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Relationship between Quality and Editorial Leadership of Biomedical Research Journals: A Comparative Study of Italian and UK Journals
Valerie Matarese
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0002512
Abstract: Background The quality of biomedical reporting is guided by statements of several organizations. Although not all journals adhere to these guidelines, those that do demonstrate “editorial leadership” in their author community. To investigate a possible relationship between editorial leadership and journal quality, research journals from two European countries, one Anglophone and one non-Anglophone, were studied and compared. Quality was measured on a panel of bibliometric parameters while editorial leadership was evaluated from journals' instructions to authors. Methodology/Principal Findings The study considered all 76 Italian journals indexed in Medline and 76 randomly chosen UK journals; only journals both edited and published in these countries were studied. Compared to UK journals, Italian journals published fewer papers (median, 60 vs. 93; p = 0.006), less often had online archives (43 vs. 74; p<0.001) and had lower median values of impact factor (1.2 vs. 2.7, p<0.001) and SCImago journal rank (0.09 vs. 0.25, p<0.001). Regarding editorial leadership, Italian journals less frequently required manuscripts to specify competing interests (p<0.001), authors' contributions (p = 0.005), funding (p<0.001), informed consent (p<0.001), ethics committee review (p<0.001). No Italian journal adhered to COPE or the CONSORT and QUOROM statements nor required clinical trial registration, while these characteristics were observed in 15%–43% of UK journals (p<0.001). At multiple regression, editorial leadership predicted 37.1%–49.9% of the variance in journal quality defined by citation statistics (p<0.0001); confounding variables inherent to a cross-cultural comparison had a relatively small contribution, explaining an additional 6.2%–13.8% of the variance. Conclusions/Significance Journals from Italy scored worse for quality and editorial leadership than did their UK counterparts. Editorial leadership predicted quality for the entire set of journals. Greater appreciation of international initiatives to improve biomedical reporting may help low-quality journals achieve higher status.
Emerging concepts in high-impact publishing: insights from the First Brazilian Colloquium on High Impact Research and Publishing
Matarese,Valerie;
Annali dell'Istituto Superiore di Sanità , 2010, DOI: 10.4415/ANN_10_04_14
Abstract: reports of scientific research are published by selective journals only when they meet stringent criteria, first and foremost of which are the quality and importance of the research. even when the research is excellent, other elements come into play to determine if the manuscript will be accepted for publication. many of these factors are under direct control of the researcher-author, but not all authors are aware of the elements of high-impact scientific writing. at the first brazilian colloquium on high impact research and publishing, editors of leading biomedical journals provided insight on the aspects of scientific reporting that favor acceptance (or immediate rejection). this commentary summarizes the editors' advice and uses the debate that followed as the basis for analyzing emerging concepts in high-impact publishing. lessons learned from this meeting are relevant to researcher-authors in other non-anglophone countries as well as to their educators and administrators who wish to improve the impact of the research that they support and finance.
Management considerations in the treatment of migraine in adolescents
Christine A Matarese, Kenneth J Mack
Adolescent Health, Medicine and Therapeutics , 2010, DOI: http://dx.doi.org/10.2147/AHMT.S7537
Abstract: nagement considerations in the treatment of migraine in adolescents Review (4251) Total Article Views Authors: Christine A Matarese, Kenneth J Mack Published Date May 2010 Volume 2010:1 Pages 21 - 30 DOI: http://dx.doi.org/10.2147/AHMT.S7537 Christine A Matarese, Kenneth J Mack Mayo Clinic, Division of Child and Adolescent Neurology, Rochester, MN, USA Abstract: Migraine is common in adolescents. It can significantly reduce quality of life, may contribute to significant school absences, and disrupt social activities. This article will address the clinical presentation, natural history, types, evaluation, diagnosis and prognosis of migraine. Common adolescent lifestyle factors such as stress, irregular mealtimes, and sleep deprivation may exacerbate migraines. Management options are discussed including lifestyle modifications, acute and preventative therapies. Features of chronic daily headache including comorbid conditions, management, and outcome are also addressed.
Prediction of under pickling defects on steel strip surface
Valentina Colla 1,Nicola Matarese and Gianluca Nastasi 2
International Journal of Soft Computing and Software Engineering , 2011, DOI: 10.7321/jscse.v1.n1.2
Abstract: An extremely important part of the finishing line is the pickling process, in which oxides formed during the hot rolling stage are removed from the surface of the steel sheets. The efficiency of the pickling process is mainly dependent on the nature of the oxide present at the surface of the steel, but, also, on process parameters such as bath composition and time duration are relevant. When acid concentration, solution temperatures and line speed are not properly balanced, in fact, sheet defects like under pickling or over pickling may happen and their occurrence does have a very serious effect on cold-reduction performance and surface appearance of the finished product. Furthermore, product damage from handling or improper equipment adjustment can render the steel unsuitable for further processing. This is the reason why it is important that process significant parameters are controlled and maintained as accurately as possible in order to avoid these undesired phenomena. In the present work, a control algorithm, composed by two different modules, i.e. decision tree and rectangular Basis Function Network, has been implemented to aim of predicting pickling defects and suggesting the optimal speed or the admissible speed range of the steel strip in the process line. In this way the most suitable line speed value can be set in an automatic way or by the technical personnel.
