Report on a pilot project to introduce a publications officer

First paragraph: Concerns about deficiencies in the reporting quality of biomedical research have been expressed for more than three decades. In spite of this, articles continue to pass through editorial and peer review processes and are published with critical aspects of their methods and results missing or inadequately described. Reporting biases also remain problematic. Together, these practices limit the integrity of biomedical literature and hinder reproducibility efforts. In an attempt to alleviate these problems, Moher and Altman recently proposed four potential contributory actions for journals and educational institutions to consider. Here, we present a description of our efforts to implement their first proposed action: the introduction of a publications officer

Assessing the utility of an institutional publications officer: a pilot assessment

Background  The scholarly publication landscape is changing rapidly. We investigated whether the introduction of an institutional publications officer might help facilitate better knowledge of publication topics and related resources, and effectively support researchers to publish.  Methods  In September 2015, a purpose-built survey about researchers’ knowledge and perceptions of publication practices was administered at five Ottawa area research institutions. Subsequently, we publicly announced a newly hired publications officer (KDC) who then began conducting outreach at two of the institutions. Specifically, the publications officer gave presentations, held one-to-one consultations, developed electronic newsletter content, and generated and maintained a webpage of resources. In March 2016, we re-surveyed our participants regarding their knowledge and perceptions of publishing. Mean scores to the perception questions, and the percent of correct responses to the knowledge questions, pre and post survey, were computed for each item. The difference between these means or calculated percentages was then examined across the survey measures.  Results  82 participants completed both surveys. Of this group, 29 indicated that they had exposure to the publications officer, while the remaining 53 indicated they did not. Interaction with the publications officer led to improvements in half of the knowledge items (7/14 variables). While improvements in knowledge of publishing were also found among those who reported not to have interacted with the publications officer (9/14), these effects were often smaller in magnitude. Scores for some publication knowledge variables actually decreased between the pre and post survey (3/14). Effects for researchers’ perceptions of publishing increased for 5/6 variables in the group that interacted with the publications officer.  Discussion  This pilot provides initial indication that, in a short timeframe, introducing an institutional publications officer may improve knowledge and perceptions surrounding publishing. This study is limited by its modest sample size and temporal relationship between the introduction of the publications officer and changes in knowledge and perceptions. A randomized trial examining the publications officer as an effective intervention is needed

Direct Determination of the Effect of Strain on Domain Morphology in Ferroelectric Superlattices with Scanning Probe Microscopy

A variant of piezo force microscopy was used to characterize the effect of strain on polarization in [(BaTiO3)n/(SrTiO3)m]p superlattices. The measurements were compared to theoretical predictions based on phase-field calculations. When polarization is constrained to be perpendicular to the substrate, the measured polarization and domain morphology agree quantitatively with the predictions. This case allows the presence of an internal electric field in the thin film to be identified. The measured trend in piezoelectric response with strain state was in qualitative agreement with predictions, and the differences were consistent with the presence of internal electrical fields. Clear differences in domain morphology with strain were observed; and in some cases, the lateral anisotropic strain appeared to influence the domain morphology. The differences in magnitude and morphology were attributed to the internal electric fields and anisotropic strains

An international survey and modified Delphi process revealed editors' perceptions, training needs, and ratings of competency-related statements for the development of core competencies for scientific editors of biomedical journals

Background: Scientific editors (i.e., those who make decisions on the content and policies of a journal) have a central role in the editorial process at biomedical journals. However, very little is known about the training needs of these editors or what competencies are required to perform effectively in this role. Methods: We conducted a survey of perceptions and training needs among scientific editors from major editorial organizations around the world, followed by a modified Delphi process in which we invited the same scientific editors to rate the importance of competency-related statements obtained from a previous scoping review. Results: A total of 148 participants completed the survey of perceptions and training needs. At least 80% of participants agreed on six of the 38 skill and expertise-related statements presented to them as being important or very important to their role as scientific editors. At least 80% agreed on three of the 38 statements as necessary skills they perceived themselves as possessing (well or very well). The top five items on participants’ list of top training needs were training in statistics, research methods, publication ethics, recruiting and dealing with peer reviewers, and indexing of journals. The three rounds of the Delphi were completed by 83, 83, and 73 participants, respectively, which ultimately produced a list of 23 “highly rated” competency-related statements and another 86 “included” items. Conclusion: Both the survey and the modified Delphi process will be critical for understanding knowledge and training gaps among scientific editors when designing curriculum around core competencies in the future

