedical qPCR studies, especially those that are based on a limited number of assayed genes. The method is based on a data-driven normalization and is useful for as little as five target genes comprising the data-set. NORMA-Gene does not require the identification and validation of reference genes allowing researchers to focus their efforts on studying target genes of biological relevance.
Determinants of antigenicity and specificity in immune response for protein sequences
Authors: Wang Yulong , Wu Wenjun , Negre Nicolas N , White Kevin P , Li Cheng , Shah Parantu K
Published: June 2011

Background

Target specific antibodies are pivotal for the design of vaccines, immunodiagnostic tests, studies on proteomics for cancer biomarker discovery, identification of protein-DNA and other interactions, and small and large biochemical assays. Therefore, it is important to understand the properties of protein sequences that are important for antigenicity and to identify small peptide epitopes and large regions in the linear sequence of the proteins whose utilization result in specific antibodies.

Results

Our analysis using protein properties suggested that sequence composition combined with evolutionary information and predicted secondary structure, as well as solvent accessibility is sufficient to predict successful peptide epitopes. The antigenicity and the specificity in immune response were also found to depend on the epitope length. We trained the B-Cell Epitope Oracle (BEOracle), a support vector machine (SVM) classifier, for the identification of continuous B-Cell epitopes with these protein properties as learning features. The BEOracle achieved an F1-measure of 81.37% on a large validation set. The BEOracle classifier outperformed the classical methods based on propensity and sophisticated methods like BCPred and Bepipred for B-Cell epitope prediction. The BEOracle classifier also identified peptides for the ChIP-grade antibodies from the modENCODE/ENCODE projects with 96.88% accuracy. High BEOracle score for peptides showed some correlation with the antibody intensity on Immunofluorescence studies done on fly embryos. Finally, a second SVM classifier, the B-Cell Region Oracle (BROracle) was trained with the BEOracle scores as features to predict the performance of antibodies generated with large protein regions with high accuracy. The BROracle classifier achieved accuracies of 75.26-63.88% on a validation set with immunofluorescence, immunohistochemistry, protein arrays and western blot results from Protein Atlas database.

Conclusions

Together our results suggest that antigenicity is a local property of the protein sequences and that protein sequence properties of composition, secondary structure, solvent accessibility and evolutionary conservation are the determinants of antigenicity and specificity in immune response. Moreover, specificity in immune response could also be accurately predicted for large protein regions without the knowledge of the protein tertiary structure or the presence of discontinuous epitopes. The dataset prepared in this work and the classifier models are available for download at https://sites.google.com/site/oracleclassifiers/.
Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon
Authors: Clepet Christian , Joobeur Tarek , Zheng Yi , Jublot Delphine , Huang Mingyun , Truniger Veronica , Boualem Adnane , Hernandez-Gonzalez Maria Elena , Dolcet-Sanjuan Ramon , Portnoy Vitaly , Mascarell-Creus Albert , Caño-Delgado Ana I , Katzir Nurit , Bendahmane Abdelhafid , Giovannoni James J , Aranda Miguel A , Garcia-Mas Jordi , Fei Zhangjun
Published: June 2011

Background

Melon (Cucumis melo), an economically important vegetable crop, belongs to the Cucurbitaceae family which includes several other important crops such as watermelon, cucumber, and pumpkin. It has served as a model system for sex determination and vascular biology studies. However, genomic resources currently available for melon are limited.

