Perspectives from early career researchers on the publication process in ecology – a response to Statzner & Resh (2010)

1. Two senior ecologists summarised their experience of the scientific publication process ( Statzner & Resh, Freshwater Biology, 2010 ; 55 , 2639) to generate discussion, particularly among early career researchers (ECRs). As a group of eight ECRs, we comment on the six trends they described. 2. We generally agree with most of the trends identified by Statzner & Resh (2010) , but also highlight a number of divergent perspectives and provide recommendations for change. Trends of particular concern are the use of inappropriate metrics to evaluate research quality (e.g. impact factor) and the salami slicing of papers to increase paper count. We advocate a transparent and comprehensive system for evaluating the research. 3. We stress the importance of impartiality and independence in the peer review process. We therefore suggest implementation of double‐blind review and quality control measures for reviewers and possibly editors. Besides such structural changes, editors should be confident to overrule biased reviewer recommendations, while reviewers should provide helpful reviews but be explicit if a submission does not meet quality standards. Authors should always conduct a thorough literature search and acknowledge historical scientific ideas and methods. Additionally, authors should report low‐quality copy editing and reviews to the editors. 4. Both early and late career researchers should jointly implement these recommendations to reverse the negative trends identified by Statzner & Resh (2010) . However, more senior scientists will always have to take the lead with respect to structural changes in the publication system given that they occupy the majority of decision‐making positions.     

A Quality Control System Involving Peer Review of Abnormal Cervical Smears

An internal quality control system which is used in the centralized cytology laboratory of a population-based cervical cancer screening programme in Florence is described. It includes a peer review procedure. Abnormal cervical smears are circulated among all the cytologists and a consensus on the final diagnosis is reached. This daily procedure is designed to evaluate the performance of each cytologist and of the laboratory as a whole but can also be considered a valuable training opportunity. During an 18-month period 1197 smears were reviewed by 15 readers using a reporting form with six main categories of reporting (from ‘regative’ to ‘invasive carcinoma’), plus an ‘unsatisfactory’ category. Overall the concordance between the 15 cytologists, assessed using the kappa statistic (range 0.46–0.71; median 0.60), was good. the level of agreement increased when a weighted kappa statistic (range 0.55–0.78; median 0.68) was used. Kappa values were also calculated for specific categories and suggested an increasing concordance with increasing severity of the lesions, the categories of ‘severe dysplasia’ and ‘invasive carcinoma’ showing the highest agreement. the poor results for the ‘moderate dysplasia’ confirmed the need for combining this group with the ‘severe dysplasia’, as proposed in the Bethesda system.     

教育中的同伴效应研究述评：概念、模型与方法

教育中的同伴效应是指宿舍、班级、年级或学校内同伴的背景、行为及产出对学生产出或行为的影响。教育中的同伴效应起初使用的是同质性模型,即认为无论个体如何选择同伴,总效益是不变的,同伴效应是一种零和现象。进而发展到异质性模型,即认为同伴效应对不同个体的作用结果是不一样的,通过合理的分配能够提高总效益。研究方法则从以普通最小二乘法为主的统计关联研究,发展到借助于随机实验、自然实验以及准实验的因果推断研究。同伴效应的研究为正确地认识和评价相关教育政策,获得最优组织学校教学的方式,提高教学效率提供了依据。     

Process Development in Biotechnology – A Re‐Evaluation

This review considers some process development problems in biotechnology and presents examples of solutions, which were developed in cooperation with industrial partners. These processes include the production of restriction endonuclease EcoRI by recombinant Escherichia coli, which is toxic to the cell, penicillin V by Penicillium chrysogenum, xylanase by Aspergillus awamori, cephalosporin C by Acremonium chrysogenum, erythritol by Moniliella tomentosa var pollinis, and alkaline serine protease by Bacillus licheniformis. Special attention is given to the practical aspects of product development.     

Respecting Autonomy Over Time: Policy and Empirical Evidence on Re‐Consent in Longitudinal Biomedical Research

Re‐consent in research, the asking for a new consent if there is a change in protocol or to confirm the expectations of participants in case of change, is an under‐explored issue. There is little clarity as to what changes should trigger re‐consent and what impact a re‐consent exercise has on participants and the research project. This article examines applicable policy statements and literature for the prevailing arguments for and against re‐consent in relation to longitudinal cohort studies, tissue banks and biobanks. Examples of re‐consent exercises are presented, triggers and non‐triggers for re‐consent discussed and the conflicting attitudes of commentators, participants and researchers highlighted. We acknowledge current practice and argue for a greater emphasis on ‘responsive autonomy,’ that goes beyond a one‐time consent and encourages greater communication between the parties involved. A balance is needed between respecting participants' wishes on how they want their data and samples used and enabling effective research to proceed.     

