An Elastic Interaction-Based Loss Function for Medical Image Segmentation

Deep learning techniques have shown their success in medical image segmentation since they are easy to manipulate and robust to various types of datasets. The commonly used loss functions in the deep segmentation task are pixel-wise loss functions. This results in a bottleneck for these models to achieve high precision for complicated structures in biomedical images. For example, the predicted small blood vessels in retinal images are often disconnected or even missed under the supervision of the pixel-wise losses. This paper addresses this problem by introducing a long-range elastic interaction-based training strategy. In this strategy, convolutional neural network (CNN) learns the target region under the guidance of the elastic interaction energy between the boundary of the predicted region and that of the actual object. Under the supervision of the proposed loss, the boundary of the predicted region is attracted strongly by the object boundary and tends to stay connected. Experimental results show that our method is able to achieve considerable improvements compared to commonly used pixel-wise loss functions (cross entropy and dice Loss) and other recent loss functions on three retinal vessel segmentation datasets, DRIVE, STARE and CHASEDB1

ISCEV guidelines for calibration and verification of stimuli and recording instruments (2023 update)

This document developed by the International Society for Clinical Electrophysiology of Vision (ISCEV) provides guidance for calibration and verification of stimulus and recording systems specific to clinical electrophysiology of vision. This guideline provides additional information for those using ISCEV Standards and Extended protocols and supersedes earlier Guidelines. The ISCEV guidelines for calibration and verification of stimuli and recording instruments (2023 update) were approved by the ISCEV Board of Directors 01, March 2023

Combining Contrast Invariant L1 Data Fidelities with Nonlinear Spectral Image Decomposition

This paper focuses on multi-scale approaches for variational methods and corresponding gradient flows. Recently, for convex regularization functionals such as total variation, new theory and algorithms for nonlinear eigenvalue problems via nonlinear spectral decompositions have been developed. Those methods open new directions for advanced image filtering. However, for an effective use in image segmentation and shape decomposition, a clear interpretation of the spectral response regarding size and intensity scales is needed but lacking in current approaches. In this context, $L^1$ data fidelities are particularly helpful due to their interesting multi-scale properties such as contrast invariance. Hence, the novelty of this work is the combination of $L^1$-based multi-scale methods with nonlinear spectral decompositions. We compare $L^1$ with $L^2$ scale-space methods in view of spectral image representation and decomposition. We show that the contrast invariant multi-scale behavior of $L^1-TV$ promotes sparsity in the spectral response providing more informative decompositions. We provide a numerical method and analyze synthetic and biomedical images at which decomposition leads to improved segmentation.Comment: 13 pages, 7 figures, conference SSVM 201

Pre-exposure prophylaxis for preventing acquisition of HIV: A cross-sectional study of patients, prescribers, uptake, and spending in the United States, 2015-2016

BACKGROUND: In 2015, there were approximately 40,000 new HIV diagnoses in the United States. Pre-exposure prophylaxis (PrEP) is an effective strategy that reduces the risk of HIV acquisition; however, uptake among those who can benefit from it has lagged. In this study, we 1) compared the characteristics of patients who were prescribed PrEP with individuals newly diagnosed with HIV infection, 2) identified the specialties of practitioners prescribing PrEP, 3) identified metropolitan statistical areas (MSAs) within the US where there is relatively low uptake of PrEP, and 4) reported median amounts paid by patients and third-party payors for PrEP. METHODS AND FINDINGS: We analyzed prescription drug claims for individuals prescribed PrEP in the Integrated Dataverse (IDV) from Symphony Health for the period of September 2015 to August 2016 to describe PrEP patients, prescribers, relative uptake, and payment methods in the US. Data were available for 75,839 individuals prescribed PrEP, and findings were extrapolated to approximately 101,000 individuals, which is less than 10% of the 1.1 million adults for whom PrEP was indicated. Compared to individuals with newly diagnosed HIV infection, PrEP patients were more likely to be non-Hispanic white (45% versus 26.2%), older (25% versus 19% at ages 35-44), male (94% versus 81%), and not reside in the South (30% versus 52% reside in the South).Using a ratio of the number of PrEP patients within an MSA to the number of newly diagnosed individuals with HIV infection, we found MSAs with relatively low uptake of PrEP were concentrated in the South. Of the approximately 24,000 providers who prescribed PrEP, two-thirds reported primary care as their specialty. Compared to the types of payment methods that people living with diagnosed HIV (PLWH) used to pay for their antiretroviral treatment in 2015 to 2016 reported in the Centers for Disease Control and Prevention (CDC) HIV Surveillance Special Report, PrEP patients were more likely to have used commercial health insurance (80% versus 35%) and less likely to have used public healthcare coverage or a publicly sponsored assistance program to pay for PrEP (12% versus 45% for Medicaid). Third-party payors covered 95% of the costs of PrEP. Overall, we estimated the median annual per patient out-of-pocket spending on PrEP was approximately US$72. Limitations of this study include missing information on prescription claims of patients not included in the database, and for those included, some patients were missing information on patient diagnosis, race/ethnicity, educational attainment, and income (34%-36%). CONCLUSIONS: Our findings indicate that in 2015-2016, many individuals in the US who could benefit from being on PrEP were not receiving this HIV prevention medication, and those prescribed PrEP had a significantly different distribution of characteristics from the broader population that is at risk for acquiring HIV. PrEP patients were more likely to pay for PrEP using commercial or private insurance, whereas PLWH were more likely to pay for their antiretroviral treatment using publicly sponsored programs. Addressing the affordability of PrEP and otherwise promoting its use among those with indications for PrEP represents an important opportunity to help end the HIV epidemic

