Direct Observation of Vortex Dynamics in Superconducting Films with Regular Arrays of Defects

Experimentally realizable devices for controlling the motion of magnetic flux quanta in anisotropic superconductors

A new generation of microscopic ratchet systems is currently being developed for controlling the motion of electrons and fluxons, as well as for particle separation and electrophoresis. Virtually all of these use static spatially asymmetric potential energies to control transport properties. Here we propose completely new types of ratchet-like systems that do not require fixed spatially asymmetric potentials in the samples. As specific examples of this novel general class of ratchets, we propose devices that control the motion of flux quanta in superconductors and could address a central problem in many superconducting devices; namely, the removal of trapped magnetic flux that produces noise. In layered superconductors there are two interpenetrating perpendicular vortex lattices consisting of Josephson vortices (JVs) and pancake vortices (PVs). We show that, owing to the JV-PV mutual interaction and asymmetric driving, the a.c. motion of JVs and/or PVs can provide a net d.c. vortex current. This controllable vortex motion can be used for making pumps, diodes and lenses of quantized magnetic flux. These proposed devices sculpt the microscopic magnetic flux profile by simply modifying the time dependence of the a.c. drive, without the need for samples with static pinning--for example, without lithography or irradiation.

Kinetically locked-in colloidal transport in an array of optical tweezers

We describe measurements of colloidal transport through arrays of micrometer-scale potential wells created with holographic optical tweezers. Varying the orientation of the trap array relative to the external driving force results in a hierarchy of lock-in transitions analogous to symmetry-selecting processes in a wide variety of systems. Focusing on colloid as a model system provides the first opportunity to observe the microscopic mechanisms of kinetic lock-in transitions and reveals a new class of statistically locked-in states. This particular realization also has immediate applications for continuously fractionating particles, biological cells, and macromolecules.

Rectification and phase locking for particles on symmetric two-dimensional periodic substrates

We demonstrate a rectification phenomenon for overdamped particles interacting with a 2D symmetric periodic substrate when driven with a dc and a circular ac drive. As a function of longitudinal dc amplitude, the longitudinal velocity increases in a series of quantized steps distinct from Shapiro steps with transverse rectification occurring near these transitions. The rectification phenomenon is explained using symmetry arguments and a simple model.

Mode locking of vortex matter driven through mesoscopic channels

We investigated the driven dynamics of vortices confined to mesoscopic flow channels by means of a dc-rf interference technique. The observed mode-locking steps in the IV curves provide detailed information on how both the number of vortex rows and the lattice structure in each flow channel change with magnetic field. Minima in flow stress occur when an integer number of rows is moving coherently, while maxima appear when the incoherent motion of mixed n and n+/-1 row configurations is predominant. Simulations show that the enhanced pinning at mismatch originates from quasistatic fault zones with misoriented edge dislocations induced by disorder in the channel edges.

Vortex configurations, matching, and domain structure in large arrays of artificial pinning centers

High-resolution scanning Hall probe microscopy has been used to image vortex configurations in very large periodic arrays of artificial pinning sites. Strong matching effects are seen at fields where either one or two vortices can sit at a site; with three vortices per site, however, no clear matching is observed. Matching effects have also been observed at several fractional multiples of the matching field, including 1/5, 1/4, 1/3, 1/2, and 3/4. These fractional values are characterized by striking domain structure and grain boundaries.

Reservoirs of human immunodeficiency virus type 1: the main obstacles to viral eradication

Highly active antiretroviral therapy (HAART) has led to profound decreases in morbidity and mortality rates in human immunodeficiency virus type 1 (HIV-1)-infected persons, at least in the developed world. Many infected persons have plasma levels of HIV-1 RNA that are less than the limits of detection of most clinical assays as a result of combination antiretroviral therapy. Nonetheless, HIV-1 has not been eradicated by HAART. This has been shown to be because of latent HIV-1 replication-competent provirus in resting CD4+ T lymphocytes, cryptic viral replication below the limits of detection of most clinical assays, and, possibly, the presence of viral sanctuary sites. An understanding of these reservoirs for HIV-1 in the setting of virally suppressive HAART will be critical for the development of new approaches to induce HIV-1 remissions and for the exploration of the possibility of viral eradication in the future.

Vortex lattice melting in layered superconductors with periodic columnar pins

The melting of the vortex lattice in highly anisotropic, layered superconductors with commensurate, periodic columnar pins is studied in a geometry where magnetic field and columnar pins are normal to the layers. Thermodynamic properties and equilibrium density distributions are obtained from numerical minimization of an appropriate free-energy functional. We find a line of first-order transitions that ends at a critical point as the pin concentration is increased. We quantitatively determine the location of this critical point and show that it is experimentally accessible.