Re‐approaching the small island effect

Aim To propose a new approach to the small island effect (SIE) and a simple mathematical procedure for the estimation of its upper limit. The main feature of the SIE is that below an upper size threshold an increase of species number with increase of area in small islands is not observed. Location Species richness patterns from different taxa and insular systems are analysed. Methods Sixteen different data sets from 12 studies are analysed. Path analysis was used for the estimation of the upper limit of the SIE. We studied each data set in order to detect whether there was a certain island size under which the direct effects of area were eliminated. This detection was carried out through the sequential exclusion of islands from the largest to the smallest. For the cases where an SIE was detected, a log‐log plot of species number against area is presented. The relationships between habitat diversity, species number and area are studied within the limits of the SIE. In previous studies only area was used for the detection of the SIE, whereas we also encompass habitat diversity, a parameter with well documented influence on species richness, especially at small scales. Results An SIE was detected in six out of the 16 studied cases. The upper limit of the SIE varies, depending on the characteristics of the taxon and the archipelago under study. In general, the values of the upper limit of the SIE calculated according to the approach undertaken in our study differ from the values calculated in previous studies. Main conclusions Although the classical species–area models have been used to estimate the upper limit of the SIE, we propose that the detection of this phenomenon should be undertaken independently from the species–area relationship, so that the net effects of area are calculated excluding the surrogate action of area on other variables, such as environmental heterogeneity. The SIE appears when and where area ceases to influence species richness directly. There are two distinct SIE patterns: (1) the classical SIE where both the direct and indirect effects of area are eliminated and (2) the cryptic SIE where area affects species richness indirectly. Our approach offers the opportunity of studying the different factors influencing biodiversity on small scales more accurately. The SIE cannot be considered a general pattern with fixed behaviour that can be described by the same model for different island groups and taxa. The SIE should be recognized as a genuine but idiosyncratic phenomenon.     

Re‐engineering the μ‐conotoxin SIIIA scaffold

Voltage‐gated sodium (Na_v) channels are responsible for generation and propagation of action potentials throughout the nervous system. Their malfunction causes several disorders and chronic conditions including neuropathic pain. Potent subtype specific ligands are essential for deciphering the molecular mechanisms of Na_v channel function and development of effective therapeutics. µ‐Conotoxin SIIIA is a potent mammalian Na_v1.2 channel blocker that exhibits analgesic activity in rodents. We undertook to reengineer loop 1 through a strategy involving charge alterations and truncations which led to the development of µ‐SIIIA mimetics with novel selectivity profiles. A novel [N5K/D15A]SIIIA(3–20) mutant with enhanced net positive charge showed a dramatic increase in its Na_v1.2 potency (IC₅₀ of 0.5 nM vs. 9.6 nM for native SIIIA) though further truncations led to loss of potency. Unexpectedly, it appears that SIIIA loop 1 significantly influences its Na_v channel interactions despite loop 2 and 3 residues constituting the pharmacophore. This minimal functional conotoxin scaffold may allow further development of selective Na_V blockers. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 347–354, 2014.     

Re‐evaluating the stability of COMU in different solvents

COMU is uronium‐type coupling reagent based on OxymaPure. It showed several advantages over classical benzotriazole‐based coupling reagents such as higher solubility, water‐soluble byproduct, and monitoring the reaction by changing of color. Although COMU is well known to perform excellent in solution, but its hydrolytic stability in DMF limits its use in automatic peptide synthesizer. Herein, we evaluated the hydrolytic stability of COMU in γ‐valerolactone (GVL), acetonitrile (ACN) and N‐formylmorpholine (NFM) and compared its stability against DMF. The stability of COMU after 24 h was found to be 88 and 89% in GVL and ACN, respectively, when compared in DMF (14%). Further, the demanding Aib‐ACP decapeptide and JR decapeptide were successfully synthesized using COMU dissolved in GVL or ACN while Fmoc amino acids were dissolved in DMF. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.     

