bluuebunny/crossref_metadata_2025_split huggingface dataset:
BayMiR: inferring evidence for endogenous miRNA-induced gene repression from mRNA expression profiles
Authors: Radfar Hossein , Wong Willy , Morris Quaid 
Published: August 2013

Abstract

Background
Popular miRNA target prediction techniques use sequence features to determine the functional miRNA target sites. These techniques commonly ignore the cellular conditions in which miRNAs interact with their targets in vivo. Gene expression data are rich resources that can complement sequence features to take into account the context dependency of miRNAs.

Results
We introduce BayMiR, a new computational method, that predicts the functionality of potential miRNA target sites using the activity level of the miRNAs inferred from genome-wide mRNA expression profiles. We also found that mRNA expression variation can be used as another predictor of functional miRNA targets. We benchmarked BayMiR, the expression variation, Cometa, and the TargetScan “context scores” on two tasks: predicting independently validated miRNA targets and predicting the decrease in mRNA abundance in miRNA overexpression assays. BayMiR performed better than all other methods in both benchmarks and, surprisingly, the variation index performed better than Cometa and some individual determinants of the TargetScan context scores. Furthermore, BayMiR predicted miRNA target sets are more consistently annotated with GO and KEGG terms than similar sized random subsets of genes with conserved miRNA seed regions. BayMiR gives higher scores to target sites residing near the poly(A) tail which strongly favors mRNA degradation using poly(A) shortening. Our work also suggests that modeling multiplicative interactions among miRNAs is important to predict endogenous mRNA targets.

Conclusions
We develop a new computational method for predicting the target mRNAs of miRNAs. BayMiR applies a large number of mRNA expression profiles and successfully identifies the mRNA targets and miRNA activities without using miRNA expression data. The BayMiR package is publicly available and can be readily applied to any mRNA expression data sets.
Differential arthritogenicity of Staphylococcus aureusstrains isolated from biological samples
Authors: Colavite-Machado Priscila Maria , Ishikawa Larissa Lumi Watanabe , Donegá França Thaís Graziela , Zorzella-Pezavento Sofia Fernanda Gonçalves , da Rosa Larissa Camargo , Chiuso-Minicucci Fernanda , da Cunha Maria de Lourdes Ribeiro de Souza , Garlet Gustavo Pompermaier , Sartori Alexandrina 
Published: August 2013

Abstract

Background

Staphylococcus aureus is the most common agent of septic arthritis that is a severe, rapidly progressive and destructive joint disease. Superantigens produced by S. aureus are considered the major arthritogenic factors. In this study, we compared the arthritogenic potential of five superantigen-producing staphylococcal strains.

Methods
Male C57BL/6 mice were intravenously infected with ATCC 19095 SEC+, N315 ST5 TSST-1+, S-70 TSST-1+, ATCC 51650 TSST-1+ and ATCC 13565 SEA+ strains. Clinical parameters as body weight, arthritis incidence and clinical score were daily evaluated. Joint histopathological analysis and spleen cytokine production were evaluated at the 14th day after infection.

Results
Weight loss was observed in all infected mice. ATCC 19095 SEC+, N315 ST5 TSST-1+ and S-70 TSST-1+ were arthritogenic, being the highest scores observed in ATCC 19095 SEC+ infected mice. Intermediate and lower clinical scores were observed in N315 ST5 TSST-1+ and S-70 TSST-1+ infected mice, respectively. The ATCC 13565 SEA+ strain caused death of 85% of the animals after 48 h. Arthritis triggered by the ATCC 19095 SEC+ strain was characterized by accentuated synovial hyperplasia, inflammation, pannus formation, cartilage destruction and bone erosion. Similar joint alterations were found in N315 ST5 TSST-1+ infected mice, however they were strikingly more discrete. Only minor synovial proliferation and inflammation were triggered by the S-70 TSST-1+ strain. The lowest levels of TNF-α, IL-6 and IL-17 production in response to S. aureus stimulation were found in cultures from mice infected with the less arthritogenic strains (S-70 TSST-1+ and ATCC 51650 TSST-1+). The highest production of IL-17 was detected in mice infected with the most arthritogenic strains (ATCC 19095 SEC+ and N315 ST5 TSST-1+).

