Tsunoda et al. (2001) recently studied the nature of object representation in monkey inferotemporal cortex using a combination of optical imaging and extracellular recordings. In particular, they examined IT neuron responses to complex natural objects and "simplified" versions thereof. In that study, in 42% of the cases, optical imaging revealed a decrease in the number of activation patches in IT as stimuli were "simplified". However, in 58% of the cases, "simplification" of the stimuli actually led to the appearance of additional activation patches in IT. Based on these results, the authors propose a scheme in which an object is represented by combinations of active and inactive columns coding for individual features. We examine the patterns of activation caused by the same stimuli as used by Tsunoda et al. in our model of object recognition in cortex (Riesenhuber 99). We find that object-tuned units can show a pattern of appearance and disappearance of features identical to the experiment. Thus, the data of Tsunoda et al. appear to be in quantitative agreement with a simple object-based representation in which an object's identity is coded by its similarities to reference objects. Moreover, the agreement of simulations and experiment suggests that the simplification procedure used by Tsunoda (2001) is not necessarily an accurate method to determine neuronal tuning.

A fundamental question in visual neuroscience is how to represent image structure. The most common representational schemes rely on differential operators that compare adjacent image regions. While well-suited to encoding local relationships, such operators have significant drawbacks. Specifically, each filter's span is confounded with the size of its sub-fields, making it difficult to compare small regions across large distances. We find that such long-distance comparisons are more tolerant to common image transformations than purely local ones, suggesting they may provide a useful vocabulary for image encoding. . We introduce the "Dissociated Dipole," or "Sticks" operator, for encoding non-local image relationships. This operator de-couples filter span from sub-field size, enabling parametric movement between edge and region-based representation modes. We report on the perceptual plausibility of the operator, and the computational advantages of non-local encoding. Our results suggest that non-local encoding may be an effective scheme for representing image structure.

Numerous psychophysical experiments have shown an important role for attentional modulations in vision. Behaviorally, allocation of attention can improve performance in object detection and recognition tasks. At the neural level, attention increases firing rates of neurons in visual cortex whose preferred stimulus is currently attended to. However, it is not yet known how these two phenomena are linked, i.e., how the visual system could be "tuned" in a task-dependent fashion to improve task performance. To answer this question, we performed simulations with the HMAX model of object recognition in cortex [45]. We modulated firing rates of model neurons in accordance with experimental results about effects of feature-based attention on single neurons and measured changes in the model's performance in a variety of object recognition tasks. It turned out that recognition performance could only be improved under very limited circumstances and that attentional influences on the process of object recognition per se tend to display a lack of specificity or raise false alarm rates. These observations lead us to postulate a new role for the observed attention-related neural response modulations.

Local descriptors are increasingly used for the task of object recognition because of their perceived robustness with respect to occlusions and to global geometrical deformations. Such a descriptor--based on a set of oriented Gaussian derivative filters-- is used in our recognition system. We report here an evaluation of several techniques for orientation estimation to achieve rotation invariance of the descriptor. We also describe feature selection based on a single training image. Virtual images are generated by rotating and rescaling the image and robust features are selected. The results confirm robust performance in cluttered scenes, in the presence of partial occlusions, and when the object is embedded in different backgrounds.

<p>A series of experiments were designed to study alternative estrus synchronization and resynchronization protocols to facilitate the use of artificial insemination in cattle. </p><p>Studies were conducted to study the effects of estradiol cypionate (ECP) on follicular dynamics, time of ovulation, and pregnancy rate to timed-AI (TAI) in CIDR-based protocols. Although administration of 1 mg ECP did not result in synchronous follicular wave emergence, a dose of 0.5 mg ECP synchronized LH release and ovulation. Administration of ECP 24 h after CIDR removal resulted in acceptable pregnancy rate. However, treatment with ECP at CIDR removal resulted in acceptable pregnancy rate only if follicular wave emergence was synchronized with estradiol-17â (E-17â). </p><p>The efficacy of two estradiol preparations (5 mg of E-17â or estadiol valerate; EV) and reduced doses of EV on CL and ovarian follicular dynamics and superovulatory response were examined. When doses of 5 mg were compared, EV treatment resulted in a more variable interval to follicular wave emergence and a lower superovulatory response than E-17â. However, EV at a dose of 1 or 2 mg was efficacious in synchronizing follicle wave emergence in CIDR-treated cattle.</p><p>Pregnancy rates were compared following TAI in cattle given a new or previously used CIDR and injections of estradiol, with or without progesterone, to synchronize follicular wave emergence. Pregnancy rate following TAI did not differ between cattle treated with a new or once-used CIDR, but pregnancy rate was lower in cattle treated with one or two twice-used CIDR. The addition of an injection of progesterone to the estradiol treatment at CIDR insertion did not enhance pregnancy rate. </p><p>The efficacy of progestins (used CIDR and MGA), and E-17â, ECP, GnRH, or progesterone treatment for resynchronization of estrus in cattle not pregnant following TAI were investigated. Progestin treatment resulted in the majority of nonpregnant heifers detected in estrus over a 4-d interval. Conception rates were higher in heifers resynchronized with a once-used CIDR than with MGA. GnRH at CIDR insertion synchronized follicular wave emergence in cows, but did not increase conception rate in heifers. E-17â at CIDR insertion (1.5 mg) and removal (0.5 mg) resulted in decreased pregnancy rate following TAI. In summary, protocols described in this thesis resulted in acceptable pregnancy rates following TAI and resynchronization of previously inseminated heifers with progestins resulted in variable estrus and pregnancy rates.</p>

