Metamorphosis and Taxonomy of Andreev Bound States

We analyze the spatial and energy dependence of the local density of states in a SNS junction. We model our system as a one-dimensional tight-binding chain which we solve exactly by numerical diagonalization. We calculate the dependence of the Andreev bound states on position, phase difference, gate voltage, and coupling with the superconducting leads. Our results confirm the physics predicted by certain analytical approximations, but reveal a much richer set of phenomena beyond the grasp of these approximations, such as the metamorphosis of the discrete states of the normal link (the normal bound states) into Andreev bound states as the leads become superconducting.Comment: 23 pages, 15 figure

Radiation therapy and photodynamic therapy for biliary tract and ampullary carcinomas

The purpose of radiation therapy for unresectable biliary tract cancer is to prolong survival or prolong stent patency, and to provide palliation of pain. For unresectable bile duct cancer, there are a number of studies showing that radiation therapy is superior to the best supportive care. Although radiation therapy is used in many institutions, no large randomized controlled trials (RCTs) have been performed to date and the evidence level supporting the superiority of this treatment is low. Because long-term relief of jaundice is difficult without using biliary stenting, a combination of radiation therapy and stent placement is commonly used. As radiation therapy, external-beam radiation therapy is usually performed, but combined use of intraluminal brachytherapy with external beam radiation therapy is more useful for making the treatment more effective. There are many reports demonstrating improved response rates as well as extended survival and time to recurrence achieved by this combination therapy. Despite the low level of the evidence, this combination therapy is performed at many institutions. It is expected that multiinstitutional RCTs will be carried out. Unresectable gallbladder cancer with a large focus is usually extensive, and normal organs with high radio sensitivity exist contiguously with it. Therefore, only limited anticancer effects are to be expected from external beam radiation therapy for this type of cancer. The number of reports on ampullary cancer is small and the role of radiation therapy in this cancer has not been established. Combination treatment for ampullary cancer consists of either a single use of intraoperative radiation therapy, postoperative external beam radiation therapy or intraluminal brachytherapy, or a combination of two or three of these therapies. Intraoperative radiation therapy is superior in that it enables precise irradiation to the target site, thereby protecting adjacent highly radiosensitive normal tissues from irradiation. There are reports showing extended survival, although not significant, in groups undergoing intraoperative or postoperative radiation therapy compared with groups without radiation therapy. To date, there are no reports of large RCTs focusing on the significance of radiation therapy as a postoperative adjuvant treatment, so its usefulness as a postoperative adjuvant treatment is not proven. An alternative treatment is photodynamic therapy. There is an RCT demonstrating that, in unresectable bile duct cancer, extended survival and improved quality of life (QOL) have been achieved through a combination of photodynamic therapy and biliary stenting, compared with biliary stenting alone. Results from large RCTs are desired

A system for phenotype harmonization in the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine (TOPMed) program

Genotype-phenotype association studies often combine phenotype data from multiple studies to increase statistical power. Harmonization of the data usually requires substantial effort due to heterogeneity in phenotype definitions, study design, data collection procedures, and data-set organization. Here we describe a centralized system for phenotype harmonization that includes input from phenotype domain and study experts, quality control, documentation, reproducible results, and data-sharing mechanisms. This system was developed for the National Heart, Lung, and Blood Institute’s Trans-Omics for Precision Medicine (TOPMed) program, which is generating genomic and other -omics data for more than 80 studies with extensive phenotype data. To date, 63 phenotypes have been harmonized across thousands of participants (recruited in 1948–2012) from up to 17 studies per phenotype. Here we discuss challenges in this undertaking and how they were addressed. The harmonized phenotype data and associated documentation have been submitted to National Institutes of Health data repositories for controlled access by the scientific community. We also provide materials to facilitate future harmonization efforts by the community, which include 1) the software code used to generate the 63 harmonized phenotypes, enabling others to reproduce, modify, or extend these harmonizations to additional studies, and 2) the results of labeling thousands of phenotype variables with controlled vocabulary terms

The effectiveness of ectomycorrhizal fungi in increasing the growth of Eucalyptus globulus Labill. in relation to root colonization and hyphal development in soil

Forty-seven different isolates of ectomycorrhizal fungi, from the different genera, were screened for their effectiveness in increasing the growth of Eucalyptus globulin La hi 11. where supply of P is deficient. Plants were grown in a P-delicient sand, in pots, in a temperature- control led glasshouse. Seedlings we re harvested 6-S and K7 d after planting, and were assessed for dry matter production and mywirrhizal colonization. Selected treatments were also assessed for P concentrations in the plant and hyphal development in the soil. Dry weights of inoculated plants ranged from 50 to 350% of the dry Weights of uninoculated plants. Growth increases in response to ectorriycorrhizal inoculation corresponded with increased P uptake by the plant.‘Early’colonizing fungal species (Descolea maculata, Hebeloma westraliens, Laccaria laccata and Pisolithus tinctorius) were generally more effective in increasing plant growth than‘late’colonizing species (Cortinarius spp. and Hyutenmgium spp.), although there was also variation in effectiveness among isolates of the same fungal species. Plant dry weights were positively correlated (r2= 0·79-0·84) with the length of colonized root, indicating that fungi which colonized roots extensively were The most effective in increasing plant growth. For some fungi, however, plant growth responses to inoculation were not related to colonized root length. These responses could not.be related to the development of hyphae in soil by the mycorrhizal fungi

Improving the colonization capacity and effectiveness of ectomycorrhizal fungal cultures by association with a host plant and re-isolation

