title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1933 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: FDAAA legislation is working, but methodological flaws undermine the reliability of clinical trials: a cross-sectional study link: https://peerj.com/articles/1015 last-modified: 2015-06-25 description: The relationship between clinical research and the pharmaceutical industry has placed clinical trials in jeopardy. According to the medical literature, more than 70% of clinical trials are industry-funded. Many of these trials remain unpublished or have methodological flaws that distort their results. In 2007, it was signed into law the Food and Drug Administration Amendments Act (FDAAA), aiming to provide publicly access to a broad range of biomedical information to be made available on the platform ClinicalTrials (available at https://www.clinicaltrials.gov). We accessed ClinicalTrials.gov and evaluated the compliance of researchers and sponsors with the FDAAA. Our sample comprised 243 protocols of clinical trials of biological monoclonal antibodies (mAb) adalimumab, bevacizumab, infliximab, rituximab, and trastuzumab. We demonstrate that the new legislation has positively affected transparency patterns in clinical research, through a significant increase in publication and online reporting rates after the enactment of the law. Poorly designed trials, however, remain a challenge to be overcome, due to a high prevalence of methodological flaws. These flaws affect the quality of clinical information available, breaching ethical duties of sponsors and researchers, as well as the human right to health. creator: Douglas H. Marin dos Santos creator: Álvaro N. Atallah uri: https://doi.org/10.7717/peerj.1015 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2015 Marin dos Santos and Atallah title: Imbalance in the blood antioxidant system in growth hormone-deficient children before and after 1 year of recombinant growth hormone therapy link: https://peerj.com/articles/1055 last-modified: 2015-06-25 description: The aim of our study was to examine the effects of 12-month therapy with recombinant growth hormone (rGH) on the blood antioxidant system in children with growth hormone deficiency (GHD). Total antioxidant capacity (TAC) of plasma was measured by FRAP (ferric reducing antioxidant power or ferric reducing ability of plasma); activities of superoxide dismutase (SOD) and catalase (CAT) in erythrocytes were assessed; non-protein thiols (NT) and ceruloplasmin (CP) levels were also measured. These parameters were determined before and after 12 month of rGH treatment. Eleven treatment-naive prepubertal children with growth hormone deficiency were included in the study. Another 11 prepubertal children comprised a control group. Before rGH treatment, TAC of plasma and NT level in the control group were significantly lower (726 ± 196 vs. 525 ± 166 µmol/L, P = 0.0182 and 0.92 ± 0.18 vs. 0.70 ± 0.22 µmol/ml, P = 0.0319, before and after the therapy, respectively). The only parameter that significantly (19.6 ± 4.7 vs. 14.5 ± 3.4 Units/g Hb, P = 0.0396) exceeded the same in the control group after rGH therapy was SOD activity. However, none of the measured parameters of antioxidant system in GHD children, except for TAC (525 ± 166 vs. 658 ± 115 µmol/L, P = 0.0205), exhibited significant improvement toward the end of the 12-month treatment period, although non-significant changes in CAT activity and CP level were also observed. This work has demonstrated that some parameters of the blood antioxidant system are out of balance and even impaired in GHD children. A 12-month treatment with rGH resulted in a partial improvement of the antioxidant system. creator: Maria S. Pankratova creator: Adil A. Baizhumanov creator: Alexander I. Yusipovich creator: Maria Faassen creator: Tatyana Yu. Shiryaeva creator: Valentina A. Peterkova creator: Svetlana S. Kovalenko creator: Tatiana A. Kazakova creator: Georgy V. Maksimov uri: https://doi.org/10.7717/peerj.1055 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Pankratova et al. title: Staphylococcus Aureus carriage and long-term Rituximab treatment for Granulomatosis with polyangiitis link: https://peerj.com/articles/1051 last-modified: 2015-06-25 description: Objective. Chronic nasal carriage of Staphylococcus aureus (SA) increases the risk of relapse while Rituximab (RTX) is an effective agent for inducing and maintaining remission in patients with Granulomatosis with polyangiitis (GPA). We investigated whether B cell depletion and hypogammaglobulinemia that occur during RTX treatment increase the risk of chronic SA nasal carriage and subsequent disease flares, in GPA patients on long-term RTX maintenance therapy.Methods. Retrospective cohort study from a disease registry involving 29 GPA patients receiving RTX