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This paper presents a portable paper-based microfluidic platform for multiplexed electrochemical detection of antibody markers of human immunodeficiency virus (HIV) and hepatitis C virus (HCV) in serum samples. To our best knowledge, this is the first paper-based electrochemical immunosensing platform, with multiplexing and telemedicine capabilities, for diagnosing HIV/HCV co-infection. The platform consists of an electrochemical microfluidic paper-based immunosensor array (E-μPIA) and a handheld multi-channel potentiostat, and is capable of performing enzyme-linked immunosorbent assays simultaneously on eight samples within 20 min (using a prepared E-μPIA). The multiplexing feature of the platform allows it to produce multiple measurement data for HIV and HCV markers from a single run, and its wireless communication module can transmit the results to a remote site for telemedicine. The unique integration of paper-based microfluidics and mobile instrumentation renders our platform portable, low-cost, user-friendly, and high-throughput. [ABSTRACT FROM AUTHOR]

In this paper, we establish and analyze a stochastic human immunodeficiency virus model with both virus-to-cell and cell-to-cell transmissions and Ornstein–Uhlenbeck process, in which we suppose that the virus-to-cell infection rate and the cell-to-cell infection rate satisfy the Ornstein–Uhlenbeck process. First, we validate that there exists a unique global solution to the stochastic model with any initial value. Then, we adopt a stochastic Lyapunov function technique to develop sufficient criteria for the existence of a stationary distribution of positive solutions to the stochastic system, which reflects the strong persistence of all CD4+ T cells and free viruses. In particular, under the same conditions as the existence of a stationary distribution, we obtain the specific form of the probability density around the quasi-chronic infection equilibrium of the stochastic system. Finally, numerical simulations are conducted to validate these analytical results. Our results suggest that the methods used in this paper can be applied to study other viral infection models in which the infected CD4+ T cells are divided into latently infected and actively infected subgroups. [ABSTRACT FROM AUTHOR]

In this paper, we investigate a stochastic human immunodeficiency virus (HIV) model with logistic growth and Ornstein-Uhlenbeck process, which is used to describe the pathogenesis and transmission dynamics of HIV in the population. We first validate that the stochastic system has a unique global solution with any initial value. Then we use a novel Lyapunov function method to establish sufficient conditions for the existence of a stationary distribution of the system, which shows the coexistence of all CD4+ T cells and free viruses. Especially, under some mild conditions which are used to ensure the local asymptotic stability of the quasi-chronic infection equilibrium of the stochastic system, we obtain the specific expression of covariance matrix in the probability density around the quasi-chronic infection equilibrium of the stochastic system. In addition, for completeness, we also obtain sufficient criteria for elimination of all infected CD4+ T cells and free virus particles. Finally, several examples together with comprehensive numerical simulations are conducted to support our analytic results. [ABSTRACT FROM AUTHOR]

In this paper, a reaction–diffusion–chemotaxis HIV-1 model with a cytotoxic T lymphocyte (CTL) immune response and general sensitivity is investigated. We first prove the global classical solvability and L ∞ -boundedness for the considered model in a bounded domain with arbitrary spatial dimensions, which extends the previous existing results. Then, we apply the global existence result to the case with a linear proliferation immune response and an incidence rate. We study the spatiotemporal dynamics about the three types of spatially homogeneous steady states: infection-free steady state S 0 , CTL-inactivated infection steady state S 1 , and CTL-activated infection steady state S ∗. Our analyses indicate that S 0 is globally asymptotically stable if the basic reproduction number R 0 is less than 1; if R 0 is between 1 and a threshold, then S 1 is globally asymptotically stable. However, if R 0 is larger than the threshold, then the chemoattraction and chemorepulsion can destabilize S ∗ , and thus, a spatiotemporal pattern forms as the chemotactic sensitivity crosses certain critical values. We obtain two kinds of important patterns, which are induced by chemotaxis: stationary Turing pattern and irregular oscillatory pattern. We also find that different chemotactic response functions can affect system's dynamics. Based on some empirical parameter values, numerical simulations are given to illustrate the effectiveness of the theoretical predications. [ABSTRACT FROM AUTHOR]

