Peer review golden rules and good practice checklist

Irene Hames 한국과학학술지편집인협의회 2016 Science Editing Vol.3 No.1

This is a republication of Appendix 1, The Golden Rules and the Peer-Review Good Practice Checklist, from the author’s book, Peer Review and Manuscript Management in Scientific Journals: guidelines for good practice, published in 2007 by Wiley-Blackwell in association with ALPSP (the Association of Learned and Professional Society Publishers), with the permission of the author and publisher (ISBN: 978-1-4051-3159-9, http://eu.wiley.com/WileyCDA/WileyTitle/productCd-1405131594.html).

The changing face of peer review

Irene Hames 한국과학학술지편집인협의회 2014 Science Editing Vol.1 No.1

It is a time of great innovation in peer review. Traditional models are being adapted and completely new ones introduced. Independent peer-review services are also starting to be offered by organizations outside the traditional journal ecosphere. In both new and established systems, the importance of increasing openness, transparency, and interaction between peer-review participants is being recognized, and these are being introduced to varying degrees. Concern with the ‘wastage’ of review effort in traditional peer review, where manuscripts often go from journal to journal, being reviewed afresh at each, before being accepted for publication, is also being addressed. Reviews are being transferred (‘cascaded’) and shared between some journals. The separation of the two basic functions of peer review—critical review and selection—as originally introduced by the journal PLOS ONE has been a major innovation, leading to the publication of sound work irrespective of its perceived novelty, interest, or importance. Post-publication review is also becoming more important and is another growth area. The concept of ‘portable’ reviews has been introduced, where authors can take reviews with them—either after they have obtained them from a peer-review provider in return for a fee or had their manuscript reviewed and declined at some journals—and include them with submissions to journals. The dynamics of publication are changing alongside, with journals able to ‘bid’ for papers that have been reviewed by independent organizations and make publishing offers to the authors. A number of innovations and ‘alternative’ peer-review models are described. They all, however, face many of the same issues as traditional peer review, and the same basic principles of good and ethical practice apply.

Peer review at the beginning of the 21st century

Irene Hames 한국과학학술지편집인협의회 2014 Science Editing Vol.1 No.1

Vigorous debate currently surrounds peer review, and polarized views are often expressed. Despite criticisms about the process, studies have found that it is still valued by researchers, with rigorous peer review being rated by authors as the most important service they expect to receive when paying to have their papers published open access. The expectations of peer review and what it can achieve need, however, to be realistic. Peer review is also only as good and effective as the people managing the process, and the large variation in standards that exists is one of the reasons some of the research and related communities have become critical of and disillusioned with the traditional model of peer review. The role of the editor is critical. All editors must act as proper editors, not just moving manuscripts automatically through the various stages, but making critical judgements throughout the process to reach sound and unbiased editorial decisions. New models and innovations in peer review are appearing. Many issues, however, remain the same: rigorous procedures and high ethical standards should be in place, those responsible for making decisions and managing the process need to be trained to equip them for their roles and responsibilities, and systems need to be adapted to deal with new challenges such as the increasing amounts of data being generated and needing to be taken into account when assessing the validity and soundness of work and the conclusions being drawn.

Multisite phosphorylation of C-Nap1 releases it from Cep135 to trigger centrosome disjunction

Hardy, Tara,Lee, Miseon,Hames, Rebecca S.,Prosser, Suzanna L.,Cheary, Donna-Marie,Samant, Mugdha D.,Schultz, Francisca,Baxter, Joanne E.,Rhee, Kunsoo,Fry, Andrew M. The Company of Biologists 2014 Journal of cell science Vol.127 No.11

<P><B>ABSTRACT</B></P><P>During mitotic entry, centrosomes separate to establish the bipolar spindle. Delays in centrosome separation can perturb chromosome segregation and promote genetic instability. However, interphase centrosomes are physically tethered by a proteinaceous linker composed of C-Nap1 (also known as CEP250) and the filamentous protein rootletin. Linker disassembly occurs at the onset of mitosis in a process known as centrosome disjunction and is triggered by the Nek2-dependent phosphorylation of C-Nap1. However, the mechanistic consequences of C-Nap1 phosphorylation are unknown. Here, we demonstrate that Nek2 phosphorylates multiple residues within the C-terminal domain of C-Nap1 and, collectively, these phosphorylation events lead to loss of oligomerization and centrosome association. Mutations in non-phosphorylatable residues that make the domain more acidic are sufficient to release C-Nap1 from the centrosome, suggesting that it is an increase in overall negative charge that is required for this process. Importantly, phosphorylation of C-Nap1 also perturbs interaction with the core centriolar protein, Cep135, and interaction of endogenous C-Nap1 and Cep135 proteins is specifically lost in mitosis. We therefore propose that multisite phosphorylation of C-Nap1 by Nek2 perturbs both oligomerization and Cep135 interaction, and this precipitates centrosome disjunction at the onset of mitosis.</P>