Result

We constructed eleven full-length enriched and four standard cDNA libraries from fruits, flowers, leaves, roots, cotyledons, and calluses of four different melon genotypes, and generated 71,577 and 22,179 ESTs from full-length enriched and standard cDNA libraries, respectively. These ESTs, together with ~35,000 ESTs available in public domains, were assembled into 24,444 unigenes, which were extensively annotated by comparing their sequences to different protein and functional domain databases, assigning them Gene Ontology (GO) terms, and mapping them onto metabolic pathways. Comparative analysis of melon unigenes and other plant genomes revealed that 75% to 85% of melon unigenes had homologs in other dicot plants, while approximately 70% had homologs in monocot plants. The analysis also identified 6,972 gene families that were conserved across dicot and monocot plants, and 181, 1,192, and 220 gene families specific to fleshy fruit-bearing plants, the Cucurbitaceae family, and melon, respectively. Digital expression analysis identified a total of 175 tissue-specific genes, which provides a valuable gene sequence resource for future genomics and functional studies. Furthermore, we identified 4,068 simple sequence repeats (SSRs) and 3,073 single nucleotide polymorphisms (SNPs) in the melon EST collection. Finally, we obtained a total of 1,382 melon full-length transcripts through the analysis of full-length enriched cDNA clones that were sequenced from both ends. Analysis of these full-length transcripts indicated that sizes of melon 5' and 3' UTRs were similar to those of tomato, but longer than many other dicot plants. Codon usages of melon full-length transcripts were largely similar to those of Arabidopsis coding sequences.

Conclusion

The collection of melon ESTs generated from full-length enriched and standard cDNA libraries is expected to play significant roles in annotating the melon genome. The ESTs and associated analysis results will be useful resources for gene discovery, functional analysis, marker-assisted breeding of melon and closely related species, comparative genomic studies and for gaining insights into gene expression patterns.
Ten-Color flow cytometry reveals distinct patterns of expression of CD124 and CD126 by developing thymocytes
Authors: Tan Chibing , Taylor Ashlee A , Coburn Matthew Z , Marino Julie H , Van De Wiele C Justin , Teague T Kent
Published: June 2011

Background

We have developed a 12-parameter/10-color flow cytometric staining method for the simultaneous detection and characterization of 21 mouse thymocyte subpopulations that represent discreet stages of T cell development. To demonstrate the utility of this method, we assessed cytokine receptor expression on mouse thymocyte subsets. These experiments revealed distinct patterns of surface expression of receptors for the cytokines IL-4 and IL-6.

Results

The IL-4 receptor α chain (CD124) was highly expressed on the earliest thymocyte subsets, then downregulated prior to T cell receptor β-selection and finally upregulated in the CD4/CD8 double positive cells prior to positive selection. The IL-6 receptor α chain (CD126) showed a different pattern of expression. It was expressed on the most mature subsets within the CD4 and CD8 single positive (SP) compartments and was absent on all other thymocytes with the exception of a very small cKit-CD4-CD8-population. Intracellular staining of SP thymocytes for phosphorylated STAT-1 demonstrated that IL-6 signaling was confined to the most mature SP subsets.

Conclusions

This 12-parameter staining methodology uses only commercially available fluorochrome-coupled monoclonal antibodies and therefore could be employed by any investigator with access to a 4-laser flow cytometer. This novel staining scheme allowed us to easily phenotype thymocyte subpopulations that span across development, from the early thymic progenitors (ETPs) to the most mature subsets of the CD4 and CD8 single positive populations.
The non-motile phenotype of Salmonella hha ydgT mutants is mediated through PefI-SrgD
Authors: Wallar Lauren E , Bysice Andrew M , Coombes Brian K
Published: June 2011

Background

Two ancestral nucleoid-associated proteins called Hha and YdgT contribute to the negative regulation of several virulence-associated genes inSalmonella entericaserovar Typhimurium. Our previous work showed that Hha and YdgT proteins are required for negative regulation ofSalmonellaPathogenicity Island-2 and thathha ydgTdouble mutants are attenuated for murine infection. Interestingly,hha ydgTmutant bacteria exhibited a non-motile phenotype suggesting that Hha and YdgT have a role in flagellar regulation.

Results

In this study we show that the non-motile phenotype ofhha ydgTmutants is due to decreased levels of the master transcriptional regulator FlhD4C2resulting in down-regulation of class II/III and class III flagellar promoters and lack of surface flagella on these cells. The horizontally acquiredpefI-srgDregion was found to be partially responsible for this phenotype since deletion ofpefI-srgDin ahha ydgTdeletion background resulted in transient restoration of class II/III and III transcription, expression of surface flagella, and motility in the quadruple mutant.