maintenance (median RTX dose of 9 g) during a median period of 49 months. Nasal swabs were collected prior and during RTX for a median of 3 and 9 swabs respectively. Persistent SA nasal carriage was defined with the presence of SA in more than 75% of nasal swabs.Results. SA nasal carriage did not change during RTX (p = 0.297). However, the rate of positive nasal swabs in GPA patients with transient SA nasal carriage during RTX maintenance increased from 0 prior RTX to 0.42 during RTX (p = 0.017). Persistent SA nasal carriage did not increase the risk of relapses (p = 0.844), of hypogammaglobulinemia (p = 0.122) and of severe infections (p = 0.144), but reduced the risk of chronic infections (p = 0.044). Change in SA carriage status during RTX did not influence the risk of relapses (p = 0.756), hypogammaglobulinamia (p = 0.474) and infections, either severe (p = 0.913) or chronic (p = 0.121).Conclusion. Long-term RTX maintenance therapy in GPA patients did not significantly influence SA nasal carriage status. Persistent SA carriage during long-term RTX treatment did not seem to increase the risk of relapses, but seemed to decrease the risk of hypogammaglobulinemia associated chronic infections. creator: Emilio Besada creator: Wenche Koldingsnes creator: Johannes C. Nossent uri: https://doi.org/10.7717/peerj.1051 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Besada et al. title: Parents’ evaluation of support in Australian hospitals following stillbirth link: https://peerj.com/articles/1049 last-modified: 2015-06-25 description: The present study evaluated the level of support and satisfaction among parents of stillborn babies in Australian hospitals. One-hundred and eighty-nine mothers and fathers completed an online survey designed by the researcher based on the guidelines designed by the Perinatal Society of Australia and New Zealand. Support was inconsistent with guidelines implemented on average only 55% of the time. Areas of support regarding creating memories, birth options and autopsy were most problematic. A significant positive correlation was found between support and satisfaction and there is indication that there has been some increase in support and satisfaction over time. There has been a significant increase in both support and satisfaction since the release of the guidelines in 2009. Creating memories was regarded by parents as the most influential to their grief. It is recommended that health professionals review guidelines and seek feedback from parents as to how they can improve the support they provide. creator: Melanie L. Basile creator: Einar B. Thorsteinsson uri: https://doi.org/10.7717/peerj.1049 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Basile and Thorsteinsson title: Family structure as a predictor of screen time among youth link: https://peerj.com/articles/1048 last-modified: 2015-06-25 description: The family plays a central role in the development of health-related behaviors among youth. The objective of this study was to determine whether non-traditional parental structure and shared custody arrangements predict how much time youth spend watching television, using a computer recreationally, and playing video games. Participants were a nationally representative sample of Canadian youth (N = 26,068) in grades 6–10 who participated in the 2009/10 Health Behaviour in School-aged Children Survey. Screen time in youth from single parent and reconstituted families, with or without regular visitation with their non-residential parent, was compared to that of youth from traditional dual-parent families. Multiple imputation was used to account for missing data. After multiple imputation, the relative odds of being in the highest television, computer use, video game, and total screen time quartiles were not different in boys and girls from non-traditional families by comparison to boys and girls from traditional dual-parent families. In conclusion, parental structure and child custody arrangements did not have a meaningful impact on screen time among youth. creator: Rachel McMillan creator: Michael McIsaac creator: Ian Janssen uri: https://doi.org/10.7717/peerj.1048 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 McMillan et al. title: A Bayesian approach to optimizing cryopreservation protocols link: https://peerj.com/articles/1039 last-modified: 2015-06-25 description: Cryopreservation is beset with the challenge of protocol alignment across a wide range of cell types and process variables. By taking a cross-sectional assessment of previously published cryopreservation data (sample means and standard errors) as preliminary meta-data, a decision tree learning analysis (DTLA) was performed to develop an understanding of target survival using optimized pruning methods based on different approaches. Briefly, a clear direction