Chronic viral infection compromises the quality of circulating mucosal-invariant T cells and follicular T helper cells via expression of both activating and inhibitory receptors

Chronic viral infection results in impaired immune responses rendering viral persistence. Here, we investigated the role of immune activation and compared the quality of T-cell responses in chronic HBV, HCV, and HIV infections. Cytokines were measured using a commercial Bio-plex Pro Human Cytokine Grp I Panel 17-plex kit (BioRad, Hercules, CA, USA). Inflammation was assessed by measuring an array of plasma cytokines, and peripheral CD4+ T cells including circulating Tfh cells, CD8+ T cells, and TCR iVα7.2+ MAIT cells in chronic HBV, HCV, and HIV-infected patients and healthy controls. The cells were characterized based markers pertaining to immune activation (CD69, ICOS, and CD27) proliferation (Ki67), cytokine production (TNF-α, IFN-γ) and exhaustion (PD-1). The cytokine levels and T cell phenotypes together with cell markers were correlated with surrogate markers of disease progression. The activation marker CD69 was significantly increased in CD4+ hi T cells, while CD8+ MAIT cells expressing IFN-γ were significantly increased in chronic HBV, HCV and HIV infections. Six cell phenotypes, viz., TNF-α+CD4+ lo T cells, CD69+CD8+ T cells, CD69+CD4+ MAIT cells, PD-1+CD4+ hi T cells, PD-1+CD8+ T cells, Ki67+CD4+ MAIT cells were independently associated with decelerating the plasma viral load (PVL). TNF-α levels showed a positive correlation with increase in cytokine levels and decrease in PVL. Chronic viral infection negatively impacts the quality of peripheral MAIT cells and TFH cells via expression of both activating and inhibitory receptors.

Plasma interleukin-7 correlation with human immunodeficiency virus RNA and CD4+ T cell counts, and interleukin-5 with circulating hepatitis B virus DNA may have implications in viral control

Chronic viral infections represent a leading cause of global morbidity and mortality. Chronic HBV, HCV, and HIV infections result in cytokine perturbations that may hold key implications in understanding the complex disease mechanisms driving virus persistence and/or resolution. Here, we determined the levels of various plasma cytokines using a commercial Bio-Plex Luminex cytokine array in chronic HBV (n = 30), HCV (n = 15), and HIV (n = 40) infections and correlated with corresponding plasma viral loads (PVLs) and liver parameters. We observed differential perturbations in cytokine profiles among the study groups. The cytokines levels positively correlated with PVL and liver transaminases. The monocyte-derived cytokines viz., MIP-1β, IL-8, and TNF-α, and Th2 cytokines like IL-4, IL-5, and IL-13 showed a better correlation with liver enzymes as compared to their corresponding PVLs. Our investigation also identified two cytokines viz., IL-5 and IL-7 that inversely correlated with HBV DNA and HIV PVLs, respectively. Regression analysis adjusted for age showed that every increase of IL-5 by one unit was associated with a reduction in HBV PVL by log10 0.4, whereas, every elevation by a unit of IL-7 was associated with decreased HIV PVL by log10 2.5. We also found that IL-7 levels correlated positively with absolute CD4+ T cell counts in HIV-infected patients. We concluded that plasma IL-5 and IL-7 may likely have a key role on viral control in HBV and HIV infections, respectively. A noteworthy increase in cytokines appears to bear protective and pathological significance, and indeed is reflective of the host's versatile immune armory against viral persistence.

Low SARS-CoV-2 viral load among vaccinated individuals infected with Delta B.1.617.2 and Omicron BA.1.1.529 but not with Omicron BA.1.1 and BA.2 variants