Conclusion

These data extend our current understanding of the mechanisms through which Hha and YdgT regulate flagellar biosynthesis and further describe howS. Typhimurium has integrated horizontal gene acquisitions into ancestral regulatory networks.
The Arabidopsis translocator protein (AtTSPO) is regulated at multiple levels in response to salt stress and perturbations in tetrapyrrole metabolism
Authors: Balsemão-Pires Emilia , Jaillais Yvon , Olson Bradley JSC , Andrade Leonardo R , Umen James G , Chory Joanne , Sachetto-Martins Gilberto
Published: June 2011

Background

The translocator protein 18 kDa (TSPO), previously known as the peripheral-type benzodiazepine receptor (PBR), is important for many cellular functions in mammals and bacteria, such as steroid biosynthesis, cellular respiration, cell proliferation, apoptosis, immunomodulation, transport of porphyrins and anions. Arabidopsis thaliana contains a single TSPO/PBR-related gene with a 40 amino acid N-terminal extension compared to its homologs in bacteria or mammals suggesting it might be chloroplast or mitochondrial localized.

Results

To test if the TSPO N-terminal extension targets it to organelles, we fused three potential translational start sites in the TSPO cDNA to the N-terminus of GFP (AtTSPO:eGFP). The location of the AtTSPO:eGFP fusion protein was found to depend on the translational start position and the conditions under which plants were grown. Full-length AtTSPO:eGFP fusion protein was found in the endoplasmic reticulum and in vesicles of unknown identity when plants were grown in standard conditions. However, full length AtTSPO:eGFP localized to chloroplasts when grown in the presence of 150 mM NaCl, conditions of salt stress. In contrast, when AtTSPO:eGFP was truncated to the second or third start codon at amino acid position 21 or 42, the fusion protein co-localized with a mitochondrial marker in standard conditions. Using promoter GUS fusions, qRT-PCR, fluorescent protein tagging, and chloroplast fractionation approaches, we demonstrate that AtTSPO levels are regulated at the transcriptional, post-transcriptional and post-translational levels in response to abiotic stress conditions. Salt-responsive genes are increased in a tspo-1 knock-down mutant compared to wild type under conditions of salt stress, while they are decreased when AtTSPO is overexpressed. Mutations in tetrapyrrole biosynthesis genes and the application of chlorophyll or carotenoid biosynthesis inhibitors also affect AtTSPO expression.

Conclusion

Our data suggest that AtTSPO plays a role in the response of Arabidopsis to high salt stress. Salt stress leads to re-localization of the AtTSPO from the ER to chloroplasts through its N-terminal extension. In addition, our results show that AtTSPO is regulated at the transcriptional level in tetrapyrrole biosynthetic mutants. Thus, we propose that AtTSPO may play a role in transporting tetrapyrrole intermediates during salt stress and other conditions in which tetrapyrrole metabolism is compromised.
Concordance of self-reported and medical chart information on cancer diagnosis and treatment
Authors: Gupta Vinay , Gu Kai , Chen Zhi , Lu Wei , Shu Xiao Ou , Zheng Ying
Published: June 2011

Background

Self-reported information is an important tool for collecting clinical information for epidemiologic studies and in clinical settings where electronic medical records are not employed and shared.

Methods

Using data collected from the Shanghai Breast Cancer Survival Study (SBCSS), a population-based, prospective cohort study of 5,042 women diagnosed with breast cancer in Shanghai, China, we compared the concordance of patient questionnaire responses to a survey administered approximately 6 months after cancer diagnosis with medical chart information obtained from the diagnostic hospitals for several disease and treatment-related variables.