Native Thrombocidin-1 and Unfolded Thrombocidin-1 Exert Antimicrobial Activity via Distinct Structural Elements

Chemokines (chemotactic cytokines) can have direct antimicrobial activity, which is apparently related to the presence of a distinct positively charged patch on the surface. However, chemokines can retain antimicrobial activity upon linearization despite the loss of their positive patch, thus questioning the importance of this patch for activity. Thrombocidin-1 (TC-1) is a microbicidal protein isolated from human blood platelets. TC-1 only differs from the chemokine NAP-2/CXCL7 by a two-amino acid C-terminal deletion, but this truncation is crucial for antimicrobial activity. We assessed the structure-activity relationship for antimicrobial activity of TC-1. Reduction of the charge of the TC-1-positive patch by replacing lysine 17 with alanine reduced the activity against bacteria and almost abolished activity against the yeast Candida albicans. Conversely, augmentation of the positive patch by increasing charge density or size resulted in a 2-3-fold increased activity against Staphylococcus aureus, Escherichia coli, and Bacillus subtilis but did not substantially affect activity against C. albicans. Reduction of TC-1 resulted in loss of the folded conformation, but this disruption of the positive patch did not affect antimicrobial activity. Using overlapping 15-mer synthetic peptides, we demonstrate peptides corresponding to the N-terminal part of TC-1 to have similar antimicrobial activity as intact TC-1. Although we demonstrate that the positive patch is essential for activity of folded TC-1, unfolded TC-1 retained antimicrobial activity despite the absence of a positive patch. This activity is probably exerted by a linear peptide stretch in the N-terminal part of the molecule. We conclude that intact TC-1 and unfolded TC-1 exert antimicrobial activity via distinct structural elements

A food web model for the Baffin Bay coastal and shelf ecosystem. Part 1 : Ecopath Technical Report

This work was undertaken as part of a multidisciplinary research project funded by the Marine Observation Prediction and Assessment Network - MEOPAR (at ULaval), Canadian Institute of Health Research – CIHR (at University of Ottawa), and Sentinel North (at ULaval), and hosted at Université Laval, in Canada. The objective of the overall project is to support the food security (i.e., the availability and access to sufficient, safe, nutritious food that meets dietary preference) of Inuit communities of the Eastern Canadian Arctic, as well as to explore ways to adapt to effects of climate change. Inuit fish and hunt local marine species, from invertebrates to fish and marine mammals, which make a large part of their diet and are central to their food security. With temperatures increasing twice as fast as the global average and sea ice becoming thinner and forming later, climate change effects on the distribution and abundance of Arctic marine species are already taking place. To better understand the effects of climate change in important subsistence species, a multi-species model (Ecopath with Ecosim) will be used to inform the development of an integrated ecosystem assessment. The model will be used as a tool to co-create scenarios of ecosystem change with the community of Qikiqtarjuaq, Nunavut, to inform adaptation strategies regarding food security (e.g., potential of new fisheries in the region). This report describes the development of an Ecopath model of the Baffin Bay coastal and shelf ecosystem. The methodology, data used to construct the model, data gaps and limitations are described

Hyperosmotic stress induces metacaspase - and mitochondria - dependent apoptosis in Saccharomyces cerevisiae

