Coloration, Camouflage, and Sexual Dichromatism in the Northern Pacific Rattlesnake (Crotalus oreganus)

In some viperid snakes, natural selection has shaped coloration and patterning to match local habitats, and for males to show greater warning coloration than females due to a less sedentary lifestyle. The Northern Pacific Rattlesnake (Crotalus oreganus) is likely the most abundant ambush predator in eastern Washington, yet little is known about its color variation, how color patterns interact with their habitats, and if male and female snakes show differences in patterning or color. To explore how snake color might interact with the colors of their environment, I used standardized digital photography to record both snake and substrate coloration. I sampled 127 rattlesnakes from overwintering hibernacula and compared their coloration to that of the surrounding habitat. I also used satellite imagery and land cover classification to investigate possible relationships between snake coloration and habitat at a broader landscape level. The hypothesis that C. oreganus shows sexual dichromatism (inter-sexual differences in color and/or pattern) was also tested by comparing both overall snake color, and the strength of contrast in tail bands between the sexes. I found that C. oreganus varies in color significantly, both locally between hibernacula, and regionally. Snake coloration was not associated with the degree of forested area within a 0.5 km radius of the hibernacula, and no significant differences in color were observed between the sexes. Despite this, the color of male and female snakes interacted differently with the habitat surrounding the hibernacula, where male snakes showed increased Red/Blue color ratios in high forested areas, while females showed lower ratios. Importantly, males showed significantly greater contrast in their tail bands than did females, suggesting increased selection for warning patterns and coloration in male snakes. Sexual dimorphism is usually attributed to sexual selection. In contrast, the sexually dichromatic warning coloration observed in this study is an example of “Ecologically Caused Sexual Dimorphism”, which has now been observed in at least two species of viper. My results suggest that other viper species with similar natural history traits to C. oreganus may also exhibit sexual dichromatism, where males have exaggerated warning colors in comparison to females

Phase Variation of Poly-N-Acetylglucosamine Expression in Staphylococcus aureus

Polysaccharide intercellular adhesin (PIA), also known as poly-N-acetyl-β-(1–6)-glucosamine (PIA/PNAG) is an important component of Staphylococcus aureus biofilms and also contributes to resistance to phagocytosis. The proteins IcaA, IcaD, IcaB, and IcaC are encoded within the intercellular adhesin (ica) operon and synthesize PIA/PNAG. We discovered a mechanism of phase variation in PIA/PNAG expression that appears to involve slipped-strand mispairing. The process is reversible and RecA-independent, and involves the expansion and contraction of a simple tetranucleotide tandem repeat within icaC. Inactivation of IcaC results in a PIA/PNAG-negative phenotype. A PIA/PNAG-hyperproducing strain gained a fitness advantage in vitro following the icaC mutation and loss of PIA/PNAG production. The mutation was also detected in two clinical isolates, suggesting that under certain conditions, loss of PIA/PNAG production may be advantageous during infection. There was also a survival advantage for an icaC-negative strain harboring intact icaADB genes relative to an isogenicicaADBC deletion mutant. Together, these results suggest that inactivation of icaC is a mode of phase variation for PIA/PNAG expression, that high-level production of PIA/PNAG carries a fitness cost, and that icaADB may contribute to bacterial fitness, by an unknown mechanism, in the absence of an intact icaC gene and PIA/PNAG production

A Critical Review onMathematical Descriptions to Study Flux Processes and Environmental-Related Interactions ofMangroves

Trees are resources that provide multiple benefits, such as the conservation of fauna, both terrestrial and marine, a source of food and raw material, and offering protection in storms, which makes it practical to understand their behavior against different phenomena. Such understanding may be possible through process modeling. Studies confirm that mangrove forests can store more carbon than other forests, influencing the fight against global warming. Thus, a critical and systematic review was carried out regarding studies focusing on mangroves to collect information on the models that have been applied and the most influential variables highlighted by other authors. Applying a systematic search for the most relevant topics related to mangroves (basic as well as recent information), it is possible to group models and methods carried out by other authors to respond to certain behaviors presented by mangroves. Moreover, possible structuring of a mathematical model applied to a species of interest thanks to the analyzed references could provide justified information to the authorities on the importance of these forests and the benefits of their preservation and regeneration-recovery.Trees are resources that provide multiple benefits, such as the conservation of fauna, both terrestrial and marine, a source of food and raw material, and offering protection in storms, which makes it practical to understand their behavior against different phenomena. Such understanding may be possible through process modeling. Studies confirm that mangrove forests can store more carbon than other forests, influencing the fight against global warming. Thus, a critical and systematic review was carried out regarding studies focusing on mangroves to collect information on the models that have been applied and the most influential variables highlighted by other authors. Applying a systematic search for the most relevant topics related to mangroves (basic as well as recent information), it is possible to group models and methods carried out by other authors to respond to certain behaviors presented by mangroves. Moreover, possible structuring of a mathematical model applied to a species of interest thanks to the analyzed references could provide justified information to the authorities on the importance of these forests and the benefits of their preservation and regeneration-recovery

