Survey-gap analysis in expeditionary research: where do we go from here?

Research expeditions into remote areas to collect biological specimens provide vital information for understanding biodiversity. However, major expeditions to little-known areas are expensive and time consuming, time is short, and well-trained people are difficult to find. In addition, processing the collections and obtaining accurate identifications takes time and money. In order to get the maximum return for the investment, we need to determine the location of the collecting expeditions carefully. In this study we used environmental variables and information on existing collecting localities to help determine the sites of future expeditions. Results from other studies were used to aid in the selection of the environmental variables, including variables relating to temperature, rainfall, lithology and distance between sites. A survey gap analysis tool based on 'ED complementarity' was employed to select the sites that would most likely contribute the most new taxa. The tool does not evaluate how well collected a previously visited site survey site might be; however, collecting effort was estimated based on species accumulation curves. We used the number of collections and/or number of species at each collecting site to eliminate those we deemed poorly collected. Plants, birds, and insects from Guyana were examined using the survey gap analysis tool, and sites for future collecting expeditions were determined. The south-east section of Guyana had virtually no collecting information available. It has been inaccessible for many years for political reasons and as a result, eight of the first ten sites selected were in that area. In order to evaluate the remainder of the country, and because there are no immediate plans by the Government of Guyana to open that area to exploration, that section of the country was not included in the remainder of the study. The range of the ED complementarity values dropped sharply after the first ten sites were selected. For plants, the group for which we had the most records, areas selected included several localities in the Pakaraima Mountains, the border with the south-east, and one site in the north-west. For birds, a moderately collected group, the strongest need was in the north-west followed by the east. Insects had the smallest data set and the largest range of ED complementarity values; the results gave strong emphasis to the southern parts of the country, but most of the locations appeared to be equidistant from one another, most likely because of insufficient data. Results demonstrate that the use of a survey gap analysis tool designed to solve a locational problem using continuous environmental data can help maximize our resources for gathering new information on biodiversity. (c) 2005 The Linnean Society of London.

Surface microbial consortia from Livarot, a French smear-ripened cheese

The surface microflora (902 isolates) of Livarot cheeses from three dairies was investigated during ripening. Yeasts were mainly identified by Fourier transform infrared spectroscopy. Geotrichum candidum was the dominating yeast among 10 species. Bacteria were identified using Biotype 100 strips, dereplicated by repetitive extragenic palindromic PCR (rep-PCR); 156 representative strains were identified by either BOX-PCR or (GTG) 55-PCR, and when appropriate by 16S rDNA sequencing and SDS-PAGE analysis. Gram-positive bacteria accounted for 65% of the isolates and were mainly assigned to the genera Arthrobacter, Brevibacterium, Corynebacterium, and Staphylococcus. New taxa related to the genera Agrococcus and Leucobacter were found. Yeast and Gram-positive bacteria strains deliberately added as smearing agents were sometimes undetected during ripening. Thirty-two percent of the isolates were Gram-negative bacteria, which showed a high level of diversity and mainly included members of the genera Alcaligenes, Hafnia, Proteus, Pseudomonas, and Psychrobacter. Whatever the milk used (pasteurized or unpasteurized), similar levels of biodiversity were observed in the three dairies, all of which had efficient cleaning procedures and good manufacturing practices. It appears that some of the Gramnegative bacteria identified should now be regarded as potentially useful in some cheese technologies. The assessment of their positive versus negative role should be objectively examined.

Macroalgae Decrease Growth and Alter Microbial Community Structure of the Reef-Building Coral, Porites astreoides

With the continued and unprecedented decline of coral reefs worldwide, evaluating the factors that contribute to coral demise is of critical importance. As coral cover declines, macroalgae are becoming more common on tropical reefs. Interactions between these macroalgae and corals may alter the coral microbiome, which is thought to play an important role in colony health and survival. Together, such changes in benthic macroalgae and in the coral microbiome may result in a feedback mechanism that contributes to additional coral cover loss. To determine if macroalgae alter the coral microbiome, we conducted a field-based experiment in which the coral Porites astreoides was placed in competition with five species of macroalgae. Macroalgal contact increased variance in the coral-associated microbial community, and two algal species significantly altered microbial community composition. All macroalgae caused the disappearance of a γ-proteobacterium previously hypothesized to be an important mutualist of P. astreoides. Macroalgal contact also triggered: 1) increases or 2) decreases in microbial taxa already present in corals, 3) establishment of new taxa to the coral microbiome, and 4) vectoring and growth of microbial taxa from the macroalgae to the coral. Furthermore, macroalgal competition decreased coral growth rates by an average of 36.8%. Overall, this study found that competition between corals and certain species of macroalgae leads to an altered coral microbiome, providing a potential mechanism by which macroalgae-coral interactions reduce coral health and lead to coral loss on impacted reefs.

