Automatic segmentation of up to ten layer boundaries in SD-OCT images of the mouse retina with and without missing layers due to pathology

Accurate quantification of retinal layer thicknesses in mice as seen on optical coherence tomography (OCT) is crucial for the study of numerous ocular and neurological diseases. However, manual segmentation is time-consuming and subjective. Previous attempts to automate this process were limited to high-quality scans from mice with no missing layers or visible pathology. This paper presents an automatic approach for segmenting retinal layers in spectral domain OCT images using sparsity based denoising, support vector machines, graph theory, and dynamic programming (S-GTDP). Results show that this method accurately segments all present retinal layer boundaries, which can range from seven to ten, in wild-type and rhodopsin knockout mice as compared to manual segmentation and has a more accurate performance as compared to the commercial automated Diver segmentation software.OCIS codes: (100.0100) Image processing, (170.4470) Ophthalmology, (100.2960) Image analysis, (100.5010) Pattern recognition, (110.4500) Optical coherence tomography     

Introduction to the BIOMED 2014 feature issue

The guest editors introduce a feature issue containing papers based on research presented at the BIOMED 2014 conference, held in Miami, FL, April 26–30, 2014.OCIS codes: (000.1200) Announcements, awards, news, and organizational activities; (170.0170) Medical optics and biotechnologySince 1994, the Optical Society of America has been organizing biennial topical meetings in the field of biomedical optics. These BIOMED conferences address the forefront research and development areas in the biomedical sciences ranging from molecular level progress in our understanding of bio-processes, to new and improved advances in instrumentation, to state-of-the-art techniques to diagnose and treat diseases. The papers published in this feature issue of Biomedical Optics Express cover a representative cross section of research presented at this year’s BIOMED meeting [1], held in Miami, FL, from 26–30 April 2014.The meeting covered plenary, invited and contributed talks, as well as posters in the following topical categories: (1) Biophysics, Biology and Biophotonics: the Crossroads; (2) BioNanophotonic and Molecular Probes; (3) Optical Microscopy: Techniques and Applications; (4) Photoacoustic Imaging and Spectroscopy; (5) Optical Coherence Tomography with Applications; (6) Optical Imaging and Tomography with Applications; and (7) Optical Spectroscopy with Applications. The conference was organized by the Conference Chairs Dr. Vadim Backman (USA) and Dr. Stefan Andersson-Engels (Sweden), and Vice Conference Chairs Dr. Stephen Boppart (USA) and Dr. Christoph Hitzenberger (Austria).The editors of this feature issue and organizers of the conference would like to take the opportunity to thank the authors and the reviewers for their contributions to this feature issue, as well as the presenters and attendees of the conference for their scientific presentations and discussions which were essential for the scientific success of BIOMED 2014.Finally, the organizers are pleased to announce that the next conference in this series, BIOMED 2016, will be held at the Westin Diplomat Resort & Spa in Hollywood, FL (Ft. Lauderdale Area), from 24–28 April 2016.     

Systematic Review and Meta-analysis of Circulatory Disease from Exposure to Low-Level Ionizing Radiation and Estimates of Potential Population Mortality Risks

Background: Although high doses of ionizing radiation have long been linked to circulatory disease, evidence for an association at lower exposures remains controversial. However, recent analyses suggest excess relative risks at occupational exposure levels.Objectives: We performed a systematic review and meta-analysis to summarize information on circulatory disease risks associated with moderate- and low-level whole-body ionizing radiation exposures.Methods: We conducted PubMed/ISI Thomson searches of peer-reviewed papers published since 1990 using the terms “radiation” AND “heart” AND “disease,” OR “radiation” AND “stroke,” OR “radiation” AND “circulatory” AND “disease.” Radiation exposures had to be whole-body, with a cumulative mean dose of < 0.5 Sv, or at a low dose rate (< 10 mSv/day). We estimated population risks of circulatory disease from low-level radiation exposure using excess relative risk estimates from this meta-analysis and current mortality rates for nine major developed countries.Results: Estimated excess population risks for all circulatory diseases combined ranged from 2.5%/Sv [95% confidence interval (CI): 0.8, 4.2] for France to 8.5%/Sv (95% CI: 4.0, 13.0) for Russia.Conclusions: Our review supports an association between circulatory disease mortality and low and moderate doses of ionizing radiation. Our analysis was limited by heterogeneity among studies (particularly for noncardiac end points), the possibility of uncontrolled confounding in some occupational groups by lifestyle factors, and higher dose groups (> 0.5 Sv) generally driving the observed trends. If confirmed, our findings suggest that overall radiation-related mortality is about twice that currently estimated based on estimates for cancer end points alone (which range from 4.2% to 5.6%/Sv for these populations).     