Prova tipográfica (In Press)During the last years, several reports described an apoptosis-like programmed cell death process in yeast in response to different environmental aggressions. Here, evidence is presented that hyperosmotic stress induces in Saccharomyces cerevisiae a cell death process accompanied by morphological and biochemical indicators of apoptotic programmed cell death, namely chromatin condensation along the nuclear envelope, mitochondrial swelling and reduction of cristae number, production of reactive oxygen species and DNA strand breaks, with maintenance of plasma membrane integrity. Disruption of AIF1 had no effect on cell survival, but lack of Yca1p drastically reduced metacaspase activation and decreased cell death indicating that this death process was associated to activation of this protease. Supporting the involvement of mitochondria and cytochrome c in caspase activation, the mutant strains cyc1Δ cyc7Δ and cyc3Δ, both lacking mature cytochrome c, displayed a decrease in caspase activation associated to increased cell survival when exposed to hyperosmotic stress. These findings indicate that hyperosmotic stress triggers S. cerevisiae into an apoptosis-like programmed cell death that is mediated by a caspase-dependent mitochondrial pathway partially dependent on cytochrome c

Free energy and molecular dynamics calculations for the cubic-tetragonal phase transition in zirconia

The high-temperature cubic-tetragonal phase transition of pure stoichiometric zirconia is studied by molecular dynamics (MD) simulations and within the framework of the Landau theory of phase transformations. The interatomic forces are calculated using an empirical, self-consistent, orthogonal tight-binding (SC-TB) model, which includes atomic polarizabilities up to the quadrupolar level. A first set of standard MD calculations shows that, on increasing temperature, one particular vibrational frequency softens. The temperature evolution of the free energy surfaces around the phase transition is then studied with a second set of calculations. These combine the thermodynamic integration technique with constrained MD simulations. The results seem to support the thesis of a second-order phase transition but with unusual, very anharmonic behaviour above the transition temperature

Protecting Young Children Against Skin Cancer: Parental Beliefs, Roles, And Regret

Objective: To examine the role of parental beliefs, roles, and anticipated regret toward performing childhood sun-protective behaviours. Methods: Parents (N = 230; 174 mothers, 56 fathers), recruited using a nonrandom convenience sample, of at least 1 child aged between 2 and 5 years completed an initial questionnaire assessing demographics and past behaviour as well as theory of planned behaviour global (attitude, subjective norm, and perceived behavioural control) and belief-based (behavioural, normative, and control beliefs) measures, role construction, and anticipated regret regarding their intention and behaviour to protect their child from the sun. Two weeks later, participants completed a follow-up questionnaire assessing their sun protection of their child during the previous 2 weeks. Results: Hierarchical multiple regression analysis identified attitude, perceived behavioural control, role construction, anticipated regret, past behaviour, and a normative belief (“current partner/other family members”) as significant predictors of parents' intention to participate in sun-protective behaviour for their child. Intention and past behaviour were significant predictors of parents' follow-up sun-protective behaviour. The regression models explained 64% and 36% of the variance in intention and behaviour, respectively. Conclusions: The findings of this study highlight the importance of anticipated regret and role-related beliefs alongside personal, normative, and control beliefs in determining parents' intentional sun-protective behaviour for their children. Findings may inform the development of parent- and community-based sun protection intervention programs to promote parents' sun-safety behaviours for their children to prevent future skin cancer incidence

A Dual-Color Fluorescence-Based Platform to Identify Selective Inhibitors of Akt Signaling

Background: Inhibition of Akt signaling is considered one of the most promising therapeutic strategies for many cancers. However, rational target-orientated approaches to cell based drug screens for anti-cancer agents have historically been compromised by the notorious absence of suitable control cells. Methodology/Principal Findings: In order to address this fundamental problem, we have developed BaFiso, a live-cell screening platform to identify specific inhibitors of this pathway. BaFiso relies on the co-culture of isogenic cell lines that have been engineered to sustain interleukin-3 independent survival of the parental Ba/F3 cells, and that are individually tagged with different fluorescent proteins. Whilst in the first of these two lines cell survival in the absence of IL-3 is dependent on the expression of activated Akt, the cells expressing constitutively-activated Stat5 signaling display IL-3 independent growth and survival in an Akt-independent manner. Small molecules can then be screened in these lines to identify inhibitors that rescue IL-3 dependence. Conclusions/Significance: BaFiso measures differential cell survival using multiparametric live cell imaging and permits selective inhibitors of Akt signaling to be identified. BaFiso is a platform technology suitable for the identification of smal