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BMC Series Focus Issue

December: Methods and Methodologies

Reliable and reproducible methods are the building blocks of every study and lay the foundations for new discoveries and advancements. This month, we would like to highlight some new experimental methods, data analyses and software reported in the BMC series journals. 

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Guidelines and reporting

The ARRIVE guidelines 2.0: Updated guidelines for reporting animal research
Nathalie Percie du Sert, Viki Hurst, […]Hanno Würbel 
BMC Veterinary Research 16, 242 (2020)

Navigating the qualitative manuscript writing process: some tips for authors and reviewers
Chris Roberts, Koshila Kumar & Gabrielle Finn 
BMC Medical Education 20, 439 (2020)

Experimental methods, devices and software

A novel cell permeability assay for macromolecules
Yensi Flores Bueso, Sidney Walker, Jennifer Quinn & Mark Tangney
BMC Molecular and Cell Biology 21, 75 (2020)

Dissecting the pathobiology of altered MRI signal in amyotrophic lateral sclerosis: A post mortem whole brain sampling strategy for the integration of ultra-high-field MRI and quantitative neuropathology 
Menuka Pallebage-Gamarallage, Sean Foxley, Ricarda A. L. Menke, Istvan N. Huszar, Mark Jenkinson, Benjamin C. Tendler, Chaoyue Wang, Saad Jbabdi, Martin R. Turner, Karla L. Miller & Olaf Ansorge
BMC Neuroscience 19, 11 (2018)

Saving time maintaining reliability: a new method for quantification of Tetranychus urticae damage in Arabidopsis whole rosettes
Dairon Ojeda-Martinez, Manuel Martinez, Isabel Diaz & M. Estrella Santamaria 
BMC Plant Biology 20, 397 (2020) 

A novel target enrichment strategy in next-generation sequencing through 7-deaza-dGTP-resistant enzymatic digestion
Peng Peng, Yanjuan Xu, Adrian M. Di Bisceglie & Xiaofeng Fan 
BMC Research Notes 13, 445 (2020)

Development and application of green and sustainable analytical methods for flavonoid extraction from Passiflora waste
Danielle da Silva Francischini, Ana Paula Lopes, Mateus Lodi Segatto, Aylon Matheus Stahl & Vânia Gomes Zuin 
BMC Chemistry 14, 56 (2020)

Rapid identification of capsulated Acinetobacter baumannii using a density-dependent gradient test
Hadas Kon, David Schwartz, Elizabeth Temkin, Yehuda Carmeli & Jonathan Lellouche 
BMC Microbiology 20, 285 (2020) 

Rapid and easy-to-use ES cell manipulation device with a small groove near culturing wells
Shun-ichi Funano, Daisuke Tone, Hideki Ukai, Hiroki R. Ueda & Yo Tanaka 
BMC Research Notes 13, 453 (2020) 

Millefy: visualizing cell-to-cell heterogeneity in read coverage of single-cell RNA sequencing datasets
Haruka Ozaki, Tetsutaro Hayashi, Mana Umeda & Itoshi Nikaido 
BMC Genomics 21, 177 (2020) 

DNA barcoding reveals cryptic diversity in the underestimated genus Triplophysa (Cypriniformes: Cobitidae, Nemacheilinae) from the northeastern Qinghai-Tibet Plateau
Tai Wang, Yan-ping Zhang, Zhuo-yu Yang, Zhe Liu & Yan-yan Du 
BMC Evolutionary Biology 20, 151 (2020)

Long-term expansion, genomic stability and in vivo safety of adult human pancreas organoids
Nikitas Georgakopoulos, Nicole Prior, Brigitte Angres, Gianmarco Mastrogiovanni, Alex Cagan, Daisy Harrison, Christopher J. Hindley, Robert Arnes-Benito, Siong-Seng Liau, Abbie Curd, Natasha Ivory, Benjamin D. Simons, Inigo Martincorena, Helmut Wurst, Kourosh Saeb-Parsy & Meritxell Huch 
BMC Developmental Biology 20, 4 (2020)

Establishing a sensitive fluorescence-based quantification method for cyclic nucleotides
Nadine Gruteser, Viktoria Kohlhas, Sabine Balfanz, Arne Franzen, Anne Günther, Andreas Offenhäusser, Frank Müller, Viacheslav Nikolaev, Martin J. Lohse & Arnd Baumann 
BMC Biotechnology 20, 47 (2020) 

MADloy: robust detection of mosaic loss of chromosome Y from genotype-array-intensity data
Juan R. González, Marcos López-Sánchez, Alejandro Cáceres, Pere Puig, Tonu Esko & Luis A. Pérez-Jurado 
BMC Bioinformatics 21, 533 (2020) 