A review of efficacy studies of 6-month short-course therapy for tuberculosis among patients infected with human immunodeficiency virus: differences in study outcomes

Six-month regimens that include rifampin for the treatment of tuberculosis in patients without human immunodeficiency virus (HIV) infection are recommended because of low percentage of relapses. Whether a similar duration of therapy should be used to treat tuberculosis in HIV-infected patients is unclear. Six studies of patients with HIV-infection and 3 of patients without HIV infection were reviewed and compared. The studies differed in terms of design, eligibility criteria, site of disease, frequency of dosing, dose administration methods, and outcome definitions. Among HIV-infected patients, the following percentages were found: cure, 59.4%--97.1%; treatment success, 34.0%--100%; effective treatment, 29.4%--88.2%; and relapse, 0%--10%. In those without HIV infection, percentages were as follows: cure, 62.3%--88.0%; treatment success, 91.2%--98.8%; effective treatment, 70.6%--83.8%; and relapse, 0%--3.4%. Although the rate of relapse appeared to be higher in some studies of HIV-infected patients with tuberculosis, this review demonstrates the limitation in the use of relapse as the exclusive outcome of interest when comparing studies.

Reduction in CD8+ cell noncytotoxic anti-HIV activity in individuals receiving highly active antiretroviral therapy during primary infection

Recent advances in the ability to detect people at the early stages of HIV infection now permit the initiation of antiretroviral treatment before the full complement of antiviral immune responses has evolved. However, the influence of early treatment interventions on the developing anti-HIV immune response is unknown. This study investigates the impact of standard highly active antiretroviral therapy (HAART) during the primary stages of HIV infection on the plasma HIV-1 RNA level, CD4(+) and CD8(+) lymphocyte counts, and the CD8(+) cell anti-HIV response. Individuals treated with HAART within 6 months of infection showed dramatic and rapid reductions in HIV-1 RNA levels along with modest increases in CD4(+) cell number and decreases in CD8(+) cell numbers. A significant reduction in the level of CD8(+) cell noncytotoxic suppression of HIV replication was observed over time in most participants receiving HAART. Importantly, those individuals choosing not to receive therapy maintained low but detectable HIV-1 RNA levels and showed no reduction in their CD8(+) cell antiviral response. These results suggest that either continued antigenic challenge is required to sustain CD8(+) cell-mediated anti-HIV activity, or that HAART has some inhibitory effect on this important immunologic function during the early stages of infection.

Local Observation of Field Polarity Dependent Flux Pinning by Magnetic Dipoles

A scanning Hall probe microscope is used to study flux pinning in a thin superconducting Pb film covering a square array of single-domain Co dots with in-plane magnetization. We show that single flux quanta of opposite sign thread the superconducting film below T(c) at the opposite poles of these dipoles. Depending on the polarity of the applied field, flux lines are attracted to a specific pole of the dipoles, due to the direct interaction with the vortexlike structures induced by the local stray field.

Symmetry-induced formation of antivortices in mesoscopic superconductors

Recent progress in nanotechnology has stimulated interest in mesoscopic superconductors as components for quantum computing and cryoelectronics. The critical parameters for superconductivity (current and field) of a mesoscopic sample are determined by the pattern of vortices in it, which in turn is controlled by the symmetry imposed by the shape of the sample (see ref. 1 and references therein). Hitherto it has been unclear what happens when the number of vortices is not consistent with the natural symmetry. Here we show that additional vortex-antivortex pairs nucleate spontaneously so as to preserve the symmetry of the sample. For example, in a square with three vortices, the spontaneously generated pair, along with the original three vortices, distribute themselves so that the four vortices sit in the four corners, with the antivortex in the centre. The measured superconducting phase boundary (of superconducting transition temperature Tc versus magnetic field strength) is in very good agreement with the calculations, giving direct experimental evidence for these symmetry-induced vortex-antivortex pairs. Vortex entry into the sample is also changed: vortices enter a square in fours, with antivortices generated to preserve the imposed vorticity. The symmetry-induced nucleation of antivortices is not restricted to superconductors, but should also apply to symmetrically confined superfluids and Bose-Einstein condensates.

