PET-BIDS, an extension to the brain imaging data structure for positron emission tomography

The Brain Imaging Data Structure (BIDS) is a standard for organizing and describing neuroimaging datasets, serving not only to facilitate the process of data sharing and aggregation, but also to simplify the application and development of new methods and software for working with neuroimaging data. Here, we present an extension of BIDS to include positron emission tomography (PET) data, also known as PET-BIDS, and share several open-access datasets curated following PET-BIDS along with tools for conversion, validation and analysis of PET-BIDS datasets

PET-BIDS, an extension to the brain imaging data structure for positron emission tomography

The Brain Imaging Data Structure (BIDS) is a standard for organizing and describing neuroimaging datasets. It serves not only to facilitate the process of data sharing and aggregation, but also to simplify the application and development of new methods and software for working with neuroimaging data. Here, we present an extension of BIDS to include positron emission tomography (PET) data (PET-BIDS). We describe the PET-BIDS standard in detail and share several open-access datasets curated following PET-BIDS. Additionally, we highlight several tools which are already available for converting, validating and analyzing PET-BIDS datasets.Competing Interest StatementThe authors have declared no competing interest

The past, present, and future of the Brain Imaging Data Structure (BIDS)

The Brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is meant as a history of how the standard has developed and grown over time. We outline the principles behind the project, the mechanisms by which it has been extended, and some of the challenges being addressed as it evolves. We also discuss the lessons learned through the project, with the aim of enabling researchers in other domains to learn from the success of BIDS

Frictional properties of basalt experimental faults and implications for volcano-tectonic settings and geo-energy sites

We performed a suite of experiments aimed at examining the frictional properties of unaltered basalts at conditions considered to be representative of slip at shallow depths in volcano-tectonic environments and in-situ geo-energy basaltic sites. Scientific drilling and field studies on exhumed subsurface faults and fractures analogues suggest that, frictional sliding in basalts can occur in shear zones within a volume of wear debris or along localized joint surfaces. To illuminate how microstructural heterogeneities affect the nucleation of slip instabilities in basalts, we sheared simulated fault gouge and bare rock surfaces at low normal stresses (4\u201330 MPa) at ambient temperature, under room-dry and wet conditions. We performed velocity steps (0.1\u2013300 \u3bcm/s) and slide-hold-slides (30\u20133000 s holds) to determine the frictional stability and healing properties of basalts. In all the tests, we observed high friction coefficient associated with important frictional restrengthening. Overall, our results show that microstructural heterogeneities strongly affect the friction velocity dependence of basalts: while for normal stresses 6510 MPa, shear localization accompanied by cataclasis and grain size reduction favors the transition to velocity weakening behavior of powdered samples, on bare surfaces gouge production during shearing promotes a transition to a velocity strengthening behavior. Our results imply that at the tested conditions, friction instabilities may promptly nucleate in shear zones where deformation within (unaltered) basaltic gouge layers is localized, such as those located along volcanic flanks, while joint surfaces characterized by rough rock-on-rock contacts are less prone to unstable slip, which is suppressed at velocities 6510 \u3bcm/s

The role of high molecular weight hyaluronic acid in mucoadhesion on an ocular surface model

Hyaluronic acid (HA) is frequently formulated in eye drops to improve the stability of the tear film by hydration and lubrication. Mucoadhesion is related to the ocular residence time and therefore to the effectiveness of the eye drops. The ocular residence time of the HA formulation is correlated with the ability of HA to create specific strong interactions in the ocular surface with the mucus layer, mainly composed of a mixture of secreted mucins (MUC; gel forming MUC5AC and MUC2) and shed membrane-bound soluble mucins (MUC1, MUC4, and MUC16). Dry eye disease (DED) is a multifactorial pathology of the preocular tear film with possible damage to the ocular surface classified in two types: (1) aqueous-deficient dry eye and (2) evaporative dry eye, caused by a decrease in goblet cell density that reduces MUC expression and/or by meibomian gland dysfunction, that results in a drop in the lipidic fraction of the tear film.In this work, the binding affinity between HA and MUC2 has been evaluated with three complementary ap-proaches because the secreted MUCs play a pivotal role in the viscoelastic properties of the tear film: 1. Rheo-logical analysis, measuring the mucoadhesive index and the complex viscosity in relation to MM (Molecular Mass) and concentration; 2. Fluorescence analysis, using a fluorescent hydrophobic probe, to investigate the conformational change of MUC2 during the interaction with the HA polymer; 3. Surface plasmon resonance analysis, used to measure the affinity between MUC2 (immobilized on the surface of a sensor chip) and the HA polymers that flowed on it at the molecular level.For all these tests, the mucoadhesive performance of the natural HA linearly increases with the MM, whereas cross-linked HA and other emollient and gelling agents (formulated in artificial tears) do not show the same mucoadhesive properties (with the exception of xanthan gum). The mucoadhesive performance of high MM HA has also been confirmed in conditions that simulate the pathological condition of the tear film during DED by decreasing the MUC2 or oleic acid concentration. Physico-chemical analysis of a series of marketed artificial tears confirms the linear correlation between the MM of the HA used in the products and the mucoadhesive index measured on the ocular surface model