Conclusions
Together these results demonstrated that S. aureus strains, isolated from biological samples, were able to induce a typical septic arthritis in mice. These results also suggest that the variable arthritogenicity of these strains was, at least in part, related to their differential ability to induce IL-17 production.
Detection of the V1016G mutation in the voltage-gated sodium channel gene of Aedes aegypti (Diptera: Culicidae) by allele-specific PCR assay, and its distribution and effect on deltamethrin resistance in Thailand
Authors: Stenhouse Steven A , Plernsub Suriya , Yanola Jintana , Lumjuan Nongkran , Dantrakool Anchalee , Choochote Wej , Somboon Pradya 
Published: August 2013

Abstract

Background
Resistance to pyrethroid insecticides is widespread among populations of Aedes aegypti, the main vector for the dengue virus. Several different point mutations within the voltage-gated sodium channel (VGSC) gene contribute to such resistance. A mutation at position 1016 in domain II, segment 6 of the VGSC gene in Ae. aegypti leads to a valine to glycine substitution (V1016G) that confers resistance to deltamethrin.

Methods
This study developed and utilized an allele-specific PCR (AS-PCR) assay that could be used to detect the V1016G mutation. The assay was validated against a number of sequenced DNA samples of known genotype and was determined to be in complete agreement. Larvae and pupae were collected from various localities throughout Thailand. Samples were reared to adulthood and their resistance status against deltamethrin was determined by standard WHO susceptibility bioassays. Deltamethrin-resistant and susceptible insects were then genotyped for the V1016G mutation. Additionally, some samples were genotyped for a second mutation at position 1534 in domain III (F1534C) which is also known to confer pyrethroid resistance.

Results
The bioassay results revealed an overall mortality of 77.6%. Homozygous 1016G individuals survived at higher rates than either heterozygous or wild-type (1016 V) mosquitoes. The 1016G mutation was significantly and positively associated with deltamethrin resistance and was widely distributed throughout Thailand. Interestingly, wild-type 1016 V mosquitoes tested were homozygous for the 1534C mutation, and all heterozygous mosquitoes were also heterozygous for 1534C. Mutant homozygous (G/G) mosquitoes expressed the wild-type (F/F) at position 1534. However, the presence of the 1534C mutation was not associated with deltamethrin resistance.

Conclusions
Our bioassay results indicate that all populations sampled display some degree of resistance to deltamethrin. Homozygous 1016G mosquitoes were far likelier to survive such exposure. However, resistance in some populations cannot be explained due to kdr mutations and indicates that other resistance mechanisms are operating. The presence of this mutation alone does not fully explain the resistance phenotype we see among Thai Ae. aegypti populations.
DNA barcode assessment of Gracilaria salicornia (Gracilariaceae, Rhodophyta) from Southeast Asia
Authors: Yang Mi Yeon , Geraldino Paul John L , Kim Myung Sook 
Published: August 2013

Abstract

Background
DNA barcoding is becoming a widely applied tool for the quick and accurate identification of species. The evolution of the mitochondrial cytochrome c oxidase subunit I (COI) gene is sufficiently rapid to allow discrimination between closely related species and biogeographic subgroups within species. Gracilaria salicornia was originally described as being from Manila, the Philippines, and is distributed throughout Asia and the Indian Ocean. To more accurately define this species and its genetic diversity owing to the confusion of identification historically, DNA barcoding using the 5’ end of the COI gene of the mitochondrial genome was applied to specimens collected from the Philippines, Malaysia, Thailand, China, and Japan, and they were compared to other gracilarian species.

Results
Within species, the COI marker yielded two clusters with nucleotide divergences of 0.0–1.3%. This divergence is slightly higher than the typical intraspecific variation for red algae. A total of eight COI haplotypes were found for G. salicornia, comprising the following groups: H1–H3 from the Philippines; H4 from Okinawa in Japan; H5–H7 from Malaysia, Thailand, and China; and H8 from Thailand.