High pressure and low temperature study of ammonia borane and lithium amidoborane

Hydrogen has been considered as a potentially efficient and environmentally friendly alternative energy solution. However, one of the most important scientific and technical challenges that the "hydrogen economy" faces is the development of safe and economically viable on-board hydrogen storage for fuel cell applications, especially to the transportation sector. Ammonia borane (BH3NH 3), a solid state hydrogen storage material, possesses exceptionally high hydrogen content (19.6 wt%).However, a fairly high temperature is required to release all the hydrogen atoms, along with the emission of toxic borazine. Recently research interests are focusing on the improvement of H2 discharge from ammonia borane (AB) including lowering the dehydrogenation temperature and enhancing hydrogen release rate using different techniques. Till now the detailed information about the bonding characteristics of AB is not sufficient to understand details about its phases and structures. ^ Elemental substitution of ammonia borane produces metal amidoboranes. Introduction of metal atoms to the ammonia borane structure may alter the bonding characteristics. Lithium amidoborane is synthesized by ball milling of ammonia borane and lithium hydride. High pressure study of molecular crystal provides unique insight into the intermolecular bonding forces and phase stability. During this dissertation, Raman spectroscopic study of lithium amidoborane has been carried out at high pressure in a diamond anvil cell. It has been identified that there is no dihydrogen bond in the lithium amidoborane structure, whereas dihydrogen bond is the characteristic bond of the parent compound ammonia borane. It has also been identified that the B-H bond becomes weaker, whereas B-N and N-H bonds become stronger than those in the parent compound ammonia borane. At high pressure up to 15 GPa, Raman spectroscopic study indicates two phase transformations of lithium amidoborane, whereas synchrotron X-ray diffraction data indicates only one phase transformation of this material. ^ Pressure and temperature has a significant effect on the structural stability of ammonia borane. This dissertation explored the phase transformation behavior of ammonia borane at high pressure and low temperature using in situ Raman spectroscopy. The P-T phase boundary between the tetragonal (I4mm) and orthorhombic (Pmn21) phases of ammonia borane has been determined. The transition has a positive Clapeyron slope which indicates the transition is of exothermic in nature. Influence of nanoconfinemment on the I4mm to Pmn2 1 phase transition of ammonia borane was also investigated. Mesoporus silica scaffolds SBA-15 with pore size of ~8 nm and MCM-41 with pore size of 2.1-2.7 nm, were used to nanoconfine ammonia borane. During cooling down, the I4mm to Pmn21 phase transition was not observed in MCM-41 nanoconfined ammonia borane, whereas the SBA-15 nanocondfined ammonia borane shows the phase transition at ~195 K. Four new phases of ammonia borane were also identified at high pressure up to 15 GPa and low temperature down to 90 K.^

Estudo da capacidade de remoção de óleo solúvel, em águas produzidas, por bentonitas hidrofobizadas

In this study we evaluated the capacity removal of PAHs in an oily solution between the bentonite hydrofobized with linseed oil and paraffin with natural bentonite. Analyses of natural bentonite and hydrofobized were made by the characterization techniques: (1) Thermogravimetric Analysis (TGA), which aimed to evaluate the thermal events due to mass loss, both associated with the exit of moisture and decomposition of clay as due to hidrofobizante loss agent. (2) Analysis of X-ray diffraction (XRD) in order to determine the mineralogical phases that make up the structure of clay and (3) Spectrophotometry in the infrared region used to characterize the functional groups of both the matrix mineral (bentonite) and the hidrofobizantes agents (linseed oil and paraffin). We used a factorial design 24 with the following factors; hidrofobizante, percent hidrofobizante, adsorption time and volume of the oily solution. Analyzing the factorial design 24 was seen that none of the factors apparently was more important than the others and, as all responses showed significant values in relation to the ability of oil removal was not possible to evaluate a difference in the degree of efficiency the two hidrofobizantes. For the new study compared the efficiency of the modified clay, with each hidrofobizante separately in relation to their natural form. As such, there are four new factorial designs 23 using natural bentonite as a differentiating factor. The factors used were bentonite (with and without hydrophobization), exposure time of the adsorbent material to the oily solution and volume of an oily solution, trying to interpret how these factors could influence the process of purifying water contaminated with PAHs. Was employed as a technique for obtaining responses to fluorescence spectroscopy, as already known from literature that PAHs, for presenting combined chains due to condensation of the aromatic rings fluoresce quite similar when excited in the ultraviolet region and as an auxiliary technique to gas chromatography / mass spectrometry (GC-MS) used for the analysis of PAHs in order to complement the study of fluorescence spectroscopy, since the spectroscopic method only allows you an idea of total number of fluorescent species contained in the oil soluble. The result shows an excellent adsorption of PAHs and other fluorescent species assigned to the main effect of the first factor, hydrophobization for the first planning 23 BNTL 5%, for 93% the sixth stop in the second test (+-+),factorial design 23 BNTL 10%, the fourth test (++-) with 94.5% the third factorial design 23 BNTP 5%, the second test (+--) with 91% and the fourth and final planning 23 BNTP 10%, the last test ( + + +) with 88%. Compared with adsorption of bentonite in its natural form. This work also shows the maximum adsorption of each hidrofobizante

