Population organization and communication in microorganisms

This review concentrates on the history of the subfield of microbiology referred to as the population organization- and communication-related research direction (POCRRD). The focal points of POCRRD include intercellular interactions, information exchange between cells, and multicellular structures (colonies, biofilms, flocs, etc.). Special attention in this review is given to the contribution of Russian scientists to the development of POCRRD. In terms of POCRRD, microorganisms are viewed as social creatures that constantly communicate and form supraorganismic, intrinsically heterogeneous systems.     

Review of cytologic slides from the national women's hospital, New Zealand, cohort of women with cervical intraepithelial neoplasia 3 diagnosed in 1955-1976

OBJECTIVE: To review cytologic slides, mostly at least 25 years old, from women attending National Women's Hospital, Auckland, who had been diagnosed histologically with cervical carcinoma in situ in 1955-1976. STUDY DESIGN: Smears comprised all those from the 2 years following diagnosis as well as all subsequent smears for women who developed "microinvasive" or invasive lower genital tract cancer. The Victorian Cytology Service performed the review using the Australian Modified Bethesda System. was 0.97. RESULTS: Nine percent of 4,930 retrieved slides were technically unsatisfactory. Original (Papanicolaou) and review coding were available for 4,477 slides. Using categories of equivalence, smears coded as normal (original, 59.2%; review, 61.4%) or showing possible or definite high grade abnormalities (original, 25.9%; review, 29.6%) were found in similar proportions. The kappa statistic (0.79) indicated a high level of agreement between original and review coding. In comparison with the review, the sensitivity of the original coding in detecting high grade abnormalities was 0.80, while the ability of the original assessment to categorize smears as not high grade (specificity) CONCLUSION: This comprehensive review found nearly all archived cytology slides to be technically satisfactory and the broad diagnostic cytologic categories from earlier periods (apart from benign lesions) to be concordant with those currently used.     

Gene transfer: regulatory issues and their impact on the clinical investigator and the good manufacturing production facility

The first human gene-transfer study was submitted to the Recombinant DNA Advisory Committee (RAC) in 1988, thus initiating a new era in clinical research. As per the RAC Website (last updated 22nd November 2002), almost 550 human gene-transfer studies have been submitted to the RAC. However, there are currently no licensed gene-therapy products available in the USA. The natural evolution of the review process to accommodate these novel protocols, as well as the death of Jesse Gelsinger in 1999, have led to significant changes in the initial and ongoing review of gene-transfer studies. However, the basic framework of the review process remains unchanged.Gene-transfer protocols require oversight by the Food and Drug Administration (FDA), the Recombinant DNA Advisory Committee (RAC), the Institutional Biosafety Committee (IBC), and the Institutional Review Board (IRB). Such oversight includes both initial review of the protocol and ongoing review of the study through the review of annual reports, adverse events, and proposed amendments to the study. In addition to such review of the protocol, the product itself is required by the FDA to be prepared under current good manufacturing practices (cGMP). This article discusses both regulatory oversight and current GMP issues in depth.     

对基金项目开展网络同行评议的几点思考

国家自然科学基金委生命科学部六处(畜牧兽医与水产和动物学科)通过对2003年基金项目开展网上评议,使我们真正体会到网上评议的优越性,不仅大大提高工作效率,还使同行专家评审意见全文反馈终于成为可能。但是,若要使网上评议更加科学、公正,除了进一步完善专家库外,国家自然科学基金委还需建设一个“基金项目评议的信息资源链接平台”和“专家评议的反评估网络数据库”,从而完善同行评议网络体系。     

How Long Is Too Long in Contemporary Peer Review? Perspectives from Authors Publishing in Conservation Biology Journals

