Correction to: Metabolic pathway of 6-aminohexanoate in the nylon oligomer-degrading bacterium Arthrobacter sp. KI72: identification of the enzymes responsible for the conversion of 6-aminohexanoate to adipate

Applied Microbiology and Biotechnology - The original publication of this paper contains mistakes for Tables 1 and 2 legends as well as the sublabels in Figs. 2, 4, 5, 6, and 7.     

Expression of Concern

“MiRNA‐218 regulates osteoclast differentiation and inflammation response in periodontitis rats through MMP9”, Cell. Microbiol. 2019;21:e12979, by Jie Guo, Xuemin Zeng, Jie Miao, Chunpeng Liu, Fulan Wei, Dongxu Liu, Zhong Zheng, Kang Ting, Chunling Wang, and Yi Liu. The Editors of Cellular Microbiology and the publisher John Wiley & Sons agree to publish an Expression of Concern regarding the above article, published online in Cellular Microbiology on November 16, 2018, in Wiley Online Library ( https://onlinelibrary.wiley.com/doi/full/10.1111/cmi.12979 ). In September 2019, the journal was contacted regarding concerns about the data presented in Figures 6 and 7 because of high level of similarities in the graphs presented in these figures. The different bars in the graphs show identical height. The standard deviation bars are also of identical length. Although one graph expresses the number of TRAP‐positive cells (Figure 6b) and the other graphs express the relative mRNA expression of different osteoclast‐related genes (Figure 6c‐g), all graphs are identical. The bars in the graphs in Figure 7 that represent 5 different osteoclast genes show the same height. Figures 6 and 7 show identical mRNA expression for a series of different genes: V‐ATPase, NFATc1, CTSK, DC‐STAMP and TRAP. In December 2019, the journal requested the authors to provide the raw data of the experiments presented in the article and for explanations of the similarities. The authors responded that the similarities were due to unintentional errors and provided Excel spread sheets containing processed data in March 2020. The data provided in the Excel sheets that were sent by the authors were analyzed and it was concluded that the calculations as shown in the Excel sheets are correct. However, the concerns raised regarding similarities in the heights of bars representing different parameters and narrow range of standard deviations presented in Figures 6–7 remained. The authors disagree with the concerns raised. In addition, the editors were concerned by manipulations of western blot images to represent single bands instead of doublets for COL1 in Figures 5 and 8 and for MMP9 in Figures 3A and C, 4C, 5A and D, and 8A. The first issue concerning COL1 bands has been addressed and corrected during the peer‐review process. The latter has been clarified after publication and following a request from the editors for the raw data of all figures in the article. In the published article, western blots of MMP‐9 in Figures 3A and C, 4C, 5A and D, and 8A show active‐MMP‐9 only and do not include pro‐MMP‐9 bands that were present in the original western blot experiments. The authors explained that on the original blots that were provided during the peer‐review process, MMP‐9 show doublets that represent pro‐MMP‐9 and active‐MMP‐9. As no significant difference was found for pro‐MMP‐9, the authors only presented single bands for active‐MMP‐9 in the publication version. The authors’ institution, Shandong University, did not respond to a request from the Publisher and the Editor‐in‐Chief to investigate whether the data arose from the originally reported experiments, are unmodified, and are suitable for publication. As a result, the journal is issuing this expression of concern to readers.     

ERRATUM

The legends to Figures 9, 10 and 11 were incorrect. They shouldhave read: Fig.9. Complete Linkage dendrograms with all the variables ofsegmentation for the organisms (b) and their diffraction patterns(a). Flg. 10. Complete linkage dendrograms without variables 4 and5 for the organisms (b) and their diffraction patterns (a). Fig. ll. Complete linkage dendrograms for the organisms witha major degree of segmentation (b) and their diffraction patterns(a).     

ERRATUM: A review of the genus Eodiaptomus Kiefer, 1932, with the description of E. sanuamuangae n.sp. from Thailannd, and a redescriptionn of E.lumholtzi (Sars, 1889) from Australia (Copepoda, Calanoida)

Hydrobiologia 361: 169–189, 1998. Due to technical problems, Figures 73–84 and Figures 85–94 were unfortunately omitted from pages 182 and 183, respectively, of the above volume, duplicates of Figures 1–6 appearing in their place. We now present the correct Figures with their captions, on pages 214 and 215 of this volume. Additionally there are four corrections to Table 1, which appeared on pages 186-188     

Correction to: How whale and dolphin barnacles attach to their hosts and the paradox of remarkably versatile attachment structures in cypris larvae

Organisms Diversity & Evolution - A typographical error was found in the Table 1 and Figures 5 and 9 legends. The specie name "Lepas anatifera" should have been "Lepas...     