The human immunodeficiency virus (HIV) interacts with the immune cells within the human body, where the environment is uncertain and noisy. Stochastic models can successfully encapsulate the effect of such a noisy environment compared to their deterministic counterparts. The human immune system is complex but well-coordinated with various immune cells like C D 4 + T cells, dendritic cells, and cytotoxic T-lymphocyte (CTL) cells, among many others. The CTL can kill the antigenic cells after its recognition. However, the efficacy of CTL in removing the infected C D 4 + T cells is progressively compromised in HIV-infected individuals. This paper considers a noise-induced HIV-immune cell interaction model with immune impairment. A multiplicative white noise is introduced in the infection rate parameter to represent the fluctuations around the average value of the rate parameter as a causative effect of the noise. We analyzed the deterministic and stochastic models and prescribed sufficient conditions for infection eradication and persistence. It is determined under what parametric restrictions the asymptotic solutions of the noise-induced system will be a limiting case of the deterministic solutions. Simulation results revealed that the solutions of the deterministic system either converge to a CTL-dominated interior equilibrium or a CTL-free immunodeficient equilibrium, depending on the initial values of the system. Stochastic analysis divulged that higher noise might be helpful in the infection removal process. The extinction time of infected C D 4 + T cells for some fixed immune impairment gradually decreases with increasing noise intensity and follows the power law. [ABSTRACT FROM AUTHOR]

In this paper, we present a detailed dynamics study of the catalytic core domain (CCD) of HIV-1 integrase using both polarized and nonpolarized force fields. The numerical results reveal the critical role of protein polarization in stabilizing Mg2+ coordination complex in CCD. Specifically, when nonpolarized force field is used, a remarkable drift of the Mg2+ complex away from its equilibrium position is observed, which causes the binding site blocked by the Mg2+ complex. In contrast, when polarized force field is employed in MD simulation, HIV-1 integrase CCD structure is stabilized and both the position of the Mg2+ complex and the binding site are well preserved. The detailed analysis shows the transition of α-helix to 310-helix adjacent to the catalytic loop (residues 139–147), which correlates with the dislocation of the Mg2+ complex. The current study demonstrates the importance of electronic polarization of protein in stabilizing the metal complex in the catalytic core domain of HIV-1 integrase. [ABSTRACT FROM AUTHOR]

To enhance my research, I would like to share my knowledge of Herpes simplex virus-2 (HSV-2) and HIV/AIDS (Acquired Immunodeficiency Syndrome) through a mathematical model. The study's objective is to develop and examine the co-disease model for the modern era using mathematical modeling. Based on their modes of transmission, HSV-2 and HIV/AIDS are currently the leading causes of death from infectious and severe chronic diseases. Depending on the severity of HIV-2's chronic disease, the model is divided into five phases: the first two HIV-2 stages and the remaining three HIV stages. Ordinary differential equations (ODEs) are arranged differently by each individual. Investigations into the mathematical equation model have revealed the points of equilibrium between the free and endemic models. A study of the developed model was conducted using the basic reproduction numbers [ R 0 ] of HSV-2 and HIV. The results demonstrate that if R 0 < 1 , the free equilibrium of disease is asymptotically locally stable. When R 0 > 1 , equilibrium endemic states are regarded as existing. Finally, MATLAB software was used to simulate the numerical equations of the model. [ABSTRACT FROM AUTHOR]

