Miracle-dz/UniFAR-FTUs huggingface dataset:
AN ABSTRACT OF THE THESIS OF Ida M. Royer for the degree of Master of Science in Oceanography presented on June 2, 2008. Title: An Investigation into Nitrogen Uptake by Emiliania huxleyi during Continuous Darkness

approved: __________________________________________________________ Fredrick G. Prahl Experiments were conducted with two strains of the coccolithophorid Emiliania huxleyi. Previous experiments with CCMP1742 and 372 at a light intensity of 60 μEin/m-s showed that during five-day periods of continuous darkness, strain 1742 was taking up nitrate from the media while strain 372 was not. The nitrate uptake in strain 1742 was concurrent with an increase in particulate nitrogen. This observation, combined with the fact that carbon-rich alkenones decreased during the same dark period, led to the hypothesis that amino acids were being synthesized during the continuous darkness period in E. huxleyi strain 1742. This thesis presents results from three separate continuous darkness experiments with E. huxleyi strains 1742 and 372, run at a light intensity of 165 μEin/m-s. These experiments were conducted to determine whether 1) amino acids are synthesized in E. huxleyi strain 1742 during continuous darkness, 2) this strain is physiologically unique in this regard, and 3) any amino acid accumulation is compound-specific. Two separate and independent methods for amino acid determination were utilized: gas chromatography paired with a flame ionization detector (GC-FID) and the ninhydrin method. Alkenones, media nutrients, and particulate organic carbon and particulate nitrogen (PN) were also measured. Results showed that no dark-period nutrient uptake or PN accumulation occurred in strain 372, in agreement with previous findings. No accumulation of amino acids was displayed in this strain during the continuous darkness period. CCMP1742 displayed nitrogen uptake, PN accumulation, and amino acid synthesis during the first experiment, but not the second or third experiments. The argument is presented that the increased light intensity of 165 μEin/m-s inhibited the above dark-period nitrogen dynamics. This inhibition may have been overcome in the first experiment due to a previous nutrient stress experienced by the cells used to inoculate the experiment culture. Future experiments should utilize NO3 to track the media nitrogen into cells, and also investigate the effects of light intensity and nutrient stress on dark-period protein production. ©Copyright by Ida M. Royer June 1, 2008 All Rights Reserved An Investigation into Nitrogen Uptake by Emilania huxleyi during Continuous Darkness
Distribution of Bacteria and Archaea in meromictic tropical Lake Kivu (Africa)

Lake Kivu is a meromictic lake in East Africa with enormous amounts of dissolved methane (CH4) and carbon dioxide (CO2) in its deep waters and surprisingly low CH4 in the surface waters. We applied 454 pyrosequencing of 16S rRNA gene fragments to study the bacterial and archaeal community compositions (BCC and ACC, respectively) to provide insight into the ecology of the microbes in Lake Kivu. The vertical distribution of electron donors and acceptors in the chemically stratified water column may be responsible for the stratified distribution of microbial populations, suggesting well-defined functional specialization. The highest microbial richness was detected in the anoxic zone, which hosted high percentages of bacterial sequences related to uncultured and poorly described phyla. This suggests an under-representation of anoxic environments in current databases and the presence of previously undescribed taxa. Microbial diversity is made up of 2 fractions: abundant species (e.g. Galand et al. 2009) and rare species. Abundant species were more stable than rare species over time. The detection of rare candidate divisions (e.g. OP3, WS3, GN02) co-occurring with sulphur-oxidising Epsilonproteobacteria, sulphate-reducing Deltaproteobacteria, hydrogen-oxidising Dehalococcoidetes and methanogens might indicate interactions in the carbon and sulphur cycles in the anoxic waters.
Fetishism and Curiosity

Introduction: Fetishisms.Part 1 What price Hollywood? Americanitis - European intellectuals and Hollywood melodrama social hieroglyphics - reflections on Two films by Douglas Sirk close-ups and commodities. Part 2 Dialectics of division: Pandora's box - topographies of curiosity cosmetics and abjection - Cindy Sherman 1977-87 the hole and the zero - Godard's visions of femininity. Part 3 Dollar-book Freud: from Log Cabin to Xanadu - psychoanalysis and history in "Citizen Kane" The carapace that failed - Osmane Sembene's Xala Netherworlds and the unconscious - Oedipus and Blue Velvet changing objects, preserving time.
Quality improvement through public reporting: The surgeon scorecard – are we there yet?

