New Descriptor for Glomerulus Detection in Kidney Microscopy Image

Glomerulus detection is a key step in histopathological evaluation of microscopy images of kidneys. However, the task of automatic detection of glomeruli poses challenges due to the disparity in sizes and shapes of glomeruli in renal sections. Moreover, extensive variations of their intensities due to heterogeneity in immunohistochemistry staining are also encountered. Despite being widely recognized as a powerful descriptor for general object detection, the rectangular histogram of oriented gradients (Rectangular HOG) suffers from many false positives due to the aforementioned difficulties in the context of glomerulus detection. A new descriptor referred to as Segmental HOG is developed to perform a comprehensive detection of hundreds of glomeruli in images of whole kidney sections. The new descriptor possesses flexible blocks that can be adaptively fitted to input images to acquire robustness to deformations of glomeruli. Moreover, the novel segmentation technique employed herewith generates high quality segmentation outputs and the algorithm is assured to converge to an optimal solution. Consequently, experiments using real world image data reveal that Segmental HOG achieves significant improvements in detection performance compared to Rectangular HOG. The proposed descriptor and method for glomeruli detection present promising results and is expected to be useful in pathological evaluation

Unveiling the RNA virosphere associated with marine microorganisms

The study of extracellular DNA viral particles in the ocean is currently one of the most advanced fields of research in viral metagenomic analysis. However, even though the intracellular viruses of marine microorganisms might be the major source of extracellular virus particles in the ocean, the diversity of these intracellular viruses is not well understood. Here, our newly developed method, referred to herein as fragmented and primer ligated dsRNA sequencing (flds) version 2, identified considerable genetic diversity of marine RNA viruses in cell fractions obtained from surface seawater. The RNA virus community appears to cover genome sequences related to more than half of the established positive‐sense ssRNA and dsRNA virus families, in addition to a number of unidentified viral lineages, and such diversity had not been previously observed in floating viral particles. In this study, more dsRNA viral contigs were detected in host cells than in extracellular viral particles. This illustrates the magnitude of the previously unknown marine RNA virus population in cell fractions, which has only been partially assessed by cellular metatranscriptomics and not by contemporary viral metagenomic studies. These results reveal the importance of studying cell fractions to illuminate the full spectrum of viral diversity on Earth

Microbial diversity in deep-sea methane seep sediments presented by SSU rRNA gene tag sequencing

http://www.godac.jamstec.go.jp/darwin/cruise/yokosuka/yk06-03/

Fermi level tuning of Ag-doped Bi2Se3 topological insulator

The temperature dependence of the resistivity (rho) of Ag-doped Bi2Se3 (AgxBi2-xSe3) shows insulating behavior above 35 K, but below 35 K, rho suddenly decreases with decreasing temperature, in contrast to the metallic behavior for non-doped Bi2Se3 at 1.5-300 K. This significant change in transport properties from metallic behavior clearly shows that the Ag doping of Bi2Se3 can effectively tune the Fermi level downward. The Hall effect measurement shows that carrier is still electron in AgxBi2-xSe3 and the electron density changes with temperature to reasonably explain the transport properties. Furthermore, the positive gating of AgxBi2-xSe3 provides metallic behavior that is similar to that of non-doped Bi2Se3, indicating a successful upward tuning of the Fermi level

Algivore or phototroph?: Plakobranchus ocellatus (Gastropoda) continuously acquires kleptoplasts and nutrition from multiple algal species in nature

The sea slug Plakobranchus ocellatus (Sacoglossa, Gastropoda) retains photosynthetically active chloroplasts from ingested algae (functional kleptoplasts) in the epithelial cells of its digestive gland for up to 10 months. While its feeding behavior has not been observed in natural habitats, two hypotheses have been proposed: 1) adult P. ocellatus uses kleptoplasts to obtain photosynthates and nutritionally behaves as a photoautotroph without replenishing the kleptoplasts; or 2) it behaves as a mixotroph (photoautotroph and herbivorous consumer) and replenishes kleptoplasts continually or periodically. To address the question of which hypothesis is more likely, we examined the source algae for kleptoplasts and temporal changes in kleptoplast composition and nutritional contribution. By characterizing the temporal diversity of P. ocellatus kleptoplasts using rbcL sequences, we found that P. ocellatus harvests kleptoplasts from at least 8 different siphonous green algal species, that kleptoplasts from more than one species are present in each individual sea slug, and that the kleptoplast composition differs temporally. These results suggest that wild P. ocellatus often feed on multiple species of siphonous algae from which they continually obtain fresh chloroplasts. By estimating the trophic position of wild and starved P. ocellatus using the stable nitrogen isotopic composition of amino acids, we showed that despite the abundance of kleptoplasts, their photosynthates do not contribute greatly to the nutrition of wild P. ocellatus, but that kleptoplast photosynthates form a significant source of nutrition for starved sea slugs. The herbivorous nature of wild P. ocellatus is consistent with insights from molecular analyses indicating that kleptoplasts are frequently replenished from ingested algae, leading to the conclusion that natural populations of P. ocellatus do not rely on photosynthesis but mainly on the digestion of ingested algae

