Channel catfish (Ictalurus punctatus) are raised for aquaculture in ponds characterized by dramatic swings in dissolved oxygen concentration. If morning dissolved oxygen concentration falls below approximately 3.0 mg/L catfish consume less feed, leading to a reduction in growth and production. Although the effects of low oxygen on channel catfish appetite have been described, the underlying mechanisms responsible for those effects are unknown. Increased production of the neuropeptides corticotropin-releasing factor (CRF) and urotensin I (UI) are implicated in other fishes as neuropeptides that reduce appetite once an environmental stressor is detected. This project characterizes the hematological responses and transcriptional response of the hypothalamus to acute, chronic, and cyclical (repeating periods of hypoxia and normoxia) hypoxia. During acute (12 hours) hypoxia, venous PO2 decreased within 6 hours, coupled with an increase in hematocrit and decreased blood osmolality. These changes reversed within 12 hours after returning to normoxia but were not coupled with a change in transcription of the genes for CRF and UI. If this pattern of hypoxia and normoxia is repeated cyclically for 5 days, the same physiological responses repeat continually. During chronic hypoxia up to 5 days in duration, channel catfish have a similar hematological response, but did not recover to normoxic control values over the duration of the challenge. Likewise, no significant change in gene expression of CRF or UI were detected during chronic hypoxia. The hypothalamic transcriptome was analyzed during a 12-hour exposure to hypoxia followed by a 12-hour normoxic recovery. Across all time points, 190 genes were differentially expressed, with the greatest numbers occurring during periods of hypoxia. Differentially expressed genes were grouped into Gene Ontology biological processes and were most overrepresented by the term “response to hypoxia,†which included genes involved with angiogenesis, red blood cell production, and negative feedback to hypoxia-inducible factor proteins. Although this study did not find a change in hypothalamic transcription of CRF and UI, it did identify multiple adaptive responses that work together to reduce the severity of hypoxia along with several gene candidates for future hypoxia studies.

Commercial catfish production is an inveterate industry within the southeastern United States. Bacterial disease is a significant detriment to global aquaculture, including the United States catfish industry. Among them, an atypical strain of the bacterium Aeromonas hydrophila has plagued the industry since the late 2000s. Atypical A. hydrophila (aAh) outbreaks are largely acute, resulting in catastrophic losses. The disease ecology, prevalence, and genetic distribution are poorly understood. Atypical Aeromonas hydrophila displays a rapid onset with few warning signs of the impending disease, making it difficult for early detection. At present there are two recognized haplotypes of aAh. This project aimed to investigate changes in the spatial and temporal distributions of these haplotypes. The analysis of clinical isolates from different geographic regions across multiple years revealed complete supplanting by the younger haplotype in the Mississippi Delta within 5 years of first isolation. Comparative genomics demonstrated distinct divergences in specific virulence components between the two strains, specifically the Type VI Secretion System, which may explain putative differences in outbreak dynamics and recent displacement of one strain by the other. Also, a rapid, non-lethal screening method was validated that can detect aAh within the catfish host. This method affords data collection regarding infection severity prior to onset of disease and, can predict aAh prevalence at the fish- and pond-levels. The occupancy model indicates more than half the population within a pond may be infected with aAh despite no overt signs of disease. Additionally, aAh is commonly present in approximately 10% of the population, providing the first evidence of a carrier state in this disease. Lastly, a compartmental SLIR model was used to investigate disease dynamics of aAh in catfish aquaculture ponds. Simulations suggest the introduction hypothesis does affect estimated pond profit and antibiotic intervention is an economical treatment for aAh. Routine monitoring was less economical and could dramatically reduce profit in some scenarios. Overall, this work expands our current knowledge of aAh in catfish aquaculture and lays the foundation for future studies investigating aAh management and mitigation of bacterial disease in catfish aquaculture.

