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https://www.readbyqxmd.com/read/30002819/isee-interactive-summarizedexperiment-explorer
#1
Kevin Rue-Albrecht, Federico Marini, Charlotte Soneson, Aaron T L Lun
Data exploration is critical to the comprehension of large biological data sets generated by high-throughput assays such as sequencing. However, most existing tools for interactive visualisation are limited to specific assays or analyses. Here, we present the iSEE (Interactive SummarizedExperiment Explorer) software package, which provides a general visual interface for exploring data in a SummarizedExperiment object. iSEE is directly compatible with many existing R/Bioconductor packages for analysing high-throughput biological data, and provides useful features such as simultaneous examination of (meta)data and analysis results, dynamic linking between plots and code tracking for reproducibility...
2018: F1000Research
https://www.readbyqxmd.com/read/30002818/dopamine-synergizes-with-caffeine-to-increase-the-heart-rate-of-daphnia
#2
Aman Kundu, Gyanesh Singh
Dopamine is a key neurotransmitter, and is widely used as a central nervous system (CNS) agent.  Dopamine plays an important role in humans, including a major role in reward and motivation behaviour. Several addictive drugs are well known to increase neuronal dopamine activity. We selected Daphnia , an important model organism, to investigate the effect(s) of selected CNS agents on heart rate. Dopamine's effects on Daphnia 's heart has not been previously reported. Caffeine is a well-known and widely consumed stimulant...
2018: F1000Research
https://www.readbyqxmd.com/read/30002817/recent-advances-in-understanding-liver-fibrosis-bridging-basic-science-and-individualized-treatment-concepts
#3
REVIEW
Ralf Weiskirchen, Sabine Weiskirchen, Frank Tacke
Hepatic fibrosis is characterized by the formation and deposition of excess fibrous connective tissue, leading to progressive architectural tissue remodeling. Irrespective of the underlying noxious trigger, tissue damage induces an inflammatory response involving the local vascular system and the immune system and a systemic mobilization of endocrine and neurological mediators, ultimately leading to the activation of matrix-producing cell populations. Genetic disorders, chronic viral infection, alcohol abuse, autoimmune attacks, metabolic disorders, cholestasis, alterations in bile acid composition or concentration, venous obstruction, and parasite infections are well-established factors that predispose one to hepatic fibrosis...
2018: F1000Research
https://www.readbyqxmd.com/read/30002816/state-of-the-art-of-the-fontan-strategy-for-treatment-of-univentricular-heart-disease
#4
REVIEW
Jelle P G van der Ven, Eva van den Bosch, Ad J C C Bogers, Willem A Helbing
In patients with a functionally univentricular heart, the Fontan strategy achieves separation of the systemic and pulmonary circulation and reduction of ventricular volume overload. Contemporary modifications of surgical techniques have significantly improved survival. However, the resulting Fontan physiology is associated with high morbidity. In this review, we discuss the state of the art of the Fontan strategy by assessing survival and risk factors for mortality. Complications of the Fontan circulation, such as cardiac arrhythmia, thromboembolism, and protein-losing enteropathy, are discussed...
2018: F1000Research
https://www.readbyqxmd.com/read/30002815/one-environmental-health-an-emerging-perspective-in-toxicology
#5
REVIEW
Adam Pérez, John Pierce Wise
The One Environmental Health research approach, a subspecialty of the One Health initiative, focuses on toxic chemicals. Distinct disciplines work together to give a holistic perspective of a health concern through discrete disciplines, including, but not limited to, public health and the medical and veterinary sciences. In this article, we illustrate the concept of One Environmental Health with two case studies. One case study focuses on alligators and contributions to the field of endocrine disruption. The other case study focuses on whales and contributions to understanding carcinogenic metals...
2018: F1000Research
https://www.readbyqxmd.com/read/30002814/recent-advances-in-understanding-inherited-disorders-of-keratinization
#6
REVIEW
Theodore Zaki, Keith Choate
The ichthyoses are a heterogeneous group of skin diseases characterized by localized or generalized scaling or both. Other common manifestations include palmoplantar keratoderma, erythroderma, recurrent infections, and hypohidrosis. Abnormal barrier function is a cardinal feature of the ichthyoses, which results in compensatory hyperproliferation and transepidermal water loss. Barrier function is maintained primarily by the stratum corneum, which is composed of cornified cells surrounded by a corneocyte lipid envelope and intercellular lipid layers...
2018: F1000Research
https://www.readbyqxmd.com/read/29983926/the-cytoscape-automation-app-article-collection
#7
EDITORIAL
Barry Demchak, David Otasek, Alexander R Pico, Gary D Bader, Keiichiro Ono, Brett Settle, Eric Sage, John H Morris, William Longabaugh, Christian Lopes, Michael Kucera, Adam Treister, Benno Schwikowski, Piet Molenaar, Trey Ideker
Cytoscape is the premiere platform for interactive analysis, integration and visualization of network data. While Cytoscape itself delivers much basic functionality, it relies on community-written apps to deliver specialized functions and analyses. To date, Cytoscape's CyREST feature has allowed researchers to write workflows that call basic Cytoscape functions, but provides no access to its high value app-based functions. With Cytoscape Automation, workflows can now call apps that have been upgraded to expose their functionality...
