Analysis of systems of constructed facilities,

Massachusetts Institute of Technology, Dept. of Civil Engineering. Thesis. 1971. Ph.D.Vita.Includes bibliographical references.by Andrew C. Lemer.Ph.D

Phylogeny of Amphidinium (Dinophyceae) from Guam and Okinawa, with descriptions of A. pagoense sp. nov. and A. uduigamense sp. nov.

Marine benthic dinoflagellates within the genus Amphidinium were isolated from Guam and Okinawa. Isolated strains were identified to species-level using phylogenetic analyses of 28S rRNA and ITS-5.8S rRNA genes as well as microscopy. Of the six isolated strains, two were new species: A. pagoense sp. nov. and A. uduigamense sp. nov. Other isolates included strains of A. massartii and A. operculatum from Guam, and two strains of A. operculatum from Okinawa. Both new species were described using light and electron microscopy (SEM and TEM). The combination of characteristics that make A. pagoense sp. nov. unique includes a pair of centrally-located pyrenoids, variable cell shape, absence of scales and a long, curved ventral ridge. For A. uduigamense sp. nov., a combination of several morphological features distinguishes it from other species. These include a constriction near the anterior of the hypocone, two centrally located pyrenoids, a longitudinal flagellum inserted in the posterior one-third of the cell, cell size, cell division in the motile stage and the absence of scales. Toxicity was confirmed in these two novel species by testing methanol extracts in an Artemia bioassay. Previously unrecorded ITS rRNA gene sequences from A. operculatum were also sequenced from both locations. Species identified and newly described in this study expand the taxonomic knowledge of Amphidinium in the Pacific.journal articl

Housekeeping Mutualisms: Do More Symbionts Facilitate Host Performance?

Mutualisms often involve one host supporting multiple symbionts, whose identity, density and intraguild interactions can influence the nature of the mutualism and performance of the host. However, the implications of multiple co-occurring symbionts on services to a host have rarely been quantified. In this study, we quantified effects of decapod symbionts on removal of sediment from their coral host. Our field survey showed that all common symbionts typically occur as pairs and never at greater abundances. Two species, the crab Trapezia serenei and the shrimp Alpheus lottini, were most common and co-occurred more often than expected by chance. We conducted a mesocosm experiment to test for effects of decapod identity and density on sediment removal. Alone, corals removed 10% of sediment, but removal increased to 30% and 48% with the presence of two and four symbionts, respectively. Per-capita effects of symbionts were independent of density and identity. Our results suggest that symbiont density is restricted by intraspecific competition. Thus, increased sediment removal from a coral host can only be achieved by increasing the number of species of symbionts on that coral, even though these species are functionally equivalent. Symbiont diversity plays a key role, not through added functionality but by overcoming density limitation likely imposed by intraspecific mating systems

Agrammatic but numerate

A central question in cognitive neuroscience concerns the extent to which language enables other higher cognitive functions. In the case of mathematics, the resources of the language faculty, both lexical and syntactic, have been claimed to be important for exact calculation, and some functional brain imaging studies have shown that calculation is associated with activation of a network of left-hemisphere language regions, such as the angular gyrus and the banks of the intraparietal sulcus. We investigate the integrity of mathematical calculations in three men with large left-hemisphere perisylvian lesions. Despite severe grammatical impairment and some difficulty in processing phonological and orthographic number words, all basic computational procedures were intact across patients. All three patients solved mathematical problems involving recursiveness and structure-dependent operations (for example, in generating solutions to bracket equations). To our knowledge, these results demonstrate for the first time the remarkable independence of mathematical calculations from language grammar in the mature cognitive system

The Children and Young People's Health Partnership Evelina London Model of Care: process evaluation protocol

Introduction Children and young people (CYP) in the UK have poor health outcomes, and there is increasing emergency department and hospital outpatient use. To address these problems in Lambeth and Southwark (two boroughs of London, UK), the local Clinical Commissioning Groups, Local Authorities and Healthcare Providers formed The Children and Young People’s Health Partnership (CYPHP), a clinical-academic programme for improving child health. The Partnership has developed the CYPHP Evelina London model, an integrated healthcare model that aims to deliver effective, coordinated care in primary and community settings and promote better self-management to over approximately 90 000 CYP in Lambeth and Southwark. This protocol is for the process evaluation of this model of care. Methods and analysis Alongside an impact evaluation, an in-depth, mixed-methods process evaluation will be used to understand the barriers and facilitators to implementing the model of care. The data collected mapped onto a logic model of how CYPHP is expected to improve child health outcomes. Data collection and analysis include qualitative interviews and focus groups with stakeholders, a policy review and a quantitative analysis of routine clinical and administrative data and questionnaire data. Information relating to the context of the trial that may affect implementation and/or outcomes of the CYPHP model of care will be documented. Ethics and dissemination The study has been reviewed by NHS REC Cornwall & Plymouth (17/SW/0275). The findings of this process evaluation will guide the scaling up and implementation of the CYPHP Evelina London Model of Care across the UK. Findings will be disseminated through publications and conferences, and implementation manuals and guidance for others working to improve child health through strengthening health systems. Trial registration number NCT03461848