The use of drugs derived from benzothiadiazine, which is a bicyclic heterocyclic benzene derivative, has become a widespread treatment for diseases such as hypertension (treated with diuretics such as bendroflumethiazide or chlorothiazide), low blood sugar (treated with non-diuretic diazoxide), or the human immunodeficiency virus, among others. In this work, we have investigated the interactions of benzothiadiazine with the basic components of cell membranes and solvents, such as phospholipids, cholesterol, ions, and water. The analysis of the mutual microscopic interactions is of central importance to elucidate the local structure of benzothiadiazine as well as the mechanisms responsible for the access of benzothiadiazine to the interior of the cell. We have performed molecular dynamics simulations of benzothiadiazine embedded in three different model zwitterionic bilayer membranes made by dimyristoylphosphatidylcholine, dioleoylphosphatidylcholine, 1,2-dioleoyl-sn-glycero-3-phosphoserine, and cholesterol inside aqueous sodium-chloride solution in order to systematically examine microscopic interactions of benzothiadiazine with the cell membrane at liquid-crystalline phase conditions. From data obtained through radial distribution functions, hydrogen-bonding lengths, and potentials of mean force based on reversible work calculations, we have observed that benzothiadiazine has a strong affinity to stay at the cell membrane interface although it can be fully solvated by water in short periods of time. Furthermore, benzothiadiazine is able to bind lipids and cholesterol chains by means of single and double hydrogen-bonds of different characteristic lengths. [ABSTRACT FROM AUTHOR]

Ellipticine is a natural product that is currently being actively investigated for its inhibitory cancer and HIV properties. Here we use path-integral molecular dynamics coupled with excited state calculations to characterize the role of nuclear quantum effects on the structural and electronic properties of ellipticine in water, a common biological solvent. Quantum effects collectively enhance the fluctuations of both light and heavy nuclei of the covalent and hydrogen bonds in ellipticine. In particular, for the ellipticine-water system, where the proton donor and acceptor have different proton affinities, we find that nuclear quantum effects (NQEs) strengthen both the strong and the weak H bonds. This is in contrast to what is observed for the cases where the proton affinity of the donors and acceptors is same. These structural fluctuations cause a significant red-shift in the absorption spectra and an increase in the broadening, bringing it into closer agreement with the experiments. Our work shows that nuclear quantum effects alter both qualitatively and quantitatively the optical properties of this biologically relevant system and highlights the importance of the inclusion of these effects in the microscopic understanding of their optical properties. We propose that isotopic substitution will produce a blue shift and a reduction in the broadening of the absorption peak. [ABSTRACT FROM AUTHOR]

Infectious diseases caused by pathogens, such as SARS-COV, H7N9, severe fever with thrombocytopenia syndrome virus, and human immunodeficiency virus, have fatal outcomes with common features of severe fever and subsequent bacterial invasion progressing to multiorgan failure. Gene biomarkers are promising to distinguish specific infections from others with similar presenting symptoms for the prescription of correct therapeutics, preventing pandemics. While routine laboratory methods based on polymerase chain reaction (PCR) to measure gene biomarkers have provided highly sensitive and specific viral detection techniques over the years, they are still hampered by their precision and resource intensity precluding their point-of-care use. Recently, there has been growing interest in employing microfluidic technologies to advance current methods for infectious disease determination via gene biomarker measurements. Here, based on the requirement of infection detection, we will review three microfluidic approaches to compartmentalize gene biomarkers: (1) microwell-based PCR platforms; (2) droplet-based PCR; and (3) point-of-care devices including centrifugal chip, SlipChip, and self-powered integrated microfluidic point-of-care low-cost enabling chip. By capturing target genes in microwells with a small sample volume (∼μl), sensitivity can be enhanced. Additionally, with the advance of significant sample volume minimization (∼pl) using droplet technology, gene quantification is possible. These improvements in cost, automation, usability, and portability have thereby allowed point-of-care applications to decentralize testing platforms from laboratory-based settings to field use against infections. [ABSTRACT FROM AUTHOR]