Delays in peer reviewed publication may have consequences for both assessment of scientific prowess in academia as well as communication of important information to the knowledge receptor community. We present an analysis on the perspectives of authors publishing in conservation biology journals regarding their opinions on the importance of speed in peer-review as well as how to improve review times. Authors were invited to take part in an online questionnaire, of which the data was subjected to both qualitative (open coding, categorizing) and quantitative analyses (generalized linear models). We received 637 responses to 6,547 e-mail invitations sent. Peer-review speed was generally perceived as slow, with authors experiencing a typical turnaround time of 14 weeks while their perceived optimal review time was six weeks. Male and younger respondents seem to have higher expectations of review speed than females and older respondents. The majority of participants attributed lengthy review times to reviewer and editor fatigue, while editor persistence and journal prestige were believed to speed up the review process. Negative consequences of lengthy review times were perceived to be greater for early career researchers and to have impact on author morale (e.g. motivation or frustration). Competition among colleagues was also of concern to respondents. Incentivizing peer-review was among the top suggested alterations to the system along with training graduate students in peer-review, increased editorial persistence, and changes to the norms of peer-review such as opening the peer-review process to the public. It is clear that authors surveyed in this study viewed the peer-review system as under stress and we encourage scientists and publishers to push the envelope for new peer-review models.     

The role of community review in evaluating the risks of human genetic variation research.

The practicality and moral value of community review of human genetic research has become a focus of debate. Examples from two Native American communities are used to address four aspects of that debate: (1) the value of community review in larger, geographically dispersed populations; (2) the identification of culturally specific risks; (3) the potential conflict between individual and group assessments of research-related risks; and (4) the confusion of social categories with biological categories. Our experiences working with these two communities suggest that: (1) successful community review may require the involvement of private social units (e.g., families); (2) culturally specific implications of genetic research may be identifiable only by community members and are of valid concern in their moral universes; (3) community concerns can be incorporated into existing review mechanisms without necessarily giving communities the power to veto research proposals; and (4) the conflation of social and biological categories presents recruitment problems for genetic studies. These conclusions argue for the use of community review to identify and minimize research-related risks posed by genetic studies. Community review also can assist in facilitating participant recruitment and retention, as well as in developing partnerships between researchers and communities.     

Principles and practice in ethical review of animal experiments across Europe: summary of the report of a FELASA working group on ethical evaluation of animal experiments

This paper summarizes a more detailed report produced by the Federation of European Laboratory Animal Science Associations (FELASA 2005), which describes and explores a set of principles for the conduct of ethical review of laboratory animal use. It presents a synopsis of results from a questionnaire that elicited information on how each of 20 countries represented in FELASA currently approaches such ethical review. This information suggests that, although local practices differ, there is an emerging consensus on the key elements that any ethical review process should involve. Drawing on the questionnaire findings, this summary also includes a brief discussion to support and amplify a series of recommendations, covering the objectives of ethical review; legal requirements; the scope of work reviewed and the 'level' at which review is approached; general principles for the organization of ethical review processes; the factors considered in the review; needs for ongoing review after initial authorization; participants in the review process; wider impacts of the review process; and strategies that can help to ensure quality and consistency of review outcomes. For further information and examples of current practice, as well as more detailed discussion to support the recommendations, readers are urged to refer to the complete report, available at http://www.lal.org.uk/pdffiles/FELASA_ethics_FULL_Report. pdf or via: http://www.felasa.eu/recommendations.htm.     

Review of LCA datasets in three emerging economies: a summary of learnings

Purpose

In response to a need for interoperable LCA databases of adequate quality, a review of 40 datasets from emerging economies has been conducted with UNEP support by independent LCA experts, with the purpose to encourage improvements, either prior to publication or as part of a continuous improvement cycle. We discuss the lessons learned during this reviewing process.

Methods

The review effort had to be delivered in a set and limited timeline of 9 months and covered 20 datasets from Malaysia, ten from Brazil, and ten from Thailand. The developed review process consisted in, among others, (i) developing a set of review criteria for this specific effort, (ii) pairing a local sector reviewer with an international LCA expert to enhance capacity development, (iii) establishing a legal relationship via a non-disclosure agreement (NDA) between the data provider and the data reviewers, and (iv) providing a review report for each dataset that assesses the presence and magnitude of gaps or deficiencies relative to the criteria, as well as their implications for qualifying usage.

Results and discussion

The reviews provided solid recommendations for improvement to the majority of the datasets submitted by the three countries. This review exercise has been conducted in the given timeframe for the majority of the datasets. Many challenges have been faced along the way; among them agreeing on an NDA, the need for sufficient information, and the question of the confidentiality of the data. The developed set of criteria for this exercise have not been presented or discussed outside of the narrow review exercise and therefore can be seen as a starting point for further debates and improvements that should involve the broad LCA community.