‘One door closes, a next door opens up somewhere’: The learning of one Olympic synchronised swimmer

Although training in sport is necessary to reach Olympic status, a conditioned body is not the only outcome. Athletes also learn how to be Olympians. This learning involves taking on certain ways of acting, thinking and valuing. Such learning has implications beyond competition, as athletes eventually retire from elite sport and devote their time to other activities. This paper examines processes of learning and transition using the case of Amelia, a former Olympic synchronised swimmer. Through two in-depth interviews, empirical material was generated which focused on the learning that took place during this athlete’s career and after, during her transition to paid employment. A cultural view of learning was used as the theoretical frame to understand the athlete’s experiences. Our reading suggests that the athlete learned in various ways to be productive. Some of these ways of being were useful after retirement; others were less compatible. In fact, Amelia used a two-year period after retirement to reconstruct herself. Key to her eventual successful transition was to distance herself from the sport and to critically reflect upon her sporting experiences. We thus recommend that those involved with high-performance athletes foster a more balanced perspective that acknowledges and promotes ways of being beyond athletic involvement

Sensitization to gliadin induces moderate enteropathy and insulitis in nonobese diabetic-DQ8 mice

Celiac disease (CD) is frequently diagnosed in patients with type 1 diabetes (T1D), and T1D patients can exhibit Abs against tissue transglutaminase, the auto-antigen in CD. Thus, gliadin, the trigger in CD, has been suggested to have a role in T1D pathogenesis. The objective of this study was to investigate whether gliadin contributes to enteropathy and insulitis in NOD-DQ8 mice, an animal model that does not spontaneously develop T1D. Gliadin-sensitized NOD-DQ8 mice developed moderate enteropathy, intraepithelial lymphocytosis, and barrier dysfunction, but not insulitis. Administration of anti-CD25 mAbs before gliadin-sensitization induced partial depletion of CD25+Foxp3+ T cells and led to severe insulitis, but did not exacerbate mucosal dysfunction. CD4+T cells isolated from pancreatic lymph nodes of mice that developed insulitis showed increased proliferation and proinflammatory cytokines after incubation with gliadin but not with BSA. CD4+ T cells isolated from nonsensitized controls did not response to gliadin or BSA. In conclusion, gliadin sensitization induced moderate enteropathy in NOD-DQ8 mice. However, insulitis development required gliadin-sensitization and partial systemic depletion of CD25+Foxp3+ T cells. This humanized murine model provides a mechanistic link to explain how the mucosal intolerance to a dietary protein can lead to insulitis in the presence of partial regulatory T cell deficiency.Facultad de Ciencias Exacta

Cell proliferation, cell cycle abnormalities, and cancer outcome in patients with Barrett’s esophagus: A long-term prospective study

Purpose: Elevated cellular proliferation and cell cycle abnormalities, which have been associated with premalignant lesions, may be caused by inactivation of tumor suppressor genes. We measured proliferative and cell cycle fractions of biopsies from a cohort of patients with Barrett's esophagus to better understand the role of proliferation in early neoplastic progression and the association between cell cycle dysregulation and tumor suppressor gene inactivation. Experimental Design: Cell proliferative fractions (determined by Ki67/DNA multiparameter flow cytometry) and cell cycle fractions (DNA content flow cytometry) were measured in 853 diploid biopsies from 362 patients with Barrett's esophagus. The inactivation status of CDKN2A and TP53 was assessed in a subset of these biopsies in a cross-sectional study. A prospective study followed 276 of the patients without detectable aneuploidy for an average of 6.3 years with esophageal adenocarcinoma as an endpoint. Results: Diploid S and 4N (G2/tetraploid) fractions were significantly higher in biopsies with TP53 mutation and LOH. CDKN2A inactivation was not associated with higher Ki67-positive, diploid S, G1, or 4N fractions. High Ki67-positive and G1 phase fractions were not associated with the future development of esophageal adenocarcinoma (p=0.13 and p=0.15, respectively), while high diploid S phase and 4N fractions were (p=0.03 and p<0.0001, respectively). Conclusions: High Ki67-positive proliferative fractions were not associated with inactivation of CDKN2A and TP53 or future development of cancer in our cohort of patients with Barrett's esophagus. Bi-allelic inactivation of TP53 was associated with elevated 4N fractions, which have been associated with the future development of esophageal adenocarcinoma

