Custom Biomedical FAIR Data Analysis in the Cloud Using CAVATICA.

The historically fragmented biomedical data ecosystem has moved towards harmonization under the findable, accessible, interoperable, and reusable (FAIR) data principles, creating more opportunities for cloud-based research. This shift is especially opportune for scientists across diverse domains interested in implementing creative, nonstandard computational analytic pipelines on large and varied datasets. However, executing custom cloud analyses may present difficulties, particularly for investigators lacking advanced computational expertise.

Cryptic mtDNA Diversity of (Onuphidae, Annelida) in the Northwestern Atlantic Ocean.

Marine annelid taxonomy is experiencing a period of rapid revision, with many previously "cosmopolitan" species being split into species with more limited geographic ranges. This is exemplified by the genus, which has recently witnessed dozens of new species descriptions rooted in genetic analyses. In the northwestern Atlantic, the name (Bosc 1802) has been applied to populations from Cape Cod through the Gulf of Mexico, Central America, and Brazil.

A Review of Ecology: Current Knowledge, Open Questions, and Future Threats for an Ecosystem Engineering Polychaete.

A well-known example of marine ecosystem engineering is the annelid genus , which builds large tubes in coastal sediments worldwide. Early studies of were among the first to recognize the importance of facilitation in ecology, and has become a key marine soft-sediment application of the ecosystem engineering concept. Here, I review our current knowledge of ecology, including its natural history, ecosystem engineering effects, and trophic relationships.

Grazer Interactions with Invasive (Rhodophyta): Comparisons to Related Unrelated Native Algae.

Ecosystem responses to invasion are strongly influenced by interactions between invaders and native species. If native species provide biotic resistance by consuming or competing with an invader, the invasion may be slowed, and/or invasive populations may be limited. If local herbivores recognize an invasive plant as being similar to native species, they may graze it more readily.

Helium ion beam imaging for image guided ion radiotherapy.

Background: Ion beam radiotherapy provides potential for increased dose conformation to the target volume. To translate it into a clinical advantage, it is necessary to guarantee a precise alignment of the actual internal patient geometry with the treatment beam. This is in particular challenging for inter- and intrafractional variations, including movement.

Theoretical and experimental comparison of proton and helium-beam radiography using silicon pixel detectors.

Ion-beam radiography (iRad) could potentially improve the quality control of ion-beam therapy. The main advantage of iRad is the possibility to directly measure the integrated stopping power. Until now there is no clinical implementation of iRad.

F-Radiolabeling and In Vivo Analysis of SiFA-Derivatized Polymeric Core-Shell Nanoparticles.

Nanoparticles represent the most widely studied drug delivery systems targeting cancer. Polymeric nanoparticles can be easily generated through a microemulsion polymerization. Herein, the synthesis, radiolabeling, and in vivo evaluation of nanoparticles (NPs) functionalized by an organosilicon fluoride acceptor (SiFA) are reported which can be radiolabeled without further chemical modifications.

Investigation of mixed ion fields in the forward direction for 220.5 MeV/u helium ion beams: comparison between water and PMMA targets.

Currently there is a rising interest in helium ion beams for radiotherapy. For benchmarking of the physical beam models used in treatment planning, there is a need for experimental data on the composition and spatial distribution of mixed ion fields. Of particular interest are the attenuation of the primary helium ion fluence and the build-up of secondary hydrogen ions due to nuclear interactions.

Recent Advances in the Development and Application of Radiolabeled Kinase Inhibitors for PET Imaging.

Over the last 20 years, intensive investigation and multiple clinical successes targeting protein kinases, mostly for cancer treatment, have identified small molecule kinase inhibitors as a prominent therapeutic class. In the course of those investigations, radiolabeled kinase inhibitors for positron emission tomography (PET) imaging have been synthesized and evaluated as diagnostic imaging probes for cancer characterization. Given that inhibitor coverage of the kinome is continuously expanding, in vivo PET imaging will likely find increasing applications for therapy monitoring and receptor density studies both in- and outside of oncological conditions.

Endoscopic cyclophotocoagulation combined with phacoemulsification versus phacoemulsification alone in medically controlled glaucoma.

Purpose: To compare the outcomes of combined endoscopic cyclophotocoagulation (ECP) and phacoemulsification cataract extraction versus cataract extraction alone in eyes with medically controlled open-angle glaucoma (OAG) and visually significant cataract.

Setting: Clinical practices of glaucoma specialists and comprehensive ophthalmologists.

Design: Prospective nonrandomized matched-control study.

Origination and immigration drive latitudinal gradients in marine functional diversity.

Global patterns in the functional attributes of organisms are critical to understanding biodiversity trends and predicting biotic responses to environmental change. In the first global marine analysis, we find a strong decrease in functional richness, but a strong increase in functional evenness, with increasing latitude using intertidal-to-outer-shelf bivalves as a model system (N = 5571 species). These patterns appear to be driven by the interplay between variation in origination rates among functional groups, and latitudinal patterns in origination and range expansion, as documented by the rich fossil record of the group.

Latanoprost-induced prostaglandin-associated periorbitopathy.

Purpose: To report, with supporting photo-documentation, cases of latanoprost-induced prostaglandin-associated periorbitopathy (PAP).

Case Series: Retrospective small case series with three cases. Chart review with photo-documentation of clinical features of prostaglandin-associated periorbitopathy resulting from latanoprost use.

Out of the tropics, but how? Fossils, bridge species, and thermal ranges in the dynamics of the marine latitudinal diversity gradient.