Characterization and significance of ACE2 and Mas receptor in human colon adenocarcinoma.

NTRODUCTION: A new arm of the renin-angiotensin system (RAS) has been recently characterized; this includes angiotensin converting enzyme (ACE)2 and angiotensin (Ang)1-7, a heptapeptide acting through the Mas receptor (MasR). Recent studies show that Ang1-7 has an antiproliferative action on lung adenocarcinoma cells. The aim of this study was to characterize RAS expression in human colon adenocarcinoma and to investigate whether Ang1-7 exerts an antiproliferative effect on human colon adenocarcinoma cells. MATERIALS AND METHODS: Gene, protein expression and enzymatic activity of the main components of the RAS were determined on non-neoplastic colon mucosa as well as on the tumor mass and the mucosa taken 5 cm distant from it, both collected from patients with colon adenocarcinoma. Two different human colon cancer cell lines were treated with AngII and Ang1-7. RESULTS: The novel finding of this study was that MasR was significantly upregulated in colon adenocarcinoma compared with non-neoplastic colon mucosa, which showed little or no expression of it. ACE gene expression and enzymatic activity were also increased in the tumors. However, AngII and Ang1-7 did not have any pro-/antiproliferative effects in the cell lines studied. CONCLUSIONS: The data suggest that upregulation of the MasR could be used as a diagnostic marker of colon adenocarcinoma

The clinical and dermoscopic features of invasive cutaneous squamous cell carcinoma depend on the histopathological grade of differentiation

Background Little is known about the variability of the dermoscopic criteria of squamous cell carcinoma (SCC) according to the histopathological differentiation grade. Objectives To evaluate whether specific dermoscopic criteria can predict the diagnosis of poorly differentiated SCC compared with well- and moderately differentiated SCC. Methods Clinical and dermoscopic images of SCCs were retrospectively evaluated for the presence of predefined criteria. Univariate and adjusted odds ratios were calculated. Discriminant functions were used to plot receiver-operator characteristic curves. Results Of 143 SCCs included, 48 (33·5%) were well differentiated, 45 (31·5%) were moderately differentiated and 50 (35·0%) were poorly differentiated. Flat tumours had a fourfold increased probability of being poorly differentiated. Dermoscopically, the presence of a predominantly red colour posed a 13-fold possibility of poor differentiation, whereas a predominantly white and white-yellow colour decreased the odds of poorly differentiated SCC by 97% each. The presence of vessels in more than 50% of the tumour's surface, a diffuse distribution of vessels and bleeding were significantly associated with poor differentiation, while scale/keratin was a potent predictor of well- or moderately differentiated tumours. Conclusions Dermoscopy may be regarded as a reliable preoperative tool to distinguish poorly from well- and moderately differentiated SCC. Given that poor differentiation of SCC represents an independent risk factor for recurrence, metastasis and disease-specific death, identifying poorly differentiated tumours in vivo may enhance their appropriate management. What's already known about this topic? While the dermoscopic criteria of squamous cell carcinoma (SCC) have been well described, little is currently known about the variability of these criteria with respect to the histopathological grade of differentiation in SCC. What does this study add? Poorly differentiated SCC is dermoscopically typified by a predominantly red colour, attributed to the presence of bleeding and/or dense vascularity. Identifying poorly differentiated tumours in vivo may enhance their appropriate management