Results

Of 5,042 SBCSS participants, medical chart information was available for 4,948 women (98.1%). Concordance between patient self-reported and medical chart information was high for the majority of disease-related variables, including: diagnosing hospital (agreement: 98.7%, kappa: 0.99), type of surgery conducted (94.0%, 0.53), ER/PR status (94.5%, 0.91), and tumor position (98.2%, 0.97), as well as for important calendar dates, such as date of diagnosis, surgery, and first chemotherapy treatment. The 10 most commonly used chemotherapeutic drugs were all reported with agreement rates of at least 82%, with associated kappa values that ranged from 0.41 for calcium folinate to 0.76 for vinorelbine.

Conclusions

Our study found high validity for patient self-reported information for a variety of disease and treatment-related variables, suggesting the utility of self-reports as an important source of clinical information for both epidemiological research and patient care.
Fully covered self-expanding metal stents placed temporarily in the bile duct: safety profile and histologic classification in a porcine model
Authors: Bakhru Mihir R , Foley Patricia L , Gatesman Jeremy , Schmitt Timothy , Moskaluk Christopher A , Kahaleh Michel
Published: June 2011

Background

Fully covered Self-Expanding metal stents (FCSEMS) have been shown efficacious in palliating malignant biliary obstructions. There is little data analyzing mucosal response to their temporary placement in the bile duct.

Methods

Ten mini pigs underwent endoscopic placement of a FCSEMS (Wallflex, Boston Scientific). FCSEMS were kept in place for three months. At the end of the 3 months, FCSEMS were removed endoscopically. Five pigs were euthanized and their bile ducts harvested. The other five were kept alive for another month post removal. A single pathologist, created a scoring system (to determine degree of inflammation, fibrosis, and epithelial injury), examined all specimens in a blinded fashion.

Results

Four FCSEMS spontaneously migrated in the duodenum. On post mortem examination, mild mucosal thickness was noted in three bile duct specimens while superficial inflammation of the bile duct was noted in five animals. Histologic examination of the bile duct revealed focal acute inflammation in both groups. For the 5 animals euthanized immediately after stent removal, there was a tendency to have superficial mucosal erosion and fibrosis. In contrast, increased chronic inflammation was more commonly seen in the animals 1 month post stent removal, with all animals in this group showing moderate degrees of mononuclear inflammatory cell mucosal infiltrates. No severe inflammatory or fibrotic duct injury was observed in any of the study animals, with degree of injury graded as mild to moderate.

Conclusion

FCSEMS appear to induce minimal tissue overgrowth or fibrosis post placement. Ease of removability and no significant histologic injury are advantages noted with FCSEMS., however, further studies are needed to evaluate treating benign biliary strictures with FCSEMS in humans.
Early acquisition and high nasopharyngeal co-colonisation by Streptococcus pneumoniae and three respiratory pathogens amongst Gambian new-borns and infants
Authors: Kwambana Brenda A , Barer Michael R , Bottomley Christian , Adegbola Richard A , Antonio Martin
Published: June 2011

Background

Although Haemophilus influenzae type b (Hib), Staphylococcus aureus and Moraxella catarrhalis are important causes of invasive and mucosal bacterial disease among children, co-carriage with Streptococcus pneumoniae during infancy has not been determined in West Africa.

Methods

Species specific PCR was applied to detect each microbe using purified genomic DNA from 498 nasopharyngeal (NP) swabs collected from 30 Gambian neonates every two weeks from 0 to 6 months and bi-monthly up to 12 months.

Results

All infants carried S. pneumoniae, H. influenzae and M. catarrhalis at several time points during infancy. S.pneumoniae co-colonized the infant nasopharynx with at least one other pathogen nine out of ten times. There was early colonization of the newborns and neonates, the average times to first detection were 5, 7, 3 and 14 weeks for S. pneumoniae, H. influenzae, M. catarrhalis and S. aureus respectively. The prevalence of S. pneumoniae, H. influenzae and M. catarrhalis increased among the neonates and exceeded 80% by 13, 15 and 23 weeks respectively. In contrast, the prevalence of S. aureus decreased from 50% among the newborns to 20% amongst nine-week old neonates. S. pneumoniae appeared to have a strong positive association with H. influenzae (OR 5.03; 95% CI 3.02, 8.39; p < 0.01) and M. catarrhalis (OR 2.20; 95% CI 1.29; p < 0.01) but it was negatively associated with S. aureus (OR 0.53; 95% CI 0.30, 0.94; p = 0.03).