Stressful Life Events and Behavior Change: A Qualitative Examination of African American Women\u27s Participation in a Weight Loss Program

We qualitatively assessed how life stressors affected African American women\u27s participation in a weight reduction program. A sample of 9 women, who completed a behavioral lifestyle intervention, participated in individual, structured, in-depth interviews. Life stressors, ranging from personal illness to changes in employment status, had varied effects on participation. Some women coped with life stressors by using them as a motivational tool to improve their own health, while others reported limited ability to devote time to attend meetings or engage in the prescribed lifestyle changes due to life stressors. A critical key to improving weight loss outcomes for African American women may be using intervention strategies that teach positive coping skills to alter maladaptive responses to life stressors

Species-level classification of the vaginal microbiome

Background The application of next-generation sequencing to the study of the vaginal microbiome is revealing the spectrum of microbial communities that inhabit the human vagina. High-resolution identification of bacterial taxa, minimally to the species level, is necessary to fully understand the association of the vaginal microbiome with bacterial vaginosis, sexually transmitted infections, pregnancy complications, menopause, and other physiological and infectious conditions. However, most current taxonomic assignment strategies based on metagenomic 16S rDNA sequence analysis provide at best a genus-level resolution. While surveys of 16S rRNA gene sequences are common in microbiome studies, few well-curated, body-site-specific reference databases of 16S rRNA gene sequences are available, and no such resource is available for vaginal microbiome studies. Results We constructed the Vaginal 16S rDNA Reference Database, a comprehensive and non-redundant database of 16S rDNA reference sequences for bacterial taxa likely to be associated with vaginal health, and we developed STIRRUPS, a new method that employs the USEARCH algorithm with a curated reference database for rapid species-level classification of 16S rDNA partial sequences. The method was applied to two datasets of V1-V3 16S rDNA reads: one generated from a mock community containing DNA from six bacterial strains associated with vaginal health, and a second generated from over 1,000 mid-vaginal samples collected as part of the Vaginal Human Microbiome Project at Virginia Commonwealth University. In both datasets, STIRRUPS, used in conjunction with the Vaginal 16S rDNA Reference Database, classified more than 95% of processed reads to a species-level taxon using a 97% global identity threshold for assignment. Conclusions This database and method provide accurate species-level classifications of metagenomic 16S rDNA sequence reads that will be useful for analysis and comparison of microbiome profiles from vaginal samples. STIRRUPS can be used to classify 16S rDNA sequence reads from other ecological niches if an appropriate reference database of 16S rDNA sequences is available

The Vaginal Microbiome: Disease, Genetics and the Environment

The vagina is an interactive interface between the host and the environment. Its surface is covered by a protective epithelium colonized by bacteria and other microorganisms. The ectocervix is nonsterile, whereas the endocervix and the upper genital tract are assumed to be sterile in healthy women. Therefore, the cervix serves a pivotal role as a gatekeeper to protect the upper genital tract from microbial invasion and subsequent reproductive pathology. Microorganisms that cross this barrier can cause preterm labor, pelvic inflammatory disease, and other gynecologic and reproductive disorders. Homeostasis of the microbiome in the vagina and ectocervix plays a paramount role in reproductive health. Depending on its composition, the microbiome may protect the vagina from infectious or non-infectious diseases, or it may enhance its susceptibility to them. Because of the nature of this organ, and the fact that it is continuously colonized by bacteria from birth to death, it is virtually certain that this rich environment evolved in concert with its microbial flora. Specific interactions dictated by the genetics of both the host and microbes are likely responsible for maintaining both the environment and the microbiome. However, the genetic basis of these interactions in both the host and the bacterial colonizers is currently unknown. _Lactobacillus_ species are associated with vaginal health, but the role of these species in the maintenance of health is not yet well defined. Similarly, other species, including those representing minor components of the overall flora, undoubtedly influence the ability of potential pathogens to thrive and cause disease. Gross alterations in the vaginal microbiome are frequently observed in women with bacterial vaginosis, but the exact etiology of this disorder is still unknown. There are also implications for vaginal flora in non-infectious conditions such as pregnancy, pre-term labor and birth, and possibly fertility and other aspects of women’s health. Conversely, the role of environmental factors in the maintenance of a healthy vaginal microbiome is largely unknown. To explore these issues, we have proposed to address the following questions:

*1.	Do the genes of the host contribute to the composition of the vaginal microbiome?* We hypothesize that genes of both host and bacteria have important impacts on the vaginal microbiome. We are addressing this question by examining the vaginal microbiomes of mono- and dizygotic twin pairs selected from the over 170,000 twin pairs in the Mid-Atlantic Twin Registry (MATR). Subsequent studies, beyond the scope of the current project, may investigate which host genes impact the microbial flora and how they do so.
*2.	What changes in the microbiome are associated with common non-infectious pathological states of the host?* We hypothesize that altered physiological (e.g., pregnancy) and pathologic (e.g., immune suppression) conditions, or environmental exposures (e.g., antibiotics) predictably alter the vaginal microbiome. Conversely, certain vaginal microbiome characteristics are thought to contribute to a woman’s risk for outcomes such as preterm delivery. We are addressing this question by recruiting study participants from the ~40,000 annual clinical visits to women’s clinics of the VCU Health System.
*3.	What changes in the vaginal microbiome are associated with relevant infectious diseases and conditions?* We hypothesize that susceptibility to infectious disease (e.g. HPV, _Chlamydia_ infection, vaginitis, vaginosis, etc.) is impacted by the vaginal microbiome. In turn, these infectious conditions clearly can affect the ability of other bacteria to colonize and cause pathology. Again, we are exploring these issues by recruiting participants from visitors to women’s clinics in the VCU Health System.

Three kinds of sequence data are generated in this project: i) rDNA sequences from vaginal microbes; ii) whole metagenome shotgun sequences from vaginal samples; and iii) whole genome shotgun sequences of bacterial clones selected from vaginal samples. The study includes samples from three vaginal sites: mid-vaginal, cervical, and introital. The data sets also include buccal and perianal samples from all twin participants. Samples from these additional sites are used to test the hypothesis of a per continuum spread of bacteria in relation to vaginal health. An extended set of clinical metadata associated with these sequences are deposited with dbGAP. We have currently collected over 4,400 samples from ~100 twins and over 450 clinical participants. We have analyzed and deposited data for 480 rDNA samples, eight whole metagenome shotgun samples, and over 50 complete bacterial genomes. These data are available to accredited investigators according to NIH and Human Microbiome Project (HMP) guidelines. The bacterial clones are deposited in the Biodefense and Emerging Infections Research Resources Repository ("http://www.beiresources.org/":http://www.beiresources.org/). 

In addition to the extensive sequence data obtained in this study, we are collecting metadata associated with each of the study participants. Thus, participants are asked to complete an extensive health history questionnaire at the time samples are collected. Selected clinical data associated with the visit are also obtained, and relevant information is collected from the medical records when available. This data is maintained securely in a HIPAA-compliant data system as required by VCU’s Institutional Review Board (IRB). The preponderance of these data (i.e., that judged appropriate by NIH staff and VCU’s IRB are deposited at dbGAP ("http://www.ncbi.nlm.nih.gov/gap":http://www.ncbi.nlm.nih.gov/gap). Selected fields of this data have been identified by NIH staff as ‘too sensitive’ and are not available in dbGAP. Individuals requiring access to these data fields are asked to contact the PI of this project or NIH Program Staff. 
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The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies

Background Characterizing microbial communities via next-generation sequencing is subject to a number of pitfalls involving sample processing. The observed community composition can be a severe distortion of the quantities of bacteria actually present in the microbiome, hampering analysis and threatening the validity of conclusions from metagenomic studies. We introduce an experimental protocol using mock communities for quantifying and characterizing bias introduced in the sample processing pipeline. We used 80 bacterial mock communities comprised of prescribed proportions of cells from seven vaginally-relevant bacterial strains to assess the bias introduced in the sample processing pipeline. We created two additional sets of 80 mock communities by mixing prescribed quantities of DNA and PCR product to quantify the relative contribution to bias of (1) DNA extraction, (2) PCR amplification, and (3) sequencing and taxonomic classification for particular choices of protocols for each step. We developed models to predict the “true” composition of environmental samples based on the observed proportions, and applied them to a set of clinical vaginal samples from a single subject during four visits. Results We observed that using different DNA extraction kits can produce dramatically different results but bias is introduced regardless of the choice of kit. We observed error rates from bias of over 85% in some samples, while technical variation was very low at less than 5% for most bacteria. The effects of DNA extraction and PCR amplification for our protocols were much larger than those due to sequencing and classification. The processing steps affected different bacteria in different ways, resulting in amplified and suppressed observed proportions of a community. When predictive models were applied to clinical samples from a subject, the predicted microbiome profiles were better reflections of the physiology and diagnosis of the subject at the visits than the observed community compositions. Conclusions Bias in 16S studies due to DNA extraction and PCR amplification will continue to require attention despite further advances in sequencing technology. Analysis of mock communities can help assess bias and facilitate the interpretation of results from environmental samples