Clinical methods, data analyses and software 

Cost of the Diet: a method and software to calculate the lowest cost of meeting recommended intakes of energy and nutrients from local foods
Amy Deptford, Tommy Allieri, Rachel Childs, Claudia Damu, Elaine Ferguson, Jennie Hilton, Paul Parham, Abigail Perry, Alex Rees, James Seddon & Andrew Hall 
BMC Nutrition 3, 26 (2017)

TumorTracer: a method to identify the tissue of origin from the somatic mutations of a tumor specimen
Andrea Marion Marquard, Nicolai Juul Birkbak, Cecilia Engel Thomas, Francesco Favero, Marcin Krzystanek, Celine Lefebvre, Charles Ferté, Mariam Jamal-Hanjani, Gareth A. Wilson, Seema Shafi, Charles Swanton, Fabrice André, Zoltan Szallasi & Aron Charles Eklund 
BMC Medical Genomics 8, 58 (2015)

Non-rigid image registration of 4D-MRI data for improved delineation of moving tumors
Stefan Weick, Kathrin Breuer, Anne Richter, Florian Exner, Serge-Peer Ströhle, Paul Lutyj, Jörg Tamihardja, Simon Veldhoen, Michael Flentje & Bülent Polat 
BMC Medical Imaging 20, 41 (2020) 

A new method for evaluation of patellar height and the position of the joint line before and after total knee arthroplasty
Hua Han & Xiaohui Zhang 
BMC Musculoskeletal Disorders 21, 768 (2020)

Improved and standardized method for assessing years lived with disability after burns and its application to estimate the non-fatal burden of disease of burn injuries in Australia, New Zealand and the Netherlands
Inge Spronk, Dale W. Edgar, Margriet E. van Baar, Fiona M. Wood, Nancy E. E. Van Loey, Esther Middelkoop, Babette Renneberg, Caisa Öster, Lotti Orwelius, Asgjerd L. Moi, Marianne Nieuwenhuis, Cornelis H. van der Vlies, Suzanne Polinder & Juanita A. Haagsma 
BMC Public Health 20, 121 (2020) 

Going web or staying paper? The use of web-surveys among older people
Susanne Kelfve, Marie Kivi, Boo Johansson & Magnus Lindwall 
BMC Medical Research Methodology 20, 252 (2020) 

Improving the health of workers with a low socioeconomic position: Intervention Mapping as a useful method for adaptation of the Participatory Approach
R. Schaap, F. G. Schaafsma, A. R. Bosma, M. A. Huysmans, C. R. L. Boot & J. R. Anema 
BMC Public Health 20, 961 (2020) 

Methodology for assessment of public health emergency preparedness and response synergies between institutional authorities and communities
Daniel H. de Vries, John Kinsman, Judit Takacs, Svetla Tsolova & Massimo Ciotti 
BMC Health Services Research 20, 411 (2020) 

Comparison of deep learning with regression analysis in creating predictive models for SARS-CoV-2 outcomes
Ahmed Abdulaal, Aatish Patel, Esmita Charani, Sarah Denny, Saleh A. Alqahtani, Gary W. Davies, Nabeela Mughal & Luke S. P. Moore 
BMC Medical Informatics and Decision Making 20, 299 (2020) 

Achilles tendon enthesitis evaluated by MRI assessments in patients with axial spondyloarthritis and psoriatic arthritis: a report of the methodology of the ACHILLES trial
Xenofon Baraliakos, Philipp Sewerin, Eugenio de Miguel, Effie Pournara, Christine Kleinmond, Annette Wiedon & Frank Behrens 
BMC Musculoskeletal Disorders 21, 767 (2020) 

Hair cortisol-a method to detect chronic cortisol levels in patients with Prader-Willi syndrome
Hasanain Hamid Shukur, Yolanda B. de Rijke, Elisabeth F. C. van Rossum, Laith Hussain-Alkhateeb & Charlotte Höybye 
BMC Endocrine Disorders 20, 166 (2020) 

Identifying Phenogroups in patients with subclinical diastolic dysfunction using unsupervised statistical learning
Yvonne E. Kaptein, Ilya Karagodin, Hongquan Zuo, Yu Lu, Jun Zhang, John S. Kaptein & Jennifer L. Strande 
BMC Cardiovascular Disorders 20, 367 (2020) 

Reviews on the topic

The development of body and organ shape
Ansa E. Cobham & Christen K. Mirth 
BMC Zoology 5, 14 (2020) 

Resilient Health Care: a systematic review of conceptualisations, study methods and factors that develop resilience
Mais Iflaifel, Rosemary H. Lim, Kath Ryan & Clare Crowley 
BMC Health Services Research 20, 324 (2020) 

An overview of the methodological aspects and policy implications of willingness-to-pay studies in oral health: a scoping review of existing literature
Navid Saadatfar & Mohammad Pooyan Jadidfard 
BMC Oral Health 20, 323 (2020)

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