Preclinical characterization of alginate‐poly‐L‐lysine encapsulated HepaRG for extracorporeal liver supply

We recently demonstrated that HepaRG cells encapsulated into 1.5% alginate beads are capable of self‐assembling into spheroids. They adequately differentiate into hepatocyte‐like cells, with hepatic features observed at Day 14 post‐encapsulation required for external bioartificial liver applications. Preliminary investigations performed within a bioreactor under shear stress conditions and using a culture medium mimicking acute liver failure (ALF) highlighted the need to reinforce beads with a polymer coating. We demonstrated in a first step that a poly‐l ‐lysine coating improved the mechanical stability, without altering the metabolic activities necessary for bioartificial liver applications (such as ammonia and lactate elimination). In a second step, we tested the optimized biomass in a newly designed perfused dynamic bioreactor, in the presence of the medium model for pathological plasma for 6 h. Performances of the biomass were enhanced as compared to the steady configuration, demonstrating its efficacy in decreasing the typical toxins of ALF. This type of bioreactor is easy to scale up as it relies on the number of micro‐encapsulated cells, and could provide an adequate hepatic biomass for liver supply. Its design allows it to be integrated into a hybrid artificial/bioartificial liver setup for further clinical studies regarding its impact on ALF animal models.     

Listening to the Call of Dance: Re‐thinking Authenticity and ‘Essentialism’

A sustained and devastating critique has been aimed in recent years at a metaphysics of truth which understands truth and authenticity as essence, as fixed, self‐identical and persistent over time. So successful has this critique been that it is now possible to speak of authenticity only in terms of a certain ‘strategic’ or politically necessary engagement, on the part of subaltern groups, with an essentialist metaphysics. While the critique is a necessary one, taken on its own it has resulted in a reductionist presumption that we are only ever going to encounter versions of truth that we have already understood, for purposes of critique, as so many versions of ‘essentialism’. By contrast, in the ceremonial performances of dance described in this issue of TAJA, across a broad spectrum of cultures, we witness the striking persistence and centrality of references to virtuosity, appropriate ‘feeling’ and to the experience of a kind of integrity, coherence and ‘truth’ in a good performance. The commentary argues that these distinctions rest on traditions that move us quite far from an essentialism both of the spirit and of the body, requiring instead a fresh effort of understanding on our part. Utilising other traditions to develop a better, less reified understanding of truth criteria can help arrest a certain hyper‐expansion of ‘the political’ that threatens to leave no other terms alive with which to inform its own vision of the relation between past, present and future.     

Re‐evaluating fall cankerworm management thresholds for urban and suburban forests

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Evidence‐based restoration in the Anthropocene—from acting with purpose to acting for impact

The recognition that we are in the distinct new epoch of the Anthropocene suggests the necessity for ecological restoration to play a substantial role in repairing the Earth's damaged ecosystems. Moreover, the precious yet limited resources devoted to restoration need to be used wisely. To do so, we call for the ecological restoration community to embrace the concept of evidence‐based restoration. Evidence‐based restoration involves the use of rigorous, repeatable, and transparent methods (i.e. systematic reviews) to identify and amass relevant knowledge sources, critically evaluate the science, and synthesize the credible science to yield robust policy and/or management advice needed to restore the Earth's ecosystems. There are now several examples of restoration‐relevant systematic reviews that have identified instances where restoration is entirely ineffective. Systematic reviews also serve as a tool to identify the knowledge gaps and the type of science needed (e.g. repeatable, appropriate replication, use of controls) to improve the evidence base. The restoration community, including both scientists and practitioners, needs to make evidence‐based restoration a reality so that we can move from best intentions and acting with so‐called “purpose” to acting for meaningful impact. Doing so has the potential to serve as a rallying point for reframing the Anthropocene as a so‐called “good” epoch.     

The Validation of Peer Review through Research Impact Measures and the Implications for Funding Strategies

There is a paucity of data in the literature concerning the validation of the grant application peer review process, which is used to help direct billions of dollars in research funds. Ultimately, this validation will hinge upon empirical data relating the output of funded projects to the predictions implicit in the overall scientific merit scores from the peer review of submitted applications. In an effort to address this need, the American Institute of Biological Sciences (AIBS) conducted a retrospective analysis of peer review data of 2,063 applications submitted to a particular research program and the bibliometric output of the resultant 227 funded projects over an 8-year period. Peer review scores associated with applications were found to be moderately correlated with the total time-adjusted citation output of funded projects, although a high degree of variability existed in the data. Analysis over time revealed that as average annual scores of all applications (both funded and unfunded) submitted to this program improved with time, the average annual citation output per application increased. Citation impact did not correlate with the amount of funds awarded per application or with the total annual programmatic budget. However, the number of funded applications per year was found to correlate well with total annual citation impact, suggesting that improving funding success rates by reducing the size of awards may be an efficient strategy to optimize the scientific impact of research program portfolios. This strategy must be weighed against the need for a balanced research portfolio and the inherent high costs of some areas of research. The relationship observed between peer review scores and bibliometric output lays the groundwork for establishing a model system for future prospective testing of the validity of peer review formats and procedures.