Contributions to unsupervised and supervised learning with applications in digital image processing

311 p. : il.

Reconstructing an 83-Year Time Series of Daily Sea Surface Temperature at Pacific Grove, California

Daily sea surface temperatures have been acquired at the Hopkins Marine Station in Pacific Grove, California since January 20, 1919.This time series is one of the longest oceanographic records along the U.S. west coast. Because of its length it is well-suited for studying climate-related and oceanic variability on interannual, decadal, and interdecadal time scales. The record, however, is not homogeneous, has numerous gaps, contains possible outliers, and the observations were not always collected at the same time each day. Because of these problems we have undertaken the task of reconstructing this long and unique series. We describe the steps that were taken and the methods that were used in this reconstruction. Although the methods employed are basic, we believe that they are consistent with the quality of the data. The reconstructed record has values at every time point, original, or estimated, and has been adjusted for time-of-day variations where this information was available. Possible outliers have also been examined and replaced where their credibility could not be established. Many of the studies that have employed the Hopkins time series have not discussed the issue of data quality and how these problems were addressed. Because of growing interest in this record, it is important that a single, well-documented version be adopted, so that the results of future analyses can be directly compared. Although additional work may be done to further improve the quality of this record, it is now available via the internet. [PDF contains 48 pages]

Response of multiple simultaneously recorded macaque area LIP neurons in a memory saccade task

Cells in the lateral intraparietal cortex (LIP) of rhesus macaques respond vigorously and in spatially-tuned fashion to briefly memorized visual stimuli. Responses to stimulus presentation, memory maintenance, and task completion are seen, in varying combination from neuron to neuron. To help elucidate this functional segmentation a new system for simultaneous recording from multiple neighboring neurons was developed. The two parts of this dissertation discuss the technical achievements and scientific discoveries, respectively.

Technology. Simultanous recordings from multiple neighboring neurons were made with four-wire bundle electrodes, or tetrodes, which were adapted to the awake behaving primate preparation. Signals from these electrodes were partitionable into a background process with a 1/f-like spectrum and foreground spiking activity spanning 300-6000 Hz. Continuous voltage recordings were sorted into spike trains using a state-of-the-art clustering algorithm, producing a mean of 3 cells per site. The algorithm classified 96% of spikes correctly when tetrode recordings were confirmed with simultaneous intracellular signals. Recording locations were verified with a new technique that creates electrolytic lesions visible in magnetic resonance imaging, eliminating the need for histological processing. In anticipation of future multi-tetrode work, the chronic chamber microdrive, a device for long-term tetrode delivery, was developed.

Science. Simultaneously recorded neighboring LIP neurons were found to have similar preferred targets in the memory saccade paradigm, but dissimilar peristimulus time histograms, PSTH). A majority of neighboring cell pairs had a difference in preferred directions of under 45° while the trial time of maximal response showed a broader distribution, suggesting homogeneity of tuning with het erogeneity of function. A continuum of response characteristics was present, rather than a set of specific response types; however, a mapping experiment suggests this may be because a given cell's PSTH changes shape as well as amplitude through the response field. Spike train autocovariance was tuned over target and changed through trial epoch, suggesting different mechanisms during memory versus background periods. Mean frequency-domain spike-to-spike coherence was concentrated below 50 Hz with a significant maximum of 0.08; mean time-domain coherence had a narrow peak in the range ±10 ms with a significant maximum of 0.03. Time-domain coherence was found to be untuned for short lags (10 ms), but significantly tuned at larger lags (50 ms).

