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1.  VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics 
Nucleic Acids Research  2011;40(Database issue):D729-D734.
VectorBase (http://www.vectorbase.org) is a NIAID-supported bioinformatics resource for invertebrate vectors of human pathogens. It hosts data for nine genomes: mosquitoes (three Anopheles gambiae genomes, Aedes aegypti and Culex quinquefasciatus), tick (Ixodes scapularis), body louse (Pediculus humanus), kissing bug (Rhodnius prolixus) and tsetse fly (Glossina morsitans). Hosted data range from genomic features and expression data to population genetics and ontologies. We describe improvements and integration of new data that expand our taxonomic coverage. Releases are bi-monthly and include the delivery of preliminary data for emerging genomes. Frequent updates of the genome browser provide VectorBase users with increasing options for visualizing their own high-throughput data. One major development is a new population biology resource for storing genomic variations, insecticide resistance data and their associated metadata. It takes advantage of improved ontologies and controlled vocabularies. Combined, these new features ensure timely release of multiple types of data in the public domain while helping overcome the bottlenecks of bioinformatics and annotation by engaging with our user community.
doi:10.1093/nar/gkr1089
PMCID: PMC3245112  PMID: 22135296
2.  The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima 
Chipman, Ariel D. | Ferrier, David E. K. | Brena, Carlo | Qu, Jiaxin | Hughes, Daniel S. T. | Schröder, Reinhard | Torres-Oliva, Montserrat | Znassi, Nadia | Jiang, Huaiyang | Almeida, Francisca C. | Alonso, Claudio R. | Apostolou, Zivkos | Aqrawi, Peshtewani | Arthur, Wallace | Barna, Jennifer C. J. | Blankenburg, Kerstin P. | Brites, Daniela | Capella-Gutiérrez, Salvador | Coyle, Marcus | Dearden, Peter K. | Du Pasquier, Louis | Duncan, Elizabeth J. | Ebert, Dieter | Eibner, Cornelius | Erikson, Galina | Evans, Peter D. | Extavour, Cassandra G. | Francisco, Liezl | Gabaldón, Toni | Gillis, William J. | Goodwin-Horn, Elizabeth A. | Green, Jack E. | Griffiths-Jones, Sam | Grimmelikhuijzen, Cornelis J. P. | Gubbala, Sai | Guigó, Roderic | Han, Yi | Hauser, Frank | Havlak, Paul | Hayden, Luke | Helbing, Sophie | Holder, Michael | Hui, Jerome H. L. | Hunn, Julia P. | Hunnekuhl, Vera S. | Jackson, LaRonda | Javaid, Mehwish | Jhangiani, Shalini N. | Jiggins, Francis M. | Jones, Tamsin E. | Kaiser, Tobias S. | Kalra, Divya | Kenny, Nathan J. | Korchina, Viktoriya | Kovar, Christie L. | Kraus, F. Bernhard | Lapraz, François | Lee, Sandra L. | Lv, Jie | Mandapat, Christigale | Manning, Gerard | Mariotti, Marco | Mata, Robert | Mathew, Tittu | Neumann, Tobias | Newsham, Irene | Ngo, Dinh N. | Ninova, Maria | Okwuonu, Geoffrey | Ongeri, Fiona | Palmer, William J. | Patil, Shobha | Patraquim, Pedro | Pham, Christopher | Pu, Ling-Ling | Putman, Nicholas H. | Rabouille, Catherine | Ramos, Olivia Mendivil | Rhodes, Adelaide C. | Robertson, Helen E. | Robertson, Hugh M. | Ronshaugen, Matthew | Rozas, Julio | Saada, Nehad | Sánchez-Gracia, Alejandro | Scherer, Steven E. | Schurko, Andrew M. | Siggens, Kenneth W. | Simmons, DeNard | Stief, Anna | Stolle, Eckart | Telford, Maximilian J. | Tessmar-Raible, Kristin | Thornton, Rebecca | van der Zee, Maurijn | von Haeseler, Arndt | Williams, James M. | Willis, Judith H. | Wu, Yuanqing | Zou, Xiaoyan | Lawson, Daniel | Muzny, Donna M. | Worley, Kim C. | Gibbs, Richard A. | Akam, Michael | Richards, Stephen
PLoS Biology  2014;12(11):e1002005.
Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history.
Author Summary
Arthropods are the most abundant animals on earth. Among them, insects clearly dominate on land, whereas crustaceans hold the title for the most diverse invertebrates in the oceans. Much is known about the biology of these groups, not least because of genomic studies of the fruit fly Drosophila, the water flea Daphnia, and other species used in research. Here we report the first genome sequence from a species belonging to a lineage that has previously received very little attention—the myriapods. Myriapods were among the first arthropods to invade the land over 400 million years ago, and survive today as the herbivorous millipedes and venomous centipedes, one of which—Strigamia maritima—we have sequenced here. We find that the genome of this centipede retains more characteristics of the presumed arthropod ancestor than other sequenced insect genomes. The genome provides access to many aspects of myriapod biology that have not been studied before, suggesting, for example, that they have diversified receptors for smell that are quite different from those used by insects. In addition, it shows specific consequences of the largely subterranean life of this particular species, which seems to have lost the genes for all known light-sensing molecules, even though it still avoids light.
doi:10.1371/journal.pbio.1002005
PMCID: PMC4244043  PMID: 25423365
3.  Recurrent pneumonia . . . Not! 
Paediatrics & Child Health  2013;18(9):459-460.
PMCID: PMC3885099  PMID: 24426804
4.  Social Cognitive Theory Predictors of Exercise Behavior in Endometrial Cancer Survivors 
Objective
This study evaluated whether social cognitive theory (SCT) variables, as measured by questionnaire and ecological momentary assessment (EMA), predicted exercise in endometrial cancer survivors.
Methods
One hundred post-treatment endometrial cancer survivors received a 6-month home-based exercise intervention. EMAs were conducted using hand-held computers for 10- to 12-day periods every 2 months. Participants rated morning self-efficacy and positive and negative outcome expectations using the computer, recorded exercise information in real time and at night, and wore accelerometers. At the midpoint of each assessment period participants completed SCT questionnaires. Using linear mixed-effects models, we tested whether morning SCT variables predicted minutes of exercise that day (Question 1) and whether exercise minutes at time point Tj could be predicted by questionnaire measures of SCT variables from time point Tj-1 (Question 2).
Results
Morning self-efficacy significantly predicted that day’s exercise minutes (p<.0001). Morning positive outcome expectations was also associated with exercise minutes (p=0.0003), but the relationship was attenuated when self-efficacy was included in the model (p=0.4032). Morning negative outcome expectations was not associated with exercise minutes. Of the questionnaire measures of SCT variables, only exercise self-efficacy predicted exercise at the next time point (p=0.003).
Conclusions
The consistency of the relationship between self-efficacy and exercise minutes over short (same day) and longer (Tj to Tj-1) time periods provides support for a causal relationship. The strength of the relationship between morning self-efficacy and exercise minutes suggest that real-time interventions that target daily variation in self-efficacy may benefit endometrial cancer survivors’ exercise adherence.
doi:10.1037/a0031712
PMCID: PMC4057057  PMID: 23437853
Social Cognitive Theory; self-efficacy; exercise; cancer survivors; ecological momentary assessment
5.  MexY-Promoted Aminoglycoside Resistance in Pseudomonas aeruginosa: Involvement of a Putative Proximal Binding Pocket in Aminoglycoside Recognition 
mBio  2014;5(2):e01068-14.