The rapid spread of SARS-CoV-2 variants in the global population is indicative of the development of selective advantages in emerging virus strains. Here, we performed a case-control investigation of the clinical and demographic characteristics, clinical history, and virological markers to predict disease progression in hospitalized adults for COVID-19 between December 2021 and January 2022 in Chennai, India. COVID-19 diagnosis was made by a commercial TaqPath COVID-19 RT-PCR, and WGS was performed with the Ion Torrent Next Generation Sequencing System. High-quality (<5% of N) complete sequences of 73 Omicron B.1.1.529 variants were randomly selected for phylogenetic analysis. SARS-CoV-2 viral load, number of comorbidities, and severe disease presentation were independently associated with a shorter time-to-death. Strikingly, this was observed among individuals infected with Omicron BA.2 but not among those with the BA.1.1.529, BA.1.1, or the Delta B.1.617.2 variants. Phylogenetic analysis revealed severe cases predominantly clustering under the BA.2 lineage. Sequence analyses showed 30 mutation sites in BA.1.1.529 and 33 in BA.1.1. The mutations unique to BA.2 were T19I, L24S, P25del, P26del, A27S, V213G, T376A, D405N and R408S. Low SARS-CoV-2 viral load among vaccinated individuals infected with Delta B.1.617.2 and the Omicron BA.1.1.529 variant but not with Omicron BA.1.1 or BA.2 suggests that the newer strains are largely immune escape variants. The number of vaccine doses received was independently associated with increased odds of developing asymptomatic disease or recovery. We propose that the novel mutations reported herein could likely bear a significant impact on the clinical characteristics, disease progression, and epidemiological aspects of COVID-19. Surging rates of mutations and the emergence of eclectic variants of SARS-CoV-2 appear to impact disease dynamics.

Dengue Infection - Recent Advances in Disease Pathogenesis in the Era of COVID-19

The dynamics of host-virus interactions, and impairment of the host’s immune surveillance by dengue virus (DENV) serotypes largely remain ambiguous. Several experimental and preclinical studies have demonstrated how the virus brings about severe disease by activating immune cells and other key elements of the inflammatory cascade. Plasmablasts are activated during primary and secondary infections, and play a determinative role in severe dengue. The cross-reactivity of DENV immune responses with other flaviviruses can have implications both for cross-protection and severity of disease. The consequences of a cross-reactivity between DENV and anti-SARS-CoV-2 responses are highly relevant in endemic areas. Here, we review the latest progress in the understanding of dengue immunopathogenesis and provide suggestions to the development of target strategies against dengue.

cGAS and DDX41-STING mediated intrinsic immunity spreads intercellularly to promote neuroinflammation in SOD1 ALS model

Neuroinflammation exacerbates the progression of SOD1-driven amyotrophic lateral sclerosis (ALS), although the underlying mechanisms remain largely unknown. Herein, we demonstrate that misfolded SOD1 (SOD1^Mut)-causing ALS results in mitochondrial damage, thus triggering the release of mtDNA and an RNA:DNA hybrid into the cytosol in an mPTP-independent manner to activate IRF3- and IFNAR-dependent type I interferon (IFN-I) and interferon-stimulating genes. The neuronal hyper-IFN-I and pro-inflammatory responses triggered in ALS-SOD1^Mut were sufficiently robust to cause a strong physiological outcome in vitro and in vivo. cGAS/DDX41-STING-signaling is amplified in bystander cells through inter-neuronal gap junctions. Our results highlight the importance of a common DNA-sensing pathway between SOD1 and TDP-43 in influencing the progression of ALS.

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Constitutive basal activation of IFN-I was found in the SOD1-ALS animal model

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SOD1-ALS damaged mitochondria to release mtDNA and RNA:DNA to activate the STING-pathway

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Blocking cGAS and STING diminishes neurodegeneration in vivo in the SOD1-ALS model

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Connexin and pannexin channels are required to propagate neuroinflammation in SOD1-ALS

Factors Associated With the Decay of Anti-SARS-CoV-2 S1 IgG Antibodies Among Recipients of an Adenoviral Vector-Based AZD1222 and a Whole-Virion Inactivated BBV152 Vaccine

Background

The magnitude of protection conferred following recovery from COVID-19 or by vaccine administration, and the duration of protective immunity developed, remains ambiguous.

Methods

We investigated the factors associated with anti-SARS-CoV-2 S1 IgG decay in 519 individuals who recovered from COVID-19 illness or received COVID-19 vaccination with two commercial vaccines, viz., an adenoviral vector-based (AZD1222) and a whole-virion-based inactivated (BBV152) vaccine in Chennai, India from March to December 2021. Blood samples collected during regular follow-up post-infection/-vaccination were examined for anti-SARS-CoV-2 S1 IgG by a commercial automated chemiluminescent immunoassay (CLIA).