Medical humanities in healthcare education in Italy: a literature review
Fieschi,Laura; Matarese,Maria; Vellone,Ercole; Alvaro,Rosaria; De Marinis,Maria Grazia;
Annali dell'Istituto Superiore di Sanità , 2013, DOI: 10.4415/ANN_13_01_10
Abstract: objective. the introduction of medical humanities (mh) in undergraduate medical education in italy has been an issue of debate since the 90's and few years later it was extended to other healthcare degrees. the aims of this italian literature review, after considering the international scene, are: to evaluate the extent to which the interest in this subject has gradually developed throughout the country; which professional groups have contributed to the debate; to identify which theoretical constructs led to the introduction of mh in undergraduate medical education; to identify whether a clear and shared definition of mh exists in italian literature; to verify what kinds of mh experiences have been accomplished in italy. materials and methods. a comprehensive literature search was conducted, including electronic databases, bibliographies, manual sorting of articles in paper format, congress proceedings. results. the analysis of the chosen articles underlines that, however limited, italian literature does not present a very different picture from the international scene. it emerges that teaching mh is believed to be an important feature in undergraduate education of healthcare professionals who intend to propose a bio-psychological-social approach to care, in spite of the difficulty to measure its short and long term effectiveness. the lack of a multidisciplinary, multi-professional approach is also evident. conclusion. further research aiming to implement the quantity and quality of mh studies in the curricula of undergraduate healthcare education is desirable.
Antioxidant Properties of Aminoethylcysteine Ketimine Decarboxylated Dimer: A Review
Alberto Macone,Mario Fontana,Marco Barba,Bruno Botta,Mirella Nardini,Francesca Ghirga,Andrea Calcaterra,Laura Pecci,Rosa Marina Matarese
International Journal of Molecular Sciences , 2011, DOI: 10.3390/ijms12053072
Abstract: Aminoethylcysteine ketimine decarboxylated dimer is a natural sulfur-containing compound detected in human plasma and urine, in mammalian brain and in many common edible vegetables. Over the past decade many studies have been undertaken to identify its metabolic role. Attention has been focused on its antioxidant properties and on its reactivity against oxygen and nitrogen reactive species. These properties have been studied in different model systems starting from plasma lipoproteins to specific cellular lines. All these studies report that aminoethylcysteine ketimine decarboxylated dimer is able to interact both with reactive oxygen and nitrogen species (hydrogen peroxide, superoxide anion, hydroxyl radical, peroxynitrite and its derivatives). Its antioxidant activity is similar to that of Vitamin E while higher than other hydrophilic antioxidants, such as trolox and N-acetylcysteine.
Resveratrol Couples Apoptosis with Autophagy in UVB-Irradiated HaCaT Cells
Nicoletta Vitale, Annamaria Kisslinger, Simona Paladino, Claudio Procaccini, Giuseppe Matarese, Giovanna Maria Pierantoni, Francesco Paolo Mancini, Donatella Tramontano
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0080728
Abstract: UVB radiation causes about 90% of non-melanoma skin cancers by damaging DNA either directly or indirectly by increasing levels of reactive oxygen species (ROS). Skin, chronically exposed to both endogenous and environmental pro-oxidant agents, contains a well-organised system of chemical and enzymatic antioxidants. However, increased or prolonged free radical action can overwhelm ROS defence mechanisms, contributing to the development of cutaneous diseases. Thus, new strategies for skin protection comprise the use of food antioxidants to counteract oxidative stress. Resveratrol, a phytoalexin from grape, has gained a great interest for its ability to influence several biological mechanisms like redox balance, cell proliferation, signal transduction pathways, immune and inflammatory response. Therefore, the potential of resveratrol to modify skin cell response to UVB exposure could turn out to be a useful option to protect skin from sunlight-induced degenerative diseases. To investigate into this matter, HaCaT cells, a largely used model for human skin keratinocytes, were treated with 25 or 100 μM resveratrol for 2 and 24 hours prior to UVB irradiation (10 to 100 mJ/cm2). Cell viability and molecular markers of proliferation, oxidative stress, apoptosis, and autophagy were analyzed. In HaCaT cells resveratrol pretreatment: reduces UVB-induced ROS formation, enhances the detrimental effect of UVB on HaCaT cell vitality, increases UVB-induced caspase 8, PARP cleavage, and induces autophagy. These findings suggest that resveratrol could exert photochemopreventive effects by enhancing UVB-induced apoptosis and by inducing autophagy, thus reducing the odds that damaged cells could escape programmed cell death and initiate malignant transformation.
Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data
Ciira wa Maina ,Antti Honkela,Filomena Matarese,Korbinian Grote,Hendrik G. Stunnenberg,George Reid,Neil D. Lawrence ,Magnus Rattray
PLOS Computational Biology , 2014, DOI: doi/10.1371/journal.pcbi.1003598
Abstract: Gene transcription mediated by RNA polymerase II (pol-II) is a key step in gene expression. The dynamics of pol-II moving along the transcribed region influence the rate and timing of gene expression. In this work, we present a probabilistic model of transcription dynamics which is fitted to pol-II occupancy time course data measured using ChIP-Seq. The model can be used to estimate transcription speed and to infer the temporal pol-II activity profile at the gene promoter. Model parameters are estimated using either maximum likelihood estimation or via Bayesian inference using Markov chain Monte Carlo sampling. The Bayesian approach provides confidence intervals for parameter estimates and allows the use of priors that capture domain knowledge, e.g. the expected range of transcription speeds, based on previous experiments. The model describes the movement of pol-II down the gene body and can be used to identify the time of induction for transcriptionally engaged genes. By clustering the inferred promoter activity time profiles, we are able to determine which genes respond quickly to stimuli and group genes that share activity profiles and may therefore be co-regulated. We apply our methodology to biological data obtained using ChIP-seq to measure pol-II occupancy genome-wide when MCF-7 human breast cancer cells are treated with estradiol (E2). The transcription speeds we obtain agree with those obtained previously for smaller numbers of genes with the advantage that our approach can be applied genome-wide. We validate the biological significance of the pol-II promoter activity clusters by investigating cluster-specific transcription factor binding patterns and determining canonical pathway enrichment. We find that rapidly induced genes are enriched for both estrogen receptor alpha (ER) and FOXA1 binding in their proximal promoter regions.
Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data
Ciira wa Maina,Antti Honkela,Filomena Matarese,Korbinian Grote,Hendrik G. Stunnenberg,George Reid,Neil D. Lawrence,Magnus Rattray
Quantitative Biology , 2013,
Abstract: Gene transcription mediated by RNA polymerase II (pol-II) is a key step in gene expression. The dynamics of pol-II moving along the transcribed region influence the rate and timing of gene expression. In this work we present a probabilistic model of transcription dynamics which is fitted to pol-II occupancy time course data measured using ChIP-Seq. The model can be used to estimate transcription speed and to infer the temporal pol-II activity profile at the gene promoter. Model parameters are estimated using either maximum likelihood estimation or via Bayesian inference using Markov chain Monte Carlo sampling. The Bayesian approach provides confidence intervals for parameter estimates and allows the use of priors that capture domain knowledge, e.g. the expected range of transcription speeds, based on previous experiments. The model describes the movement of pol-II down the gene body and can be used to identify the time of induction for transcriptionally engaged genes. By clustering the inferred promoter activity time profiles, we are able to determine which genes respond quickly to stimuli and group genes that share activity profiles and may therefore be co-regulated. We apply our methodology to biological data obtained using ChIP-seq to measure pol-II occupancy genome-wide when MCF-7 human breast cancer cells are treated with estradiol (E2). The transcription speeds we obtain agree with those obtained previously for smaller numbers of genes with the advantage that our approach can be applied genome-wide. We validate the biological significance of the pol-II promoter activity clusters by investigating cluster-specific transcription factor binding patterns and determining canonical pathway enrichment. We find that rapidly induced genes are enriched for both estrogen receptor alpha (ER$\alpha$) and FOXA1 binding in their proximal promoter regions.
Integrative Analysis of Deep Sequencing Data Identifies Estrogen Receptor Early Response Genes and Links ATAD3B to Poor Survival in Breast Cancer
Kristian Ovaska,Filomena Matarese,Korbinian Grote,Iryna Charapitsa,Alejandra Cervera,Chengyu Liu,George Reid,Martin Seifert,Hendrik G. Stunnenberg,Sampsa Hautaniemi
PLOS Computational Biology , 2013, DOI: 10.1371/journal.pcbi.1003100
Abstract: Identification of responsive genes to an extra-cellular cue enables characterization of pathophysiologically crucial biological processes. Deep sequencing technologies provide a powerful means to identify responsive genes, which creates a need for computational methods able to analyze dynamic and multi-level deep sequencing data. To answer this need we introduce here a data-driven algorithm, SPINLONG, which is designed to search for genes that match the user-defined hypotheses or models. SPINLONG is applicable to various experimental setups measuring several molecular markers in parallel. To demonstrate the SPINLONG approach, we analyzed ChIP-seq data reporting PolII, estrogen receptor (), H3K4me3 and H2A.Z occupancy at five time points in the MCF-7 breast cancer cell line after estradiol stimulus. We obtained 777 early responsive genes and compared the biological functions of the genes having binding within 20 kb of the transcription start site (TSS) to genes without such binding site. Our results show that the non-genomic action of via the MAPK pathway, instead of direct binding, may be responsible for early cell responses to activation. Our results also indicate that the responsive genes triggered by the genomic pathway are transcribed faster than those without binding sites. The survival analysis of the 777 responsive genes with 150 primary breast cancer tumors and in two independent validation cohorts indicated the ATAD3B gene, which does not have binding site within 20 kb of its TSS, to be significantly associated with poor patient survival.
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