Conclusion
Although this work concentrated on a limited geographical region of a widespread taxon, the data shows intraspecific molecular divergences in G. salicornia and provides further evidence that DNA barcodes are useful tools for identifying species boundaries and examining biogeographical haplotypes for the genus Gracilaria.
TLR2 & Co: a critical analysis of the complex interactions between TLR2 and coreceptors
Authors: van Bergenhenegouwen Jeroen , Plantinga Theo S , Joosten Leo A B , Netea Mihai G , Folkerts Gert , Kraneveld Aletta D , Garssen Johan , Vos Arjan P 
Published: August 2013

ABSTRACTTLRs play a major role in microbe-host interactions and innate immunity. Of the 10 functional TLRs described in humans, TLR2 is unique in its requirement to form heterodimers with TLR1 or TLR6 for the initiation of signaling and cellular activation. The ligand specificity of TLR2 heterodimers has been studied extensively, using specific bacterial and synthetic lipoproteins to gain insight into the structure-function relationship, the minimal active motifs, and the critical dependence on TLR1 or TLR6 for activation. Different from that for specific well-defined TLR2 agonists, recognition of more complex ligands like intact microbes or molecules from endogenous origin requires TLR2 to interact with additional coreceptors. A breadth of data has been published on ligand-induced interactions of TLR2 with additional pattern recognition receptors such as CD14, scavenger receptors, integrins, and a range of other receptors, all of them important factors in TLR2 function. This review summarizes the roles of TLR2 in vivo and in specific immune cell types and integrates this information with a detailed review of our current understanding of the roles of specific coreceptors and ligands in regulating TLR2 functions. Understanding how these processes affect intracellular signaling and drive functional immune responses will lead to a better understanding of host-microbe interactions and will aid in the design of new agents to target TLR2 function in health and disease.
Quantum Chemical Designing of Efficient TC4-Based Sensitizers by Modification of Auxiliary Donor and π-Spacer
Authors: Abdullah Muhammad Imran , Janjua Muhammad Ramzan Saeed Ashraf , Nazar Muhammad Faizan , Mahmood Asif 
Published: August 2013

Abstract
In the present study, ten metal-free dyes for dye-sensitized solar cells (DSSCs) have been designed. These dyes have designed by structural modification of TC4. Density functional theory was used for structure optimization and determination of photophysical properties. These dyes contain triphenylamine as electron donor and cyanoacrylic acid as electron acceptor. Five π-spacers are used to connect the donor and acceptor. Two auxiliary donors are also used to assist the donor. Results of this study indicate that stronger electron-donating auxiliary groups and longer π-conjugation enhance, while electron-withdrawing fluorine at a π-spacer decreases the performance of dyes in DSSC. As compared to auxiliary electron donors, π-spacers have a strong impact on the performance of the dyes in the DSSCs. Major absorption peaks of all dyes were in the visible region. These absorption peaks are associated with the π–π* transitions of the entire molecule. From calculations it is clear that all dyes will be good photosensitizers in DSSC. The present calculations will provide new ways for experimentalists to synthesize high-performance dyes.
Do bisphosphonates inhibit direct fracture healing?
Authors: Savaridas T. , Wallace R. J. , Salter D. M. , Simpson A. H. R. W. 
Published: August 2013