Quantification of viral load: clinical relevance for human immunodeficiency virus, hepatitis B virus and hepatitis C virus infection

Quantitative determination of viral load using nucleic acid amplification techniques represents the most accurate prognostic marker for human immunodeficiency virus type 1 (HIV-1) infection, independently of CD4+ cell count. Overall, the different methods for HIV-1 RNA determination (RT-PCR, nucleic acid sequence-based amplification, branched DNA) show a good reproducibility (0.5 log), however for low copy numbers and in HIV-1-infected children the variability may exceed 0.7 log. In non-HIV-1 subtype B infections the copy number is underestimated. While serology permits an accurate follow-up of hepatitis B virus (HBV) infection, HBV DNA quantification is used for monitoring of antiviral therapy, determination of infectiosity and in combination with serological markers for the resolution of unusual profiles, i.e. isolated anti-HBc reactivity. The prognostic relevance of hepatitis C virus (HCV) RNA determination is of limited value for the long-term prognosis of chronic hepatitis C, however the viral load may predict the outcome of antiviral therapy. Genetic diversity represents a challenge for HCV RNA quantification.

Reservoirs for HIV-1: mechanisms for viral persistence in the presence of antiviral immune responses and antiretroviral therapy

The success of combination antiretroviral therapy for HIV-1 infection has generated interest in mechanisms by which the virus can persist in the body despite the presence of drugs that effectively inhibit key steps in the virus life cycle. It is becoming clear that viral reservoirs established early in the infection not only prevent sterilizing immunity but also represent a major obstacle to curing the infection with the potent antiretroviral drugs currently in use. Mechanisms of viral persistence are best considered in the context of the dynamics of viral replication in vivo. Virus production in infected individuals is largely the result of a dynamic process involving continuous rounds of de novo infection of and replication in activated CD4(+) T cells with rapid turnover of both free virus and virus-producing cells. This process is largely, but not completely, interrupted by effective antiretroviral therapy. After a few months of therapy, plasma virus levels become undetectable in many patients. Analysis of viral decay rates initially suggested that eradication of the infection might be possible. However, there are several potential cellular and anatomical reservoirs for HIV-1 that may contribute to long-term persistence of HIV-1. These include infected cell in the central nervous system and the male urogenital tract. However, the most worrisome reservoir consists of latently infected resting memory CD4(+) T cells carrying integrated HIV-1 DNA. Definitive demonstration of the presence of this form of latency required development of methods for isolating extremely pure populations of resting CD4(+) T cells and for demonstrating that a small fraction of these cells contain integrated HIV-1 DNA that is competent for replication if the cells undergo antigen-driven activation. Most of the latent virus in resting CD4(+) T cells is found in cells of the memory phenotype. The half-life of this latent reservoir is extremely long (44 months). At this rate, eradication of this reservoir would require over 60 years of treatment. Thus, latently infected resting CD4(+) T cells provide a mechanism for life-long persistence of replication-competent forms of HIV-1, rendering unrealistic hopes of virus eradication with current antiretroviral regimens. The extraordinary stability of the reservoir may reflect gradual reseeding by a very low level of ongoing viral replication and/or mechanisms that contribute to the intrinsic stability of the memory T cell compartment. Given the substantial long-term toxicities of current combination therapy regimens, novel approaches to eradicating this latent reservoir are urgently needed.

Determinants of virological response to antiretroviral therapy: implications for long-term strategies

A variety of factors can contribute to the failure of combination antiretroviral therapy to durably suppress viral replication in patients infected with human immunodeficiency virus (HIV). Patients who have a low CD4(+) T cell count or high plasma viral load before therapy is initiated are at high risk for subsequent virological failure. Previous therapy is also a strong determinant of subsequent virological response, presumably because of pre-existing viral resistance. Drug exposure, as determined by adherence, drug absorption, and drug metabolism, has a significant impact on future long-term virological responses. Although definitive proof is lacking, some tissues may have limited drug penetration, thus allowing for ongoing viral replication. Understanding why combination therapy fails for HIV-infected patients may allow clinicians to individualize treatment strategies. Unfortunately, almost any factor (drug, host, or viral) that leads to virological failure of an initial combination regimen is likely to persist-and perhaps become more challenging-once a salvage regimen is initiated.

Viral dynamics during active cytomegalovirus infection and pathology

The central role that cytomegalovirus (CMV) load plays in its pathogenesis is being unravelled. In AIDS patients with active CMV replication, many months prior to the development of CMV disease, elevated CMV load in the blood and urine are significantly associated with an increased risk of disease progression. In addition, elevated load in blood is associated with an increased risk of death. Intervention with ganciclovir acts to rapidly inhibit CMV replication in vivo and has allowed estimates of the clearance/replication rate of CMV to be performed. These data indicate that CMV replicates dynamically in the human host with a doubling time of approximately 1 day. This knowledge has been used to determine the relative contribution of initial viral load and rate of change of viral load as predictors of CMV disease in organ transplant recipients. The data show that both these parameters have prognostic value in multivariate models and should allow the development of novel patient management strategies.