Segurança na mudança direta de natalizumabe para fingolimode em um grupo de pacientes com esclerose múltipla e positivos para JCV

To assess safety of the switch between natalizumab and fingolimod without a washout period. Methods Prospective data on 25 JCV positive patients who underwent this medication switch were collected and analyzed. Results After a median period of nine months from the medication switch, there were no safety issues to report. The patients had good disease control and no adverse events were reported. Conclusion Washout may not be necessary in daily practice when switching from natalizumab to fingolimod. Expertise on multiple sclerosis management, however, is essential for drug switching748650652Avaliar a segurança na mudança entre natalizumabe e fingolimode sem período de washout. Métodos Dados prospectivos de 25 pacientes positivos para vírus JC que tiveram sua medicação modificada foram coletados e analisados. Resultados Após uma mediana de nove meses da troca de medicação, não havia aspectos de segurança a relatar. Os pacientes estavam com bom controle da doença e não foram relatados eventos adversos. Conclusão Washout pode não ser necessário na prática diária para a mudança entre natalizumabe e fingolimode. No entanto, expertise no manejo de esclerose múltipla é essencial para esta troca entre medicaçõe

“It’s a silver lining”: A template analysis of satisfaction and quality of life following post-mastectomy breast reconstruction

The file attached to this record is the author's final peer reviewed version.Objective: In the United Kingdom, the number of women electing to undergo post-mastectomy breast reconstruction is increasing. As a consequence exploring patient-reported outcomes in breast surgery has become increasingly important. This study aims to explore satisfaction and quality of life following post-mastectomy breast reconstruction. Design: Qualitative research design. Methods: In-depth, semi-structured telephone interviews were conducted with 25 women, (Age, M= 53.08, SD=8.41) following breast reconstruction in the United Kingdom. Data were analysed using template analysis which produced three first-level, 13 second-level and 19 third-level themes. Results: Following reconstruction women reported improved emotional functioning, although this was often accompanied with deterioration in physical, sexual and/or social functioning. Women positively appraised their breast appearance, although some reported a decline in satisfaction over time and attributed this decline to their chosen reconstructive technique. Many women accepted the inevitability of scarring and most perceived their scars as a representation of their journey, signifying survival. Generally women were satisfied with the outcome of their reconstruction, although on reflection some would not have opted for reconstruction. Following breast reconstruction women were increasingly likely to experience the fear of recurrence, attributed to no longer being able to have a mammogram on the affected breast(s). Conclusions: This study provides new insights into post-mastectomy breast reconstruction and is a novel application of the qualitative data analysis method, template analysis. Template analysis demonstrates only slight variation in some categories of experience among women, despite a heterogeneous sample. The findings allow researchers and clinicians to focus on specific dimensions of satisfaction and quality of life to positively support the needs of women following reconstructio

Twitter influence on UK vaccination and antiviral uptake during the 2009 H1N1 pandemic

Objective: Information exchange via Twitter and other forms of social media make public health communication more complex as citizens play an increasingly influential role in shaping acceptable or desired health behaviors. Taking the case of the 2009–2010 H1N1 pandemic, we explore in detail the dissemination of H1N1-related advice in the UK through Twitter to see how it was used to discourage or encourage vaccine and antiviral uptake. Methods: In three stages we conducted (1) an analysis of general content, retweeting patterns, and URL sharing, (2) a discourse analysis of the public evaluation of press releases and (3) a template analysis of conversations around vaccine and antiviral uptake, using Protection Motivation Theory (PMT) as a way of understanding how the public weighed the costs and benefits. Results: Network analysis of retweets showed that information from official sources predominated. Analysing the spread of significant messages through Twitter showed that most content was descriptive but there was some criticism of health authorities. A detailed analysis of responses to press releases revealed some scepticism over the economic beneficiaries of vaccination, that served to undermine public trust. Finally, the conversational analysis showed the influence of peers when weighing up the risks and benefits of medication. Conclusion: Most tweets linked to reliable sources, however Twitter was used to discuss both individual and health authority motivations to vaccinate. The PMT framework describes the ways individuals assessed the threat of the H1N1 pandemic, weighing this against the perceived cost of taking medication. These findings offer some valuable insights for social media communication practices in future pandemics