on the decision process for selection of methods was developed with key choices being the cooling rate, plunge temperature on the one hand and biomaterial choice, use of composites (sugars and proteins as additional constituents), loading procedure and cell location in 3D scaffolding on the other. Secondly, using machine learning and generalized approaches via the Naïve Bayes Classification (NBC) method, these metadata were used to develop posterior probabilities for combinatorial approaches that were implicitly recorded in the metadata. These latter results showed that newer protocol choices developed using probability elicitation techniques can unearth improved protocols consistent with multiple unidimensionally-optimized physical protocols. In conclusion, this article proposes the use of DTLA models and subsequently NBC for the improvement of modern cryopreservation techniques through an integrative approach. creator: Sammy Sambu uri: https://doi.org/10.7717/peerj.1039 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Sambu title: Beliefs in being unlucky and deficits in executive functioning: an ERP study link: https://peerj.com/articles/1007 last-modified: 2015-06-25 description: There has been initial evidence to support the Dysexecutive Luck hypothesis, which proposes that beliefs in being unlucky are associated with deficits in executive functioning (Maltby et al., 2013). The present study tested the Dysexecutive Luck hypothesis by examining whether deficits in the early stage of top down attentional control led to an increase of neural activity in later stages of response related selection process among those who thought themselves to be unlucky. Individuals with these beliefs were compared to a control group using an Event-Related Potential (ERP) measure assessing underlying neural activity of semantic inhibition while completing a Stroop test. Results showed stronger main interference effects in the former group, via greater reaction times and a more negative distributed scalp late ERP component during incongruent trials in the time window of 450–780 ms post stimulus onset. Further, less efficient maintenance of task set among the former group was associated with greater late ERP response-related activation to compensate for the lack of top-down attentional control. These findings provide electrophysiological evidence to support the Dysexecutive Luck hypothesis. creator: Jaime Martín del Campo Ríos creator: Giorgio Fuggetta creator: John Maltby uri: https://doi.org/10.7717/peerj.1007 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Martín del Campo et al. title: Decreasing seagrass density negatively influences associated fauna link: https://peerj.com/articles/1053 last-modified: 2015-06-23 description: Seagrass meadows globally are disappearing at a rapid rate with physical disturbances being one of the major drivers of this habitat loss. Disturbance of seagrass can lead to fragmentation, a reduction in shoot density, canopy height and coverage, and potentially permanent loss of habitat. Despite being such a widespread issue, knowledge of how such small scale change affects the spatial distribution and abundances of motile fauna remains limited. The present study investigated fish and macro faunal community response patterns to a range of habitat variables (shoot length, cover and density), including individual species habitat preferences within a disturbed and patchy intertidal seagrass meadow. Multivariate analysis showed a measurable effect of variable seagrass cover on the abundance and distribution of the fauna, with species specific preferences to both high and low seagrass cover seagrass. The faunal community composition varied significantly with increasing/decreasing cover. The faunal species composition of low cover seagrass was more similar to sandy control plots than to higher cover seagrass. Shannon Wiener Diversity (H′) and species richness was significantly higher in high cover seagrass than in low cover seagrass, indicating increasing habitat value as density increases. The results of this study underline how the impacts of small scale disturbances from factors such as anchor damage, boat moorings and intertidal vehicle use on seagrass meadows that reduce shoot density and cover can impact upon associated fauna. These impacts have negative consequences for the delivery of ecosystem services such as the provision of nursery habitat. creator: Rosemary M. McCloskey creator: Richard K.F. Unsworth uri: https://doi.org/10.7717/peerj.1053 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 McCloskey and Unsworth title: The invasive land planarian Platydemus manokwari (Platyhelminthes, Geoplanidae): records from six new localities, including the first in the USA link: https://peerj.com/articles/1037 last-modified: 2015-06-23 