O gênero Geastrum Pers. (Geastraceae, Basidiomycota): ocorrência, chave taxonômica e descrições de novas espécies do Nordeste brasileiro

Geastraceae is a monophyletic family included in the gomphoid-phalloid clade, it is composed only by two genus: Geastrum and Myriostoma. These genus are closely related in their morphology and phylogeny, both showing angiocarpic basidiomata, apical stoma, basidiospores passively released by the bellows mechanism and exoperidium dehiscent in rays, these genus are distinct by the number of stomas and pedicels. Because of dehiscense of exoperidium they are popularly known as “earthstars”. Usually they occur on decomposing leaf-litter and decaying wood. They are, thus, saprophytic, with rare exceptions of ectomycorrhizal species. Geastrum is the most diverse gasteroid genus in Brazil, with an estimated 51 records. However, there are large gaps in the geographic distribution and systematics studies about the Geastrum in this country, especially because of the characteristics found in the Brazilian territory (megadiverse, hotspots and continental size), which makes it a priority area for species inventory. Thus, this work was aimed at realizing inventory of species of Geastrum, which occur in Caatinga and Northeastern Atlantic Rainforest. At least two field expeditions were realized, during about four days on rainy season of 2013 and 2014 in the areas: Reserva Biológica de Guaribas, located in Atlantic Rainforest domain, Paraíba State and Reserva Ecológica Estadual Mata do Pau Ferro, located on “Brejos Paraibanos”, Paraíba State. Furthermore, specimens deposited in the Herbarium of the Universidade Federal do Rio Grande do Norte, which were collected in Parque Nacional Vale do Catimbau, Caatinga of Pernambuco State, were analyzed. The specimens were identified according to analysis of macro and micro morphology based on specific literature. Approximately 400 basidiomata, distributed in 73 exsiccates were analyzed. 21 species were identified, 19 are in specie level, which two are proposed to new species. (Geastrum magnosporum sp. nov. e G. pusillupilosum sp. nov.) and two in genera level (sp. e aff.). We emphasize one new record for Brazil, 12 new records for Paraíba State, four new records for semiarid region in Brazil and six new records to Atlantic Rainforest relicts “Brejo de Altitude”. So, the results improved the knowledge about Geastrum in Paraíba State by 200%, 24 % in Brazilian semiarid region and 55% in Atlantic Rainforest relicts “Brejo de Altitude”, evincing that Northeastern Brazil has high species richness.

Enhancing Quality of Life for People who are Blind or Low Vision Using Computing Technology

Thesis (Ph.D.)--University of Washington, 2016-08

Challenges Facing Long Term Foster Carers: Exploration of the Nature of Psychoanalytic Parent/Carer Support