Dynamic channel assignment algorithms allow wireless nodes to switch channels when their traffic loads exceed certain thresholds. These thresholds represent estimations of their throughput capacities. Unfortunately, the threshold estimation may not be accurate due to co-channel interference (CCI) and adjacent-channel interference (ACI), especially with high traffic loads in dense networks. When the link capacity is over-estimated, these channel assignment algorithms are not effective. This is because channel switch is not triggered even with overloaded data traffic and the link quality decreases significantly as the channel is overloaded. When the link capacity is under-estimated, the link is under utilized. Moreover, when link traffic load increases from time to time, channel switch occurs frequently. Such frequent channel switches increase latency and degrade throughput, and can even cause network wide channel oscillations. In this paper, we propose a novel threshold-based control system, called \emph{balanced control system} (BCS). The proposed threshold-based control policy consist of deciding, according to the real time traffic load and interference, whether to switch to another channel,{which channel should be switched to and how to perform the switch. Our control model is based on a fuzzy logic control. The threshold which assists to make the channel switch decisions, could be deduced dynamically according to the real-time traffic of each node. We also design a novel dynamic channel assignment scheme, which is used for the selection of the new channel. The channel switch scheduler is provided to perform channel-switch processing for sender and receiver over enhanced routing protocols. We implement our system in NS2, and the simulation results show that with our proposed system, the performance improves by 12.3\%-72.8\% in throughput and reduces 23.2\%-52.3\% in latency. / Computer and Information Science

Regulator of K+ conductance (RCK) domains control the activity of a variety of K+ channels and transporters, including the prokaryotic TrkA/H K+ transport complex and the eukaryotic BK channel, through binding of cytoplasmic ligands such as ATP, H+, and Ca2+. Thus RCK domains transduce ligand binding to gate transmembrane K+ flux in response to signaling events and cellular metabolism, in organisms ranging from bacteria to humans. In this work, I utilize the prokaryotic RCK domain containing K+ channel, MthK as a model system to provide insight toward the structural basis of ion channel gating by RCK domains. In MthK, binding of Ca2+ to an octameric ring of RCK domains (the gating ring) which is tethered to the pore of the channel, leads to a series of conformational changes that facilitates channel opening and K+ conduction. Using electrophysiology and X-ray crystallography, I identify the presence of additional Ca2+ binding sites in the MthK RCK domain, showing that each RCK domain contributes to three different regulatory Ca2+ binding sites, two of which are located at the interfaces between adjacent RCK domains. The additional Ca2+ binding sites, resulting in a stoichiometry of 24 Ca2+ ions per channel, is consistent with the steep relation between [Ca2+] and MthK channel activity. Comparison of Ca2+ bound and unliganded RCK domains suggests a physical mechanism for Ca2+-dependent conformational changes that underlie gating in this class of channels. To gain insight toward mechanisms of RCK domain activation, I crystallized and solved the structure of the RCK domain of MthK bound with Ba2+. The Ba2+-bound RCK domain was assembled as an octomeric gating ring, as observed in structures of the full-length MthK channel, and shows Ba2+ bound at several positions, one of which overlaps with a known Ca2+ binding site. Functionally, I determined that Ba2+ could activate reconstituted MthK channels as observed in electrophysiological recordings. These results suggest a working hypothesis for a sequence of ligand-dependent conformational changes that may underlie RCK domain activation and channel gating. In an effort to more accurately describe the Ca2+-dependent gating process in MthK, I crystallized and solved structures of mutant and wild-type RCK domains, and found that distinct Ca2+ activation sites near the N- and C-termini of the RCK domain (termed C1 and C3, respectively) are allosterically coupled to one another, to affect tuning of Ca2+ affinity and Ca2+-dependent channel activation. These results define a structural mechanism of allosteric modulation in a ligand-gated K+ channel, and provide a framework for understanding similar mechanisms in related RCK-containing channels and transporters. / Biochemistry

<p> In this thesis, we present three algorithms for blind estimation of the finite impulse response (FIR) channels in the presence of unknown noise. The algorithms are developed considering different available system resources: 1) If only one receiving antenna is available, based on the single-input-single-output (SISO) system model, with the output being up-sampled, we develop the maximum a posteriori (MAP) algorithm for Gaussian distributed noise. With large enough samples being collected, during which the channel keeps invariant, an efficient implementation of the MAP algorithm is also obtained; 2) If two receiving antennae can be affordable, based on the singleinput-multiple-output (SIMO) system model and up-sampling both the outputs, we develop a subspace based algorithm utilizing Canonical Correlation Decomposition (CCD) to obtain the subspaces, and a maximum likelihood (ML) based algorithm which starts from the Gaussian distributed projection error from the noise subspace onto the COD-estimated signal subspace. The developed channel estimators achieve superior performance measured by the normalized root mean square error (NRMSE), compared with some existing second-order-statistics (SOS) based methods while keeping the computation complexity comparable. When more than two receiving antennae are available, by treating them as one group and applying the MAP algorithm or separating them into two groups and applying the CCD based algorithms, the channels can still be blindly estimated with or without up-sampling the outputs. </p> / Thesis / Master of Applied Science (MASc)