Enteric helminths of the mallard Anas platyrhynchos L., 1758 in the north-western part of Poland

Although the mallard, Anas platyrhynchos, is the most common wild duck in Poland, as well as in the entire Palearctic, it is extremely rarely studied by comprehensive parasitological surveys. The aim of this study was to present a synthesis on the species composition of enteric helminths of the mallard in north-western Poland. The study was carried out in 1999-2006 and involved parasitic worms isolated from the alimentary tracts of 187 mallards (Anseriformes: Anatidae). Following isolation, the parasites were preserved in 70% ethylene and stained (flatworms) or viewed in transient light (nematodes and acanthocephalans). Taxonomic identity of the worms was determined using taxonomic keys and numerous original papers. The studies have revealed that the parasitic community of this host in the north-west part of Poland is relatively complex, composed of 51 species of helminths of four systematic groups: 16 digenean species, 23 tapeworms, 9 nematodes, and 3 acanthocephalans. The material also revealed five new to Polish fauna parasitic species: one trematode (Echinostoma miyagawai) and four tapeworms (Microsomacanthus baeri, M. pachycephala, Monotestilepis tadornae, and Sobolevicanthus aculeostileticus). On the other hand, for another 11 species (Prosthogonimus ovatus, Psilotrema simillimum, Australapatemon minor, Leucochloridiomorpha lutea, Psilostomum brevicolle, Echinocotyle rosseteri, Fimbriarioides sp., Retinometra giranensis, Anisakinae gen. sp., Pseudocapillaria mergi i Polymorphus magnus) the mallard was found to be a new host.     

The next step from high-flux dialysis: application of sorbent technology.

The current foci of renal replacement therapy with dialysis are middle molecular weight toxins, consisting of small proteins, polypeptides and products of glycosylation and lipoxygenation. Conventional high-flux dialysis is not efficient at removing these molecules, explaining the increased interest in using sorbents to supplement dialysis techniques. Prototype biocompatible sorbents have been developed and investigated for middle molecule removal; these have been shown, in man, to remove beta(2)-microglobulin, angiogenin, leptin, cytokines and other molecules, without reducing platelets and leukocytes. Extensive clinical studies are underway to demonstrate the clinical utility and safety of adding routinely a sorbent hemoperfusion device to hemodialysis.     

Delay of cytoreductive surgery and heated intraperitoneal chemotherapy in patients with appendiceal neoplasm

Cytoreductive surgery/heated intraperitoneal chemotherapy (CRS/HIPEC) has been shown to be effective for selected patients with advanced appendiceal cancer. We propose that delaying CRS/HIPEC leads to disease progression and affects outcome. A retrospective analysis of a prospective database was carried out. Patients were divided into two groups based on time from diagnosis to CRS/HIPEC (less than 6 months = early, greater than 6 months = delayed). Comparison was made of Peritoneal Cancer Index (PCI), Prior Surgery Score (PSS), complete cytoreduction (CC), and lymph node status. Overall survival (OS) was calculated using Kaplan-Meier estimates. Of 127 patients, 50 had disseminated peritoneal adenomucinosis and 77 had peritoneal mucinous carcinomatosis (PMCA). Of patients with PMCA, 41 had early CRS/HIPEC and 36 delayed. PCI was less than 20 in 46 and 17 per cent (P = 0.007) of the early and delayed groups, respectively. CC was achieved in 88 and 61 per cent (P = 0.009) of the early and delayed groups, respectively. PSS was (2 of 3) in 51 and 91 per cent (P = 0.001) of the early and delayed groups, respectively. Five-year OS was 54 per cent for the early group and 45 per cent for the delayed group (P = 0.2). Delaying CRS/HIPEC was associated with higher tumor load and lower chance for complete cytroreduction. Longer follow-up and larger numbers are needed to determine if OS difference will reach statistical significance.     