Fracture repair occurs by two broad mechanisms: direct healing, and indirect healing with callus formation. The effects of bisphosphonates on fracture repair have been assessed only in models of indirect fracture healing. A rodent model of rigid compression plate fixation of a standardised tibial osteotomy was used. Ten skeletally mature Sprague–Dawley rats received daily subcutaneous injections of 1 µg/kg ibandronate (IBAN) and ten control rats received saline (control). Three weeks later a tibial osteotomy was rigidly fixed with compression plating. Six weeks later the animals were killed. Fracture repair was assessed with mechanical testing, radiographs and histology. The mean stress at failure in a four-point bending test was significantly lower in the IBAN group compared with controls (8.69 Nmm-2 (sd 7.63) vs 24.65 Nmm-2 (sd 6.15); p = 0.017). On contact radiographs of the extricated tibiae the mean bone density assessment at the osteotomy site was lower in the IBAN group than in controls (3.7 mmAl (sd 0.75) vs 4.6 mmAl (sd 0.57); p = 0.01). In addition, histological analysis revealed progression to fracture union in the controls but impaired fracture healing in the IBAN group, with predominantly cartilage-like and undifferentiated mesenchymal tissue (p = 0.007). Bisphosphonate treatment in a therapeutic dose, as used for risk reduction in fragility fractures, had an inhibitory effect on direct fracture healing. We propose that bisphosphonate therapy not be commenced until after the fracture has united if the fracture has been rigidly fixed and is undergoing direct osteonal healing. Cite this article: Bone Joint J 2013;95-B:1263–8.
Surgeon level data
Authors: Perry D. C. , Parsons N. , Costa M. L. 
Published: August 2013

The variation in surgical performance, both between centres and individual surgeons, has recently been of significant political, media and public interest. Within the United Kingdom, a government agenda to increase accountability amongst surgeons has led to the online publication of ‘surgeon-level’ data. Surgeons, journalists and the public need to understand these data if they are to be useful in driving up standards of surgical care. This Editorial describes the use of Funnel Plots, which are the common means by which such data are presented, and discusses how the plots are generated. Cite this article: Bone Joint J 2013;95-B:1156–7.
Towards a narrative concept of citizenship: Implications for citizenship education as children’s identity-making
Authors: Kim Byung-Geuk 
Published: August 2013

Abstract
This article offers a narrative concept of citizenship in order to suggest a model of citizenship education as opposed to the factual, values-oriented model currently emphasized in Korea. Korea’s current approach to citizenship education is shaped by a mandated moral education curriculum meant to instil selected national values and moral virtues in children through a top-down method of teaching and learning citizenship. The article develops a different concept of citizenship in order to inspire the practice of citizenship education as children’s identity-making. The new concept, which employs a narrative inquiry methodology for the autobiographical inquiry, is found to be in fundamental conflict with Korea’s current practice of citizenship education: the narrative concept of citizenship attends to children’s lived experiences as a starting point for citizenship education that educates children about who they are and how they live as citizens. In contrast, the predetermined values-/virtues-oriented view of citizenship underpinning the established teaching practices in Korea educates children to be knowledgeable about citizenship values or virtues without establishing the relevance of this knowledge in their lives. This study suggests that, given the goals and standards of citizenship education, the narrative concept of citizenship would be far more effective in that it allows children to see themselves in multiple dimensions of good citizenship.
Switching sides: The struggle between national identity and globalized pedagogy in the development of an early literacy programme in Cambodia
Authors: Courtney Jane , Gravelle Maggie 
Published: August 2013

Abstract
In 2006 a bi-lateral donor working with the Ministry of Education, Youth and Sport (MoEYS) in Cambodia identified the need for improving the quality of literacy. The bilateral donor outsourced the contract to a team of British consultants to design and lead an early literacy project working alongside Khmer national consultants. This article begins by discussing and analysing how globalized perceptions of teaching, learning and national identity were enshrined in the development of training and classroom materials for both teacher and pupils. It uses the example of the place of phonics in the teaching of reading to explore the contradictions in practice between donor and low income countries. By examining the perceptions and assumptions made by all parties and analysing the discourse that took place in the development process it is possible to identify how national education and perceptions of identity and citizenship come into conflict with what was identified as a ‘global pedagogy’. As more agencies become involved and agendas change, the conflict between issues of national identity, citizenship and global pedagogy become increasingly blurred leaving the authors the task of unpacking the relative importance of these concepts on the impact of the project. We conclude that in educational project design there is a need to strike a balance between the influences exerted through international practice and priorities against the effects of local conditions, culture and context.
Revisiting the notion of political black cinema: A comparative analysis of Melvin Van Peebles and Ousmane Sembene
Authors: Ryan Connor 
Published: August 2013

