Modeling HIV Drug Resistance

Despite the development of antiviral drugs and the optimization of therapies, the emergence of drug resistance remains one of the most challenging issues for successful treatments of HIV-infected patients. The availability of massive HIV drug resistance data provides us not only exciting opportunities for HIV research, but also the curse of high dimensionality. We provide several statistical learning methods in this thesis to analyze sequence data from different perspectives. We propose a hierarchical random graph approach to identify possible covariation among residue-specific mutations. Viral progression pathways were inferred using an EM-like algorithm in literature, and we present a normalization method to improve the accuracy of parameter estimations. To predict the drug resistance from genotypic data, we also build a novel regression model utilizing the information from progression pathways. Finally, we introduce a computational approach to determine viral fitness, for which our initial computational results closely agree with experimental results. Work on two other topics are presented in the Appendices. Latent class models find applications in several areas including social and biological sciences. Finding explicit maximum likelihood estimation has been elusive. We present a positive solution to a conjecture on a special latent class model proposed by Bernd Sturmfels from UC Berkeley. Monomial ideals provide ubiquitous links between combinatorics and commutative algebra. Irreducible decomposition of monomial ideals is a basic computational problem and it finds applications in several areas. We present two algorithms for finding irreducible decomposition of monomial ideals

Solving the 100 Swiss Francs Problem

Sturmfels offered 100 Swiss Francs in 2005 to a conjecture, which deals with a special case of the maximum likelihood estimation for a latent class model. This paper confirms the conjecture positively

4-(2-Chloro­ethoxy)phthalonitrile

In the title compound, C10H7ClN2O, the O and both C atoms of the chloroethoxy group are disordered over two positions, the occupancy factor of the major disorder component refining to 0.54 (2)

Semi-blind joint channel estimation and symbol detection for RIS-empowered multiuser mmWave Systems

In this letter, we propose a semi-blind joint channel estimation and symbol detection scheme for reconfigurable intelligent surface (RIS)-empowered multiuser millimeter wave (mmWave) systems. Combined with the coding scheme at user equipments (UEs) and RIS reflection coefficient design, we prove that the received signals at the base station (BS) follow a PARATUCK2 tensor model, and then a two-stage fitting algorithm is derived by exploiting the low-rank structure of mmWave channel. Without a dedicated training stage, the proposed scheme can jointly detect information symbols of all UEs and estimate the channels of the UEs-RIS and RIS-BS links. In comparison to the existing methods, the proposed system can increase spectrum efficiency and obtain better channel estimation and symbol detection performance. Numerical results are presented to verify the effectiveness of the proposed scheme

Secrecy Outage Probability of Relay Selection Based Cooperative NOMA for IoT Networks

As an important partner of fifth generation (5G) communication, the internet of things (IoT) is widely used in many fields with its characteristics of massive terminals, intelligent processing, and remote control. In this paper, we analyze security performance for the cooperative non-orthogonal multiple access (NOMA) networks for IoT, where the multi-relay Wyner model with direct link between the base station and the eavesdropper is considered. In particular, secrecy outage probability (SOP) for two kinds of relay selection (RS) schemes (i.e., single-phase RS (SRS) and two-phase RS (TRS)) is developed in the form of closed solution. As a benchmark for comparison, the SOP for random RS (RRS) is also obtained. To gain more meaningful insights, approximate derivations of SOP under the high signal-to-noise ratio (SNR) region are provided. Results of statistical simulation confirm the theoretical analysis and testify that: i) Compared with RRS scheme, SRS and TRS may improve secure performance because of obtaining smaller SOPs; ii) There exists secrecy performance floor for the SOP in strong SNR regime, which is dominated by NOMA protocol; iii) The security performance can be enhanced by augmenting the quantity of relays for SRS and TRS strategies. The purpose of this work is to provide theoretical basis for the analysis and design of anti-eavesdropping for NOMA systems in IoT

Covert communication in downlink NOMA systems with channel uncertainty

With the gradual promotion of the fifth generation (5G) mobile communication and Internet of Things (IoT) applications, wireless communication transmission will be more vulnerable to illegal interceptions and/or attacks. To ensure communication security, we study covert communication of downlink nonorthogonal multiple access (NOMA) systems, where the channel knowledge of users is uncertain. A multiantenna transmitter tries to covertly transmit information to a covert user (strong user) through the shield of a public communication link (weak user), while the warden tries to detect the communication behavior between the transmitter and the covert user. To improve security and energy efficiency, the ${k}$ th best antenna of the transmitter is selected, since the optimal antenna may be not available due to some schedule and/or other reasons. Aiming to evaluate the proposed framework performance, we start by deriving exact expressions for the minimum detection error probability and the optimal detection threshold of the warden, followed by a calculation analysis of the expected minimum detection error probability (EMDEP) and the outage probability of NOMA users. The asymptotic behavior for the outage probability is investigated at high signal-to-noise ratio (SNR) to acquire greater useful insights. With the goal of improving the system covertness performance, we propose that a scheme is optimized to enhance the covert throughput of the system to the maximum. Simulation results show that the following hold: 1) channel estimation errors have a significant effect on system performance; 2) reliability performance tends to build up, as the total number of antennas grows large; and 3) as the transmitting power and number of antennas increases, there is an upper bound for maximizing the covert throughput

The prospective outcome of the monkeypox outbreak in 2022 and characterization of monkeypox disease immunobiology

A new threat to global health re-emerged with monkeypox’s advent in early 2022. As of November 10, 2022, nearly 80,000 confirmed cases had been reported worldwide, with most of them coming from places where the disease is not common. There were 53 fatalities, with 40 occurring in areas that had never before recorded monkeypox and the remaining 13 appearing in the regions that had previously reported the disease. Preliminary genetic data suggest that the 2022 monkeypox virus is part of the West African clade; the virus can be transmitted from person to person through direct interaction with lesions during sexual activity. It is still unknown if monkeypox can be transmitted via sexual contact or, more particularly, through infected body fluids. This most recent epidemic’s reservoir host, or principal carrier, is still a mystery. Rodents found in Africa can be the possible intermediate host. Instead, the CDC has confirmed that there are currently no particular treatments for monkeypox virus infection in 2022; however, antivirals already in the market that are successful against smallpox may mitigate the spread of monkeypox. To protect against the disease, the JYNNEOS (Imvamune or Imvanex) smallpox vaccine can be given. The spread of monkeypox can be slowed through measures such as post-exposure immunization, contact tracing, and improved case diagnosis and isolation. Final Thoughts: The latest monkeypox epidemic is a new hazard during the COVID-19 epidemic. The prevailing condition of the monkeypox epidemic along with coinfection with COVID-19 could pose a serious condition for clinicians that could lead to the global epidemic community in the form of coinfection