ABSTRACT
The resistance-nodulation-division (RND) family multidrug efflux system MexXY-OprM is a major determinant of aminoglycoside resistance in Pseudomonas aeruginosa, although the details of aminoglycoside recognition and export by MexY, the substrate-binding RND component of this efflux system, have not been elucidated. To identify regions/residues of MexY important for aminoglycoside resistance, plasmid-borne mexY was mutagenized and mutations that impaired MexY-promoted aminoglycoside (streptomycin) resistance were identified in a ΔmexY strain of P. aeruginosa. Sixty-one streptomycin-sensitive mexY mutants were recovered; among these, 7 unique mutations that yielded wild-type levels of MexY expression were identified. These mutations compromised resistance to additional aminoglycosides and to other antimicrobials and occurred in both the transmembrane and periplasmic regions of the protein. Mapping of the mutated residues onto a 3-dimensional structure of MexY modeled on Escherichia coli AcrB revealed that these tended to occur in regions implicated in general pump operation (transmembrane domain) and MexY trimer assembly (docking domain) and, thus, did not provide insights into aminoglycoside recognition. A region corresponding to a proximal binding pocket connected to a periplasm-linked cleft, part of a drug export pathway of AcrB, was identified in MexY and proposed to play a role in aminoglycoside recognition. To test this, selected residues (K79, D133, and Y613) within this pocket were mutagenized and the impact on aminoglycoside resistance was assessed. Mutations of D133 and Y613 compromised aminoglycoside resistance, while, surprisingly, the K79 mutation enhanced aminoglycoside resistance, confirming a role for this putative proximal binding pocket in aminoglycoside recognition and export.
IMPORTANCE
Bacterial RND pumps do not typically accommodate highly hydrophilic agents such as aminoglycosides, and it is unclear how those, such as MexY, which accommodate these unique substrates, do so. The results presented here indicate that aminoglycosides are likely not captured and exported by this RND pump component in a unique manner but rather utilize a previously defined export pathway that involves a proximal drug-binding pocket that is also implicated in the export of nonaminoglycosides. The observation, too, that a mutation in this pocket enhances MexY-mediated aminoglycoside resistance (K79A), an indication that it is not optimally designed to accommodate these agents, lends further support to earlier proposals that antimicrobials are not the intended pump substrates.
doi:10.1128/mBio.01068-14
PMCID: PMC3994515  PMID: 24757215
6.  Accelerometry and Self-report in Sedentary Populations 
Objectives
To determine whether self-reported exercise duration and intensity matched accelerometer data in sedentary endometrial cancer survivors and age-matched controls.
Methods
Participants were asked to wear an accelerometer and self-report exercise bouts, duration, and intensity for one week. Self-reported duration was compared with accelerometer data.
Results
Self-reported exercise-bout duration matched accelerometer duration 93% for survivors and 99% for controls. Self-reported exercise-bout intensity matched accelerometer intensity 70% for survivors and 66% for controls. There were no significant differences between groups.
Conclusions
Sedentary endometrial cancer survivors and controls self-reported duration and intensity of physical activity consistent with accelerometer data.
PMCID: PMC3979893  PMID: 20950160
accelerometry; self-report; physical activity; sedentary; cancer survivors
7.  Regulation of adipose oestrogen output by mechanical stress 
Nature communications  2013;4:1821.
Adipose stromal cells are the primary source of local estrogens in adipose tissue, aberrant production of which promotes oestrogen receptor-positive breast cancer. Here we show that extracellular matrix compliance and cell contractility are two opposing determinants for oestrogen output of adipose stromal cells. Using synthetic extracellular matrix and elastomeric micropost arrays with tunable rigidity, we find that increasing matrix compliance induces transcription of aromatase, a rate-limiting enzyme in oestrogen biosynthesis. This mechanical cue is transduced sequentially by discoidin domain receptor 1, c-Jun N-terminal kinase 1, and phosphorylated JunB, which binds to and activates two breast cancer-associated aromatase promoters. In contrast, elevated cell contractility due to actin stress fibre formation dampens aromatase transcription. Mechanically stimulated stromal oestrogen production enhances oestrogen-dependent transcription in oestrogen receptor-positive tumour cells and promotes their growth. This novel mechanotransduction pathway underlies communications between extracellular matrix, stromal hormone output, and cancer cell growth within the same microenvironment.
doi:10.1038/ncomms2794
PMCID: PMC3921626  PMID: 23652009
8.  Mexican-American and Puerto Rican Breast Cancer Survivors’ Perspectives on Exercise: Similarities and Differences 
Qualitative data was collected from Mexican-American (MA) and Puerto Rican (PR) breast cancer survivors to gain their perspectives on the relevant issues surrounding breast cancer survivorship and exercise. Six focus groups, a total of 31 participants were convened (three in Puerto Rico and three in Texas). Responses were analyzed and compared between the Mexican-American and Puerto Rican groups. Follow-up sessions were conducted at the sites to review the initial results and to validate a culturally adapted exercise intervention trial. A total of 900 responses were catalogued into 27 codes. Both groups had similar descriptions of exercise and barriers to exercise. Both groups expressed lack of information regarding their exercise capabilities. The groups differed in their responses to perceived safety in their community and how to deliver a culturally adapted exercise intervention in their community. We found important cultural differences and similarities in relevant factors of exercise and breast cancer survivorship.