Characterization of the neural mechanisms supporting the implementation of cognitive control in human decision making

Humans are particularly adept at modifying their behavior in accordance with changing environmental demands. Through various mechanisms of cognitive control, individuals are able to tailor actions to fit complex short- and long-term goals. The research described in this thesis uses functional magnetic resonance imaging to characterize the neural correlates of cognitive control at two levels of complexity: response inhibition and self-control in intertemporal choice. First, we examined changes in neural response associated with increased experience and skill in response inhibition; successful response inhibition was associated with decreased neural response over time in the right ventrolateral prefrontal cortex, a region widely implicated in cognitive control, providing evidence for increased neural efficiency with learned automaticity. We also examined a more abstract form of cognitive control using intertemporal choice. In two experiments, we identified putative neural substrates for individual differences in temporal discounting, or the tendency to prefer immediate to delayed rewards. Using dynamic causal models, we characterized the neural circuit between ventromedial prefrontal cortex, an area involved in valuation, and dorsolateral prefrontal cortex, a region implicated in self-control in intertemporal and dietary choice, and found that connectivity from dorsolateral prefrontal cortex to ventromedial prefrontal cortex increases at the time of choice, particularly when delayed rewards are chosen. Moreover, estimates of the strength of connectivity predicted out-of-sample individual rates of temporal discounting, suggesting a neurocomputational mechanism for variation in the ability to delay gratification. Next, we interrogated the hypothesis that individual differences in temporal discounting are in part explained by the ability to imagine future reward outcomes. Using a novel paradigm, we imaged neural response during the imagining of primary rewards, and identified negative correlations between activity in regions associated the processing of both real and imagined rewards (lateral orbitofrontal cortex and ventromedial prefrontal cortex, respectively) and the individual temporal discounting parameters estimated in the previous experiment. These data suggest that individuals who are better able to represent reward outcomes neurally are less susceptible to temporal discounting. Together, these findings provide further insight into role of the prefrontal cortex in implementing cognitive control, and propose neurobiological substrates for individual variation.

Proteolytic processing of the nonstructural proteins of dengue 2 virus

The genomes of many positive stranded RNA viruses and of all retroviruses are translated as large polyproteins which are proteolytically processed by cellular and viral proteases. Viral proteases are structurally related to two families of cellular proteases, the pepsin-like and trypsin-like proteases. This thesis describes the proteolytic processing of several nonstructural proteins of dengue 2 virus, a representative member of the Flaviviridae, and describes methods for transcribing full-length genomic RNA of dengue 2 virus. Chapter 1 describes the in vitro processing of the nonstructural proteins NS2A, NS2B and NS3. Chapter 2 describes a system that allows identification of residues within the protease that are directly or indirectly involved with substrate recognition. Chapter 3 describes methods to produce genome length dengue 2 RNA from cDNA templates.

The nonstructural protein NS3 is structurally related to viral trypsinlike proteases from the alpha-, picorna-, poty-, and pestiviruses. The hypothesis that the flavivirus nonstructural protein NS3 is a viral proteinase that generates the termini of several nonstructural proteins was tested using an efficient in vitro expression system and antisera specific for the nonstructural proteins NS2B and NS3. A series of cDNA constructs was transcribed using T7 RNA polymerase and the RNA translated in reticulocyte lysates. Proteolytic processing occurred in vitro to generate NS2B and NS3. The amino termini of NS2B and NS3 produced in vitro were found to be the same as the termini of NS2B and NS3 isolated from infected cells. Deletion analysis of cDNA constructs localized the protease domain necessary and sufficient for correct cleavage to the first 184 amino acids of NS3. Kinetic analysis of processing events in vitro and experiments to examine the sensitivity of processing to dilution suggested that an intramolecular cleavage between NS2A and NS2B preceded an intramolecular cleavage between NS2B and NS3. The data from these expression experiments confirm that NS3 is the viral proteinase responsible for cleavage events generating the amino termini of NS2B and NS3 and presumably for cleavages generating the termini of NS4A and NS5 as well.

Biochemical and genetic experiments using viral proteinases have defined the sequence requirements for cleavage site recognition, but have not identified residues within proteinases that interact with substrates. A biochemical assay was developed that could identify residues which were important for substrate recognition. Chimeric proteases between yellow fever and dengue 2 were constructed that allowed mapping of regions involved in substrate recognition, and site directed mutagenesis was used to modulate processing efficiency.

