Determination of Biological Species of Ganoderma Boninense (Pat.) and Their Pathogenic Potential on Oil Palm (Elaeis Guineensis Jacq.) Seedlings

A total of 5 Ganoderma isolates from oil palm (Elaeis guineensis Jacq.) and coconut (Cocos nucifera L.) hosts were used in the determination of Ganoderma boninense based on monokaryotic mating compatibilities. Ganoderma specimens collected from both oil palm and coconut hosts fell into 2 types; one was reddish brown with a varnished dorsal surface ('laccate') represented by isolates EGB-01, CN-Ll and CN-L2 and the other a dull brown non-varnished dorsal surface ('non laccate') represented by EG-NL and CN-NL. The isolate WD814 identified as G. boninense by the Forestry and Forest Products Research Institute (FFRRI) at Tsukuba, Japan, was included as an outgroup sample. The present study showed that based on sexual compatibilities of monosporus cultures obtained from a single fruitbody, the mating pattern of G. boninense was heterothallic and tetrapolar. The cultures fell into 4 distinct sex groups from which 4 monokaryon testers were successfully obtained. When tested for intergroup compatibilities, isolates CN-Ll and WD814 were compatible with EGB-Ol, whereas CN-L2, EG-NL and CN-NL were not. Thus. monokaryon compatibility crosses confirmed that although EGB-01, CN-L 1 and WD814 were from oil palm, coconut and Livistona palm hosts respectively, they all belonged to the same biological species. The pathogenic potential of isolates from oil palm and coconut hosts were tested on oil palm seedlings over a 12-month period in glasshouse trials. Only EGB- 01 and CN-Ll isolates were found to be pathogenic on oil palm seedlings, with both showing 100% infection. Totally no infection was established in palms inoculated with the non-G. boninense isolates EG-NL, CN-NL and CN-L2. When infected seedlings were uprooted, the point of entry of G. boninenese was found to be the larger primary root of the plant. A scanning electron micrograph (SEM) of a newly infected root showed that the fungi colonised the epidermis, cortex, endodermis, lacunae, as well as plugged the xylem and phloem tissues. This indicates that fungal colonisation was not restricted to any particular tissue. This study concluded firstly, more than one species of laccate Ganoderma can be found on coconut stumps. Secondly, G. boninense isolated from oil palm and coconut stumps were pathogenic on oil palms. Thirdly, the non G. boninense specimens (EG-NL, CN-NL and CNL2) were not pathogenic to oil palms

Chemical weathering of new pyroclastic deposits from Mt. Merapi (Java), Indonesia.

The Java Island, Indonesia with abundant amount of pyroclastic deposits is located in the very active and dynamic Pacific Ring of Fires. Studying the geochemical weathering indices of these pyroclastic deposits is important to get a clear picture about weathering profiles on deposits resulting from the eruption of Mt. Merapi. Immediately after the first phase of the eruption (March to June 2006), moist and leached pyroclastic deposits were collected. These pyroclastic deposits were found to be composed of volcanic glass, plagioclase feldspar in various proportions, orthopyroxene, clinopyroxene, olivine, amphibole and titanomagnetite. The total elemental composition of the bulk samples (including trace elements and heavy metals) was determined by wet chemical methods and X-ray fluorescence (XRF) analyses. Weathering of the pyroclastic deposits was studied using various weathering indices. The Ruxton ratio, weathering index of Parker, Vought resudual index and chemical index of weathering of moist pyroclastic deposits were lower than those of the leached samples, but the alteration indices (chemical and plagioclase) were slightly higher in the moist compared to the leached pyroclastic deposits

Linear density perturbations in multifield coupled quintessence

18 pages, 8 figures, version to be submitted to PRD, refs. added19 pages, 9 figures, version accepted for publication by PRD, refs. added, extra Consistency Test section added19 pages, 9 figures, version accepted for publication by PRD, refs. added, extra Consistency Test section adde

Impact of a dedicated cancer-associated thrombosis service on clinical outcomes: a mixed-methods evaluation of a clinical improvement exercise