EasyGO: Gene Ontology-based annotation and functional enrichment analysis tool for agronomical species

Following the publication of our recent article (Kapp et al., BMC Genomics 2006, 7:231), we (the authors) regrettably found several errors in the published Table 5. This correction article not only describes what makes the published Table 5 incorrect, it also presents the correct Table 5.     

Algorithm of OMA for large-scale orthology inference

Since the publication of our article (Roth, Gonnet, and Dessimoz: BMC Bioinformatics 2008 9: 518), we have noticed several errors, which we correct in the following.     

ERRATUM

In this paper, Figures 5 and 6 were unfortunately printed (throughno fault of the authors) in the wrong positions. The diagramon page 291 should correctly be positioned on page 292 and viceversa. The captions are in the correct positions.     

Positioning of anchor groups in protein loop prediction: the importance of solvent accessibility and secondary structure elements

The prediction of loop regions in the process of protein structure prediction by homology is still an unsolved problem. In an earlier publication, we could show that the correct placement of the amino acids serving as an anchor group to be connected by a loop fragment with a predicted geometry is a highly important step and an essential requirement within the process (Lessel and Schomburg, Proteins 1999; 37:56-64). In this article, we present an analysis of the quality of possible loop predictions with respect to gap length, fragment length, amino acid type, secondary structure, and solvent accessibility. For 550 insertions and 544 deletions, we test all possible positions for anchor groups with an inserted loop of a length between 3 and 12 amino acids. We could show that approximately 80% of the indel regions could be predicted within 1.5 A RMSD from a knowledge-based loop data base if criteria for the correct localization of anchor groups could be found and the loops can be sorted correctly. From our analysis, several conclusions regarding the optimal placement of anchor groups become obvious: (1) The correct placement of anchor groups is even more important for longer gap lengths, (2) medium length fragments (length 5-8) perform better than short or long ones, (3) the placement of anchor groups at hydrophobic amino acids gives a higher chance to include the best possible loop, (4) anchor groups within secondary structure elements, in particular beta-sheets are suitable, (5) amino acids with lower solvent accessibility are better anchor group. A preliminary test using a combination of the anchor group positioning criteria deduced from our analysis shows very promising results.     

Tension receptors on the apodemes of muscles in the walking legs of the crab,Cancer magister †

1. Mechanoreceptors monitoring tension in working muscles are described in the Decapoda Crustacea.

2. The receptors are associated with apodemes of muscles in the walking leg and are well‐developed in the extensor and flexor of the meropodite (Figures 1, 2).

3. The unbranched dendrites of the receptor neurones innervate the tissues surrounding the insertions of the muscle fibres (Figures 3, 4, 5(A)).

4. The receptors show spontaneous activity with the M‐C joint at resting position and this activity increases when the muscle is stretched by holding the joint at a different position (Figure 7).

5. Isometric tension increase in the muscle recruits sensory units (Figures 8, 10(A)) and increases the activity of units firing (Figure 9).

6. Apodeme receptors may be an entirely distinct input channel from chordotonal organs (Figure 10(B,C)). Joint movements produced by a standard muscle stimulus against increasing loads reveal very different responses (Figure 11).

7. Attempts to determine whether chordotonal organs (CP1, Figures 5(B), 6) monitor isometric muscle tension (Figure 12) suggest possible complexities in their dynamic responses.

8. Abbreviations used in this paper are FASN flexor apodeme sensory nerve, EASN extensor apodeme sensory nerve, BASN bender apodeme sensory nerve, and OASN opener apodeme sensory nerve.     

How to Get the Most out of Your Curation Effort

Large-scale annotation efforts typically involve several experts who may disagree with each other. We propose an approach for modeling disagreements among experts that allows providing each annotation with a confidence value (i.e., the posterior probability that it is correct). Our approach allows computing certainty-level for individual annotations, given annotator-specific parameters estimated from data. We developed two probabilistic models for performing this analysis, compared these models using computer simulation, and tested each model's actual performance, based on a large data set generated by human annotators specifically for this study. We show that even in the worst-case scenario, when all annotators disagree, our approach allows us to significantly increase the probability of choosing the correct annotation. Along with this publication we make publicly available a corpus of 10,000 sentences annotated according to several cardinal dimensions that we have introduced in earlier work. The 10,000 sentences were all 3-fold annotated by a group of eight experts, while a 1,000-sentence subset was further 5-fold annotated by five new experts. While the presented data represent a specialized curation task, our modeling approach is general; most data annotation studies could benefit from our methodology.     