Conclusions

This hands-on exercise provided some valuable insights into the road towards global consensus and guidance on data review. Beyond this time-constrained effort, a broader discussion and consensus at international level on the review of datasets and a continuous effort in reviewing datasets is desirable. Four key aspects were identified as necessary to consider: review criteria, review process, reviewers’ selection criteria, and development of a legal basis which protects the confidentiality of the data, as well as the position of the reviewers. This last aspect is sensitive as, in LCA datasets reviews, companies and/or countries might disclose some information with high stakes regarding competition and trade.

     

An analysis of book review criteria and motivation

Abstract. The book review process for multi-authored volumes such as symposia proceedings and compendia is analysed and discussed. The criteria used in book reviewing as listed by Keddy (1991) as well as a set of new ones have been screened in a selection of 142 multi-authored volumes reviewed in Ecology, Journal of Ecology, Vegetatio, and Journal of Vegetation Science. Too often many important book review criteria have not been taken into account at all. Use of a standard set of book review criteria is suggested to avoid personal bias as much as possible.     

Critical review: a summary of the current state-of-practice

Purpose

Much collective wisdom and experience have been gained as an increasing number of Life Cycle Assessment (LCA) reviews are conducted. However, specifics on how and when to conduct critical review of LCA studies are still lacking. Toward this need, a technical session entitled “LCA Critical Review” was held during the Life Cycle Management (LCM) conference in Gothenburg, Sweden, 26 August 2013. The goal of the session was to have experts address LCA critical review as well as engage attendees in discussing gaps in the current guidance and how the review process can be improved.

Methods

The LCM session consisted of six presentations followed by open discussion with all session attendees. This paper begins with a review of the current state-of-the-practice in LCA critical review (CR) followed by a summary of the LCM session. It concludes with suggestions for how the newly drafted technical specification, ISO TS 14071 Critical review processes and reviewer competencies, can be improved as it is being developed.

Results and discussion

ISO TS 14071 promises to provide additional guidance to move the practice forward. But at only eight pages in length, its potential effectiveness appears moderate. Additional detailed guidance is needed to move the critical review process toward increased uniformity and clarity of practice, for example, when critical review is necessary.

Conclusions

A session on LCA critical review is planned to be held during the Life Cycle Management 2015 conference which will occur in Bordeaux, France (http://lcm2015.org/). Discussion on these issues related to LCA review will be continued.     

The evolution of peer review as a basis for scientific publication: directional selection towards a robust discipline?

Peer review is pivotal to science and academia, as it represents a widely accepted strategy for ensuring quality control in scientific research. Yet, the peer‐review system is poorly adapted to recent changes in the discipline and current societal needs. We provide historical context for the cultural lag that governs peer review that has eventually led to the system's current structural weaknesses (voluntary review, unstandardized review criteria, decentralized process). We argue that some current attempts to upgrade or otherwise modify the peer‐review system are merely sticking‐plaster solutions to these fundamental flaws, and therefore are unlikely to resolve them in the long term. We claim that for peer review to be relevant, effective, and contemporary with today's publishing demands across scientific disciplines, its main components need to be redesigned. We propose directional changes that are likely to improve the quality, rigour, and timeliness of peer review, and thereby ensure that this critical process serves the community it was created for.     

Optimization of primer-specific filter metrics for the assessment of mitochondrial DNA sequence data

Filter metrics are used as a quick assessment of sequence trace files in order to sort data into different categories (i.e. high quality, review, and low quality) without human intervention. The filter metrics consist of two numerical parameters for sequence quality assessment: trace score (TS) and contiguous read length (CRL). Primer-specific settings for the TS and CRL were established using a calibration dataset of 2817 traces and validated using a concordance dataset of 5617 traces. Prior to optimization, 57% of the traces required manual review before import into a sequence analysis program, whereas after optimization only 28% of the traces required manual review. After optimization of primer-specific filter metrics for mitochondrial DNA sequence data, an overall reduction of review of trace files translates into increased throughput of data analysis and decreased time required for manual review.     