2018: F1000Research
https://www.readbyqxmd.com/read/29983924/examine-visualizing-annotated-networks-in-cytoscape
#8
Philipp Spohr, Kasper Dinkla, Gunnar W Klau, Mohammed El-Kebir
eXamine is a Cytoscape app that displays set membership as contours on top of a node-link layout of a small graph. In addition to facilitating interpretation of enriched gene sets of small biological networks, eXamine can be used in other domains such as the visualization of communities in small social networks. eXamine was made available on the Cytoscape App Store in March 2014, has since registered more than 7,200 downloads, and has been highly rated by more than 25 users. In this paper, we present eXamine's new automation features that enable researchers to compose reproducible analysis workflows to generate visualizations of small, set-annotated graphs...
2018: F1000Research
https://www.readbyqxmd.com/read/29983922/defining-fgf21-resistance-during-obesity-controversy-criteria-and-unresolved-questions
#9
Kathleen R Markan
The term "FGF21 resistance" was first used to describe increased circulating FGF21 levels concomitant to decreased FGF21 receptor complex expression in white adipose tissue of obese mice.  Since this initial report, the term has been associated with a wide range of pathological states, including human obesity, in which circulating FGF21 levels are elevated. However, the notion of "FGF21 resistance" has been controversial partly due to difficulty in delineating the mechanisms underlying the physiological versus pharmacological effects of FGF21...
2018: F1000Research
https://www.readbyqxmd.com/read/29983921/role-of-extracellular-matrix-in-breast-cancer-development-a-brief-update
#10
REVIEW
Manoj Kumar Jena, Jagadeesh Janjanam
Evidence is increasing on the crucial role of the extracellular matrix (ECM) in breast cancer progression, invasion and metastasis with almost all mortality cases owing to metastasis. The epithelial-mesenchymal transition is the first signal of metastasis involving different transcription factors such as Snail, TWIST, and ZEB1. ECM remodeling is a major event promoting cancer invasion and metastasis; where matrix metalloproteinases (MMPs) such as MMP-2, -9, -11, and -14 play vital roles degrading the matrix proteins for cancer spread...
2018: F1000Research
https://www.readbyqxmd.com/read/29983918/case-report-case-report-on-multiple-extradural-thoracic-lesions-with-myelopathy-as-the-clinical-presentation-in-a-systemic-sarcoidosis-another-tale-of-a-lurking-entity
#11
Sunil Munakomi
Herein, we report a rare case study of a sarcoidosis presenting with the features of compressive myelopathy. There were multiple extra-dural lesions in the thoracic region. Computerized Tomography (CT) of the chest revealed fibrotic changes with a pleural based nodular lesion in the right lung. The patient underwent laminectomy and partial excision of both the lesions. The histology revealed presence of non-caseating granulomas. The patient made a good recovery following adjuvant medical management with steroid and Methotrexate...
2018: F1000Research
https://www.readbyqxmd.com/read/29983917/development-of-a-human-leukocyte-antigen-based-hiv-vaccine
#12
REVIEW
Yufei Wang
Human immunodeficiency virus (HIV) carries abundant human cell proteins, particularly human leukocyte antigen (HLA) molecules when the virus leaves host cells. Immunization in macaques with HLAs protects the animals from simian immunodeficiency virus infection. This finding offers an alternative approach to the development of HLA molecule-based HIV vaccines. Decades of studies have enhanced a great deal of our understanding of the mechanisms of allo-immune response-mediated anti-HIV immunity. These include cell-mediated immunity, innate immunity, and antibody response...
2018: F1000Research
https://www.readbyqxmd.com/read/29983916/apkc-the-kinase-that-phosphorylates-cell-polarity
#13
REVIEW
Yang Hong
Establishing and maintaining cell polarity are dynamic processes that necessitate complicated but highly regulated protein interactions. Phosphorylation is a powerful mechanism for cells to control the function and subcellular localization of a target protein, and multiple kinases have played critical roles in cell polarity. Among them, atypical protein kinase C (aPKC) is likely the most studied kinase in cell polarity and has the largest number of downstream substrates characterized so far. More than half of the polarity proteins that are essential for regulating cell polarity have been identified as aPKC substrates...