Many viruses which cause disease including human immunodeficiency virus (HIV) and influenza are “enveloped” by a membrane and infection of a host cell begins with joining or “fusion” of the viral and target cell membranes. Fusion is catalyzed by viral proteins in the viral membrane. For HIV and for the influenza virus, these fusion proteins contain an ∼20-residue apolar “fusion peptide” that binds to target cell membranes and plays a critical role in fusion. For this study, the HIV fusion peptide (HFP) and influenza virus fusion peptide (IFP) were chemically synthesized with uniform 13C, 15N labeling over large contiguous regions of amino acids. Two-dimensional 13C–13C and 15N–13C spectra were obtained for the membrane-bound fusion peptides and an amino acid-type 13C assignment was obtained for the labeled residues in HFP and IFP. The membrane used for the HFP sample had a lipid headgroup and cholesterol composition comparable to that of host cells of the virus, and the 13C chemical shifts were more consistent with β strand conformation than with helical conformation. The membrane used for the IFP sample did not contain cholesterol, and the chemical shifts of the dominant peaks were more consistent with helical conformation than with β strand conformation. There were additional peaks in the IFP spectrum whose shifts were not consistent with helical conformation. An unambiguous 13C and 15N assignment was obtained in an HFP sample with more selective labeling, and two shifts were identified for the Leu-9 CO, Gly-10 N, and Gly-10 Cα nuclei. These sets of two shifts may indicate two β strand registries such as parallel and antiparallel. Although most spectra were obtained on a 9.4 T instrument, one 13C–13C correlation spectrum was obtained on a 16.4 T instrument and was better resolved than the comparable 9.4 T spectrum. More selective labeling and higher field may, therefore, be approaches to obtaining unambiguous assignments for membrane-associated fusion peptides. [ABSTRACT FROM AUTHOR]

In view of the complex procedure of nucleic acid extraction, there exists a huge challenge for the widespread use of point-of-care diagnostics for nucleic acid testing. To achieve point-of-care applications in a more rapid and cost-efficient manner, we designed a snake pipe-shaped microfluidic chip so as to accomplish reagents-prestored, time-saving, operation-simple nucleic acid extraction. All reagents needed for this process, including lysis buffer, wash buffer, elution buffer, and so on, were preloaded in the snake pipe and securely isolated by membrane valves, without the need for using any specialized equipment. By an integrated chip and a powerful ultrasonic, this device could complete virus nucleic acid extraction from sophisticated serum samples in less than 1 min. We used hepatitis B virus (HBV) and human immunodeficiency virus (HIV) mixed with different sources of serum as samples to be extracted. The coefficient of variation of HBV and HIV extraction on-chip was 1.32% and 2.74%, respectively, and there were no significant differences between on-chip and commercial instrument extraction (P > 0.05, α = 0.05) in different dilution ratios, which showed that the extraction device we established had excellent stability and sensitivity. [ABSTRACT FROM AUTHOR]

At present, the calculated binding free energy obtained using the molecular mechanics/Poisson-Boltzmann (Generalized-Born) surface area (MM/PB(GB)SA) method is overestimated due to the lack of knowledge of suitable interior dielectric constants in the simulation on the interaction of Human Immunodeficiency Virus (HIV-1) protease systems with inhibitors. Therefore, the impact of different values of the interior dielectric constant and the entropic contribution when using the MM/PB(GB)SA method to calculate the binding free energy was systemically evaluated. Our results show that the use of higher interior dielectric constants (1.4–2.0) can clearly improve the predictive accuracy of the MM/PBSA and MM/GBSA methods, and computational errors are significantly reduced by including the effects of electronic polarization and using a new highly efficient interaction entropy (IE) method to calculate the entropic contribution. The suitable range for the interior dielectric constant is 1.4–1.6 for the MM/PBSA method; within this range, the correlation coefficient fluctuates around 0.84, and the mean absolute error fluctuates around 2 kcal/mol. Similarly, an interior dielectric constant of 1.8–2.0 produces a correlation coefficient of approximately 0.76 when using the MM/GBSA method. In addition, the entropic contribution of each individual residue was further calculated using the IE method to predict hot-spot residues, and the detailed binding mechanisms underlying the interactions of the HIV-1 protease, its inhibitors, and bridging water molecules were investigated. In this study, the use of a higher interior dielectric constant and the IE method can improve the calculation accuracy of the HIV-1 system. [ABSTRACT FROM AUTHOR]