The ability of an ectomycorrhizal fungus to colonize plant roots (colonization capacity) and to increase plant growth at a deficient supply of P (effectiveness) declines after repeated subculture on agar media. We attempted to revitalize selected isolates of ectomycorrhizal fungi by inoculating them onto a compatible host (Eucalyptus globulus) and reisolating them from ectomycorrhizas and basidiomes. The growth on agar of the reisolated fungal cultures and the original fungal cultures was measured over 14 d. Seedlings of E. globulus were also inoculated with either the original fungal isolates or their reisolates and were grown in pots containing a P-deficient sand, in a temperature-controlled glasshouse. Seedlings were harvested 49 and 93 d after planting and were assessed for mycorrhizal colonization, dry weights and P concentrations. The reisolates generally grew at a faster rate on agar, and colonized plant roots more quickly, than the original isolates. Plants inoculated with the reisolates also had increased dry weights by day 93, which could be attributed to increased P uptake by the plant. We concluded that reisolating ectomycorrhizal fungi from mycorrhizas and basidiomes can increase the colonization capacity and effectiveness of isolates which have been grown on agar media for extended periods. This result, and the high cost of maintaining cultures emphasizes the need to examine alternative methods of storage of fungal isolates

Commercial inoculation of eucalypts with ectomycorrhizal fungi

Four eucalypt species (Eucalyptus globulus, E. nitens, E. regnans and E. diversicolor) were inoculated with alginate beads (Mycobead ™) encapsulating two ectomycorrhizal fungi (Hebeloma westraliense and Laccaria laccata). A commercial fluid drill, used for sowing seed, was slightly modified and was used to deposit 5-1 0 Mycobeads into a steamed peat: perlite (2: 1 v/v) seedling substrate immediately prior to sowing pre-soaked seed. The substrate contained basal nutrients minus nitrogen and phosphorus. Over 100,000 seedlings were sown in this way. Three weeks after sowing, seedlings were watered twice weekly with a complete liquid feed which included nitrogen and phosphorus at moderately deficient levels. Otherwise, standard practices used in production nurseries were maintained throughout. Three months after inoculating seed, all seedlings of all four eucalypt species were mycorrhizal and the majority of seedling trays contained Hebeloma and Laccaria sporocarps

The survival and development of inoculant ectomycorrhizal fungi on roots of outplanted Eucalyptus globulus Labill

The survival and development of two inoculant ectomycorrhizal fungi (Hebeloma westraliense Bough. Tom. and Mal. and Setchelliogaster sp. nov.) on roots of outplanted Eucalyptus globulus Labill. was examined at two expasture field sites in the south-west of Western Australia. Site 1 was a gravelly yellow duplex soil, and Site 2 was a yellow sandy earth. Plants were grown in steamed or unsteamed soil, in root bags designed as field containers for young growing trees. Three, 6 and 12 months after outplanting, plants were removed from these bags and assessed for dry weights of shoots and ectomycorrhizal colonization of roots. The inoculant ectomycorrhizal fungi (identified on the basis of the colour and morphology of their mycorrhizas) survived on roots of E. globulus for at least 12 months after outplanting at both field sites. At Site 1, however, colonization of new fine roots by the inoculant fungi was low (less than 20% of fine root length). Inoculation had no effect on the growth of E. globulus at this site. In contrast, at Site 2 the inoculant ectomycorrhizal fungi colonized up to 30–50% of new fine root length during the first 6 months after outplanting. There was a corresponding growth response to ectomycorrhizal inoculation at this site, with a close relationship (r2=0.82**) between plant growth at 12 months and root colonization at 3 months. Plant growth at 12 months was related less closely with root colonization at 6 or 12 months. Root colonization by lsquoresidentrsquo ectomycorrhizal fungi increased with time at both field sites. At Site 2, this increase appeared to be at the expense of colonization by the inoculant fungi, which was reduced to less than 10% of fine root length at 12 months. Steaming the soil had little effect on colonization by the inoculant ectomycorrhizal fungi at either field site, but decreased colonization by the resident ectomycorrhizal fungi

The effect of soil pH on the ability of ectomycorrhizal fungi to increase the growth of Eucalyptus globulus Labill

We examined the effect of two levels of soil pH (5 and 6) on the ability (effectiveness) of ectomycorrhizal fungi to increase the growth of Eucalyptus globulus Labill. at a deficient supply of P. Plants were inoculated with one of six fungal isolates [Laccaria laccata (Scop. ex Fr.) Berk. and Br. (isolates A and B), Pisolithus tinctorius (Pers.) Coker and Couch (isolates A and B), Descolea maculata Bough. and Mal. and Setchelliogaster sp. nov.] and were grown in a P-deficient sand, in pots, in a temperature-controlled glasshouse. Seedlings were harvested 89 days after planting and were assessed for dry matter production, tissue P concentrations, ectomycorrhizal colonization of roots and hyphal development in soil. Uninoculated plants had less than 5% of their fine root length colonized by ectomycorrhizal fungi. In contrast, inoculated plants had 30% or greater of their fine root length ectomycorrhizal. Inoculation increased the uptake of P and growth of plants for all isolates and at both levels of soil pH, although growth responses to inoculation were greater at pH 6, particularly for the two L. laccata isolates. Isolates which colonized roots most extensively increased plant growth to the greatest extent. D. maculata was the most effective fungal isolate at pH 5, and both D. maculata and L. laccata A were most effective at pH 6. The effects of soil pH on plant growth were also related to some extent to the effects of soil pH on colonized root length. Growth responses to inoculation were related less well to hyphal development in soil. The L. laccata isolates formed more hyphae in soil (on a per pot, per m of fine root, and per m of colonized fine root basis) than other fungal isolates, but were not always more effective in increasing plant grown