Laparoscopic splenectomy: outcome and efficacy for massive and supramassive spleens

BackgroundMassive and supramassive splenomegaly are relative contraindications to pure laparoscopic splenectomy (LS).MethodsA retrospective review of adult patients was conducted for splenectomy occurring from 1999 to 2009. Massive and supramassive spleens were defined as craniocaudad length ≥ 17 cm or weight ≥ 600 g and craniocaudad length ≥ 22 cm or weight ≥ 1,600 g, respectively.ResultsLS was done for 22 and open splenectomy for 21 patients, of which 12 and 14 were supramassive. Spleen weight and craniocaudad length were comparable. LS was associated with lower blood loss (308 vs 400 mL, P = .24), shorter length of stay (3 vs 4.5 days, P = .054), and similar morbidity (17% vs 14%). Two reoperations and 1 death occurred with open splenectomy. Operative times were longer for LS (195 vs 105 min, P = .008), while the conversion rate was 25%.ConclusionsIn cases of massive and supramassive splenomegaly, better outcomes are accomplished with LS than open splenectomy, and are comparable to hand-assisted LS.     

New 2-Thiopyridines as Potential Candidates for Killing both Actively Growing and Dormant Mycobacterium tuberculosis Cells

From in vivo observations, a majority of M. tuberculosis cells in latently infected individuals are in a dormant and probably nonculturable state, display little metabolic activity, and are phenotypically resistant to antibiotics. Despite many attempts, no specific antimicrobials effective against latent tuberculosis have yet been found, partly because of a lack of reliable and adequate in vitro models for screening of drug candidates. We propose here a novel in vitro model of M. tuberculosis dormancy that meets the important criteria of latency, namely, nonculturability of cells, considerable reduction of metabolic activity, and significant phenotypic resistance to the first-line antibiotics rifampin and isoniazid. Using this model, we found a new group of 2-thiopyridine derivatives that had potent antibacterial activity against both actively growing and dormant M. tuberculosis cells. By means of the model of M. tuberculosis nonculturability, several new 2-thiopyridine derivatives were found to have potent antitubercular activity. The compounds are effective against both active and dormant M. tuberculosis cells. The bactericidal effects of compounds against dormant M. tuberculosis was confirmed by using three different in vitro models of tuberculosis dormancy. The model of nonculturability could be used as a reliable tool for screening drug candidates, and 2-thiopyridine derivatives may be regarded as prominent compounds for further development of new drugs for curing latent M. tuberculosis infection.     

Mantle–slab interaction and redox mechanism of diamond formation

Subduction tectonics imposes an important role in the evolution of the interior of the Earth and its global carbon cycle; however, the mechanism of the mantle–slab interaction remains unclear. Here, we demonstrate the results of high-pressure redox-gradient experiments on the interactions between Mg-Ca-carbonate and metallic iron, modeling the processes at the mantle–slab boundary; thereby, we present mechanisms of diamond formation both ahead of and behind the redox front. It is determined that, at oxidized conditions, a low-temperature Ca-rich carbonate melt is generated. This melt acts as both the carbon source and crystallization medium for diamond, whereas at reduced conditions, diamond crystallizes only from the Fe-C melt. The redox mechanism revealed in this study is used to explain the contrasting heterogeneity of natural diamonds, as seen in the composition of inclusions, carbon isotopic composition, and nitrogen impurity content.Subduction of crustal material plays an important role in the global carbon cycle (1–6). Depending on oxygen fugacity and pressure-temperature (P-T) conditions, carbon exists in the Earth''s interior in the form of carbides, diamond, graphite, hydrocarbons, carbonates, and CO₂ (7–11). In the upper mantle, the oxygen fugacity (fO₂) varies from one to five log units below the fayalite-magnetite-quartz (FMQ) buffer, with a trend of a decrease with depth (6, 12–15). At a depth of ∼250 km, mantle is reported to become metal saturated (16, 17), which holds true for all mantle regions below, including the transition zone and lower mantle. The subduction of the oxidized crustal material occurs to depths greater than 600 km (4–6). The main carbon-bearing minerals of the subducted materials are carbonates, which are thermodynamically stable up to P-T conditions of the lower mantle (10, 11, 18). As evidenced by the compositions of inclusions in diamond, which vary from strongly reduced, e.g., metallic iron and carbides (19–23), to oxidized, e.g., carbonates and CO₂ (6, 20, 24–28), carbonates may be involved in the reactions with reduced deep-seated rocks, including Fe⁰-bearing species (29–31). A scale of these reactions is determined mainly by the capacity of subducted carbonate-bearing domains. An important consequence of such an interaction is that it can produce diamond. However, studies on diamond synthesis via the reactions between oxidized and reduced phases are limited (32–35).To understand the mechanisms of the interaction of carbon-bearing oxidized- and reduced-mineral assemblages, we performed high-pressure experiments with an iron-carbonate system; an approach was used that enabled the creation of an oxygen fugacity gradient in the capsules (Materials and Methods and SI Materials and Methods).