As national healthcare reform continues to place greater emphasis on providing high value care, measures designed to track clinical performance remain relatively overlooked. To that extent, several organizations have attempted to create objective grading systems to evaluate orthopaedic surgeon quality and performance. While attempting to address these issues, ProPublica’s Surgeon Scorecard has provoked national debate among patient advocates and healthcare providers. The methodology behind the Scorecard was developed at the Harvard School of Public Health with an aim to provide a more robust means of comparing surgical performance and outcomes for patients and healthcare organizations. Currently, the Scorecard assesses eight elective surgical procedures, including total knee and hip arthroplasty, through the use of the Medicare Claims Dataset. The impact of the Scorecard on orthopaedic practice has yet to be established. In this discussion, we analyze the Scorecard from the perspective of various stakeholders to identify its benefits and shortcomings, as well as offer direction for further improvement.
BEST PRACTICE AS ACTUAL AND RELATIVE BENCHMARK TO INEFFICIENT UNITS : MULTISET DEA ANALYSIS

The direction in research of the efficiency of decision-making units in this paper is an efficient→multi-inefficient→multi-efficient unit. So, the general purpose of this paper is twofold: (1) identification of «hidden» inefficient units within a multi-set, among efficient units of the basic set, and (2) achieving the efficiency in such identified inefficient units. This indicates (warns of! ) a negative efficient→inefficient process, so as to provide a timely response and thereby prevent multi-inefficiency. The specific goal is to assess the efficiency of the Serbian railway passenger stations, first within the basic set of the Passenger Transport Section Belgrade, then in the multi-set of the Passenger Transport Sections, and finally in the superset, the Passenger Transport Sector. This is achieved by means of the multi-set DEA (Data Envelopment Analysis) method, which is a system for: (i) relative efficiency assessment, in the first iteration, through the basic set analysis, and (ii) decrease in efficiency of potentially inefficient units, in subsequent iterations, through the multi-set analysis. The result is that the efficient stations Požarevac and Pančevo Bridge are at the initial level, and the (newly) efficient Požarevac, Novi Sad and Inđija at the final level. The best practice station remains the Požarevac Station, which is multi-efficient, and therefore the role model to inefficient stations. The conclusion is drawn that the solution resulting from the multi-set DEA analysis is more realistic, and less relative, because it applies to a wider analysed set of decision-making units, i.e., a larger coverage when considering the issue. This is important for fitting into the new era of growing globalization, and therefore our recommendation is the integral multi-set, as opposed to the individual single set approach.
Decision Diagrams - from A Mathematical Notion to Engineering Applications

The paper presents a historical perspective to the theory of decision dia- grams from the first definitions of the trees in mathematics re lated to the represen- tations of discrete sets to the more recent definitions of dif ferent decision trees and related diagrams that are widely used in few areas of computing. Special attention has been paid to the relationships (similarities and differenc es) between Binary decision diagrams (BDD) and Structurally synthesized binary decision diagrams (SSBDD).
A Proposed Approach for the Determination of the Accuracy of Acoustic Profilers for Field Conditions