Objectives Cancer-associated thrombosis (CAT) complex condition, which may present to any healthcare professional and at any point during the cancer journey. As such, patients may be managed by a number of specialties, resulting in inconsistent practice and suboptimal care. We describe the development of a dedicated CAT service and its evaluation. Setting Specialist cancer centre, district general hospital and primary care. Participants Patients with CAT and their referring clinicians. Intervention A cross specialty team developed a dedicated CAT service , including clear referral pathways, consistent access to medicines, patient's information and a specialist clinic. Primary and secondary outcome measures The service was evaluated using a mixed-methods evaluation , including audits of clinical practice, clinical outcomes, staff surveys and qualitative interviewing of patients and healthcare professionals. Results Data from 457 consecutive referrals over an 18-month period were evaluated. The CAT service has led to an 88% increase in safe and consistent community prescribing of low-molecular-weight heparin, with improved access to specialist advice and information. Patients reported improved understanding of their condition, enabling better self-management as well as better access to support and information. Referring clinicians reported better care standards for their patients with improved access to expertise and appropriate management. Conclusions A dedicated CAT service improves overall standards of care and is viewed positively by patients and clinicians alike. Further health economic evaluation would enhance the case for establishing this as the standard model of care

Effects of neo-adjuvant chemotherapy for oesophago-gastric cancer on neuro-muscular gastric function

Delayed gastric emptying symptoms are often reported after chemotherapy. This study aims to characterise the effects of chemotherapy on gastric neuro-muscular function. Patients undergoing elective surgery for oesophago-gastric cancer were recruited. Acetylcholinesterase, nNOS, ghrelin receptor and motilin expressions were studied in gastric sections from patients receiving no chemotherapy (n = 3) or oesophageal (n = 2) or gastric (n = 2) chemotherapy. A scoring system quantified staining intensity (0–3; no staining to strong). Stomach sections were separately suspended in tissue baths for electrical field stimulation (EFS) and exposure to erythromycin or carbachol; three patients had no chemotherapy; four completed cisplatin-based chemotherapy within 6 weeks prior to surgery. AChE expression was markedly decreased after chemotherapy (scores 2.3 ± 0.7, 0.5 ± 0.2 and 0 ± 0 in non-chemotherapy, oesophageal- and gastric-chemotherapy groups (p < 0.03 each) respectively. Ghrelin receptor and motilin expression tended to increase (ghrelin: 0.7 ± 0.4 vs 2.0 ± 0.4 and 1.2 ± 0.2 respectively; p = 0.04 and p = 0.2; motilin: 0.7 ± 0.5 vs 2.2 ± 0.5 and 2.0 ± 0.7; p = 0.06 and p = 0.16). Maximal contraction to carbachol was 3.7 ± 0.7 g and 1.9 ± 0.8 g (longitudinal muscle) and 3.4 ± 0.4 g and 1.6 ± 0.6 (circular) in non-chemotherapy and chemotherapy tissues respectively (p < 0.05 each). There were loss of AChE and reduction in contractility to carbachol. The tendency for ghrelin receptors to increase suggests an attempt to upregulate compensating systems. Our study offers a mechanism by which chemotherapy markedly alters neuro-muscular gastric function

Herpes simplex virus ICP27 protein directly interacts with the nuclear pore complex through NUP62, inhibiting host nucleocytoplasmic transport pathways

The herpes simplex virus ICP27 protein is important for the expression and nuclear export of viral mRNAs. Although several binding sites have been mapped along the ICP27 sequence for various RNA and protein partners including the transport receptor TAP of the host cell nuclear transport machinery, several aspects of ICP27 trafficking through the nuclear pore complex remain unclear. We investigated if ICP27 could interact directly with the nuclear pore complex itself, finding that ICP27 directly binds the core nucleoporin Nup62. This is confirmed through co-immunoprecipitation and in vitro binding assays with purified components. Mapping with ICP27 deletion and point mutants further shows that the interaction requires sequences in both the N and C-termini of ICP27. Expression of wildtype ICP27 protein inhibited both classical, importin α/β-dependent and transportin dependent nuclear import. In contrast, an ICP27 point mutant that does not interact with Nup62 had no such inhibitory effect. We suggest that ICP27 association with Nup62 provides additional binding sites at the nuclear pore for ICP27 shuttling thus supporting ICP27-mediated transport. We propose that ICP27 competes with some host cell transport receptors for binding, resulting in inhibition of those host transport pathways

Initial carbon storage in new tephra layers of Mt. Talang in Sumatra as affected by pioneer plants