description: The land planarian Platydemus manokwari de Beauchamp, 1963 or “New Guinea flatworm” is a highly invasive species, mainly in the Pacific area, and recently in Europe (France). We report specimens from six additional countries and territories: New Caledonia (including mainland and two of the Loyalty Islands, Lifou and Maré), Wallis and Futuna Islands, Singapore, Solomon Islands, Puerto Rico, and Florida, USA. We analysed the COI gene (barcoding) in these specimens with two sets of primers and obtained 909 bp long sequences. In addition, specimens collected in Townsville (Australia) were also sequenced. Two haplotypes of the COI sequence, differing by 3.7%, were detected: the “World haplotype” found in France, New Caledonia, French Polynesia, Singapore, Florida and Puerto Rico; and the “Australian haplotype” found in Australia. The only locality with both haplotypes was in the Solomon Islands. The country of origin of Platydemus manokwari is New Guinea, and Australia and the Solomon Islands are the countries closest to New Guinea from which we had specimens. These results suggest that two haplotypes exist in the area of origin of the species, but that only one of the two haplotypes (the “World haplotype”) has, through human agency, been widely dispersed. However, since P. manokwari is now recorded from 22 countries in the world and we have genetic information from only 8 of these, with none from New Guinea, this analysis provides only partial knowledge of the genetic structure of the invasive species. Morphological analysis of specimens from both haplotypes has shown some differences in ratio of the genital structures but did not allow us to interpret the haplotypes as different species. The new reports from Florida and Puerto Rico are firsts for the USA, for the American continent, and the Caribbean. P. manokwari is a known threat for endemic terrestrial molluscs and its presence is a matter of concern. While most of the infected territories reported until now were islands, the newly reported presence of the species in mainland US in Florida should be considered a potential major threat to the whole US and even the Americas. creator: Jean-Lou Justine creator: Leigh Winsor creator: Patrick Barrière creator: Crispus Fanai creator: Delphine Gey creator: Andrew Wee Kien Han creator: Giomara La Quay-Velázquez creator: Benjamin Paul Yi-Hann Lee creator: Jean-Marc Lefevre creator: Jean-Yves Meyer creator: David Philippart creator: David G. Robinson creator: Jessica Thévenot creator: Francis Tsatsia uri: https://doi.org/10.7717/peerj.1037 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Justine et al. title: Delivery by caesarean section and risk of childhood obesity: analysis of a Peruvian prospective cohort link: https://peerj.com/articles/1046 last-modified: 2015-06-23 description: Objectives. We aimed to assess if Caesarean section is a risk factor for overnutrition in early- and late-childhood, and to assess the magnitude of the effect of child- versus family-related variables in these risk estimates.Methods. Longitudinal data from Peruvian children from the Young Lives Study was used. Outcomes assessed were overweight, obesity, overnutrition (overweight plus obesity), and central obesity (waist circumference) at the age 5 (first follow-up) and 7 (second follow-up) years. The exposure of interests was delivery by Caesarean section. Relative risks (RR) and 95% confidence intervals (95% CI) were calculated using multivariable models adjusted for child-related (e.g., birth weight) and family-related (e.g., maternal nutritional status) variables.Results. At baseline, mean age was 11.7 (± 3.5) months and 50.1% were boys. Children born by Caesarean section were 15.6%. The 10.5% of the children were overweight and 2.4% were obese. For the obesity outcome, data from 6,038 and 9,625 children-years was included from baseline to the first and second follow-up, respectively. Compared to those who did not experience Caesarean delivery, the risk of having obesity was higher in the group born by Caesarean: RRs were higher at early-childhood (first follow-up: 2.25; 95% CI [1.36–3.74]) than later in life (second follow-up: 1.57; 95% CI [1.02–2.41]). Family-related variables had a greater effect in attenuating the risk estimates for obesity at the first, than at the second follow-up.Conclusion. Our results suggest a higher probability of developing obesity, but not overweight, among children born by Caesarean section delivery. The magnitude of risk estimates decreased over time, and family-related variables had a stronger effect on the risk estimates at early-childhood. creator: Rodrigo M. Carrillo-Larco creator: J. Jaime Miranda creator: Antonio Bernabé-Ortiz uri: https://doi.org/10.7717/peerj.1046 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Carrillo-Larco et al.