Expression in vitro revealed that the dengue protease domain efficiently processes the yellow fever polyprotein between NS2A and NS2B and between NS2B and NS3, but that the reciprocal construct is inactive. The dengue protease processes yellow fever cleavage sites more efficiently than dengue cleavage sites, suggesting that suboptimal cleavage efficiency may be used to increase levels of processing intermediates in vivo. By mutagenizing the putative substrate binding pocket it was possible to change the substrate specificity of the yellow fever protease; changing a minimum of three amino acids in the yellow fever protease enabled it to recognize dengue cleavage sites. This system allows identification of residues which are directly or indirectly involved with enzyme-substrate interaction, does not require a crystal structure, and can define the substrate preferences of individual members of a viral proteinase family.

Full-length cDNA clones, from which infectious RNA can be transcribed, have been developed for a number of positive strand RNA viruses, including the flavivirus type virus, yellow fever. The technology necessary to transcribe genomic RNA of dengue 2 virus was developed in order to better understand the molecular biology of the dengue subgroup. A 5' structural region clone was engineered to transcribe authentic dengue RNA that contains an additional 1 or 2 residues at the 5' end. A 3' nonstructural region clone was engineered to allow production of run off transcripts, and to allow directional ligation with the 5' structural region clone. In vitro ligation and transcription produces full-length genomic RNA which is noninfectious when transfected into mammalian tissue culture cells. Alternative methods for constructing cDNA clones and recovering live dengue virus are discussed.

Generation time and utilization of energy by aquatic bacteria. [Translation from: Trudy Instituta Biologii Vnutrennykh Vodnany 11(14), 198-202, 1966.]

Recent research has shown that the biomass of bacteria in lakes and other water-bodies can attain significant values. The huge production of bacteria is brought about by their great rate of reproduction. In a series of cases their biomass exceeds the biomass of phytoplankton. Therefore in a study of the biological productivity of water bodies it is necessary to calculate the biomass and production not only of the phyto- and zooplankton, but also of bacteria.The authors uses different methods and formulae to to compare the time of one generation of the bacteria.

Readout of a real-time hologram in bacteriorhodopsin film with high diffraction efficiency and intensity

A scheme for the readout of a hologram recorded in bacteriorhodopsin film with high diffraction efficiency and intensity is suggested and demonstrated. Two weak coherent continuous beams function as the recording beams, and a strong light pulse is used to read the real-time hologram. The width of the readout light pulse is modulated to be short compared with the erase time of the reading beam; the time space between two adjacent pulses is ensured to be longer than the time the beams take to recover the hologram, and high diffraction efficiency and intensity (similar to 11 mW/cm(2)) can be obtained. (C) 1996 Optical Society of America.

Fish lost at sea: the effect of soak time on pelagic longline catches

Our analyses of observer records reveal that abundance estimates are strongly influenced by the timing of longline operations in relation to dawn and dusk and soak time— the amount of time that baited hooks are available in the water. Catch data will underestimate the total mortality of several species because hooked animals are “lost at sea.” They fall off, are removed, or escape from the hook before the longline is retrieved. For example, longline segments with soak times of 20 hours were retrieved with fewer skipjack tuna and seabirds than segments with soak times of 5 hours. The mortality of some seabird species is up to 45% higher than previously estimated. The effects of soak time and timing vary considerably between species. Soak time and exposure to dusk periods have strong positive effects on the catch rates of many species. In particular, the catch rates of most shark and billfish species increase with soak time. At the end of longline retrieval, for example, expected catch rates for broadbill swordfish are four times those at the beginning of retrieval. Survival of the animal while it is hooked on the longline appears to be an important factor determining whether it is eventually brought on board the vessel. Catch rates of species that survive being hooked (e.g. blue shark) increase with soak time. In contrast, skipjack tuna and seabirds are usually dead at the time of retrieval. Their catch rates decline with time, perhaps because scavengers can easily remove hooked animals that are dead. The results of our study have important implications for fishery management and assessments that rely on longline catch data. A reduction in soak time since longlining commenced in the 1950s has introduced a systematic bias in estimates of mortality levels and abundance. The abundance of species like seabirds has been over-estimated in recent years. Simple modifications to procedures for data collection, such as recording the number of hooks retrieved without baits, would greatly improve mortality estimates.