doi:10.1007/s10903-012-9648-9
PMCID: PMC3469768  PMID: 22610693
Hispanic; breast cancer; cultural adaptation; exercise; survivorship
9.  Ensembl Genomes 2013: scaling up access to genome-wide data 
Nucleic Acids Research  2013;42(Database issue):D546-D552.
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrating resource for genome-scale data from non-vertebrate species. The project exploits and extends technologies for genome annotation, analysis and dissemination, developed in the context of the vertebrate-focused Ensembl project, and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. This article provides an update to the previous publications about the resource, with a focus on recent developments. These include the addition of important new genomes (and related data sets) including crop plants, vectors of human disease and eukaryotic pathogens. In addition, the resource has scaled up its representation of bacterial genomes, and now includes the genomes of over 9000 bacteria. Specific extensions to the web and programmatic interfaces have been developed to support users in navigating these large data sets. Looking forward, analytic tools to allow targeted selection of data for visualization and download are likely to become increasingly important in future as the number of available genomes increases within all domains of life, and some of the challenges faced in representing bacterial data are likely to become commonplace for eukaryotes in future.
doi:10.1093/nar/gkt979
PMCID: PMC3965094  PMID: 24163254
10.  Butterfly genome reveals promiscuous exchange of mimicry adaptations among species 
Dasmahapatra, Kanchon K | Walters, James R. | Briscoe, Adriana D. | Davey, John W. | Whibley, Annabel | Nadeau, Nicola J. | Zimin, Aleksey V. | Hughes, Daniel S. T. | Ferguson, Laura C. | Martin, Simon H. | Salazar, Camilo | Lewis, James J. | Adler, Sebastian | Ahn, Seung-Joon | Baker, Dean A. | Baxter, Simon W. | Chamberlain, Nicola L. | Chauhan, Ritika | Counterman, Brian A. | Dalmay, Tamas | Gilbert, Lawrence E. | Gordon, Karl | Heckel, David G. | Hines, Heather M. | Hoff, Katharina J. | Holland, Peter W.H. | Jacquin-Joly, Emmanuelle | Jiggins, Francis M. | Jones, Robert T. | Kapan, Durrell D. | Kersey, Paul | Lamas, Gerardo | Lawson, Daniel | Mapleson, Daniel | Maroja, Luana S. | Martin, Arnaud | Moxon, Simon | Palmer, William J. | Papa, Riccardo | Papanicolaou, Alexie | Pauchet, Yannick | Ray, David A. | Rosser, Neil | Salzberg, Steven L. | Supple, Megan A. | Surridge, Alison | Tenger-Trolander, Ayse | Vogel, Heiko | Wilkinson, Paul A. | Wilson, Derek | Yorke, James A. | Yuan, Furong | Balmuth, Alexi L. | Eland, Cathlene | Gharbi, Karim | Thomson, Marian | Gibbs, Richard A. | Han, Yi | Jayaseelan, Joy C. | Kovar, Christie | Mathew, Tittu | Muzny, Donna M. | Ongeri, Fiona | Pu, Ling-Ling | Qu, Jiaxin | Thornton, Rebecca L. | Worley, Kim C. | Wu, Yuan-Qing | Linares, Mauricio | Blaxter, Mark L. | Constant, Richard H. ffrench | Joron, Mathieu | Kronforst, Marcus R. | Mullen, Sean P. | Reed, Robert D. | Scherer, Steven E. | Richards, Stephen | Mallet, James | McMillan, W. Owen | Jiggins, Chris D.
Nature  2012;487(7405):94-98.