Inactivation of LLC1 gene in nonsmall cell lung cancer

Hong, Kyeong-Man,Yang, Sei-Hoon,Chowdhuri, Sinchita Roy,Player, Audrey,Hames, Megan,Fukuoka, Junya,Meerzaman, Daoud,Dracheva, Tatiana,Sun, Zhifu,Yang, Ping,Jen, Jin Alan R. Liss, Inc 2007 International journal of cancer Vol.120 No.11

<P>Serial analysis of gene expression studies led us to identify a previously unknown gene, c20orf85, that is present in the normal lung epithelium but absent or downregulated in most primary nonsmall cell lung cancers and lung cancer cell lines. We named this gene LLC1 for Low in Lung Cancer 1. LLC1 is located on chromosome 20q13.3 and has a 70% GC content in the promoter region. It has 4 exons and encodes a protein containing 137 amino acids. By in situ hybridization, we observed that LLC1 message is localized in normal lung bronchial epithelial cells but absent in 13 of 14 lung adenocarcinoma and 9 out of 10 lung squamous carcinoma samples. Methylation at CpG sites of the LLC1 promoter was frequently observed in lung cancer cell lines and in a fraction of primary lung cancer tissues. Treatment with 5-aza deoxycytidine resulted in a reduced methylation of the LLC1 promoter concomitant with the increase of LLC1 expression. These results suggest that inactivation of LLC1 by means of promoter methylation is a frequent event in nonsmall cell lung cancer and may play a role in lung tumorigenesis. © 2007 Wiley-Liss, Inc.</P>

Jaw lesions associated with impacted tooth: A radiographic diagnostic guide

Hamed Mortazavi,Maryam Baharvand 대한영상치의학회 2016 Imaging Science in Dentistry Vol.46 No.3

This review article aimed to introduce a category of jaw lesions associated with impacted tooth. General search engines and specialized databases such as Google Scholar, PubMed, PubMed Central, MedLine Plus, Science Direct, Scopus, and well-recognized textbooks were used to find relevant studies using keywords such as “jaw lesion”, “jaw disease”, “impacted tooth”, and “unerupted tooth”. More than 250 articles were found, of which approximately 80 were broadly relevant to the topic. We ultimately included 47 articles that were closely related to the topic of interest. When the relevant data were compiled, the following 10 lesions were identified as having a relationship with impacted tooth: dentigerous cysts, calcifying odontogenic cysts, unicystic (mural) ameloblastomas, ameloblastomas, ameloblastic fibromas, adenomatoid odontogenic tumors, keratocystic odontogenic tumors, calcifying epithelial odontogenic tumors, ameloblastic fibro-odontomas, and odontomas. When clinicians encounter a lesion associated with an impacted tooth, they should first consider these entities in the differential diagnosis. This will help dental practitioners make more accurate diagnoses and develop better treatment plans based on patients’ radiographs.

Photocatalytic decolourization of dyes on NiO-ZnO nano-composites

Hameed, Abdul,Montini, Tiziano,Gombac, Valentina,Fornasiero, Paolo Korean Society of Photoscience 2009 Photochemical & photobiological sciences Vol.8 No.5

NiO-ZnO nanocomposite photocatalysts were synthesized by co-precipitation/co-gel formation techniques using potassium hydroxide (KOH), sodium carbonate ($Na_2CO_3$) and oxalic acid ($H_2C_2O_4$) as precipitating agents. X-Ray diffraction (XRD) analysis was employed for the determination of crystallite size and phase purity, while BET surface areas were estimated by nitrogen physisorption analysis. The photocatalytic activities of the NiO-ZnO nanocomposites, evaluated using the photo-decolourization of two structurally different dyes, methyl orange and methylene blue, were correlated with the variation in the crystallite size of the constituents of the composites. All the three synthesized nanocomposites showed appreciable activity for the decolourization of dyes. NiO-ZnO nanocomposite derived by KOH exhibited maximum activity for the decolourization of both the dyes and the decolourization rate of methylene blue was found to be comparable with that of Degussa P-25 $TiO_2$. Finally, the activity of the most active NiO-ZnO composite with relatively large crystallite sizes was compared with the pure components and their physical mixture, synthesized by the identical synthetic route, in the same molar ratio as that of nanocomposite.