In this paper an innovative approach to estimate the accuracy of measuring devices for field measurements is proposed. The approach uses simultaneous measurements taken with identical devices close to each other. This method was successfully applied in the evaluation of the accuracy of a 1200kHz ADCP for cross-sectional measurements of current velocities in tidal channels. Measurements were carried out from measuring devices mounted on vessels moving close to each other on parallel tracks. Measurement campaigns covered tidal ranges of about 3.5 m and depth-averaged current velocities ranging from 0.30 to 1.05 m/s. Point estimates were defined by fitting a logarithmic velocity profile to the measured values. The variability of point measurements is estimated from the simultaneous measurements. The accuracy of the depth-averaged velocity values is obtained by computing several probability intervals on the basis of re-sampling techniques. The standard deviation for point measurements were found to be constant at 0.06 m/s and 0.14 m/s for distances above and below 1 m from the sea bottom, respectively. Results are in reasonable agreement with those reported by VAN RIJN et al. (2002a), despite the different instruments and experimental and environmental settings. The accuracy of an ADCPmeasuring the depth-averaged velocity values was approximately constant at ±0.015 m/s. Resulting accuracy values have been used in the calibration and validation of depth-averaged two-dimensional and three-dimensional flow models.
Molecular analysis of AbOmpA type-1 as immunogenic target for therapeutic interventions against MDR Acinetobacter baumannii infection

Introduction: Acinetobacter baumannii is associated with hospital-acquired infections. Outer membrane protein A of A.baumannii (AbOmpA) is a well-characterized virulence factor which has important roles in pathogenesis of this bacterium. Methods: Based on our PCR-sequencing of ompA gene in the clinical isolates, AbOmpA protein can be categorized into two types, named here type-1 and type-2. We are performed in silico analyses on beta-barrel domain of AbOmpA such as sequence alignments, prediction of 3D modeling and immunoinformatics. Results: High prevalence of AbOmpA type-1 were detected both in 21 multidrug-resistant (MDR) A. baumannii isolates collected from clinical settings (64% of total sequences) and in silico sequences extracted from Uniprot database (49.7% of total sequences). Multiple sequence alignments and phylogenic tree revealed AbOmpA sequences in comparison with OmpA of Enterobacteriaceae family were more heterogenic, especially at extracellular loops amino acid positions and were evolutionary far from this family. Characterization of in silico 3D molecular model of beta-barrel domain of AbOmpA type-1 showed this domain had four large extracellular loops which resemble to beta-barrel domain of Klebsiella pneumonia OmpA (KpOmpA). Immunoinformatics analyses showed the four extracellular loops had high scores as B and T cell antigenic epitopes especially in loop-1 and 3. Geometry analyses revealed extracellular loops effectively protrude to outer space of the cell. Conclusion: Beta-barrel domain of AbOmpA type-1 has all the characteristics of a promising vaccine and could be considered as an excellent target for a vaccine against MDR A. baumannii infection.
The Pennsylvania State University The Graduate School College of Engineering START-UP METHODS FOR THE DEVELOPMENT OF CARBON DIOXIDE FIXING AND BIOFUEL PRODUCING BIOCATHODES IN BIOELECTROCHEMICAL SYSTEMS

A two-step method was developed for enrichment and isolation of electrotrophic bacteria capable of CO2 fixation and biofuel production in a two chamber BES. Anaerobic enrichment cultures were first heterotrophically grown on glucose then used to inoculate BES cathode chambers. After the two weeks heterotrophic start-up, carbon dioxide was provided as sole electron acceptor and carbon source to select for bacteria able to switch to electroautotrophic growth. Biocathodic uptake of electric current increased and was sustained over a period of about two months. Maximum current density consumed was −34 ± 4 mA/m 2 (maximum current consumption: −50 ± 6 μA) at a set potential of −0.4 V. Production of organic acids (acetate: 1.90 ± 0.73 g/L, propionate: 2.09 ± 0.56 g/L, and butyrate: 2.25 ± 0.20 g/L) and volatile fatty acids (butanol: 26.82 ± 0.00 mg/L and ethanol: 16.04 ± 0.01 mg/L) were detected by either HPLC or GC measurements. Production of biohydrogen was detected during and after start-up. These metabolic end products may have resulted from microbial fermentation (electrochemically assisted) during start-up and through microbial electrosynthesis. Bacterial community analysis based on 16S rRNA gene clone library after 19 days of operation, revealed Trichococcus palustris strain DSM 9172 with 99% sequence similarity as the prevailing species in both replicate biocathode communities. Oscillibacter sp. (99% sequence similarity) and Clostridium butyricum (99% sequence similarity) were also dominant groups detected. These results suggest facultative autotrophic microorganisms (ex. acetogens) may have been attributable for consumption of electrons and CO2 electrosynthesis. 16 3.
Resonant-type Micro-probe for Vertical Profiler