Results

Age and underlying comorbidities were the two variables that were independently associated with the development of a breakthrough infection. Individuals who were >60 years of age with underlying comorbid conditions (viz., hypertension, diabetes mellitus and cardiovascular disease) had a ~15 times and ~10 times greater odds for developing a breakthrough infection and hospitalization, respectively. The time elapsed since the first booster dose was associated with attrition in anti-SARS-CoV-2 IgG, where each month passed was associated with an ebb in the anti-SARS-CoV-2 IgG antibody levels by a coefficient of -6 units.

Conclusions

Our findings advocate that the elderly with underlying comorbidities be administered with appropriate number of booster doses with AZD1222 and BBV152 against COVID-19.

T-Cell Exhaustion in Chronic Infections: Reversing the State of Exhaustion and Reinvigorating Optimal Protective Immune Responses

T-cell exhaustion is a phenomenon of dysfunction or physical elimination of antigen-specific T cells reported in human immunodeficiency virus (HIV), hepatitis B virus (HBV), and hepatitis C virus (HCV) infections as well as cancer. Exhaustion appears to be often restricted to CD8+ T cells responses in the literature, although CD4+ T cells have also been reported to be functionally exhausted in certain chronic infections. Although our understanding of the molecular mechanisms associated with the transcriptional regulation of T-cell exhaustion is advancing, it is imperative to also explore the central mechanisms that control the altered expression patterns. Targeting metabolic dysfunctions with mitochondrion-targeted antioxidants are also expected to improve the antiviral functions of exhausted virus-specific CD8+ T cells. In addition, it is crucial to consider the contributions of mitochondrial biogenesis on T-cell exhaustion and how mitochondrial metabolism of T cells could be targeted whilst treating chronic viral infections. Here, we review the current understanding of cardinal features of T-cell exhaustion in chronic infections, and have attempted to focus on recent discoveries, potential strategies to reverse exhaustion and reinvigorate optimal protective immune responses in the host.

Tuberculosis (TB)-associated immune reconstitution inflammatory syndrome in TB-HIV co-infected patients in Malaysia: prevalence, risk factors, and treatment outcomes

Background Tuberculosis-associated immune reconstitution inflammatory syndrome (TB-IRIS) is an important early complication of antiretroviral therapy (ART) in countries with high rates of endemic TB, but data from South-East Asia are incomplete. Identification of prevalence, risk factors and treatment outcomes of TB-IRIS in Malaysia was sought. Methods: A 3-year retrospective study was conducted among TB-HIV co-infected patients treated at the University of Malaya Medical Centre. Simple and adjusted logistic regressions were used to identify the predictors for TB-IRIS while Cox regression was used to assess the influence of TB-IRIS on long-term CD4 T-cell recovery. Results: One hundred and fifty-three TB-HIV patients were enrolled, of whom 106 had received both anti-TB treatment (ATT) and ART. The median (IQR) baseline CD4 T-cell count was 52 cells μL–1 (13–130 cells μL–1). Nine of 96 patients (9.4%) developed paradoxical TB-IRIS and eight developed unmasking TB-IRIS, at a median (IQR) time of 27 (12–64) and 19 (14–65) days, respectively. In adjusted logistic regression analysis, only disseminated TB was predictive of TB-IRIS [OR: 10.7 (95% CI: 1.2–94.3), P = 0.032]. Mortality rates were similar for TB-IRIS (n = 1, 5.9%) and non-TB-IRIS (n = 5, 5.7%) patients and CD4 T-cell recovery post-ART was not different between the two groups (P = 0.363). Conclusion: Disseminated TB was a strong independent predictor of TB-IRIS in Malaysian HIV-TB patients after commencing ART. This finding underscores the role of a high pathogen load in the pathogenesis of TB-IRIS; so interventions that reduce pathogen load before ART may benefit HIV patients with disseminated TB.