To date, no global data on carbon sequestration at the initial weathering phase of tephra deposits are available. To study carbon storage in the new volcanic deposit, tephra layers were reconstructed for a period of 46 months. The tephra samples were collected immediately after eruption of Mount (Mt.) Talang on 12 April 2005, over portions of the Solok District in West Sumatra, Indonesia. Pot experiments were filled with and without soil materials and covered with the collected tephra. The pot experiments were conducted in a wired house. The tephra was applied in 0, 2.5 and 5 cm depths to simulate natural tephra deposition. Every day 250 ml of filtered water was added and allowed to percolate. Solid fraction from the tephra layer was collected and analyzed at regular intervals and primary plant succession was observed over a period of 4 years. After 2 months, blue-green algae (cyanobacteria) started to colonize the bare surface tephra layer to form an algae mat. After 16 months, the surface was transformed into a green biofilm of lichen. Vascular plants (grasses and shrubs) started to be established after 2 years. Total carbon (TC) content of the tephra layer was increased significantly from 0.19 to 1.75% or eight times higher after 46 months of incubation. Higher TC storage was found in the 2.5 cm compared to that of the 5.0 cm tephra layer, which was reconstructed above the soil, with values of 1.75 and 0.89%, respectively. On the contrary, lesser amount of TC was accumulated in the single tephra layer (without soil underneath). Between 71 and 90% of TC was considered as total organic carbon (TOC). The labile organic carbon (LOC) content in the 2.5 cm and 5.0 cm of tephra layer was found to be 0.22 and 0.77%, respectively, at the end of incubation. This experiment confirmed the potential of tephra to capture carbon from the atmosphere with the help of nonvascular plants and then by vascular plants and finally sink them in the tephra layer

PatientExploreR: an extensible application for dynamic visualization of patient clinical history from electronic health records in the OMOP common data model.

MotivationElectronic health records (EHRs) are quickly becoming omnipresent in healthcare, but interoperability issues and technical demands limit their use for biomedical and clinical research. Interactive and flexible software that interfaces directly with EHR data structured around a common data model (CDM) could accelerate more EHR-based research by making the data more accessible to researchers who lack computational expertise and/or domain knowledge.ResultsWe present PatientExploreR, an extensible application built on the R/Shiny framework that interfaces with a relational database of EHR data in the Observational Medical Outcomes Partnership CDM format. PatientExploreR produces patient-level interactive and dynamic reports and facilitates visualization of clinical data without any programming required. It allows researchers to easily construct and export patient cohorts from the EHR for analysis with other software. This application could enable easier exploration of patient-level data for physicians and researchers. PatientExploreR can incorporate EHR data from any institution that employs the CDM for users with approved access. The software code is free and open source under the MIT license, enabling institutions to install and users to expand and modify the application for their own purposes.Availability and implementationPatientExploreR can be freely obtained from GitHub: https://github.com/BenGlicksberg/PatientExploreR. We provide instructions for how researchers with approved access to their institutional EHR can use this package. We also release an open sandbox server of synthesized patient data for users without EHR access to explore: http://patientexplorer.ucsf.edu.Supplementary informationSupplementary data are available at Bioinformatics online

Characterizing dual wavelength polarimetry through the eye for monitoring glucose

Diabetes is an insidious disease that afflicts millions of people worldwide and typically requires the person with the disease to monitor their blood sugar level via finger or forearm sticks multiple times daily. Therefore, the ability to noninvasively measure glucose would be a significant advancement for the diabetic community. The use of optically polarized light passed through the anterior chamber of the eye is one proposed noninvasive approach for glucose monitoring. However, the birefringence of the cornea and the difficulty in coupling the light across the eye have been major drawbacks toward realizing this approach. A dual wavelength optical polarimetric approach has been proposed as a means to potentially overcome the birefringence noise but has never been fully characterized. Therefore, in this paper an optical model has been developed along with experiments performed on New Zealand White rabbit eyes for characterizing the light path and corneal birefringence at two different wavelengths as they are passed through the anterior chamber of the eye. The results show that, without index matching, it is possible to couple the light in and out of the eye but only across a very limited range otherwise the light does not come back out of the eye. It was also shown that there is potential to use a dual wavelength approach to accommodate the birefringence noise of the cornea in the presence of eye motion. These results will be used to help guide the final design of the polarimetric system for use in noninvasive monitoring of glucose in vivo