<p>A series of experiments were designed to study alternative estrus synchronization and resynchronization protocols to facilitate the use of artificial insemination in cattle. </p><p>Studies were conducted to study the effects of estradiol cypionate (ECP) on follicular dynamics, time of ovulation, and pregnancy rate to timed-AI (TAI) in CIDR-based protocols. Although administration of 1 mg ECP did not result in synchronous follicular wave emergence, a dose of 0.5 mg ECP synchronized LH release and ovulation. Administration of ECP 24 h after CIDR removal resulted in acceptable pregnancy rate. However, treatment with ECP at CIDR removal resulted in acceptable pregnancy rate only if follicular wave emergence was synchronized with estradiol-17â (E-17â). </p><p>The efficacy of two estradiol preparations (5 mg of E-17â or estadiol valerate; EV) and reduced doses of EV on CL and ovarian follicular dynamics and superovulatory response were examined. When doses of 5 mg were compared, EV treatment resulted in a more variable interval to follicular wave emergence and a lower superovulatory response than E-17â. However, EV at a dose of 1 or 2 mg was efficacious in synchronizing follicle wave emergence in CIDR-treated cattle.</p><p>Pregnancy rates were compared following TAI in cattle given a new or previously used CIDR and injections of estradiol, with or without progesterone, to synchronize follicular wave emergence. Pregnancy rate following TAI did not differ between cattle treated with a new or once-used CIDR, but pregnancy rate was lower in cattle treated with one or two twice-used CIDR. The addition of an injection of progesterone to the estradiol treatment at CIDR insertion did not enhance pregnancy rate. </p><p>The efficacy of progestins (used CIDR and MGA), and E-17â, ECP, GnRH, or progesterone treatment for resynchronization of estrus in cattle not pregnant following TAI were investigated. Progestin treatment resulted in the majority of nonpregnant heifers detected in estrus over a 4-d interval. Conception rates were higher in heifers resynchronized with a once-used CIDR than with MGA. GnRH at CIDR insertion synchronized follicular wave emergence in cows, but did not increase conception rate in heifers. E-17â at CIDR insertion (1.5 mg) and removal (0.5 mg) resulted in decreased pregnancy rate following TAI. In summary, protocols described in this thesis resulted in acceptable pregnancy rates following TAI and resynchronization of previously inseminated heifers with progestins resulted in variable estrus and pregnancy rates.</p>

Biofilms are highly organized bacterial structures that are attached to a surface. They are ubiquitous in nature and may be detrimental, causing numerous types of illnesses in living organisms. Biofilms in the human oral cavity are the main cause of dental caries and periodontal diseases and can act as a source for pathogenic organisms to spread within the body and cause various types of systemic diseases. Streptococcus mutans is the primary etiological agent of dental caries, the single most chronic childhood disease. In many cases, quorum sensing (QS) is required for initial formation and subsequent development of biofilms and the signaling molecule autoinducer 2 (AI- 2) has been well studied as an inter-species QS signaling molecule. However, recent reports also suggest that AI-2-mediated signaling is important for intra-species biofilm formation in both Gram-negative and positive bacteria. Therefore, there is significant interest in understanding the role of different QS signals such as AI-2 in oral biofilm formation. Microfluidic devices provide biomimetic environments and offer a simple method for executing multiple stimuli experiments simultaneously, thus, can be an extremely powerful tool in the study of QS in biofilms. In this study, we report conditions that support the development of S. mutans biofilms in microchannel microfluidic devices, and the effects of extracellular addition of chemically synthesized (S)-4,5-dihydroxy-2,3-pentanedione (DPD; precursor of AI-2) on mono-species S. mutans luxS (AI-2 deficient strain) biofilm formation using a gradient generating microfluidic device. S. mutans wild type (WT) and luxS biofilms were developed in nutrient rich medium (25% brain heart infusion medium, BHI + 1% sucrose) for up to 48 h. Maximum biofilm formation with both strains was observed after 24 h, with distinct structure and organization. No changes in S. mutans luxS biofilm growth or structure were observed upon exposure to different concentrations of AI-2 in a gradient generating device (0 to 5 M). These results were also validated by using a standard 96-well plate assay and by verifying the uptake of AI-2 by S. mutans luxS. Our data suggest that extracellular addition of AI-2 does not complement the luxS deletion in S. mutans with respect to biofilm formation.