Molecular diversity of HIV-1 among people who inject drugs in Kuala Lumpur, Malaysia: massive expansion of circulating recombinant form (CRF) 33_01B and emergence of multiple unique recombinant clusters

Since the discovery of HIV-1 circulating recombinant form (CRF) 33_01B in Malaysia in the early 2000 s, continuous genetic diversification and active recombination involving CRF33_01B and other circulating genotypes in the region including CRF01_AE and subtype B' of Thai origin, have led to the emergence of novel CRFs and unique recombinant forms. The history and magnitude of CRF33_01B transmission among various risk groups including people who inject drugs (PWID) however have not been investigated despite the high epidemiological impact of CRF33_01B in the region. We update the most recent molecular epidemiology of HIV-1 among PWIDs recruited in Malaysia between 2010 and 2011 by population sequencing and phylogenetic analysis of 128 gag-pol sequences. HIV-1 CRF33_01B was circulating among 71% of PWIDs whilst a lower prevalence of other previously dominant HIV-1 genotypes [subtype B' (11%) and CRF01_AE (5%)] and CRF01_AE/B' unique recombinants (13%) were detected, indicating a significant shift in genotype replacement in this population. Three clusters of CRF01_AE/B' recombinants displaying divergent yet phylogenetically-related mosaic genomes to CRF33_01B were identified and characterized, suggestive of an abrupt emergence of multiple novel CRF clades. Using rigorous maximum likelihood approach and the Bayesian Markov chain Monte Carlo (MCMC) sampling of CRF33_01Bpol sequences to elucidate the past population dynamics, we found that the founder lineages of CRF33_01B were likely to have first emerged among PWIDs in the early 1990 s before spreading exponentially to various high and low-risk populations (including children who acquired infections from their mothers) and later on became endemic around the early 2000 s. Taken together, our findings provide notable genetic evidence indicating the widespread expansion of CRF33_01B among PWIDs and into the general population. The emergence of numerous previously unknown recombinant clades highlights the escalating genetic complexity of HIV-1 in the Southeast Asian region.

Diagonal control design for atomic force microscope piezoelectric tube nanopositioners

Atomic Force Microscopes (AFM) are used for generating surface topography of samples at micro to atomic resolutions. Many commercial AFMs use piezoelectric tube nanopositioners for scanning. Scanning rates of these microscopes are hampered by the presence of low frequency resonant modes. When inadvertently excited, these modes lead to high amplitude mechanical vibrations causing the loss of accuracy, while scanning, and eventually to break down of the tube. Feedback control has been used to damp these resonant modes. Thereby, enabling higher scanning rates. Here, a multivariable controller is designed to damp the first resonant mode along both the x and y axis. Exploiting the inherent symmetry in the piezoelectric tube, the multivariable control design problem is recast as independent single-input single-output (SISO) designs. This in conjunction with integral resonant control is used for damping the first resonant mode.

Invited review article: high-speed flexure-guided nanopositioning: mechanical design and control issues

Recent interest in high-speed scanning probe microscopy for high-throughput applications including video-rate atomic force microscopy and probe-based nanofabrication has sparked attention on the development of high-bandwidth flexure-guided nanopositioning systems (nanopositioners). Such nanopositioners are designed to move samples with sub-nanometer resolution with positioning bandwidth in the kilohertz range. State-of-the-art designs incorporate uniquely designed flexure mechanisms driven by compact and stiff piezoelectric actuators. This paper surveys key advances in mechanical design and control of dynamic effects and nonlinearities, in the context of high-speed nanopositioning. Future challenges and research topics are also discussed.

Robust interferon-α and IL-12 responses by dendritic cells are related to efficient CD4+ T-cell recovery in HIV patients on ART

Amongst HIV patients with successful virological responses to antiretroviral therapy (ART), poor CD4(+) T-cell recovery is associated with low nadir CD4(+) T-cell counts and persistent immune activation. These factors might be influenced by dendritic cell (DC) function. Interferon-α-producing plasmacytoid DC and IL-12-producing myeloid DC were quantified by flow cytometry after stimulation with agonists to TLR7/8 (CL075) or TLR9 (CpG-ODN). These were compared between patients who achieved CD4(+) T-cell counts above or below 200 cells/μL after 6 months on ART (High vs. Low groups). High Group patients had more DC producing interferon-α or IL-12 at Weeks 6 and 12 on ART than Low Group patients. The frequencies of cytokine-producing DC at Week 12 were directly correlated with CD4(+) T-cell counts at baseline and at Week 12. Patients with good recovery of CD4(+) T-cells had robust TLR-mediated interferon-α responses by plasmacytoid DC and IL-12 responses by myeloid DC during early ART (1-3 months).