Use of Toxicological Data in Estimating Reference Values for Risk Assessment

A number of programs within the U.S. Environmental Protection Agency (USEPA) currently set less-than-lifetime exposure limits in addition to the chronic reference dose (RfD) and reference concentration (RfC). A review of procedures within the USEPA for setting reference values suggests that less-thanlifetime reference values should be more routinely developed and captured in the USEPA's online IRIS database where chronic RfDs and RfCs, as well as cancer slope factors, are currently available. A review of standard testing study protocols was conducted to determine what data were available for setting acute, short-term, and longer-term reference values, as well as chronic values. This review was done from the point of view of endpoints assessed for specific organ systems (both structural and functional), life stages covered by exposure and outcome, durations of exposure covered and the outcomes evaluated for each, and evaluation of latency to response and/or reversibility of effects. This review revealed a number of data gaps and research needs, including the need for an acute and/or short-term testing protocol that can be used to set acute and shortterm reference values, a strategy for when to conduct more extensive testing based on initial screening data or other information (e.g., chemical class, pharmacokinetics, mode of action), additonal standard testing guidlines protocols to allow more complete assessment of certain organ systems and life stages, development of pharmacokinetic data for different life stages, toxicity related to aging, and latency to response, particularly long-term latency as a result of developmental exposures. The implications of this review are discussed relative to characterizing hazard data for setting reference values, and the potential effects on uncertainty factors and low-dose extrapolation.     

The sensitivity of rapid (partial) review of cervical smears

SHIELD P. W. AND COX N. C. (1998) Cytopathology 9, 84–92 The sensitivity of rapid (partial) review of cervical smears Rapid review involves a daily rapid (e.g. 30 s) review of all smears not normally double-screened. It has been suggested that the method may increase the sensitivity of cervical cytology by identifying abnormalities not reported on initial screening, true false negatives (TFN). Rapid screening is reported to have high sensitivity for cervical neoplasia when used as a preview tool. To be effective, however, in a review mode it must be able to detect TFN. Several studies have found that many TFN result from factors such as low numbers of abnormal cells or subtle expression of diagnostic criteria. Studies on the sensitivity of rapid screening for detecting TFN would therefore provide a more reliable estimate of its value as a review tool. The sensitivity of rapid re-screening was evaluated using a test set of 200 cases. Each of 15 screeners rapidly reviewed (30 s partial screen) the set over a 2-week period. The set consisted of 129 normal, 28 low-grade squamous lesions (CIN I), 37 high-grade lesions (CIN II, III and adenocarcinoma in situ (AIS)) and six invasive carcinomas. The abnormals included 20 TFN cases. The median sensitivity for abnormalities was 62%. Rapid review was more sensitive for CIN II and CIN III (67%) and invasive carcinoma (66.7%) than for CIN I (53%). Great variation was apparent in the sensitivity for individual screeners, with a range of 41–86% for all abnormalities. The sensitivity for TFN cases varied even more (10–75%, median 35%) and for most screeners was significantly (P < 0.05) lower than for cases which were detected on initial screen (53–90%, median 70.6%). Following this trial rapid review was used routinely for a period of 3 months. In this time 11 413 cases were rapidly reviewed. This led to the full review of 415 slides (3.5%) and the identification of 16 cases of undetected CIN (12 CIN I, three CIN II, one CIN III). Based on current estimates of our laboratory false-negative rate this represents between a quarter and half of the TFN cases of CIN that probably occurred in this period. In conclusion, rapid screening is likely to be significantly less sensitive when used in a review rather than a preview mode. In routine practice the method requires a daily commitment of screener time, but does provide a higher yield of TFN smears than does random review, and allows amendment of these results prior to reporting.     

Rapid rescreening of cervical smears as a quality control method in a high-risk population

