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Andreas Hartmann, Yulia Worbe, Kevin J Black
This is the fourth yearly article in the Tourette Syndrome Research Highlights series, summarizing research from 2017 relevant to Tourette syndrome and other tic disorders. The authors briefly summarize reports they consider most important or interesting. The  highlights from 2018 article is being drafted on the Authorea online authoring platform, and readers are encouraged to add references or give feedback on our selections using the comments feature on that page. After the calendar year ends, the article is submitted as the annual update for the Tics collection on F1000Research...
2018: F1000Research
Paul Brennan
Protein schematics are valuable for research, teaching and knowledge communication. However, the tools used to automate the process are challenging. The purpose of the drawProteins package is to enable the generation of schematics of proteins in an automated fashion that can integrate with the Bioconductor/R suite of tools for bioinformatics and statistical analysis. Using UniProt accession numbers, the package uses the UniProt API to get the features of the protein from the UniProt database. The features are assembled into a data frame and visualized using adaptations of the ggplot2 package...
2018: F1000Research
Gilles Didier, Alberto Valdeolivas, Anaïs Baudot
The identification of communities, or modules, is a common operation in the analysis of large biological networks. The Disease Module Identification DREAM challenge  established a framework to evaluate clustering approaches in a biomedical context, by testing the association of communities with GWAS-derived common trait and disease genes. We implemented here several extensions of the MolTi software that detects communities by optimizing multiplex (and monoplex) network modularity. In particular, MolTi now runs a randomized version of the Louvain algorithm, can consider edge and layer weights, and performs recursive clustering...
2018: F1000Research
Caroline Gremillet, Jan G Jakobsson
Background: Hip fractures yearly affect 1.6 million patients worldwide, often the elderly with complex comorbidity. Mortality following surgery for acute hip fracture is high. The high mortality rate is multifactorial; high age, comorbidities and complication/deterioration in health following surgery. Whether the anaesthesia technique affects the 30-day mortality rate has been studied widely without reaching a consensus. The primary aim of this study was to determine anaesthetic techniques used in Sweden and their impact on the 30-day mortality rate in the elderly, who underwent acute hip fracture surgery...
2018: F1000Research
Zaki Mubarak, Adintya Humaira, Basri A Gani, Zainal A Muchlisin
Background: Candida albicans is an opportunistic fungus that infects the oral cavity. Increases in colony numbers of C. albicans can be caused by multiple factors, such as smoking, a weakened immune system, taking antibiotics and with immune-compromised individuals. Smoking can increase the virulence factor of C. albicans and make it stronger. One of the virulence factors of C. albicans is the biofilm it forms. The C. albicans biofilm makes it more tolerant to extracts of the seaweed Gracil aria verrucosa , which has antifungal activity...
2018: F1000Research
Netti Aryani, Indra Suharman, Hafrijal Syandri
Background: Hemibagrus wyckii Bagridae is one of the most important economic fish species that lives in the rivers and reservoir in Riau Province, Indonesia. The present study aimed to determine the reproductive performance of H.wyckii under culture conditions. Method s : A total of 10 female and 10 male fish were selected, and weight, length, characteristics of egg and sperm, and hatchery performance were measured. Eggs were fertilized using the dry method. Egg weight and egg diameters were measured for 50 eggs per female...
2018: F1000Research
Parashkev Nachev, Geraint Rees, Richard Frackowiak
Translation in cognitive neuroscience remains beyond the horizon, brought no closer by supposed major advances in our understanding of the brain. Unless our explanatory models descend to the individual level-a cardinal requirement for any intervention-their real-world applications will always be limited. Drawing on an analysis of the informational properties of the brain, here we argue that adequate individualisation needs models of far greater dimensionality than has been usual in the field. This necessity arises from the widely distributed causality of neural systems, a consequence of the fundamentally adaptive nature of their developmental and physiological mechanisms...
2018: F1000Research
Sally Hayward, Rosalind M Harding, Helen McShane, Rachel Tanner
Migrants and ethnic minorities in the UK have higher rates of tuberculosis (TB) compared with the general population. Historically, much of the disparity in incidence between UK-born and migrant populations has been attributed to differential pathogen exposure, due to migration from high-incidence regions and the transnational connections maintained with TB endemic countries of birth or ethnic origin. However, focusing solely on exposure fails to address the relatively high rates of progression to active disease observed in some populations of latently infected individuals...