Successful discrimination of protein interactions

We present results from the prediction of protein complexes associated with the first Critical Assessment of PRediction of Interactions (CAPRI) experiment. Our algorithm, SmoothDock, comprises four steps: (1) we perform rigid body docking using the program DOT, keeping the top 20,000 structures as ranked by surface complementarity; (2) we rerank these structures according to a free energy estimate that includes both desolvation and electrostatics and retain the top 2000 complexes; (3) we cluster the filtered complexes using a pairwise root-mean-square deviation (RMSD) criterion; (4) the 25 largest clusters are subject to a smooth docking discrimination algorithm where van der Waals forces are taken into account. We predicted targets 1, 6, and 7 with RMSDs of 9.5, 2.4, and 2.6 A, respectively. More importantly, from the perspective of biological applications, our approach consistently ranked the correct model first (i.e., with highest confidence). For target 5 we identified the binding region but not the correct orientation. Although we were able to find reasonable clusters for all targets, low-affinity complexes (K(d) < nM) were harder to discriminate. For four of seven targets, the top models predicted by our automated procedure were among the best communitywide predictions.     

Retraction

Gómez-Hernández A, de las Heras N, Otero YF, Escribano ó, Gozalbo-López B, Guillén C,Cachofeiro V, Lahera V, Benito M. Differential vascular damage in non-compensated versus compensated insulin resistance. Am J Physiol Endocrinol Metab (First published May 10, 2011).doi:10.1152/ajpendo.00662.2010.This article is being retracted by the American Physiological Society at the request of the authors because it contains improperly prepared data in Figures 3A and 4B. The authors apologize to the readers for this error and for any inconvenience associated with the publication of the article.     

Ion exchange HPLC microanalysis of chondroitin sulfate: quantitative derivatization of chondroitin lyase digestion products with 2-aminopyridine

The following corrections pertain to the legends of Figures1 and 4: Disulfated disaccharide standards in Figure 1B are:peak 6, Di_E-PA; peak 7, Di_D-PA. Di_B-PA co-elutes with Di_E-PAunder the chromatographic conditions described (data not shown).Accordingly, in Figure 4H, peak 8 (39.5 min) eluted in the positionof Di_D-PA and not Di_B-PA.     

A Lagrangian model of phytoplankton photosynthetic response in the upper mixed layer

Figure 1: On the top plot, the left vertical axis label shouldread ‘Cumulative Inhibition’ instead of ‘InstantaneousInhibition’. Figures 2, 3 and 5: The horizontal time axis should begin at6 or 0600 hours instead of 18 or 1800 hours.     

Publication bias in laboratory animal research: a survey on magnitude, drivers, consequences and potential solutions

Context

Publication bias jeopardizes evidence-based medicine, mainly through biased literature syntheses. Publication bias may also affect laboratory animal research, but evidence is scarce.

Objectives

To assess the opinion of laboratory animal researchers on the magnitude, drivers, consequences and potential solutions for publication bias. And to explore the impact of size of the animals used, seniority of the respondent, working in a for-profit organization and type of research (fundamental, pre-clinical, or both) on those opinions.

Design

Internet-based survey.

Setting

All animal laboratories in The Netherlands.

Participants

Laboratory animal researchers.

Main Outcome Measure(s)

Median (interquartile ranges) strengths of beliefs on 5 and 10-point scales (1: totally unimportant to 5 or 10: extremely important).

Results

Overall, 454 researchers participated. They considered publication bias a problem in animal research (7 (5 to 8)) and thought that about 50% (32–70) of animal experiments are published. Employees (n = 21) of for-profit organizations estimated that 10% (5 to 50) are published. Lack of statistical significance (4 (4 to 5)), technical problems (4 (3 to 4)), supervisors (4 (3 to 5)) and peer reviewers (4 (3 to 5)) were considered important reasons for non-publication (all on 5-point scales). Respondents thought that mandatory publication of study protocols and results, or the reasons why no results were obtained, may increase scientific progress but expected increased bureaucracy. These opinions did not depend on size of the animal used, seniority of the respondent or type of research.

Conclusions

Non-publication of “negative” results appears to be prevalent in laboratory animal research. If statistical significance is indeed a main driver of publication, the collective literature on animal experimentation will be biased. This will impede the performance of valid literature syntheses. Effective, yet efficient systems should be explored to counteract selective reporting of laboratory animal research.     