Abstract
This article revisits Ousmane Sembene’s La Noire de ... (1966) and Melvin Van Peebles’s Sweet Sweetback’s Baaadasssss Song (1971) to put pressure on Sembene’s legacy as an advocate of African women’s rights and Van Peeble’s reputation as a provocative voice in the American Black Arts Movement. Focusing on each films’ defiant yet silent protagonists, this article questions feminism’s concern for women to speak out against patriarchy that would silence them. It asks whose liberation the films provide for, and interrogates cinema that speaks for the voiceless. This article posits that artistic voice, even when mobilized for political resistance, always presents a risk and threat of displacing violence. Speaking out against oppression, whether white supremacist, neo-imperialist or patriarchal oppression, requires the speaker to wield a certain authority that invests in other means of oppression. This article addresses the politically committed artist’s responsibility to navigate the tenuous relationship between politics and art.
Sexual behavior of in-school adolescents in Osun State, Southwest Nigeria: a comparative study
Authors: Sabageh Adedayo O. , Fatusi Adesegun O. , Sabageh Donatus , Aluko Joel A. 
Published: August 2013

Abstract
Objectives: The sexual and reproductive health of adolescents is of utmost importance in many nations (especially in developing countries). Sexual behavior varies from location to location and the outcome (when negative) creates great concerns mainly due to the consequential impact on health and development. This study aimed at comparing sexual behavior of in-school adolescents in rural and urban areas of Osun state.
Methods: A comparative cross sectional study was conducted. A total of 760 in-school adolescents were recruited using multistage sampling technique. Pre-tested questionnaires were administered after ethical considerations. Data were analysed and p-value was placed at 0.05.
Results: A total of 380 rural and 380 urban adolescents participated in this study with a mean age of 14.90±2.44 and 14.34±2.31 years, respectively. About one-fifth (20.1%) had experienced their first sex (66% of rural and 34% of urban). The mean age at first sex was 14.05 years±2.3 years (13.89±2.3 years for rural and 14.37±2.3 years for urban). Only 76 (49.7%) sexually experienced respondents had used condom in the past (45.5% of rural, 57.7% of urban). Half of the urban respondents used condom during their first sex while only a quarter of their rural counterparts had done so (p=0.003).
Conclusion: Sexual behavior was commoner among the rural respondents than their urban counterpart. There is an urgent need for sexuality education especially among rural adolescents in the study area.
A rare case of hypopituitarism with psychosis
Authors: Nwokolo M , Fletcher J 
Published: August 2013

SummaryA 46-year-old woman presented multiple times in a 4-month period with hypotension, sepsis, hypoglycaemia and psychosis. A low random cortisol in combination with her presenting complaint made adrenal insufficiency the likely diagnosis. Fluid resuscitation and i.v. steroid therapy led to clinical improvement; however, a short synacthen test (SST) demonstrated an apparently satisfactory cortisol response. The test was repeated on a later admission and revealed a peak cortisol level of 25 nmol/l (>550 nmol/l). Concurrent treatment with i.v. hydrocortisone had led to a false-negative SST. ACTH was <5 ng/l (>10 ng/l), indicating secondary adrenal failure. We discuss the challenges surrounding the diagnosis of adrenal insufficiency and hypopituitarism, the rare complication of psychosis and a presumptive diagnosis of autoimmune lymphocytic hypophysitis (ALH).Learning pointsAdrenocortical insufficiency must be considered in the shocked, hypovolaemic and hypoglycaemic patient with electrolyte imbalance. Rapid treatment with fluid resuscitation and i.v. corticosteroids is vital.Polymorphic presentations to multiple specialities are common. Generalised myalgia, abdominal pain and delirium are well recognised, psychosis is rare.A random cortisol can be taken with baseline bloods. Once the patient is stable, meticulous dynamic testing must follow to confirm the clinical diagnosis.The chronic disease progression of ALH is hypothesised to be expansion then atrophy of the pituitary gland resulting in empty sella turcica and hypopituitarism.If hypopituitarism is suspected, an ACTH deficiency should be treated prior to commencing thyroxine (T4) therapy as unopposed T4may worsen features of cortisol deficiency.