Age-validation of a leopard shark (Triakis semifasciata) recaptured after 20 years

On 10 July 1999, vertebrae bearing an oxytetracycline (OTC) time mark were retrieved from a tagged leopard shark (Triakis semifasciata) recaptured in San Francisco Bay, CA, after being at liberty for almost 20 years. An additional long-term leopard shark tag return was received in June 2001, for which growth information (but not vertebrae) was obtained. The first recapture is significant in that it represents the longest at-liberty period for an age-validated (OTC-injected) shark, extends and completes age validation for this species, spanning all age classes up to its estimated average maximum age, and provides an example of the persistence of the OTC time mark in an elasmobranch at liberty for almost 20 years. The recaptured leopard shark made in 2001 also provides valuable information on long-term growth from time of release to time of recapture. Findings are documented here so that other researchers are aware that validation is complete for this species, to present pertinent evidence of considerable interannual variability in growth in this species, and to report observations on processing difficulties relating to the ephemeral nature of the 20-yr-old OTC mark.

A study on the quality of prawns during processing in prawn-freezing factories

A study on the occurrence of defective pieces of prawns at three different stages of processing of headless shell on and peeled and deveined varieties was undertaken, each in one freezing factory. The average percentages of the defective prawns together with the standard deviation observed over a period of one year at the three stages are mentioned. Correlation is indicated between the occurrence of the defective pieces at the pre-freezing stage and those of earlier stages.

Studies on technological problems associated with the processing of cooked frozen prawns. Pt. 2. Hygienic conditions in relation to bacteriological characteristics

The importance of sanitary practices in the processing of precooked frozen shrimps has been discussed. Several typical examples have been shown to point out the different sources of contamination of the product and the extent to which each of the factors by itself or in combination affect the bacterial quality of the final product. A scheme of processing has also been suggested for controlling the microbial quality.

Influence of size, station time and satiation amount on prey handling time in Anabas testudineus (Bloch)

Satiation amount, satiation time and handling time of Anabas testudineus (Bloch), an air breathing predatory fish was experimentally estimated using guppy (Lebistes reticulatus) as prey. Weight of the fish and satiation time influenced prey handling time. As satiation time is related to the level of hunger, level of hunger was found to influence handling time of prey.

The processing of fish and other marine resources

The preservation of freshness in fish (commonly referred to as fish handling) and the conversion of fresh fish into other products can both be considered as methods of processing. In commercial practice, however, the term "processing" is confined to the conversion of fresh fish into other products.

Millisecond processing beyond chip technology: From electronics to photonics

There is a clear and increasing interest in short time annealing processing far below one second, i.e. the lower limit of Rapid Thermal Processing (RTP) called spike annealing. This was driven by the need of suppressing the so-called Transient Enhanced Diffusion in advanced boronimplanted shallow pn-junctions in silicon technology. Meanwhile the interest in flash lamp annealing (FLA) in the millisecond range spread out into other fields related to silicon technology and beyond. This paper reports on recent experiments regarding shallow junction engineering in germanium, annealing of ITO layers on glass and plastic foil to form an conductive layer as well as investigations which we did during the last years in the field of wide band gap semiconductor materials (SiC, ZnO). A more common feature evolving from our work was related to the modeling of wafer stress during millisecond thermal processing with flash lamps. Finally recent achievements in the field of silicon-based light emission basing on Metal-Oxide-Semiconductor Light Emitting Devices will be reported. © 2007 IEEE.

Effect of contact time on the acute toxicity of mercury to scale carp

The behaviour of metals in aquatic ecosystems is dependent on various environmental factors. Experiments were conducted in five different contact times (0.5, 2, 12, 24 and 48h) between soil sediment and mercury on Cyprinus carpio var communis. It was observed that contact time with soil sediment had significant effect in reducing the toxicity of mercury. Higher the time of contact, greater the effect. Medium hard water (150 mg/L CaC0 sub(3) of total hardness) had the highest effect as compared to other water in reducing the toxicity of mercury when combined with underlying soil sediment. With the increase in contact time, complexation and adsorption of inorganic mercury ions with the dissolved and particulate phases of water and soil sediment were increased; thereby bioaccumulation of mercury ions by scale carp was more. Applicability of the result of this experiment in natural ecosystems was also suggested.