This research study investigates the role and impact of psychoanalytically-informed short-term parent work with long-term foster carers of looked-after children, in support of the foster placement. The study reflects on the data gathered from four child assessments and five foster families seen by a psychoanalytic child psychotherapist for four sessions each. It draws on psychoanalytic ideas from a range of theoretical traditions, exploring such concepts as trauma, defences, compulsion to repeat, psychological-mindedness, ‘container/contained’ (Bion) and ‘holding environment’ (Winnicott). One distinctive contribution of this research is what it adds to our already existing understanding of the defences (or responses) aroused in the carer when faced with the intense and distressing affect associated with the child’s early trauma; and the impact of this legacy of trauma on the child, on the carer and on the wider Social Services system. Applying Grounded Theory and psychoanalytically-informed clinical case study methodology to the research material, the study breaks down the data analysis into seven stages of coding, from the initial reading of the data to the eventual development of two key hypotheses. One of the predominant themes that emerged from the analysis was the carer’s capacity to remain focused on the child’s emotional needs and how this in turn was linked to the direction of the therapist’s focus. The successive analyses of the data culminated in the hypothesis that the more the therapist focused on the carer and the carer’s emotional states in the course of the parent work, the more the carer was enabled to focus on the child’s emotional needs. As the system of categories emerged according to the themes exemplified in the sessions, a particular focus of analysis became the concept of psychologicalmindedness, considered under several sub-categories: displaying insightful comments; awareness of the child’s bodily states; awareness of the child’s affect; the carer’s ability to recognize the child’s defences; and the carer’s ability to make links between the child’s current difficulties and the child’s past experiences. Through this analysis it became apparent that degree of psychological-mindedness was closely linked to the individual carer’s capacity to metabolize the child’s distressed and distressing communication. This in turn led to a deeper exploration of the situations that were particularly challenging for the carers: i.e., instances when the child was compelled to repeat past traumatic emotional states and as a result was communicating intense distress. This exploration eventually generated the second hypothesis: that in reaction to the child’s distress, the response of each carer could be plotted somewhere along a spectrum, from either distancing themselves from the child’s emotional state to seeking excessive closeness with the child (merging). The next stage of the analysis developed four new categories of carer responses to the distressed child: identification and distancing from the child; identification and merging with the child; the category that describes the carer’s psychologicalmindedness as being ‘impaired’; and ‘good enough’ caring. This then led to an exploration of the carer’s own defences at these most challenging times. This research demonstrates clearly that even within the short space of four sessions of weekly psychoanalytic parent work, it is possible to achieve significant improvement in a carer’s capacity to bear the child’s compulsion to repeat early traumas, and to help the carers become more emotionally available to provide the child with effective psychological parenting at such difficult and challenging times. Key words: looked-after children; long-term foster carers; psychoanalytic short-term parent work; trauma; compulsion to repeat; psychological-mindedness; empathy; defences; psychoanalytically-informed clinical case study research methodology; Grounded Theory research methodology.

Development of error correction techniques for nitrate-N load estimation models

Excess nutrient loads carried by streams and rivers are a great concern for environmental resource managers. In agricultural regions, excess loads are transported downstream to receiving water bodies, potentially causing algal blooms, which could lead to numerous ecological problems. To better understand nutrient load transport, and to develop appropriate water management plans, it is important to have accurate estimates of annual nutrient loads. This study used a Monte Carlo sub-sampling method and error-corrected statistical models to estimate annual nitrate-N loads from two watersheds in central Illinois. The performance of three load estimation methods (the seven-parameter log-linear model, the ratio estimator, and the flow-weighted averaging estimator) applied at one-, two-, four-, six-, and eight-week sampling frequencies were compared. Five error correction techniques; the existing composite method, and four new error correction techniques developed in this study; were applied to each combination of sampling frequency and load estimation method. On average, the most accurate error reduction technique, (proportional rectangular) resulted in 15% and 30% more accurate load estimates when compared to the most accurate uncorrected load estimation method (ratio estimator) for the two watersheds. Using error correction methods, it is possible to design more cost-effective monitoring plans by achieving the same load estimation accuracy with fewer observations. Finally, the optimum combinations of monitoring threshold and sampling frequency that minimizes the number of samples required to achieve specified levels of accuracy in load estimation were determined. For one- to three-weeks sampling frequencies, combined threshold/fixed-interval monitoring approaches produced the best outcomes, while fixed-interval-only approaches produced the most accurate results for four- to eight-weeks sampling frequencies.

Note préliminaire sur quatre espèces nouvelles d'Hapalocarcinidae, avec quelques remarques au sujet du Cryptochirus rugosus Edmonson

This note briefly describes four new species of Hapalocarcinidae: Cryptochirus tri, Troglocarcinus edmonsoni, Troglocarcinus sheni, Troglocarcinus stimpsoni

Estimating Population Trends in American Woodcock (Scolopax Minor) Using Population Reconstruction Models

The American woodcock (Scolopax minor) population index in North America has declined 0.9% a year since 1968 prompting managers to identify priority information and management needs for the species (Sauer et al 2008). Managers identified a need for a population model that better informs on the status of American woodcock populations (Case et al. 2010). Population reconstruction techniques use long-term age-at-harvest data and harvest effort to estimate abundances with error estimates. Four new models were successfully developed using survey data (1999 to 2013). The optimal model estimates sex specific harvest probability for adult females at 0.148 (SE = 0.017) and all other age-sex cohorts at 0.082 (SE = 0.008) for the most current year 2013. The model estimated a yearly survival rate of 0.528 (SE = 0.008). Total abundance ranged from 5,206,000 woodcock in 2007 to 6,075,800 woodcock in 1999. This study represents the first population estimates of woodcock populations.