Conclusion

This study shows early acquisition and high co-carriage of three important respiratory pathogens with S. pneumoniae in the nasopharyngeal mucosa among Gambian neonates and infants. This has important potential implications for the aetiology of respiratory polymicrobial infections, biofilm formation and vaccine strategies.
The prevalence of HBV infection in the cohort of IDPs of war against terrorism in Malakand Division of Northern Pakistan
Authors: Khan Fawad , Akbar Haji , Idrees Muhammad , Khan Hayat , Shahzad Khuram , Kayani Mahmood A
Published: June 2011

Background

Hepatitis B is an important public health problem in the Pakistani population and is the major cause of chronic hepatitis, cirrhosis, fibrosis and hepatocellular carcinoma. High prevalence of HBV infections has been observed especially in areas of low economic status. In spite of effective immunization programs, no significant change has been observed in the epidemiology of HBV in the rural areas of Pakistan (~67.5% of the total population) mainly due to lack of interest from government authorities and poor hygienic measures. The current study was aimed at estimating the prevalence and risk factors associated with HBV infection within internally displaced persons (IDPs) due to war against terrorism in the Malakand Division of Northern Pakistan.

Methods

Blood samples from 950 IDPs suspected with HBV infection (including both males and females) were collected and processed with commercial ELISA kits for HBsAg, Anti HBs, HBeAg, Anti HBe antibodies. The samples positive by ELISA were confirmed for HBV DNA by real-time PCR analysis.

Results

The overall prevalence of HBV observed was 21.05% of which 78.5% were males and 21.5% were females. Most confirmed HBV patients belong to the Malakand and Dir (lower) district. High-risk of infection was found in the older subjects 29.13% (46-60 years), while a lower incidence (11.97%) was observed in children aged <15 years. Lack of awareness, socioecomic conditions, sexual activities and sharing of razor blades, syringes and tattooing needles were the most common risk factors of HBV infection observed during the cohort of patients.

Conclusion

The present study, revealed for the first time a high degree of prevalence of HBV infection in rural areas of Northern Pakistan. The noticed prevalence is gender- and age-dependent that might be due to their high exposures to the common risk factors. To avoid the transmission of HBV infection proper awareness about the possible risk factors and extension of immunization to the rural areas are recommended.
Association between novel PLCE1variants identified in published esophageal cancer genome-wide association studies and risk of squamous cell carcinoma of the head and neck
Authors: Ma Hongxia , Wang Li-E , Liu Zhensheng , Sturgis Erich M , Wei Qingyi
Published: June 2011

Background

Phospholipase C epsilon 1 (PLCE1) (an effector of Ras) belonging to the phospholipase family plays crucial roles in carcinogenesis and progression of several cancers, including squamous cell carcinoma of the head and neck (SCCHN). A single nucleotide polymorphism (SNP, rs2274223) in PLCE1 has been identified as a novel susceptibility locus in genome-wide association studies (GWAS) of esophageal squamous cell carcinoma (ESCC) and gastric cardia adenocarcinoma (GCA) that share similar risk factors with SCCHN. Therefore, we investigated the association between potentially functional SNPs in PLCE1 and susceptibility to SCCHN.

Methods

We genotyped three potentially functional SNPs (rs2274223A/G, rs3203713A/G and rs11599672T/G) of PLCE1 in 1,098 SCCHN patients and 1,090 controls matched by age and sex in a non-Hispanic white population.