2018: F1000Research
https://www.readbyqxmd.com/read/29983915/a-threshold-model-for-receptor-tyrosine-kinase-signaling-specificity-and-cell-fate-determination
#14
REVIEW
Allen Zinkle, Moosa Mohammadi
Upon ligand engagement, the single-pass transmembrane receptor tyrosine kinases (RTKs) dimerize to transmit qualitatively and quantitatively different intracellular signals that alter the transcriptional landscape and thereby determine the cellular response. The molecular mechanisms underlying these fundamental events are not well understood. Considering recent insights into the structural biology of fibroblast growth factor signaling, we propose a threshold model for RTK signaling specificity in which quantitative differences in the strength/longevity of ligand-induced receptor dimers on the cell surface lead to quantitative differences in the phosphorylation of activation loop (A-loop) tyrosines as well as qualitative differences in the phosphorylation of tyrosines mediating substrate recruitment...
2018: F1000Research
https://www.readbyqxmd.com/read/29983914/normal-human-lactation-closing-the-gap
#15
REVIEW
Melinda Boss, Hazel Gardner, Peter Hartmann
With the exception of infant growth, there are no well-defined parameters describing normal human lactation. This represents a major gap in the continuum of care that does not exist for other major organs. Biological normality occurs naturally and is characterized by well-integrated function. We have proposed a definition that highlights four key elements that describe parameters for biological normality: comfort, milk supply, infant health, and maternal health. Notwithstanding the current limitations, published data have been collated to provide preliminary markers for the initiation of lactation and to describe objective tests once lactation is established...
2018: F1000Research
https://www.readbyqxmd.com/read/29983913/recent-advances-in-understanding-female-gametophyte-development
#16
REVIEW
Debra J Skinner, Venkatesan Sundaresan
The haploid female gametophyte (embryo sac) is an essential reproductive unit of flowering plants, usually comprising four specialized cell types, including the female gametes (egg cell and central cell). The differentiation of these cells relies on spatial signals which pattern the gametophyte along a proximal-distal axis, but the molecular and genetic mechanisms by which cell identities are determined in the embryo sac have long been a mystery. Recent identification of key genes for cell fate specification and their relationship to hormonal signaling pathways that act on positional cues has provided new insights into these processes...
2018: F1000Research
https://www.readbyqxmd.com/read/29983912/recent-advances-in-understanding-and-managing-contact-dermatitis
#17
REVIEW
Stefan F Martin, Thomas Rustemeyer, Jacob P Thyssen
About 20% of the general population is contact-sensitized to common haptens such as fragrances, preservatives, and metals. Many also develop allergic contact dermatitis (ACD), the clinical manifestation of contact sensitization. ACD represents a common health issue and is also one of the most important occupational diseases. Although this inflammatory skin disease is mediated predominantly by memory T lymphocytes recognizing low-molecular-weight chemicals after skin contact, the innate immune system also plays an important role...
2018: F1000Research
https://www.readbyqxmd.com/read/29983911/sex-gender-differences-in-cognition-neurophysiology-and-neuroanatomy
#18
REVIEW
Lutz Jäncke
In this mini-review, I summarize and interpret the current status of sex/gender differences in terms of brain anatomy, brain function, behavior, and cognition. Based on this review and the reported findings, I conclude that most of these sex/gender differences are not large enough to support the assumption of sexual dimorphism in terms of brain anatomy, brain function, cognition, and behavior. Instead, I suggest that many brain and cognitive features are modulated by environment, culture, and practice (and several other influences)...
2018: F1000Research
https://www.readbyqxmd.com/read/29946446/tmd-symptoms-and-vertical-mandibular-symmetry-in-young-adult-orthodontic-patients-in-north-sumatra-indonesia-a-cross-sectional-study
#19
Ervina Sofyanti, Trelia Boel, Benny Soegiharto, Elza I Auerkari
Background: Temporomandibular joint disorder (TMD) includes symptoms of pain and dysfunction in the muscles of mastication and the temporomandibular joint. Differences in vertical condylar height, observed in the assessment of mandibular asymmetry, is a structural alteration that represents a risk factor for TMD. The study aimed to evaluate the association between TMD symptoms and vertical mandibular symmetry in young adult orthodontic patients in North Sumatra, Indonesia.  Methods: The cross-sectional study included 18-25-year-old (mean ± SD, 21...
2018: F1000Research
https://www.readbyqxmd.com/read/29946445/the-use-of-prp-transgenic-drosophila-to-replace-and-reduce-vertebrate-hosts-in-the-bioassay-of-mammalian-prion-infectivity
#20
Alana M Thackray, Olivier Andréoletti, Raymond Bujdoso
Prion diseases are fatal neurodegenerative conditions of humans and vertebrate species. The transmissible prion agent is a novel infectious particle composed principally of PrP Sc , an abnormal isomer of the normal host protein PrP C . The only reliable method to detect mammalian prion infectivity is by bioassay, invariably in a vertebrate host. The current prion bioassays typically involve intracerebral or peripheral inoculation of test material into the experimental host and subsequent euthanasia when clinical signs of terminal prion disease become evident...
2018: F1000Research
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