The evolutionary importance of hybridization and introgression has long been debated1. We used genomic tools to investigate introgression in Heliconius, a rapidly radiating genus of neotropical butterflies widely used in studies of ecology, behaviour, mimicry and speciation2-5 . We sequenced the genome of Heliconius melpomene and compared it with other taxa to investigate chromosomal evolution in Lepidoptera and gene flow among multiple Heliconius species and races. Among 12,657 predicted genes for Heliconius, biologically important expansions of families of chemosensory and Hox genes are particularly noteworthy. Chromosomal organisation has remained broadly conserved since the Cretaceous, when butterflies split from the silkmoth lineage. Using genomic resequencing, we show hybrid exchange of genes between three co-mimics, H. melpomene, H. timareta, and H. elevatus, especially at two genomic regions that control mimicry pattern. Closely related Heliconius species clearly exchange protective colour pattern genes promiscuously, implying a major role for hybridization in adaptive radiation.
doi:10.1038/nature11041
PMCID: PMC3398145  PMID: 22722851
11.  Yellow nails, lymphedema and chronic cough: Yellow nail syndrome in an eight-year-old girl 
Yellow nail syndrome is a rare disease and reported mainly in adults. A case of yellow nail syndrome involving an eight-year-old girl with associated discoloured yellowish nails on the fingers and toes, lymphedema and chronic cough, and sputum production is reported.
PMCID: PMC3299040  PMID: 22332131
Chronic cough; Keratosis obturans; Lymphedema; Yellow nail syndrome
12.  Design of the Steps to Health Study of Physical Activity in Survivors of Endometrial Cancer: Testing a Social Cognitive Theory Model 
Physical activity has been shown to benefit cancer survivors' physical functioning, emotional well-being, and symptoms. Physical activity may be of particular benefit to survivors of endometrial cancer because they are more likely to be obese and sedentary than the general population, as these are risk factors for the disease, and thus experience a number of related co-morbid health problems. However, there is little research systematically studying mechanisms of physical activity adherence in cancer survivor populations. This paper describes the design of the Steps to Health study, which applies a Social Cognitive Theory-based model of endometrial cancer survivors' adoption and maintenance of exercise in the context of an intervention to increase walking or other moderate intensity cardiovascular activity. In Steps to Health we will test the influence of self-efficacy and outcome expectations on adherence to exercise recommendations, as well as studying the determinants of self-efficacy. Endometrial cancer survivors who are at least 6 months post-treatment are provided with an intervention involving print materials and telephone counseling, and complete assessments of fitness, activity, self-efficacy and outcome expectations, and determinants of self-efficacy every two months for a six month period. In addition to testing an innovative model, the Steps to Health study employs multiple assessment methods, including ecological momentary assessment, implicit tests of cognitive variables, and ambulatory monitoring of physical activity. The study results can be used to develop more effective interventions for increasing physical activity in sedentary cancer survivors by taking into account the full complement of sources of self-efficacy information and outcome expectations.
doi:10.1016/j.psychsport.2010.07.010
PMCID: PMC3014624  PMID: 21218163
13.  Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species 
Nucleic Acids Research  2011;40(Database issue):D91-D97.
Ensembl Genomes (http://www.ensemblgenomes.org) is an integrative resource for genome-scale data from non-vertebrate species. The project exploits and extends technology (for genome annotation, analysis and dissemination) developed in the context of the (vertebrate-focused) Ensembl project and provides a complementary set of resources for non-vertebrate species through a consistent set of programmatic and interactive interfaces. These provide access to data including reference sequence, gene models, transcriptional data, polymorphisms and comparative analysis. Since its launch in 2009, Ensembl Genomes has undergone rapid expansion, with the goal of providing coverage of all major experimental organisms, and additionally including taxonomic reference points to provide the evolutionary context in which genes can be understood. Against the backdrop of a continuing increase in genome sequencing activities in all parts of the tree of life, we seek to work, wherever possible, with the communities actively generating and using data, and are participants in a growing range of collaborations involved in the annotation and analysis of genomes.
doi:10.1093/nar/gkr895
PMCID: PMC3245118  PMID: 22067447
14.  Analysis of high-molecular-weight fructan polymers in crude plant extracts by high-resolution LC-MS 
Analytical and Bioanalytical Chemistry  2011;401(9):2955-2963.