Challenges and opportunities of publishing supplements at <Emphasis Type="Italic">Arthritis Research &; Therapy</Emphasis>

Supplements are the cause of much debate in the world of journal publishing. Supplements are criticized for the fact that often they are funded by an external source, and journals have been known to shy away from their publication [1]. But is refusing to publish supplements the only answer? At Arthritis Research & Therapy, we feel that - if subjected to the full rigors of peer review - supplements can provide invaluable educational resources, exploring themes in a detailed and focused way that might not always be possible in the main journal.At Arthritis Research & Therapy, we have decided that the potential risk of a loss of objectivity in industry-sponsored supplements can be managed by scrupulous attention to the peer-review process. Therefore, in our experience, the benefit of publishing supplements greatly outweighs any perception of loss of objectivity. We should note that our colleagues in the pharmaceutical industry have embraced our approach with no efforts to circumvent our rules, as far as we know.We consider proceedings, review collections, and meeting abstracts for inclusion as supplements. Examples of recent supplements are easily accessed on the journal website. It will be apparent that the emphasis is on the molecular and cellular basis of immune and inflammatory mechanisms of disease. The underwriting by the sponsor of the cost of peer review and production ensures that the high-quality publication is freely available. Outlined below is the procedure that we follow when considering any potential supplements for the journal. We recognize the potential for competing interests to influence the content of articles where there is industry involvement, but we believe that by adhering to a stringent publication process we negate this risk with our supplement content.So, what is the procedure? First, in a change from the approach taken by many journals, we appoint an ''internal'' Supplement Editor (usually from the journal''s Editorial Board), whose role is to select peer reviewers and assess the suitability of the supplement articles for publication in the journal. This internal editor is selected by the Editors-in-Chief, and the sponsor''s approval is not sought in making this appointment. Before their appointment, internal editors are asked to declare any potential conflicts of interest, and full disclosures are included in both online and print versions of any supplements. In cases in which internal editors receive a stipend, this is paid for by the publisher - not the sponsor. All conflict of interest disclosures associated with supplement publications follow the National Library of Medicine policy for indexing supplement articles in MEDLINE [2].For some supplements, particularly where articles are commissioned externally, there may be an ''external'' Supplement Editor as well as the internal editor. Before their appointment, external supplement editors must be approved by the Editors-in-Chief. Their role is to identify the subject matter and propose suitable authors for the individual supplement articles, with the proviso that all content must be approved by the Editors-in-Chief. The external editor is not involved in the peer review of any of the articles once submitted. They are also asked for full conflict of interest disclosures, which are included in the supplement publication alongside those of the internal editor.One of the common criticisms levied against supplements is that the articles are not peer-reviewed to the journal''s normal standards. At Arthritis Research & Therapy, supplement articles go through the same thorough peer-review process as articles do in the main journal [3]. The Editors-in-Chief have full editorial control, including the ability to ask authors to make extensive revisions, and reserve the right to reject articles that do not meet the journal''s standards. And in accordance with the guidelines of the International Committee for Medical Journal Editors [4], all contracts clearly include information about editorial control and the role of the internal supplement editor.In addition to disclosures from the individual editors, sources of funding for a supplement are prominently displayed on the supplement title page, and funding is also acknowledged in each individual article. We ensure that supplements can be clearly distinguished as separate from the main journal content on the journal homepage. As with all of our articles, individual authors declare their conflicts of interest. This complies with the good publication practice (GPP2) guidelines [5]. We also adhere to the guidelines of the European Medical Writers Association [6] by ensuring that the involvement of any medical writers is disclosed in an article''s acknowledgments section along with their sources of funding.We hope that by ensuring that there is full transparency of disclosures from everyone involved in supplements and following strictly the peer-review procedure described above, we avoid the potential pitfalls of supplement publishing. The guidelines of the International Committee of Medical Journal Editors themselves state that supplements ''serve useful purposes'' and it is our responsibility as editors to ensure that they continue to be useful without allowing ourselves to be subject to industry influence. By publicly disclosing our policy for supplement review here, we hope that other journals will be more open about their peer-review policies for supplements and that they adopt similarly stringent practices in the future.     

Erratum to: Western Purple-Faced Langurs (Semnopithecus vetulus nestor) Feed on Ripe and Ripening Fruit in Human-Modified Environments in Sri Lanka

Erratum to: Int J Primatol (2012) 33(1): 40–72 DOI 10.1007/s10764-011-9538-3 This notice clarifies the relationship between this publication and a previous publication by the same author. The purpose of this notice is to correct the literature and ensure its integrity.     

Correction: Helicobacter pylori and gastroduodenal pathology: New threats of the old friend

Since publication of our article (Ahmed and Sechi: Ann Clin Microbiol Antimicrob 2005, 4:1), we have noticed several errors.