Wireless mesh networks have received increasing interest in recent years due to the fast expanding Wi-Fi market. More and more, individual communities and companies are beginning to set up intranets with multiple Wi-Fi access points, so that clients can communicate using wireless connections. Because the traditional IEEE 802.11 standard cannot provide efficient performance for mesh networks, the IEEE set up a task group in 2001 to establish a wireless mesh network standard, IEEE 802.11s. For compatibility, IEEE 802.11s will be an extension of the IEEE 802.11 MAC/PHY, and as a result, the new standard has inherited both the pros and cons of IEEE 802.11. Co-channel and inner-channel interference are the dominant factors affecting the system performance of wireless networks. Since there are a number of available non-overlapping channels one can always use these in order to eliminate inner-channel interference. However, the number of channels is not sufficient for an ESS Mesh if channel reuse is not considered, not only because of the network size, but also because of the non-licensed nature of the IEEE 802.11 PHY ISM band, where the network will suffer interference from other co-located networks. For this reason, channel reuse in an ESS Mesh is essential and reducing co-channel interference is a key issue in channel assignment. In this thesis, we investigate the performance of deterministic traffic scheduling with channel assignment in an ESS Mesh based on a TDMA MAC framework while still using the IEEE 802.11 PHY. We first analyze an upper bound on channel assignment performance, considering both binary interference models and cumulative interference models. Then, a scheduling solution for deterministic traffic is proposed, based on heuristic channel assignment and path selection algorithms. Our simulation results show that the scheduling solution is feasible and the performance is close to the theoretical value. / Thesis / Master of Applied Science (MASc)

The prevalence of cloud storage has yielded significant benefits to consumers. Trusted Exe- cution Environments (TEEs) have been introduced to protect program execution and data in the cloud. However, an attacker targeting the cloud storage server through side-channel attacks can still learn some data in TEEs. This data retrieval is possible through the monitor- ing and analysis of the encrypted ciphertext as well as a program's memory access patterns. As the attacks grow in complexity and accuracy, innovative protection methods must be de- signed to secure data. This thesis proposes and implements an ORAM controller primitive in TEE and protects it from all potential side-channel attacks. This thesis presents two vari- ations, each with two different encryption methods designed to mitigate attacks targeting both memory access patterns and ciphertext analysis. The latency for enabling this protec- tion is calculated and proven to be 75.86% faster overall than the previous implementation on which this thesis is based. / Master of Science / Cloud storage and computing has become ubiquitous in recent times, with usage rising ex- ponentially over the past decade. Cloud Service Providers also offer Confidential Computing services for clients requiring data computation which is encrypted and protected from the service providers themselves. While these services are protected against attackers directly looking to access secure data, they are still vulnerable against attacks which only observe, but do not interfere. Such attacks monitor a client's memory access pattern or the encrypted data in the server and can obtain sensitive information including encryption keys. This work proposes and implements an Oblivious RAM design which safeguards against the aforemen- tioned attacks by using a mix of confidential computing in hardware and special algorithms designed to randomize the client's data access patterns. The evaluation of this work shows a significant increase in performance over previous works in this domain while using the latest technology in confidential computing.

The purpose of this dissertation is to find the channel capacity in optical fiber communication systems when incoherent detection is used with single (polarization filtering) and two-polarizations (no polarization filtering). Optical fiber systems employ photodetectors that convert optical intensity to electrical current. Bandpass vector fields may be represented by four orthogonal baseband components corresponding to two quadrature phases and two orthogonal polarizations. Intensity is proportional to the sum of the squares of these four components. In the case of a coherent receiver, a strong optical local oscillator (in phase and with same polarization as the signal) is added to the signal prior to the photodetector. This results in the removal of the quadrature phase and polarization components, and reduces to the one degree of freedom (DOF) case of signal plus local oscillator shot noise for which the Shannon channel capacity formula applies. Electrical noise following the photodetector may also be neglected if there is an optical amplifier before the photodetector in the receiver. The amplifier introduces amplified spontaneous emission noise containing both quadrature phase components and both polarizations (4 DOFs), but the 2 DOF case would result if a polarization filter were used. Although the 1 and 2 DOF cases are of less practical interest than the 4 DOF case, they provide useful benchmarks for comparing performance limits. We evaluate both spectral efficiency limits (bps/Hz) in the limit of high and low SNR for the 1,2 and 4 DOF cases and also find the power efficiency (minimum number of photons per bit) for each of these cases. It is shown that for high SNR the spectral efficiency is the same independent of the number of DOFs and that the half-Gaussian distribution is the optimum distribution. We are able to thus obtain a compact equation for spectral efficiency which behaves in a similar way to the Shannon capacity formula but with the SNR scaled by a constant. We also show that for low SNR the half-Gaussian distribution is not the optimum distribution as the slope of the mutual information changes with the square of SNR which would lead to the number of photons per bit becoming infinite in the limit of SNR going to zero. We use a modified half-Gaussian distribution which has a discrete component (an impulse function at the origin) and provide a simple proof that this distribution results in a mutual information that goes to zero linearly with SNR resulting in a minimum number of photons per bit. Furthermore, by increasing the magnitude of the discrete component at the origin, it is shown that the minimum number of photons per bit for the incoherent channel approaches that of the coherent channel. / Ph. D.