Evaluation of complex physical therapy for lymphedema of the unilateral lower limbs

We evaluated the effectiveness of the complex physical therapy (CPT) for lymphedema of the unilateral lower limbs of eleven patients who had been admitted to Tokushima Rehabilitation Hospital. Ten patients were of secondary lymphedema, nine of which were after treatment of uterine cancer and one was of primary lymphedema. Our CPT consited of skin care, manual lymph drainage (MLD), compression therapy with elastic bandages or elastic stockings, and exercise therapy under compression. MLD functionally operates to enhance the lymph drainage more proximally in both contralateral and ipsilateral truncal quadrants of the torso, then in the proximal limb, and only thereafter from the distal to proximal portion of the edematous extremity. Swelling ratio of all patients on admission was 26.9± 11.8% and that at discharge was 16.8±9.4%. Edema reduction ratio (ERR) of the entire patients was 41.5± 16.5%, and 81.8% of cases were recognized as effective, in which ERR showed more than 30% at discharge. In a consensus document about the diagnosis and treatment of peripheral lymphedema in 1995, the International Society of Lymphology Executive Committee reported that most operations designed to alleviate peripheral lymphedema have not as yet been perfected or usually are still inferior to combined physiotherapy. At present lymphedema should be accurately diagnosed in the early stage and be treated with CPT correctly by clinicians who understand lymphedema thoroughly and are well trained

Metagenomic insights into zooplankton-associated bacterial communities

Zooplankton and microbes play a key role in the ocean's biological cycles by releasing and consuming copious amounts of particulate and dissolved organic matter. Additionally, zooplankton provide a complex microhabitat rich in organic and inorganic nutrients in which bacteria thrive. In this study, we assessed the phylogenetic composition and metabolic potential of microbial communities associated with crustacean zooplankton species collected in the North Atlantic. Using Illumina sequencing of the 16S rRNA gene, we found significant differences between the microbial communities associated with zooplankton and those inhabiting the surrounding seawater. Metagenomic analysis of the zooplankton-associated microbial community revealed a highly specialized bacterial community able to exploit zooplankton as microhabitat and thus, mediating biogeochemical processes generally underrepresented in the open ocean. The zooplankton-associated bacterial community is able to colonize the zooplankton's internal and external surfaces using a large set of adhesion mechanisms and to metabolize complex organic compounds released or exuded by the zooplankton such as chitin, taurine and other complex molecules. Moreover, the high number of genes involved in iron and phosphorus metabolisms in the zooplankton-associated microbiome suggests that this zooplankton-associated bacterial community mediates specific biogeochemical processes (through the proliferation of specific taxa) that are generally underrepresented in the ambient waters

A deeply branching thermophilic bacterium with an ancient acetyl-CoA pathway dominates a subsurface ecosystem

<div><p>A nearly complete genome sequence of <em>Candidatus</em> ‘Acetothermum autotrophicum’, a presently uncultivated bacterium in candidate division OP1, was revealed by metagenomic analysis of a subsurface thermophilic microbial mat community. Phylogenetic analysis based on the concatenated sequences of proteins common among 367 prokaryotes suggests that <em>Ca.</em> ‘A. autotrophicum’ is one of the earliest diverging bacterial lineages. It possesses a folate-dependent Wood-Ljungdahl (acetyl-CoA) pathway of CO₂ fixation, is predicted to have an acetogenic lifestyle, and possesses the newly discovered archaeal-autotrophic type of bifunctional fructose 1,6-bisphosphate aldolase/phosphatase. A phylogenetic analysis of the core gene cluster of the acethyl-CoA pathway, shared by acetogens, methanogens, some sulfur- and iron-reducers and dechlorinators, supports the hypothesis that the core gene cluster of <em>Ca.</em> ‘A. autotrophicum’ is a particularly ancient bacterial pathway. The habitat, physiology and phylogenetic position of <em>Ca.</em> ‘A. autotrophicum’ support the view that the first bacterial and archaeal lineages were H₂-dependent acetogens and methanogenes living in hydrothermal environments.</p> </div