Latitudinal diversity gradients are underlain by complex combinations of origination, extinction, and shifts in geographic distribution and therefore are best analyzed by integrating paleontological and neontological data. The fossil record of marine bivalves shows, in three successive late Cenozoic time slices, that most clades (operationally here, genera) tend to originate in the tropics and then expand out of the tropics (OTT) to higher latitudes while retaining their tropical presence. This OTT pattern is robust both to assumptions on the preservation potential of taxa and to taxonomic revisions of extant and fossil species.

Global environmental predictors of benthic marine biogeographic structure.

Analyses of how environmental factors influence the biogeographic structure of biotas are essential for understanding the processes underlying global diversity patterns and for predicting large-scale biotic responses to global change. Here we show that the large-scale geographic structure of shallow-marine benthic faunas, defined by existing biogeographic schemes, can be predicted with 89-100% accuracy by a few readily available oceanographic variables; temperature alone can predict 53-99% of the present-day structure along coastlines. The same set of variables is also strongly correlated with spatial changes in species compositions of bivalves, a major component of the benthic marine biota, at the 1° grid-cell resolution.

Functional groups of ecosystem engineers: a proposed classification with comments on current issues.

Ecologists have long known that certain organisms fundamentally modify, create, or define habitats by altering the habitat's physical properties. In the past 15 years, these processes have been formally defined as "ecosystem engineering", reflecting a growing consensus that environmental structuring by organisms represents a fundamental class of ecological interactions occurring in most, if not all, ecosystems. Yet, the precise definition and scope of ecosystem engineering remains debated, as one should expect given the complexity, enormity, and variability of ecological systems.

Sublethal predation and regeneration in two onuphid polychaetes: patterns and implications.

We examined sublethal predation in the polychaete Diopatra cuprea, an important ecosystem engineer of intertidal and shallow subtidal marine sediments in the western Atlantic. D. cuprea commonly loses its antennae and portions of its anterior to predator attacks; these lost body portions are subsequently regenerated.

Multistate outbreak of toxic anterior segment syndrome, 2005.

Purpose: To present the findings of an outbreak of toxic anterior segment syndrome (TASS).

Setting: Six states, 7 ophthalmology surgical centers, United States.

Methods: Cases were identified through electronic communication networks and via reports to a national TASS referral center.

Tube decoration may not be cryptic for Diopatra cuprea (Polychaeta: Onuphidae).

Previous studies have suggested several adaptive functions for the decorated tube caps of Diopatra cuprea (Polychaeta: Onuphidae). We experimentally tested the hypothesis that decoration provides crypsis. A series of field experiments quantified predation-related damage done to tube caps that were (1) devoid of decoration, (2) decorated with algae, or (3) decorated with shell fragments.

Patients' and physicians' perceptions of the travoprost dosing aid: an open-label, multicenter study of adherence with prostaglandin analogue therapy for open-angle glaucoma or ocular hypertension.

Objective: This study describes patients' and physicians' perceptions of issues related to dosing adherence with topical therapies for lowering intraocular pressure before and after use of the travoprost dosing aid (Travatan Dosing Aid, Alcon Research Ltd., Fort Worth, Texas).

Methods: The study had an open-label, multicenter, single-treatment-arm design that included sequential patients with open-angle glaucoma (with or without pigment dispersion or pseudoexfoliation component) or ocular hypertension who were taking any prostaglandin analogue monotherapy.

Comparing the fixed combination dorzolamide-timolol (Cosopt) to concomitant administration of 2% dorzolamide (Trusopt) and 0.5% timolol -- a randomized controlled trial and a replacement study.

Purpose: To compare the intraocular pressure (IOP) lowering effect of concomitant administration of 0.5% timolol and 2% dorzolamide and a fixed combination dorzolamide-timolol (Cosopt) To critically evaluate discrepancies between phase 3 clinical trials and prior replacement studies.

Design: A prospective, randomized, controlled clinical trial and a prospective, non-randomized comparative replacement trial.

Caspase-mediated proteolysis of the polyglutamine disease protein ataxin-3.

Spinocerebellar ataxia type-3, also known as Machado-Joseph Disease, is one of many inherited neurodegenerative disorders caused by polyglutamine-encoding CAG repeat expansions in otherwise unrelated disease genes. Polyglutamine disorders are characterized by disease protein misfolding and aggregation; often within the nuclei of affected neurons. Although the precise mechanism of polyglutamine-mediated cell death remains elusive, evidence suggests that proteolysis of polyglutamine disease proteins by caspases contributes to pathogenesis.

Poly-ubiquitin binding by the polyglutamine disease protein ataxin-3 links its normal function to protein surveillance pathways.

In at least nine inherited diseases polyglutamine expansions cause neurodegeneration associated with protein misfolding and the formation of ubiquitin-conjugated aggregates. Although expanded polyglutamine triggers disease, functional properties of host polyglutamine proteins also must influence pathogenesis. Using complementary in vitro and cell-based approaches we establish that the polyglutamine disease protein, ataxin-3, is a poly-ubiquitin-binding protein.

Protein aggregation and the ubiquitin proteasome pathway: gaining the UPPer hand on neurodegeneration.

Protein misfolding and aggregation are common to most neurodegenerative diseases, suggesting that abnormalities of protein homeostasis contribute to pathogenesis. Research implicates at least two components of cellular protein quality control in disease: molecular chaperones and the ubiquitin-proteasome pathway (UPP). Although evidence is more compelling for chaperone involvement, recent cell-based and genetic studies suggest that perturbations in the UPP also contribute to neurodegenerative disease processes.