The polyamidoamine (PAMAM) dendrimer prevents HIV-1 entry into target cells in vitro. Its mechanism of action, however, remains unclear and precludes the design of potent dendrimers targeting HIV-1 entry. We employed steered molecular dynamics simulations to examine whether the HIV-1 gp120-CD4 complex is a target of PAMAM. Our simulations mimicked single molecule force spectroscopy studies of the unbinding of the gp120-CD4 complex under the influence of a controlled external force. We found that the complex dissociates via complex pathways and defies the standard classification of adhesion molecules as catch and slip bonds. When the force loading rate was large, the complex behaved as a slip bond, weakening gradually. When the loading rate was small, the complex initially strengthened, akin to a catch bond, but eventually dissociated over shorter separations than with large loading rates. PAMAM docked to gp120 and destabilized the gp120-CD4 complex. The rupture force of the complex was lowered by PAMAM. PAMAM disrupted salt bridges and hydrogen bonds across the gp120-CD4 interface and altered the hydration pattern of the hydrophobic cavity in the interface. In addition, intriguingly, PAMAM suppressed the distinction in the dissociation pathways of the complex between the small and large loading rate regimes. Taken together, our simulations reveal that PAMAM targets the gp120-CD4 complex at two levels: it weakens the complex and also alters its dissociation pathway, potentially inhibiting HIV-1 entry. [ABSTRACT FROM AUTHOR]

The potential of ribonucleic acid (RNA) as both informational and ligand binding molecule have opened a scenario in the development of biosensors. An aminated diamond-based RNA aptasensor is presented for human immunodeficiency virus (HIV) trans-activator of transcription (Tat) peptide protein detection that not only gives a labeled or label-free detection method but also provides a reusable platform for a simple, sensitive, and selective detection of proteins. The immobilized procedure was based on the binding interaction between positively charged amine terminated diamond and the RNA aptamer probe molecules with the negatively charged surface carboxylic compound linker molecule such as terephthalic acid. [ABSTRACT FROM AUTHOR]

Thermal ramp rate is a major limiting factor in using real-time polymerase chain reaction (PCR) for routine diagnostics. We explored the limits of speed by using liquid for thermal exchange rather than metal as in traditional devices, and by testing different polymerases. In a clinical setting, our system equaled or surpassed state-of-the-art devices for accuracy in amplifying DNA/RNA of avian influenza, cytomegalovirus, and human immunodeficiency virus. Using Thermococcus kodakaraensis polymerase and optimizing both electrical and chemical systems, we obtained an accurate, 35 cycle amplification of an 85-base pair fragment of E. coli O157:H7 Shiga toxin gene in as little as 94.1 s, a significant improvement over a typical 1 h PCR amplification. [ABSTRACT FROM AUTHOR]

There is a widespread agreement that more effective drug delivery vehicles with more alternatives, as well as better active pharmaceutical ingredients (APIs), must be developed to improve the efficacy of microbicide products. For instance, in tropical regions, films are more appropriate than gels due to better stability of drugs at extremes of moisture and temperature. Here, we apply fundamental fluid mechanical and physicochemical transport theory to help better understand how successful microbicide API delivery depends upon properties of a film and the human reproductive tract environment. Several critical components of successful drug delivery are addressed. Among these are: elastohydrodynamic flow of a dissolved non-Newtonian film; mass transfer due to inhomogeneous dilution of the film by vaginal fluid contacting it along a moving boundary (the locally deforming vaginal epithelial surface); and drug absorption by the epithelium. Local rheological properties of the film are dependent on local volume fraction of the vaginal fluid. We evaluated this experimentally, delineating the way that constitutive parameters of a shear-thinning dissolved film are modified by dilution. To develop the mathematical model, we integrate the Reynolds lubrication equation with a mass conservation equation to model diluting fluid movement across the moving vaginal epithelial surface and into the film. This is a complex physicochemical phenomenon that is not well understood. We explore time- and space-varying boundary flux model based upon osmotic gradients. Results show that the model produces fluxes that are comparable to experimental data. Further experimental characterization of the vaginal wall is required for a more precise set of parameters and a more sophisticated theoretical treatment of epithelium. [ABSTRACT FROM AUTHOR]