We present a characterization method, which is dedicated to the measurement of the inner dimensions of high aspect ratio micro-holes, typically 100μm in diameter and 1mm in depth. Micro-probes with an integrated forcesensitive element are manufactured in silicon technology. Vertical surface profiles can be obtained through the measurement of the deflection at the end of a cantilever beam due to contact force, while scanning over the inner surface of the hole. Two alternative solutions have been developed for force sensing. The first one is based on piezoresistive detection and the other one is based on frequency shift of mechanical resonators. In this paper, the latter sensing method is presented more in detail. The operation principle, modeling and fabrication process are presented.
Using the relationship between eye diameter and body length to detect the effects of long-term starvation on Antarctic krill Euphausia superba

Body shrinkage may be one of the strategies that Antarctic krill use to cope with food scarcity, particularly during winter. Despite their demonstrated ability to shrink, there are only very limited data to determine how commonly shrinkage occurs in the wild. It has been previously shown that laboratory-shrunk krill tend to conserve the size of the eye. This study examined whether the relationship between the eye diameter and body length could be used to detect whether krill had been shrinking. By tracking individuals over time and examining specimens sampled as groups, it was demonstrated that fed and starved krill are distinguishable by the relationship between the eye diameter and body length. The eye diameter of starved krill did not decrease, even when the animals had shrunk in overall body length. The eye diameter of well-fed krill continued to increase as overall length increased. This created a distinction between fed and starved krill, while no separation was detected in terms of the body length to weight relationship. Eye growth of krill re-commenced with re-growth of krill following shrinkage although there was some time lag. It would take approximately 2 moult cycles of shrinkage at modest rates to significantly change the eye diameter to body length relationship between normal and shrunk krill. If krill starve for a prolonged period in the wild, and hence shrink, the eye diameter to body length relationship should be able to indicate this. This would be particularly noticeable at the end of winter.
How Important are Entrepreneurial Social Capital and Knowledge Structure in New Venture Innovation?

Drawing upon the resource-based view and knowledge-based theory, this research investigated the roles of entrepreneurial social capital and knowledge structure in the process of new venture innovation. A questionnaire survey was conducted on a sample of 1000 new ventures in U.S. The analysis results show that an entrepreneur's social capital influences their knowledge structure of new production development, and ultimately impacts new venture innovation. By incorporating the entrepreneur's knowledge structure with their social capital in the context of new venture innovation, this research attempted to develop a theory of action which connects individual differences with social structure.
The variability of acoustical turbulence in the atmospheric boundary layer

Outside sound propagation is affected by small‐scale turbulence in the atmospheric boundary layer through refractive processes. These effects modulate the performance of acoustical sensors, and are at the basis of the atmospheric remote sensing by sodar. Previous studies have documented the impact of a mean turbulence profile or a statistical distribution of turbulence. In this study, we use a high‐resolution atmospheric model called LES to reveal the spatial and temporal variability of the small‐scale turbulence. First, we introduce some standard results on the role of various eddy sizes on acoustical propagation. Second, we discuss the methodology to derive the acoustical refractive index fluctuations from LES data. Third, we analyze the LES prediction in the case of a fair‐weather boundary layer, emphasizing the impact of large‐scale convective organization. Finally, we discuss some challenges in attempting to predict the acoustical turbulence from present‐day weather forecasts.
INHIBITORS FROM MELIA DUBIA AGAINST SDIA MEDIATED QUORUM SENSING OF UROPATHOGENIC E. COLI