Exploring coordination-driven self-assembly with autonomous chemical robots

The work presented herein focused on the automation of coordination-driven self assembly, exploring methods that allow syntheses to be followed more closely while forming new ligands, as part of the fundamental study of the digitization of chemical synthesis and discovery. Whilst the control and understanding of the principle of pre-organization and self-sorting under non-equilibrium conditions remains a key goal, a clear gap has been identified in the absence of approaches that can permit fast screening and real-time observation of the reaction process under different conditions. A firm emphasis was thus placed on the realization of an autonomous chemical robot, which can not only monitor and manipulate coordination chemistry in real-time, but can also allow the exploration of a large chemical parameter space defined by the ligand building blocks and the metal to coordinate. The self-assembly of imine ligands with copper and nickel cations has been studied in a multi-step approach using a self-built flow system capable of automatically controlling the liquid-handling and collecting data in real-time using a benchtop MS and NMR spectrometer. This study led to the identification of a transient Cu(I) species in situ which allows for the formation of dimeric and trimeric carbonato bridged Cu(II) assemblies. Furthermore, new Ni(II) complexes and more remarkably also a new binuclear Cu(I) complex, which usually requires long and laborious inert conditions, could be isolated. The study was then expanded to the autonomous optimization of the ligand synthesis by enabling feedback control on the chemical system via benchtop NMR. The synthesis of new polydentate ligands has emerged as a result of the study aiming to enhance the complexity of the chemical system to accelerate the discovery of new complexes. This type of ligand consists of 1-pyridinyl-4-imino-1,2,3-triazole units, which can coordinate with different metal salts. The studies to test for the CuAAC synthesis via microwave lead to the discovery of four new Cu complexes, one of them being a coordination polymer obtained from a solvent dependent crystallization technique. With the goal of easier integration into an automated system, copper tubing has been exploited as the chemical reactor for the synthesis of this ligand, as it efficiently enhances the rate of the triazole formation and consequently promotes the formation of the full ligand in high yields within two hours. Lastly, the digitization of coordination-driven self-assembly has been realized for the first time using an in-house autonomous chemical robot, herein named the ‘Finder’. The chemical parameter space to explore was defined by the selection of six variables, which consist of the ligand precursors necessary to form complex ligands (aldehydes, alkineamines and azides), of the metal salt solutions and of other reaction parameters – duration, temperature and reagent volumes. The platform was assembled using rounded bottom flasks, flow syringe pumps, copper tubing, as an active reactor, and in-line analytics – a pH meter probe, a UV-vis flow cell and a benchtop MS. The control over the system was then obtained with an algorithm capable of autonomously focusing the experiments on the most reactive region (by avoiding areas of low interest) of the chemical parameter space to explore. This study led to interesting observations, such as metal exchange phenomena, and also to the autonomous discovery of self assembled structures in solution and solid state – such as 1-pyridinyl-4-imino-1,2,3-triazole based Fe complexes and two helicates based on the same ligand coordination motif.

Application of an online-biomass sensor in an optical multisensory platform prototype for growth monitoring of biotechnical relevant microorganism and cell lines in single-use shake flasks

In the context of this work we evaluated a multisensory, noninvasive prototype platform for shake flask cultivations by monitoring three basic parameters (pH, pO2 and biomass). The focus lies on the evaluation of the biomass sensor based on backward light scattering. The application spectrum was expanded to four new organisms in addition to E. coli K12 and S. cerevisiae [1]. It could be shown that the sensor is appropriate for a wide range of standard microorganisms, e.g., L. zeae, K. pastoris, A. niger and CHO-K1. The biomass sensor signal could successfully be correlated and calibrated with well-known measurement methods like OD600, cell dry weight (CDW) and cell concentration. Logarithmic and Bleasdale-Nelder derived functions were adequate for data fitting. Measurements at low cell concentrations proved to be critical in terms of a high signal to noise ratio, but the integration of a custom made light shade in the shake flask improved these measurements significantly. This sensor based measurement method has a high potential to initiate a new generation of online bioprocess monitoring. Metabolic studies will particularly benefit from the multisensory data acquisition. The sensor is already used in labscale experiments for shake flask cultivations.