Investigation of a nonlinear dynamic hydraulic system model through the energy analysis approach†

Hamed Hossein Afshari,Mostafa Ehramianpour,Morteza Mohammadi 대한기계학회 2009 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.23 No.11

The dynamics of a pressure regulator valve have been studied using the through Bondgraph simulation technique. This valve consists of several elements that can transmit, transform, store, and consume hydraulic energy. The governing equations of the system have been derived from the dynamic model. In solving system equations numerically, various pressure-flow characteristics across the regulator ports and orifices have been taken into consideration. This simulation study identifies some critical parameters that have significant effects on the transient response of the system. The results have been obtained using the MATLAB-SIMULINK environment. The main advantage of the proposed methodology is its ability to model the nonlinear behavior of the hydraulic resistance of system elements as a function of the fluid flow rate.

Review of common conditions associated with periodontal ligament widening

Hamed Mortazavi,Maryam Baharvand 대한영상치의학회 2016 Imaging Science in Dentistry Vol.46 No.4

Purpose: The aim of this article is to review a group of lesions associated with periodontal ligament (PDL) widening. Materials and Methods: An electronic search was performed using specialized databases such as Google Scholar, PubMed, PubMed Central, Science Direct, and Scopus to find relevant studies by using keywords such as “periodontium”, “periodontal ligament”, “periodontal ligament space”, “widened periodontal ligament”, and “periodontal ligament widening”. Results: Out of nearly 200 articles, about 60 were broadly relevant to the topic. Ultimately, 47 articles closely related to the topic of interest were reviewed. When the relevant data were compiled, the following 10 entities were identified: occlusal/orthodontic trauma, periodontal disease/periodontitis, pulpo-periapical lesions, osteosarcoma, chondrosarcoma, non-Hodgkin lymphoma, progressive systemic sclerosis, radiation-induced bone defect, bisphosphonate-related osteonecrosis, and osteomyelitis. Conclusion: Although PDL widening may be encountered by many dentists during their routine daily procedures, the clinician should consider some serious related conditions as well.

Assessment of Recurrence Quantification Analysis (RQA) of EEG for Development of a Novel Drowsiness Detection System

Hamed Shabani,Mohammad Mikaili,Seyed Mohammad Reza Noori 대한의용생체공학회 2016 Biomedical Engineering Letters (BMEL) Vol.6 No.3

Purpose In this paper, the aim is to detect drowsiness usingone of the well-known nonlinear signal analysis methodsknown as Recurrence Quantification Analysis (RQA). Wewant to show that by assuming brain as a chaotic system, thenumber of recurrences in the phase space of this system willincrease during drowsiness state. Methods Determinism (DET) feature extracted by Recurrencequantification analysis (RQA) method has been used to detectthese recurrences. Furthermore, eleven other features of RQAfor the purpose of comparing their capability with DETfeature have been used to detect drowsiness. Three differentfeature subsets are extracted from these twelve features. Thefirst feature subset is called DET feature. The second featuresubset is obtained by applying Linear Discriminant Analysis(LDA) technique on the twelve dimensional feature set. Thethird feature subset is made by Sequential Forward Selection(SFS) method. To reach the highest value of accuracy,specificity and sensitivity, the three evaluated feature setshave been applied to four different classifiers known as Knearestneighbor (KNN), Support Vector Machine classifier(SVM), Naïve Bayes and Fisher Linear Discriminant Analysis. A K-means clustering method has also been applied on thedata to ensure that the criteria used for labeling drowsy andalert segments are suitable. Results The Results reveal that DET feature could achievethe best performance in drowsiness detection by SVMclassifier with an accuracy of more than ninety percentage. Conclusions These findings approve that DET measure is areasonable feature for the purpose of drowsiness detection.