The main water-soluble carbohydrates in temperate forage grasses are polymeric fructans. Fructans consist of fructose chains of various chain lengths attached to sucrose as a core molecule. In grasses, fructans are a complex mixture of a large number of isomeric oligomers with a degree of polymerisation ranging from 3 to >100. Accurate monitoring and unambiguous peak identification requires chromatographic separation coupled to mass spectrometry. The mass range of ion trap mass spectrometers is limited, and we show here how monitoring selected multiply charged ions can be used for the detection and quantification of individual isomers and oligomers of high mass, particularly those of high degree of polymerization (DP > 20) in complex plant extracts. Previously reported methods using linear ion traps with low mass resolution have been shown to be useful for the detection of fructans with a DP up to 49. Here, we report a method using high-resolution mass spectrometry (MS) using an Exactive Orbitrap MS which greatly improves the signal-to-noise ratio and allows the detection of fructans up to DP = 100. High-sugar (HS) Lolium perenne cultivars with high concentrations of these fructans have been shown to be of benefit to the pastoral agricultural industry because they improve rumen nitrogen use efficiency and reduce nitrous oxide emissions from pastures. We demonstrate with our method that these HS grasses not only contain increased amounts of fructans in leaf blades but also accumulate fructans with much higher DP compared to cultivars with normal sugar levels.
Electronic supplementary material
The online version of this article (doi:10.1007/s00216-011-5374-8) contains supplementary material, which is available to authorized users.
doi:10.1007/s00216-011-5374-8
PMCID: PMC3204112  PMID: 21927982
Fructan; Porous graphitic carbon; High resolution; Degree of polymerization; High-sugar grasses
15.  Exercise Intervention for Cancer Survivors with Heart Failure: Two Case Reports 
Rationale
Cardiotoxicity is a troubling long-term side effect of chemotherapy cancer treatment, affecting therapy and quality of life (QOL). Exercise is beneficial in heart failure (HF) patients and in cancer survivors without HF, but has not been tested in cancer survivors with treatment induced HF.
Methods
We present case studies for two survivors: a 56-year old female Hodgkin’s lymphoma survivor (Pt 1) and a 44-year old male leukemia survivor (Pt 2). We conducted a 16-week exercise program with the goal of 30 minutes of exercise performed 3 times per week at a minimum intensity of 50% heart rate reserve (HRR) or ‘12’ rating of perceived exertion (RPE).
Results
Pt 1 improved from 11.5 minutes of exercise split over two bouts at an RPE of 14 to a 30 minute bout at an RPE of 15. Pt 2 improved from 11 minutes of exercise split over two bouts at an RPE of 12 to an 18 minute bout at an RPE of 12. Both improved in VO2 peak (Pt 1: 13.9 to 14.3 mlO2/kg/min; Pt 2: 12.5 to 18.7 mlO2/kg/min). Ejection fraction increased for Pt 2 (25–30% to 35–40%) but not for Pt 1 (35–40%). QOL as assessed by the SF-36 Physical Component Scale (PCS) improved from 17.79 to 25.31 for Pt 1 and the Mental Component Scale (MCS) improved from 43.84 to 56.65 for Pt 1 and from 34.79 to 44.45 for Pt 2.
Conclusions
Properly designed exercise interventions can improve physical functioning and quality of life for this growing group of survivors.
PMCID: PMC3121107  PMID: 21709755
cancer survivorship; cardiotoxicity; exercise; quality of life
16.  Dimensions of Physical Activity and their Relationship to Physical and Emotional Symptoms in Breast Cancer Survivors 
Background
Many breast cancer survivors experience long term sequelae, including fatigue, decreased physical functioning, pain, and psychological distress. Physical activity can ameliorate these problems, but there is little research on how activity should be performed to be most beneficial. This study explores how dimensions of physical activity (total energy expenditure, frequency, and duration) are associated with symptoms among breast cancer survivors.
Methods
We conducted secondary analysis of data on physical activity behavior and symptoms in a cross-sectional study (n = 148) of breast cancer survivors who were off treatment and had been diagnosed within the past 5 years.
Results
Multivariate analyses showed that total energy expenditure was associated with better general health (p=0.006) and fewer depressive symptoms (p=0.014), while frequency of activity was linearly related to physical functioning (p=0.047), pain (0.057), general health (p<0.001), and depressive symptoms (p<0.001). Duration was related to physical functioning, pain, and general health, but the worst outcomes were reported by the participants with the shortest and longest duration of activity (quadratic trend p values = 0.002, 0.003, 0.008, respectively).