2018: F1000Research
Juan Salazar, Valmore Bermúdez, Luis Carlos Olivar, Wheeler Torres, Jim Palmar, Roberto Añez, Maria Gratzia Ordoñez, José Ramón Rivas, María Sofía Martínez, Juan Diego Hernández, Modesto Graterol, Joselyn Rojas
Background: Insulin resistance (IR) is a metabolic disorder related to atherosclerosis. Its measurement is of great importance not only as a marker of diabetes but also for cardiovascular disease. The aim of this research study was to evaluate the relationship between various IR indices and coronary risk in an adult population from Maracaibo city, Venezuela. Methods: The Maracaibo City Metabolic Syndrome Prevalence Study is a descriptive, cross-sectional study with random and multi-stage sampling. In this sub study, 1272 individuals of both genders were selected with the measurement of basal insulin and coronary risk according to the Framingham-Wilson formula calibrated for our population...
2018: F1000Research
Diliana Pecheva, Christopher Kelly, Jessica Kimpton, Alexandra Bonthrone, Dafnis Batalle, Hui Zhang, Serena J Counsell
Measures obtained from diffusion-weighted imaging provide objective indices of white matter development and injury in the developing preterm brain. To date, diffusion tensor imaging (DTI) has been used widely, highlighting differences in fractional anisotropy (FA) and mean diffusivity (MD) between preterm infants at term and healthy term controls; altered white matter development associated with a number of perinatal risk factors; and correlations between FA values in the white matter in the neonatal period and subsequent neurodevelopmental outcome...
2018: F1000Research
Flavia C L Hoyte, Harold S Nelson
Allergic rhinitis affects 20 to 30% of adults in both the United States and Europe and perhaps a somewhat higher percentage of children. In addition to nasal and ocular symptoms directly related to the allergic process, interference of these symptoms with sleep leads to daytime sleepiness and impaired quality of life. Patients miss work because of symptoms but an even greater problem is interference with work productivity, or presenteeism, which has been reported to be the biggest contributor to the total economic cost of allergic rhinitis...
2018: F1000Research
Rahul S Nanchal, Jonathon D Truwit
Acute respiratory distress syndrome (ARDS) is a clinically and biologically heterogeneous disorder associated with many disease processes that injure the lung, culminating in increased non-hydrostatic extravascular lung water, reduced compliance, and severe hypoxemia. Despite enhanced understanding of molecular mechanisms, advances in ventilatory strategies, and general care of the critically ill patient, mortality remains unacceptably high. The Berlin definition of ARDS has now replaced the American-European Consensus Conference definition...
2018: F1000Research
Nomi L Harris, Heather Wiencko, Brad Chapman, Peter J A Cock, Karsten Hokamp, Hilmar Lapp, Chris Fields, Bastian Greshake Tzovaras
In 2018, the annual Bioinformatics Open Source Conference was held for the first time in conjunction with the Galaxy Community Conference, as an experiment to see if we could reach people in the bioinformatics community who aren't part of the audience attracted by ISMB. Held in June 2018 at Reed College in Portland, Oregon, GCCBOSC (Galaxy Community Conference and Bioinformatics Open Source Conference) attracted over 300 participants from around the world. The meeting started with two days of training, followed by two days of talks and poster/demo sessions (with some joint and some parallel sessions)...
2018: F1000Research
Ilijana Begcevic, Magda Tsolaki, Davor Brinc, Marshall Brown, Eduardo Martinez-Morillo, Ioulietta Lazarou, Mahi Kozori, Fani Tagaraki, Stella Nenopoulou, Mara Gkioka, Eutichia Lazarou, Bryant Lim, Ihor Batruch, Eleftherios P Diamandis
Background: Alzheimer's disease (AD) is the most common type of dementia, with progressive onset of clinical symptoms. The main pathological hallmarks are brain deposits of extracellular amyloid beta plaques and intracellular neurofibrillary tangles (NFT). Cerebrospinal fluid reflects pathological changes in the brain; amyloid beta 1-42 is a marker of amyloid plaques, while total and phosphorylated tau are markers of NFT formation. Additional biomarkers associated with disease pathogenesis are needed, for better prognosis, more specific diagnosis, prediction of disease severity and progression and for improved patient classification in clinical trials...