p16 Mutation Spectrum in the Premalignant Condition Barrett's Esophagus

Background: Mutation, promoter hypermethylation and loss of heterozygosity involving the tumor suppressor gene p16 (CDKN2a/INK4a) have been detected in a wide variety of human cancers, but much less is known concerning the frequency and spectrum of p16 mutations in premalignant conditions. Methods and Findings: We have determined the p16 mutation spectrum for a cohort of 304 patients with Barrett’s esophagus, a premalignant condition that predisposes to the development of esophageal adenocarcinoma. Forty seven mutations were detected by sequencing of p16 exon 2 in 44 BE patients (14.5%) with a mutation spectrum consistent with that caused by oxidative damage and chronic inflammation. The percentage of patients with p16 mutations increased with increasing histologic grade. In addition, samples from 3 out of 19 patients (15.8%) who underwent esophagectomy were found to have mutations. Conclusions: The results of this study suggest the environment of the esophagus in BE patients can both generate an

Core competencies for scientific editors of biomedical journals: consensus statement

Background&nbsp; Scientific editors are responsible for deciding which articles to publish in their journals. However, we have not found documentation of their required knowledge, skills, and characteristics, or the existence of any formal core competencies for this role.&nbsp; Methods&nbsp; We describe the development of a minimum set of core competencies for scientific editors of biomedical journals.&nbsp; Results&nbsp; The 14 key core competencies are divided into three major areas, and each competency has a list of associated elements or descriptions of more specific knowledge, skills, and characteristics that contribute to its fulfillment.&nbsp; Conclusions&nbsp; We believe that these core competencies are a baseline of the knowledge, skills, and characteristics needed to perform competently the duties of a scientific editor at a biomedical journal.Additional co-authors: Kurinchi Gurusamy, Farrokh Habibzadeh, Stefanie Jewell-Thomas, Diane Kelsall, José Florencio LapeñaJr, Harriet MacLehose, Ana Marusic, Joanne E. McKenzie, Jay Shah, Larissa Shamseer, Sharon Straus, Peter Tugwell, Elizabeth Wager, Margaret Winker and Getu Zhaor

NSAIDs Modulate Clonal Evolution in Barrett's Esophagus

Cancer is considered an outcome of decades-long clonal evolution fueled by acquisition of somatic genomic abnormalities (SGAs). Non-steroidal anti-inflammatory drugs (NSAIDs) have been shown to reduce cancer risk, including risk of progression from Barrett's esophagus (BE) to esophageal adenocarcinoma (EA). However, the cancer chemopreventive mechanisms of NSAIDs are not fully understood. We hypothesized that NSAIDs modulate clonal evolution by reducing SGA acquisition rate. We evaluated thirteen individuals with BE. Eleven had not used NSAIDs for 6.2±3.5 (mean±standard deviation) years and then began using NSAIDs for 5.6±2.7 years, whereas two had used NSAIDs for 3.3±1.4 years and then discontinued use for 7.9±0.7 years. 161 BE biopsies, collected at 5–8 time points over 6.4–19 years, were analyzed using 1Million-SNP arrays to detect SGAs. Even in the earliest biopsies there were many SGAs (284±246 in 10/13 and 1442±560 in 3/13 individuals) and in most individuals the number of SGAs changed little over time, with both increases and decreases in SGAs detected. The estimated SGA rate was 7.8 per genome per year (95% support interval [SI], 7.1–8.6) off-NSAIDs and 0.6 (95% SI 0.3–1.5) on-NSAIDs. Twelve individuals did not progress to EA. In ten we detected 279±86 SGAs affecting 53±30 Mb of the genome per biopsy per time point and in two we detected 1,463±375 SGAs affecting 180±100 Mb. In one individual who progressed to EA we detected a clone having 2,291±78 SGAs affecting 588±18 Mb of the genome at three time points in the last three of 11.4 years of follow-up. NSAIDs were associated with reduced rate of acquisition of SGAs in eleven of thirteen individuals. Barrett's cells maintained relative equilibrium level of SGAs over time with occasional punctuations by expansion of clones having massive amount of SGAs