Results

Although none of three SNPs was alone significantly associated with overall risk of SCCHN, their combined effects of risk alleles (rs2274223G, rs3203713G and rs11599672G) were found to be associated with risk of SCCHN in a locus-dose effect manner (P
trend = 0.046), particularly for non-oropharyngeal tumors (P
trend = 0.017); specifically, rs2274223 was associated with a significantly increased risk (AG vs. AA: adjusted OR = 1.29, 95% CI = 1.01-1.64; AG/GG vs. AA: adjusted OR = 1.30, 95% CI = 1.03-1.64), while rs11599672 was associated with a significantly decreased risk (GG vs. TT: adjusted OR = 0.54, 95% CI = 0.34-0.86; TG/GG vs. TT: adjusted OR = 0.76, 95% CI = 0.61-0.95).

Conclusions

Our findings suggest that PLCE1 variants may have an effect on risk of SCCHN associated with tobacco and alcohol exposure, particularly for those tumors arising at non-oropharyngeal sites. These findings, although need to be validated by larger studies, are consistent with those in esophageal and gastric cancers.
Expression of phosphorylated raf kinase inhibitor protein (pRKIP) is a predictor of lung cancer survival
Authors: Huerta-Yepez Sara , Yoon Nam K , Hernandez-Cueto Angeles , Mah Vei , Rivera-Pazos Clara M , Chatterjee Devasis , Vega Mario I , Maresh Erin L , Horvath Steve , Chia David , Bonavida Benjamin , Goodglick Lee
Published: June 2011

Background

Raf-1 kinase inhibitor protein (RKIP) has been reported to negatively regulate signal kinases of major survival pathways. RKIP activity is modulated in part by phosphorylation on Serine 153 by protein kinase C, which leads to dissociation of RKIP from Raf-1. RKIP expression is low in many human cancers and represents an indicator of poor prognosis and/or induction of metastasis. The prognostic power has typically been based on total RKIP expression and has not considered the significance of phospho-RKIP.

Methods

The present study examined the expression levels of both RKIP and phospho-RKIP in human lung cancer tissue microarray proteomics technology.

Results

Total RKIP and phospho-RKIP expression levels were similar in normal and cancerous tissues. phospho-RKIP levels slightly decreased in metastatic lesions. However, the expression levels of phospho-RKIP, in contrast to total RKIP, displayed significant predictive power for outcome with normal expression of phospho-RKIP predicting a more favorable survival compared to lower levels (P = 0.0118); this was even more pronounced in more senior individuals and in those with early stage lung cancer.

Conclusions

This study examines for the first time, the expression profile of RKIP and phospho-RKIP in lung cancer. Significantly, we found that phospho-RKIP was a predictive indicator of survival.
Statistics-based model for prediction of chemical biosynthesis yield from Saccharomyces cerevisiae
Authors: Varman Arul M , Xiao Yi , Leonard Effendi , Tang Yinjie J
Published: June 2011

Background

The robustness of Saccharomyces cerevisiae in facilitating industrial-scale production of ethanol extends its utilization as a platform to synthesize other metabolites. Metabolic engineering strategies, typically via pathway overexpression and deletion, continue to play a key role for optimizing the conversion efficiency of substrates into the desired products. However, chemical production titer or yield remains difficult to predict based on reaction stoichiometry and mass balance. We sampled a large space of data of chemical production from S. cerevisiae, and developed a statistics-based model to calculate production yield using input variables that represent the number of enzymatic steps in the key biosynthetic pathway of interest, metabolic modifications, cultivation modes, nutrition and oxygen availability.