Discussion/Conclusions
Greater total energy expenditure, higher physical activity frequency, and moderate duration were associated with better outcomes for most variables, although there was no relationship between any of the dimensions of physical activity and fatigue.
Implications for Cancer Survivors
The association of better outcomes with higher energy expenditure, higher frequency of activity, and moderate duration indicates that increasing activity through multiple short bouts may be the most beneficial for breast cancer survivors. However, randomized studies are needed to confirm this finding.
doi:10.1007/s11764-008-0067-9
PMCID: PMC3076788  PMID: 18923906
symptoms; depression; physical activity; breast cancer survivors
17.  An Acute Exercise Session Increases Self-Efficacy in Sedentary Endometrial Cancer Survivors and Controls 
Background
Self-efficacy can be affected by mastery experiences and somatic sensations. A novel exercise experience and associated sensations may impact self-efficacy and subsequent behaviors. We investigated the effect of a single exercise session on self-efficacy for sedentary endometrial cancer survivors compared with sedentary women of a similar age, but with no cancer history.
Methods
Twenty survivors and 19 controls completed an exercise session performed as a submaximal cycle ergometry test. Sensations and efficacy were measured before and after exercise. Repeated measures analysis of variance (ANOVA) was performed. Regression models were used to determine predictors of self-efficacy and subsequent exercise.
Results
Self-efficacy increased for both survivors and controls, but survivors had a higher rate of increase, and the change predicted subsequent exercise. The association between exercise-related somatic sensations and self-efficacy differed between the 2 groups.
Conclusions
A novel exercise experience had a larger effect on self-efficacy and subsequent exercise activity for endometrial cancer survivors than controls. Somatic sensations experienced during exercise may differ for survivors, which may be related to the experience of having cancer. Understanding factors affecting confidence in novel exercise experiences for populations with specific cancer histories is of the utmost importance in the adoption of exercise behaviors.
PMCID: PMC3024053  PMID: 21088310
special needs populations; exercise psychology; health behavior
18.  Physical Activity and Obesity in Endometrial Cancer Survivors: Associations with Pain, Fatigue, and Physical Functioning 
OBJECTIVE
This study aims to determine the prevalence of physical activity and obesity and their relationship to physical functioning, fatigue, and pain in endometrial cancer survivors.
STUDY DESIGN
Surveys were mailed to 200 survivors of endometrial cancer diagnosed within the last five years; 61% were returned. Surveys assessed physical activity, height and weight, comorbid health problems, physical functioning, fatigue, and pain.
RESULTS
Twenty-two percent exercised in the past month at the level of current public health recommendations; 41% reported no physical activity, and 38% reported some activity. Sixteen percent were overweight and 50% were obese. Both lower BMI and higher physical activity were related to better physical functioning. Higher physical activity was related to less fatigue, primarily for patients of normal BMI.
CONCLUSIONS
Results suggest endometrial cancer survivors’ obesity and inactivity contributes to poorer quality of life. This population could benefit from quality of life interventions incorporating physical activity.
doi:10.1016/j.ajog.2008.10.010
PMCID: PMC2666540  PMID: 19110220
Endometrial cancer; exercise; fatigue; obesity; pain; physical functioning
19.  Primary ciliary dyskinesia 
Paediatrics & Child Health  2008;13(8):672-674.
PMCID: PMC2606072  PMID: 19436519
20.  Extensive molecular differences between anterior- and posterior-half-sclerotomes underlie somite polarity and spinal nerve segmentation 
Background
The polarization of somite-derived sclerotomes into anterior and posterior halves underlies vertebral morphogenesis and spinal nerve segmentation. To characterize the full extent of molecular differences that underlie this polarity, we have undertaken a systematic comparison of gene expression between the two sclerotome halves in the mouse embryo.
Results
Several hundred genes are differentially-expressed between the two sclerotome halves, showing that a marked degree of molecular heterogeneity underpins the development of somite polarity.