Immunopathological factors for vertical transmission of HIV-1

With the global rise in human immunodeficiency virus-1 (HIV-1) infection in women of childbearing age, there has also been an alarming rise in the number of mother-to-child transmissions of HIV-1. Although drug therapies such as zidovudine as well as nevirapine have been demonstrated to significantly decrease the incidence of vertical transmission of HIV-1, these therapeutic regimens are still not widely available in some developing countries where maternal-to-child transmission of HIV-1 continues to occur at an alarming rate. Therefore, the continued studies of mechanisms and correlates of vertical transmission of HIV-1 are warranted. The current status of immunological and virological correlates of vertical transmission are summarized in this review. In addition, information concerning recent therapeutic agents for the prevention of HIV-1 vertical transmission is presented.

Cervicovaginal human papillomavirus infection in human immunodeficiency virus-1 (HIV)-positive and high-risk HIV-negative women

BACKGROUND

Human papillomavirus (HPV) infection is associated with precancerous cervical squamous intraepithelial lesions commonly seen among women infected with human immunodeficiency virus-1 (HIV). We characterized HPV infection in a large cohort of HIV-positive and HIV-negative women participating in the Women's Interagency HIV Study to determine the prevalence of and risk factors for cervicovaginal HPV infection in HIV-positive women.

METHODS

HIV-positive (n = 1778) and HIV-negative (n = 500) women were tested at enrollment for the presence of HPV DNA in a cervicovaginal lavage specimen. Blood samples were tested for HIV antibody status, level of CD4-positive T cells, and HIV RNA load (copies/mL). An interview detailing risk factors was conducted. Univariate and multivariate analyses were performed.

RESULTS

Compared with HIV-negative women, HIV-positive women with a CD4+ cell count of less than 200/mm3 were at the highest risk of HPV infection, regardless of HIV RNA load (odds ratio [OR] = 10.13; 95% confidence interval [CI] = 7.32-14.04), followed by women with a CD4+ count greater than 200/mm3 and an HIV RNA load greater than 20,000 copies/mL (OR = 5.78; 95% CI = 4.17-8.08) and women with a CD4+ count greater than 200/mm3 and an HIV RNA load less than 20,000 copies/mL (OR = 3.12; 95% CI = 2.36-4.12), after adjustment for other factors. Other risk factors among HIV-positive women included racial/ethnic background (African-American versus Caucasian, OR = 1.64; 95% CI = 1.19-2.28), current smoking (yes versus no; OR = 1.55; 95% CI = 1.20-1.99), and younger age (age < 30 years versus > or = 40 years; OR = 1.75; 95% CI = 1.23-2.49).

CONCLUSIONS

Although the strongest risk factors of HPV infection among HIV-positive women were indicators of more advanced HIV-related disease, other factors commonly found in studies of HIV-negative women, including racial/ethnic background, current smoking, and age, were important in HIV-positive women as well.

Human immunodeficiency virus type 1 reverse transcriptase expressing the K70E mutation exhibits a decrease in specific activity and processivity

Adefovir dipivoxil [9-(2-(bispivaloyloxymethyl)phosphonylmethoxyethyl)adenine (bis-POM PMEA)], an oral prodrug of adefovir (PMEA), is currently in phase III clinical testing for the treatment of human immunodeficiency virus-1 (HIV-1) infection. Previous in vitro experiments have shown that HIV-1 recombinant viruses expressing either a K65R or a K70E mutation in reverse transcriptase (RT) have reduced sensitivity to PMEA and that the K70E mutant also has impaired replication capacity in vitro. Genotypic analyses of samples from patients enrolled in a phase I/II clinical trial of adefovir dipivoxil demonstrated that the K70E RT mutation developed in two of 29 patients during extended therapy. To further investigate the molecular mechanisms involved in the resistance to PMEA, we cloned, expressed, and purified HIV-1 RT enzymes carrying either the K65R or K70E and, for comparison, the M184V mutation. The Km values of dNTPs for these mutant enzymes were not significantly altered from wild-type RT. The Ki values for the K65R mutant were increased from wild-type by 2-5-fold against a variety of inhibitors, whereas the Ki values for the M184V mutant were increased 12-fold specifically for 2', 3'-dideoxy-3'-thiacytidine (3TC) triphosphate. The Ki values for the K70E mutant were increased for PMEA diphosphate and 3TC triphosphate by 2-3-fold. These results are in agreement with antiviral drug susceptibility assay results. The three recombinant enzymes were also evaluated for their specific activities and processivities. All mutants were reduced in specific activity with respect to wild-type RT. In single-cycle processivity studies, the M184V mutant was, as expected, notably impaired. The K70E mutant was also slightly impaired, whereas the K65R mutant was slightly more processive than wild-type. These results with recombinant K70E RT are consistent with the reduced in vitro replication capacity of the K70E RT mutant of HIV-1 and further demonstrate that the K70E mutation confers minor PMEA and 3TC resistance to HIV-1.