Results

Based on the production data of about 40 chemicals produced from S. cerevisiae, metabolic engineering methods, nutrient supplementation, and fermentation conditions described therein, we generated mathematical models with numerical and categorical variables to predict production yield. Statistically, the models showed that: 1. Chemical production from central metabolic precursors decreased exponentially with increasing number of enzymatic steps for biosynthesis (>30% loss of yield per enzymatic step, P-value = 0); 2. Categorical variables of gene overexpression and knockout improved product yield by 2~4 folds (P-value < 0.1); 3. Addition of notable amount of intermediate precursors or nutrients improved product yield by over five folds (P-value < 0.05); 4. Performing the cultivation in a well-controlled bioreactor enhanced the yield of product by three folds (P-value < 0.05); 5. Contribution of oxygen to product yield was not statistically significant. Yield calculations for various chemicals using the linear model were in fairly good agreement with the experimental values. The model generally underestimated the ethanol production as compared to other chemicals, which supported the notion that the metabolism of Saccharomyces cerevisiae has historically evolved for robust alcohol fermentation.

Conclusions

We generated simple mathematical models for first-order approximation of chemical production yield from S. cerevisiae. These linear models provide empirical insights to the effects of strain engineering and cultivation conditions toward biosynthetic efficiency. These models may not only provide guidelines for metabolic engineers to synthesize desired products, but also be useful to compare the biosynthesis performance among different research papers.
Convergence and weaker control conditions for hybrid iterative algorithms
Authors: Wang Shuang
Published: June 2011

Very recently, Yao et al. (Appl. Math. Comput. 216, 822-829, 2010) have proposed a hybrid iterative algorithm. Under the parameter sequences satisfying some quite restrictive conditions, they derived a strong convergence theorem in a Hilbert space. In this article, under the weaker conditions, we prove the strong convergence of the sequence generated by their iterative algorithm to a common fixed point of an infinite family of nonexpansive mappings, which solves a variational inequality. It is worth pointing out that we use a new method to prove our results. An appropriate example, such that all conditions of this result that are satisfied and that other conditions are not satisfied, is provided. Furthermore, we also give a weak convergence theorem for their iterative algorithm involving an infinite family of nonexpansive mappings in a Hilbert space.

MSC: 47H05, 47H09, 47H10
Generalizations of Caristi Kirk's Theorem on Partial Metric Spaces
Authors: Karapinar Erdal
Published: June 2011

In this article, lower semi-continuous maps are used to generalize Cristi-Kirk's fixed point theorem on partial metric spaces. First, we prove such a type of fixed point theorem in compact partial metric spaces, and then generalize to complete partial metric spaces. Some more general results are also obtained in partial metric spaces.

2000 Mathematics Subject Classification 47H10,54H25
Characterization of duck enteritis virus UL53 gene and glycoprotein K
Authors: Zhang Shunchuan , Xiang Jun , Cheng Anchun , Wang Mingshu , Wu Ying , Yang Xiaoyuan , Zhu Dekang , Jia Renyong , Luo Qihui , Chen Zhengli , Chen Xiaoyue
Published: June 2011

Background

Most of the previous research work had focused on the epidemiology and prevention of duck enteritis virus (DEV). Whilst with the development of protocols in molecular biology, nowadays more and more information about the genes of DEV was reported. But little information about DEV UL53 gene and glycoprotein K(gK) was known except our reported data.

Results

In our paper, the fluorescent quantitative real-time PCR(FQ-RT-PCR) assay and nucleic acid inhibition test were used to study the transcription characteristic of the DEV UL53 gene. Except detecting the mRNA of DEV UL53 gene, the product gK encoded by UL53 gene was detected through the expression kinetics of UL53 gene by the purified rabbit anti-UL53 protein polyclonal antibodies. Western-blotting and indirect immunofluorescence assays were used to detect gK. From the results of these experiments, the UL53 gene and gK were respectively identified as a late gene and a really late protein. On the other hand, the indirect immunofluorescence assay provided another information that the intracellular localization of DEV gK was mainly distributed in cytoplasm.

Conclusions

By way of conclusions, we conceded that DEV UL53 gene is a really late gene, which is coincident with properties of UL53 homologs from other herpesvirus, such as ILTV(Infectious Laryngotracheitis virus) and HSV-1(Herpes simplex virus type 1). The properties of intracellular localization about gK protein provided a foundation for further functional analysis and further studies will be focused on constructing of the UL53 gene DEV mutant.