Conclusion
We have identified a set of genes that warrant further investigation as regulators of somite polarity and vertebral morphogenesis, as well as repellents of spinal axon growth. Moreover the results indicate that, unlike the posterior half-sclerotome, the central region of the anterior-half-sclerotome does not contribute bone and cartilage to the vertebral column, being associated instead with the development of the segmented spinal nerves.
doi:10.1186/1471-213X-9-30
PMCID: PMC2693541  PMID: 19463158
21.  Cystic fibrosis – the first interview 
Paediatrics & Child Health  2001;6(9):620-622.
PMCID: PMC2805964  PMID: 20084132
22.  The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera 
Nature Communications  2014;5:4737.
Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393 Mb) of the Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a widely recognized model species in metapopulation biology and eco-evolutionary research, which has the putative ancestral karyotype of n=31. Using a phylogenetic analyses of Nymphalidae and of other Lepidoptera, combined with orthologue-level comparisons of chromosomes, we conclude that the ancestral lepidopteran karyotype has been n=31 for at least 140 My. We show that fusion chromosomes have retained the ancestral chromosome segments and very few rearrangements have occurred across the fusion sites. The same, shortest ancestral chromosomes have independently participated in fusion events in species with smaller karyotypes. The short chromosomes have higher rearrangement rate than long ones. These characteristics highlight distinctive features of the evolutionary dynamics of butterflies and moths.
Butterflies and moths (Lepidoptera) vary in chromosome number. Here, the authors sequence the genome of the Glanville fritillary butterfly, Melitaea cinxia, show it has the ancestral lepidopteran karyotype and provide insight into how chromosomal fusions have shaped karyotype evolution in butterflies and moths.
doi:10.1038/ncomms5737
PMCID: PMC4164777  PMID: 25189940
23.  Daughters and Mothers Against Breast Cancer (DAMES): Main outcomes of a randomized controlled trial of weight loss in overweight mothers with breast cancer and their overweight daughters 
Cancer  2014;120(16):2522-2534.
BACKGROUND
Few studies to date have used the cancer diagnosis as a teachable moment to promote healthy behavior changes in survivors of cancer and their family members. Given the role of obesity in the primary and tertiary prevention of breast cancer, the authors explored the feasibility of a mother-daughter weight loss intervention.
METHODS
A randomized controlled trial of a mailed weight loss intervention was undertaken among 68 mother-daughter dyads (n = 136), each comprised of a survivor of breast cancer (AJCC stage 0-III) and her adult biological daughter. All women had body mass indices ≥ 25 kg/m2 and underwent in-person assessments at baseline, 6 months, and 12 months, with accelerometry and exercise capacity performed on a subset of individuals. All women received a personalized workbook and 6 newsletters over a 1-year period that promoted weight loss; exercise; and a nutrient-rich, low-energy density diet. A total of 25 dyads received individually tailored instruction (INDIVIDUAL), 25 dyads received team-tailored instruction (TEAM), and 18 dyads received standardized brochures (CONTROL).
RESULTS
The trial met its accrual target, experienced 90% retention, and caused no serious adverse events. Significant differences in baseline to 12-month changes were observed between INDIVIDUAL versus CONTROL mothers for body mass index, weight, and waist circumference (WC); significant differences also were observed in the WC of corresponding daughters (P < .05). Significant differences were found between INDIVIDUAL versus CONTROL and TEAM versus CONTROL dyads for WC (P = .0002 and .018, respectively), minutes per week of physical activity (P = .031 and .036, respectively), and exercise capacity (P = .047 for both).
CONCLUSIONS
Significant improvements in lifestyle behaviors and health outcomes are possible with tailored print interventions directed toward survivors of cancer and their family members. For greater impact, more research is needed to expand this work beyond the mother-daughter dyad. Cancer 2014;120:2522–2534. © 2014 The Authors. Cancer published by Wiley Periodicals, Inc. on behalf of American Cancer Society.
Obesity is a major risk factor for the incidence and mortality of several cancers. The results of this randomized controlled trial of weight loss among 136 women diagnosed with breast cancer and their biological daughters suggests that the diagnosis of cancer can be used to motivate healthy diet and exercise behaviors among survivors of cancer and their family members using mailed print interventions.
doi:10.1002/cncr.28761
PMCID: PMC4232005  PMID: 24804802
breast neoplasms; survivors; obesity; weight loss; diet; exercise; intervention studies

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