Serum HIV-1 RNA levels compared to soluble markers of immune activation to predict disease progression in HIV-1-infected individuals

We assessed the value of HIV-1 RNA level compared to soluble immune activation markers, namely neopterin, beta2-microglobulin and soluble TNF receptor 75 (sTNFR-75), to predict the change in the number of CD4+ T cells over a 1-year period, the development of AIDS, and survival (median follow-up 54 months). The study population comprised a cohort of 47 individuals for the analysis of the change in CD4+ T cells and survival (20 died), and a subgroup of 31 individuals with a baseline CD4+ T cells above 200 x 10(6)/l for the development of AIDS (11 developed AIDS). HIV-1 RNA was measured from stored sera by quantitative PCR. The CD4+ T cell count obtained at study entry strongly correlated with baseline serum HIV-1 RNA levels (r=-0.47), and to a lesser extent with neopterin (r=-0.41) and beta2-microglobulin (r=-0.29). The percentage change in CD4+ T cells over a 1-year period correlated with HIV-1 RNA levels (r=-0.32, p=0.03), however, stronger correlations were found for neopterin, beta2-microglobulin and sTNFR-75 (r=-0.51, r=-0.41, r=-0.42; p< 0.01). No progression to AIDS or death was observed in individuals with baseline HIV-1 RNA levels below 20,000 copies/ml (10 of 31 and 15 of 47 individuals, respectively). A Cox's proportional hazard model to predict AIDS revealed that HIV-1 RNA, the change in CD4+ cells over a 1-year period and sTNFR-75 levels independently predict AIDS; the change in CD4+ cells, the absolute CD4+ T cell count and neopterin were jointly significant to predict death. All results were adjusted for nucleoside monotherapy. In conclusion, to improve the predictive power, quantitation of HIV-1 RNA as a 'natural history marker' may be supplemented by measurement of sTNFR-75 for 'early'-stage disease progression and neopterin for 'late'-stage disease progression.

Kinetics of response in lymphoid tissues to antiretroviral therapy of HIV-1 infection

In lymphoid tissue, where human immunodeficiency virus-type 1 (HIV-1) is produced and stored, three-drug treatment with viral protease and reverse transcriptase inhibitors markedly reduced viral burden. This was shown by in situ hybridization and computerized quantitative analysis of serial tonsil biopsies from previously untreated adults. The frequency of productive mononuclear cells (MNCs) initially diminished with a half-life of about 1 day. Surprisingly, the amount of HIV-1 RNA in virus trapped on follicular dendritic cells (FDCs) decreased almost as quickly. After 24 weeks, MNCs with very few copies of HIV-1 RNA per cell were still detectable, as was proviral DNA; however, the amount of FDC-associated virus decreased by >/=3.4 log units. Thus, 6 months of potent therapy controlled active replication and cleared >99.9 percent of virus from the secondary lymphoid tissue reservoir.

Quantitative image analysis of HIV-1 infection in lymphoid tissue

Tracking human immunodeficiency virus-type 1 (HIV-1) infection at the cellular level in tissue reservoirs provides opportunities to better understand the pathogenesis of infection and to rationally design and monitor therapy. A quantitative technique was developed to determine viral burden in two important cellular compartments in lymphoid tissues. Image analysis and in situ hybridization were combined to show that in the presymptomatic stages of infection there is a large, relatively stable pool of virions on the surfaces of follicular dendritic cells and a smaller pool of productively infected cells. Despite evidence of constraints on HIV-1 replication in the infected cell population in lymphoid tissues, estimates of the numbers of these cells and the virus they could produce are consistent with the quantities of virus that have been detected in the bloodstream. The cellular sources of virus production and storage in lymphoid tissues can now be studied with this approach over the course of infection and treatment.