METANNOGEN: compiling features of biochemical reactions needed for the reconstruction of metabolic networks

BACKGROUND: One central goal of computational systems biology is the mathematical modelling of complex metabolic reaction networks. The first and most time-consuming step in the development of such models consists in the stoichiometric reconstruction of the network, i. e. compilation of all metabolites, reactions and transport processes relevant to the considered network and their assignment to the various cellular compartments. Therefore an information system is required to collect and manage data from different databases and scientific literature in order to generate a metabolic network of biochemical reactions that can be subjected to further computational analyses. RESULTS: The computer program METANNOGEN facilitates the reconstruction of metabolic networks. It uses the well-known database of biochemical reactions KEGG of biochemical reactions as primary information source from which biochemical reactions relevant to the considered network can be selected, edited and stored in a separate, user-defined database. Reactions not contained in KEGG can be entered manually into the system. To aid the decision whether or not a reaction selected from KEGG belongs to the considered network METANNOGEN contains information of SWISSPROT and ENSEMBL and provides Web links to a number of important information sources like METACYC, BRENDA, NIST, and REACTOME. If a reaction is reported to occur in more than one cellular compartment, a corresponding number of reactions is generated each referring to one specific compartment. Transport processes of metabolites are entered like chemical reactions where reactants and products have different compartment attributes. The list of compartmentalized biochemical reactions and membrane transport processes compiled by means of METANNOGEN can be exported as an SBML file for further computational analysis. METANNOGEN is highly customizable with respect to the content of the SBML output file, additional data-fields, the graphical input form, highlighting of project specific search terms and dynamically generated Web-links. CONCLUSION: METANNOGEN is a flexible tool to manage information for the design of metabolic networks. The program requires Java Runtime Environment 1.4 or higher and about 100 MB of free RAM and about 200 MB of free HD space. It does not require installation and can be directly Java-webstarted from

Knowledge-based energy functions for computational studies of proteins

This chapter discusses theoretical framework and methods for developing knowledge-based potential functions essential for protein structure prediction, protein-protein interaction, and protein sequence design. We discuss in some details about the Miyazawa-Jernigan contact statistical potential, distance-dependent statistical potentials, as well as geometric statistical potentials. We also describe a geometric model for developing both linear and non-linear potential functions by optimization. Applications of knowledge-based potential functions in protein-decoy discrimination, in protein-protein interactions, and in protein design are then described. Several issues of knowledge-based potential functions are finally discussed.Comment: 57 pages, 6 figures. To be published in a book by Springe

CYGD: the Comprehensive Yeast Genome Database

The Comprehensive Yeast Genome Database (CYGD) compiles a comprehensive data resource for information on the cellular functions of the yeast Saccharomyces cerevisiae and related species, chosen as the best understood model organism for eukaryotes. The database serves as a common resource generated by a European consortium, going beyond the provision of sequence information and functional annotations on individual genes and proteins. In addition, it provides information on the physical and functional interactions among proteins as well as other genetic elements. These cellular networks include metabolic and regulatory pathways, signal transduction and transport processes as well as co-regulated gene clusters. As more yeast genomes are published, their annotation becomes greatly facilitated using S.cerevisiae as a reference. CYGD provides a way of exploring related genomes with the aid of the S.cerevisiae genome as a backbone and SIMAP, the Similarity Matrix of Proteins. The comprehensive resource is available under http://mips.gsf.de/genre/proj/yeast/

The impact of out-of-hospital models of care on paediatric emergency department presentations

OBJECTIVE: To estimate the potential impact of enhanced primary care and new out-of-hospital models (OOHMs) on emergency department (ED) presentations by children and young people (CYP). DESIGN: Observational study. PATIENTS AND SETTING: Data collected prospectively on 3020 CYP 0–17.9 years from 6 London EDs during 14 days by 25 supernumerary clinicians. CYP with transient acute illness, exacerbation of long-term condition (LTC), complex LTC/disability and injury/trauma were considered manageable within OOHM. OOHMs assessed included nurse-led services, multispecialty community provider (MCP), primary and acute care system (PACS) plus current and enhanced primary care. MEASURES: Diagnosis, severity; record of investigations, management and outcome that occurred; objective assessment of clinical need and potential alternative management options/destinations. RESULTS: Of the patients 95.6% had diagnoses appropriate for OOHM. Most presentations required assessment by a clinician with skills in assessing illness (39.6%) or injuries (30.9%). One thousand two hundred and ninety-one (42.75%) required no investigations and 1007 (33.3%) were provided only with reassurance. Of the presentations 42.2% were judged to have been totally avoidable if the family had had better health education. Of the patients 26.1% were judged appropriate for current primary care (community pharmacy or general practice) with 31.5% appropriate for the combination of enhanced general practice and community pharmacy. Proportions suitable for new models were 14.1% for the nurse-led acute illness team, MCP 25.7%, GP federation CYP service 44.6%, comprehensive walk-in centre for CYP 64.3% and 75.5% for a PACS. CONCLUSIONS: High proportions of ED presentations by CYP could potentially be managed in new OOHMs or by enhancement of existing primary care