2018: F1000Research
Aye Sandar Mon, Myo Kyi Phyu, Wilaiphorn Thinkhamrop, Bandit Thinkhamrop
Background: Mothers and their newborns are vulnerable to threats to their health and survival during the postnatal period. Full postnatal care (PNC) uptake decreases maternal deaths and is also essential for first 1,000 days of newborn's life, but PNC usage is usually inadequate in rural areas. Little is known about the full PNC utilization among rural Myanmar women. This study, therefore, aimed to study the situation of the utilization of full PNC and examine its determinants. Methods: This community-based cross-sectional study was conducted in selected villages of the Magway Region, Myanmar...
2018: F1000Research
Jayaram Kancherla, Alexander Zhang, Brian Gottfried, Hector Corrada Bravo
Interactive and integrative data visualization tools and libraries are integral to exploration and analysis of genomic data. Web based genome browsers allow integrative data exploration of a large number of data sets for a specific region in the genome. Currently available web-based genome browsers are developed for specific use cases and datasets, therefore integration and extensibility of the visualizations and the underlying libraries from these tools is a challenging task. Genomic data visualization and software libraries that enable bioinformatic researchers and developers to implement customized genomic data viewers and data analyses for their application are much needed...
2018: F1000Research
Markos Erango, Arnoldo Frigessi, Leiv Arne Rosseland
Background: Cesarean delivery is performed under spinal anesthesia, and vasodilation is the main cause for a drop in blood pressure. The compression of the aorta and inferior vena cava by the gravid uterus is of additional clinical importance. Hypotension may occur during cesarean delivery even if prophylactic infusion of phenylephrine is practiced. We have tested if a 3 minute supine observation, can identify a subset of women with decreasing systolic arterial pressure (SAP) under spinal anesthesia. Methods: We performed a prospective observational study at Oslo University Hospital on healthy pregnant women for planned cesarean delivery...
2018: F1000Research
Kelly D Cobey, Manoj M Lalu, Becky Skidmore, Nadera Ahmadzai, Agnes Grudniewicz, David Moher
Background: There is no standardized definition of what a predatory journal is, nor have the characteristics of these journals been delineated or agreed upon. In order to study the phenomenon precisely a definition of predatory journals is needed. The objective of this scoping review is to summarize the literature on predatory journals, describe its epidemiological characteristics, and to extract empirical descriptions of potential characteristics of predatory journals. Methods: We searched five bibliographic databases: Ovid MEDLINE, Embase Classic + Embase, ERIC, and PsycINFO, and Web of Science on January 2 nd , 2018...
2018: F1000Research
Birgit Schmidt, Tony Ross-Hellauer, Xenia van Edig, Elizabeth C Moylan
Open peer review (OPR), as with other elements of open science and open research, is on the rise. It aims to bring greater transparency and participation to formal and informal peer review processes. But what is meant by `open peer review', and what advantages and disadvantages does it have over standard forms of review? How do authors or reviewers approach OPR? And what pitfalls and opportunities should you look out for? Here, we propose ten considerations for OPR, drawing on discussions with authors, reviewers, editors, publishers and librarians, and provide a pragmatic, hands-on introduction to these issues...
2018: F1000Research
Johannes M Dijkstra, Unni Grimholt
This correspondence concerns a publication by Malmstrøm et al. in Nature Genetics in October 2016. Malmstrøm et al. made an important contribution to fish phylogeny research by using low-coverage genome sequencing for comparison of 66 teleost (modern bony) fish species, with 64 of those 66 belonging to the species-rich clade Neoteleostei, and with 27 of those 64 belonging to the order Gadiformes. For these 66 species, Malmstrøm et al. estimated numbers of genes belonging to the major histocompatibility complex (MHC) class I lineages U and Z and concluded that in teleost fish these combined numbers are positively associated with, and a driving factor of, the rates of establishment of new fish species (speciation rates)...
2018: F1000Research
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