OBJECTIVE: Cancer of the cervix is one of the commonest cancers in South Africa. Accurate cytological diagnosis is one of the prerequisites for an effective cervical screening programme and requires the implementation of appropriate quality assurance modalities. This study was undertaken to determine if rapid review of reportedly negative cervical smears is a useful internal quality assurance modality in an unscreened population with very high rates of cervical carcinoma. METHOD: Approximately 26% of all cervical smears received at the study institution between 1 January 1998 and 31 December 2003, and initially reported as negative or inadequate, underwent rapid review. RESULTS: A total of 62,866 (26%) cervical smears out of 241,796 reportedly negative or inadequate cervical smears underwent rapid review. An amended report was sent out in 373 (0.59%) of these 62,866 cervical smears. This included 101 cases of high-grade squamous intraepithelial lesion (HSIL) and high-grade atypical squamous cells (ASC-H), 143 low-grade squamous intraepithelial lesions, 54 atypical squamous cells of undetermined significance (ASC-US) and 33 atypical glandular cells that were not reported initially. The false-negative proportion for HSIL and ASC-H (combined) in this study was 5.76%. No squamous cell carcinomas were diagnosed on rapid review but one patient with HSIL/ASC-H on review had squamous cell carcinoma on biopsy. Three cytotechnologists had a lower sensitivity of primary screening and required retraining. CONCLUSIONS: Rapid review is beneficial as an internal quality assurance modality in an unscreened high-risk population and increases the detection of women with significant cervical lesions requiring treatment. The relatively low cost of rapid review compared with other rescreening modalities makes this an attractive option in low resource settings.     

Implementing code review in the scientific workflow: Insights from ecology and evolutionary biology

Code review increases reliability and improves reproducibility of research. As such, code review is an inevitable step in software development and is common in fields such as computer science. However, despite its importance, code review is noticeably lacking in ecology and evolutionary biology. This is problematic as it facilitates the propagation of coding errors and a reduction in reproducibility and reliability of published results. To address this, we provide a detailed commentary on how to effectively review code, how to set up your project to enable this form of review and detail its possible implementation at several stages throughout the research process. This guide serves as a primer for code review, and adoption of the principles and advice here will go a long way in promoting more open, reliable, and transparent ecology and evolutionary biology.     

Max‐Bergmann award lecture:A RaPID way to discover bioactive nonstandard peptides assisted by the flexizyme and FIT systems

Although general review articles should cover various people's achievements related to the subject, this review is privileged to describe the technology developed by Suga (and colleagues) as a recipient of the Max‐Bergmann Medal in 2016. The technology consists of 3 unique and essential tools, flexizymes, FIT, and RaPID systems. This review describes the history of the development of each tool and discusses the recent applications of the RaPID system to discover potent nonstandard peptides for therapeutic and diagnostic uses.     

Signaling pathways in the epithelial origins of pulmonary fibrosis

Pulmonary fibrosis complicates a number of disease processes and leads to substantial morbidity and mortality. Idiopathic pulmonary fibrosis (IPF) is perhaps the most pernicious and enigmatic form of the greater problem of lung fibrogenesis with a median survival of three years from diagnosis in affected patients. In this review, we will focus on the pathology of IPF as a model of pulmonary fibrotic processes, review possible cellular mechanisms, review current treatment approaches and review two transgenic mouse models of lung fibrosis to provide insight into processes that cause lung fibrosis. We will also summarize the potential utility of signaling pathway inhibitors as a future treatment in pulmonary fibrosis. Finally, we will present data demonstrating a minimal contribution of epithelial-mesenchymal transition in the development of fibrotic lesions in the transforming growth factor-alpha transgenic model of lung fibrosis.     

DNA sequence analysis linguistic tools: contrast vocabularies, compositional spectra and linguistic complexity

This is a review of the methods based on counting oligomers in nucleotide and amino acid sequences. Such methods are analogous to the formal linguistic analysis of human texts. This review includes methods based on the calculation of observed occurrences (frequencies) of oligomers and their distribution, as well as those based on deviations between the observed and the expected occurrences (contrast words, genome signatures) in biological sequences. Both types of methods have a wide range of sensitivity and can identify homologous as well as functionally and taxonomically related sequences.     

森林生态系统生物物理参数遥感反演研究进展

论述了利用遥感技术反演推算森林生态系统主要生物物理参数：叶面积指数、吸收光合有效辐射、净第一性生产力和生物量的技术、方法和模型及各个参量之间的相互关系研究进展,阐述了各研究方法、模型的特点、优势及局限性。特别论述了净第一性生产力的森林冠层光合作用理论模型基础、微波遥感估算森林生物量的应用优势和理论模型,展示了遥感技术在森林生态学研究中广阔的应用前景,同时也指出现有研究中各生物物理参数的定量遥感估算还有待进一步深入研究。