Yes / The present study investigates the turbulent hydrodynamics in an open channel flow with an emergent and sparse vegetation patch placed in the middle of the channel. The dimensions of the rigid vegetation patch are 81 cm long and 24 cm wide and it is prepared by a 7× 10 array of uniform acrylic cylinders by maintaining 9 cm and 4 cm spacing between centers of two consecutive cylinders along streamwise and lateral directions respectively. From the leading edge of the patch, the observed nature of time averaged flow velocities along streamwise, lateral and vertical directions is not consistent up to half length of the patch; however the velocity profiles develop a uniform behavior after that length. In the interior of the patch, the magnitude of vertical normal stress is small in comparison to the magnitudes of streamwise and lateral normal stresses. The magnitude of Reynolds shear stress profiles decreases with increasing downstream length from the leading edge of the vegetation patch and the trend continues even in the wake region downstream of the trailing edge. The increased magnitude of turbulent kinetic energy profiles is noticed from leading edge up to a certain length inside the patch; however its value decreases with further increasing downstream distance. A new mathematical model is proposed to predict time averaged streamwise velocity inside the sparse vegetation patch and the proposed model shows good agreement with the experimental data. / Debasish Pal received financial assistance from SRIC Project of IIT Kharagpur (Project code: FVP)

The need for delivery grew significantly during the COVID-19 pandemic because people avoided activities in public to limit the spread of the virus. The purpose of this research was to evaluate how the pandemic influenced many individual's delivery preferences through the administration of a stated preference survey targeted at residents in the New River Valley, Virginia. Conclusions revealed from the survey show that people want more efficient and accessible delivery services. A new delivery ecosystem called Delivery as a Service (DaaS) was developed using the input from the survey, existing service-based models being widely implemented in many industries, and emerging technologies. This thesis details a framework for DaaS derived by defining major actors, characteristics, and a method to measure the effectiveness of a DaaS system. This comprehensive definition of integrated delivery services illustrates areas for future research to further optimize the DaaS system. DaaS has the potential to significantly change the current delivery ecosystem through increased delivery accessibility and efficiency. Goods can be brought to users at a faster rate and on a larger scale. Autonomous vehicle and drone delivery technologies can significantly reduce the cost while correspondingly reducing the time of delivery. DaaS is a concept that is needed for people to thrive in modern times and brings the opportunity to provide added benefits to even rural areas. / Master of Science / The need for delivery grew significantly during the COVID-19 pandemic because people avoided activities in public to limit the spread of the virus. The purpose of this research was to evaluate how the pandemic influenced many individual's delivery preferences through the administration of a stated preference survey targeted at residents in the New River Valley, Virginia. Conclusions revealed from the survey show that people want more efficient and accessible delivery services. A new delivery ecosystem called Delivery as a Service (DaaS) was developed using the input from the survey, existing service-based models being widely implemented in many industries, and emerging technologies. This thesis details a framework for DaaS derived by defining major actors, characteristics, and a method to measure the effectiveness of a DaaS system. This comprehensive definition of integrated delivery services illustrates areas for future research to further optimize the DaaS system. DaaS has the potential to significantly change the current delivery ecosystem through increased delivery accessibility and efficiency. Goods can be brought to users at a faster rate and on a larger scale. Autonomous vehicle and drone delivery technologies can significantly reduce the cost while correspondingly reducing the time of delivery. DaaS is a concept that is needed for people to thrive in modern times and brings the opportunity to provide added benefits to even rural areas.