Objective: To investigate the potentiality of Meliadubia stem extracts for quorum sensing (SdiA-selective) inhibitory activity against uropathogenic Escherichia coli (UPEC). Methods: The antimicrobial (cell-density) and anti-virulent (swarming motility, protein, protease, hemolysis, hemagglutination, hydrophobicity and biofilm inhibition) properties of the Meliadubia stem extracts were performed. Results: The biofilm, hemolysis, swarming motility were inhibited by 45.71%, 12.97 % and 33.33% respectively when the media were supplemented with 30 mg/ml of ethanolic extract. The GC-MS spectrum of ethanolic extract showed an array of 49 structurally unrelated compounds with the natural ligand, AHL. Their interaction with the quorum regulator, SdiA, was predicted by Glide module of Schrodinger suite and the ligands C 7, C 20, C 28 showed appreciable activity with the following G-Score 11.4, 10.7, 9.9 respectively. In vitro and in silico molecular docking analysis data showed fairly good correlation, suggesting that the ethanolic extract has the potential to attenuate the quorum sensing of UPEC . Further investigation is desired to study the antagonistic effect of the above ligand by in vitro and in vivo strategies. Conclusion : The quorum quenching activity of Meliadubia stem was proven from the overall analysis and its effect towards the inhibition of biofilm and virulence factors were analyzed.
Potential effects of climate change on a marine invasion: The importance of current context

Species invasions threaten marine biodiversity globally. There is a concern that climate change is exacerbating this problem. Here, we examined some of the potential effects of warming water temperatures on the invasion of Western Atlantic habitats by a marine predator, the Indo-Pacific lionfish (Pterois volitans and P. miles). We focussed on two temperature-dependent aspects of lionfish life-history and behaviour: pelagic larval duration, because of its link to dispersal potential, and prey consump- tion rate, because it is an important determinant of the impacts of lionfish on native prey. Using models derived from fundamental metabolic theory, we predict that the length of time spent by lionfish in the plankton in early life should decrease with warming temperatures, with a concomitant reduction in potential dispersal distance. Although the uncertainty around change in dispersal distances is large, predicted reductions are, on average, more than an order of magnitude smaller than the current rate of range expansion of lionfish in the Caribbean. Nevertheless, because shorter pelagic larval duration has the potential to increase local re- tention of larvae, local lionfish management will become increasingly important under projected climate change. Increasing tem- perature is also expected to worsen the current imbalance between rates of prey consumption by lionfish and biomass production by their prey, leading to a heightened decline in native reef fish biomass. However, the magnitude of climate-induced decline is predicted to be minor compared to the effect of current rates of lionfish population increases (and hence overall prey consumption rates) on invaded reefs. Placing the predicted effects of climate change in the current context thus reveals that, at least for the
Assessing farm sustainability with value oriented methods

Agricultural policy makers aim to combine strong economic performance with a sustainable use of natural resources. An important step is to move from trying to define sustainability towards developing concrete tools for measuring and promoting achievements in sustainability. Hence, sustainability assessment is inevitably based on strong simplifications both of the theoretical paradigm and of the characteristics of systems of concern. The most known approaches to assess sustainability performance are burden orientated: they assess the costs or potential harm of resource use. These burden-oriented approaches focus on the level of environmental impacts caused by an economic activity compared to another set of environmental impacts, while value-oriented impact assessment analyses how much value has been created with this set of environmental impacts as compared with the use of these resources by other companies. In this paper, an outline of the possibilities and limitations of value-oriented methods to assess farm sustainability will be discussed.
A Computationally Efficient Parallel Kernel Regression for Image Reconstruction

Image reconstruction is a method by which the underlying images, hidden in blurry and noisy data, can be retrieved. This is used in applications such as computer tomography (CT), magnetic resonance and radio astronomy. In recent times, a non-parametric adaptive regression method called steering kernel regression was proposed and proved to be effective. This method involves computation of local gradient at each pixel thereby making it computationally intensive. The time consuming parts of the steering kernel regression can be optimized by off-loading them onto GPUs and multi-core processors. The parallel implementation of this algorithm improved the performance of image processing applications such as denoising, deblocking and upscaling. It has given an average speedup factor of 6 on multi-core and 21 on a GPU.