Autoinducer 2 (AI-2) molecules produced by bacterial cells are thought to be involved in controlling a variety of bacterial cellular processes by coordinated gene and protein expression. Previous work in our laboratory has shown that ground beef contains compounds that can interfere with AI-2-mediated bioluminescence expression in Vibrio. harveyi. The underlying hypothesis of this work was that AI-2 molecules affect the protein expression in Escherichia coli O157:H7 and AI-2 inhibitory molecules negate the influence of AI-2 molecules. The main objectives of this study were to identify, characterize, and isolate the factors responsible for inhibition of AI-2 molecules from ground beef extracts, elucidate the role of LuxS/AI-2 cell signaling system in E. coli O157:H7 protein expression, and determine if inhibitory factors present in ground beef extract can negate the influence of AI-2 molecules on the protein expression. Using a solvent extraction procedure and gas chromatography analysis, AI-2 inhibitory factors present in ground beef extracts were identified as both medium and long chain fatty acids. When identified fatty acids were tested at different concentrations for AI-2 inhibition, AI-2 inhibition ranging from 25% to 90% was observed. Both ground beef extracts and mixture of selected fatty acids also resulted in 2- to 4-fold reduced AI-2 influenced biofilm formation by E. coli K12 cells. Identification of LuxS/AI-2-mediated protein expression in E. coli O157:H7 was conducted using two dimensional gel electrophoresis. Protein expression analysis showed that the LuxS/AI-2 system modulates the expression of proteins involved in different cellular processes such as carbohydrate and amino acid metabolism, stress response, and formation of flagella and motility. When AI-2 inhibitory factors were added along with AI-2 molecules, the expression patterns of three AI-2-influenced proteins (GlmS, SpeE, and NikA) were changed suggesting that AI-2 inhibitors can negate the influence of AI-2 molecules on protein expression of selected proteins. Collectively, these results highlight that proteins associated with different cellular processes in E. coli O157:H7 can be modulated depending on whether cells are in contact with AI-2 molecules in the presence or absence of AI-2 inhibitory factors.

Avian influenza virus (AIV) is a type A virus of the family Orthomyxoviridae and its outbreaks not only cause economic losses in poultry, but also are worldwide threats to human health. The phenotypic changes in host cells induced by pathogens are always accompanied by remarkable changes in gene expression. Therefore understanding the gene expression profile of infected cells at the global level is important to get insights into interactions between hosts and viruses. Different genomic approaches have been utilized in the current study to investigate the host-AIV interactions in chickens. The Ser to Asn mutation on position 631 in the chicken Mx1 protein was reported to result in a positive antiviral function in vitro. With AIV infection, the Mx1 mRNA expression levels in heterozygous birds were significantly up-regulated. Additional mutations on the chicken Mx1 coding region were identified by sequencing. The results showed that most identified mutations were co-segregated with S631N mutation except one insertion in the position of 1544bp in the heterozygous birds. We speculate this insertion might be related to the up-regulation of mRNA expression of heterozygous birds with AIV infection. The miRNAs play critical roles in biological processes and are important effectors in host-pathogen interactions. The miRNA deep sequencing was used to profile miRNAs in AIV infected or non-infected chickens. Differentially expressed miRNAs identified have expanded our knowledge in the functions of these potential immune related chicken miRNAs regulating host response to AIV infection. Both microarray and transcriptome analysis by RNA-Seq were used in the current study to investigate the global gene expression of host response to AIV infection. Through the comprehensive analysis, a list of strong candidate miRNAs such as miR-32 and their host target genes including Mx1 were identified for further elucidating the regulatory mechanism of host-AIV interaction. In summary, we have identified many important candidate host genes and miRNAs which play important roles in the modulation of host response to AIV infection using genomic approaches. Further investigation of underline regulatory mechanisms of these genes, miRNAs or related pathways, followed by functional analysis, could lay solid foundation for understanding cellular and molecular mechanisms of the host-AIV interactions, thereby, pave a way for the development of novel protective strategies against AIV infection in chickens.

Context. Video games are a big entertainment industry. Many video games let players play against or together. Some video games also make it possible for players to play against or together with computer controlled players, called bots. Artificial Intelligence (AI) is used to create bots. Objectives. This thesis aims to implement cooperative behaviors between two bots and determine if the behaviors lead to an increase in win ratio. This means that the bots should be able to cooperate in certain situations, such as when they are attacked or when they are attacking. Methods. The bots win ratio will be tested with a series of quantitative experiments where in each experiment two teaming bots with cooperative behavior will play against two teaming bots without any cooperative behavior. The data will be analyzed with a t-test to determine if the data are statistical significant. Results and Conclusions. The results show that cooperative behavior can increase performance of two teaming Real Time Strategy bots against a non-cooperative team with two bots. However, the performance could either be increased or decreased depending on the situation. In three cases there were an increase in performance and in one the performance was decreased. In three cases there was no difference in performance. This suggests that more research is needed for these cases.