High-speed cycloid-scan atomic force microscopy

A key hurdle in achieving high scan speeds in atomic force microscopes is that the probe is required to be scanned over the sample in a zig-zag raster pattern. The fast axis of the AFM scanner must track a signal that contains frequencies beyond its mechanical bandwidth. Consequently, fast raster scans generate distortions in the resulting image. We propose a smooth cycloid-like scan pattern that allows us to achieve scan speeds much higher than a raster scan. We illustrate how the proposed method can be implemented on a commercial AFM with minimal modifications.

Immunological profiles of immune restoration disease presenting as mycobacterial lymphadenitis and cryptococcal meningitis

OBJECTIVES

A proportion of HIV patients beginning antiretroviral therapy (ART) develop immune restoration disease (IRD). Immunological characteristics of IRD were investigated in a cohort of HIV patients beginning therapy in Kuala Lumpur, Malaysia.

METHODS

Peripheral blood mononuclear cells were collected at weeks 0, 6, 12, 24 and 48 of ART from five patients experiencing IRD [two with cryptococcal and three with Mycobacterium tuberculosis (Mtb) disease], eight non-IRD controls who had begun ART with CD4 T-cell counts of <100 cells/microL and 17 healthy controls. Leukocytes producing interferon-gamma (IFNgamma) were quantified by enzyme-linked immunospot assay after stimulation with purified protein derivative (PPD), early secretory antigenic target-6 (ESAT-6), Cryptococcus neoformans or Cytomegalovirus antigens. Plasma immunoglobulin (IgG) antibodies reactive with these antigens were assessed by enzyme-linked immunosorbent assay. Proportions of activated (HLA-DR(hi)) and regulatory (CD25 CD127(lo) and CTLA-4(+)) CD4 T-cells were quantified by flow cytometry.

RESULTS

Plasma HIV RNA declined and CD4 T-cell counts rose within 8-27 weeks on ART. Mtb IRD patients displayed elevated IFNgamma responses and/or plasma IgG to PPD, but none responded to ESAT-6. Cryptococcal IRD occurred in patients with low baseline CD4 T-cell counts and involved clear IFNgamma and antibody responses to cryptococcal antigen. Proportions of activated and regulatory CD4 T-cells declined on ART, but remained higher in patients than in healthy controls. At the time of IRD, proportions of activated CD4 T-cells and regulatory CD4 T-cells were generally elevated relative to other patients.

CONCLUSIONS

Cryptococcal and Mtb IRD generally coincide with peaks in the proportion of activated T-cells, pathogen-specific IFNgamma responses and reactive plasma IgG. IRD does not reflect a paucity of regulatory CD4 T-cells.

Rapid detection and serotyping of dengue virus by multiplex RT-PCR and real-time SYBR green RT-PCR

INTRODUCTION

Dengue fever and dengue haemorrhagic fever currently rank highly among the newly-emerging infectious diseases, and are considered to be the most important arboviral disease worldwide. The definitive diagnosis is culture analysis, but practical considerations limit its use. Also, the period for viral detection is limited. Within a day or two after fever subsides, rising levels of antibodies interfere with viral cultures. An alternative to this quandary is the use of viral RNA detection assays. In our laboratory, a reverse transcriptase polymerase chain reaction (RT-PCR) assay was developed using a set of degenerate primers.

METHODS

This multiplex RT-PCR assay was evaluated with 280 samples collected during the year 2003. These groups include prototype dengue virus (serotypes 1-4), acute serum from which the dengue virus was isolated, seronegative acute samples (culture negative) but whose convalescent samples seroconverted, and sera positive for other microbial diseases. This assay was then modified into a real-time SYBR Green RT-PCR assay. Sensitivity and specificity of both assays were compared.

RESULTS

The multiplex RT-PCR assay was able to detect 134 samples whereas SYBR Green RT-PCR assay was able to detect 178 out of 306 samples. Both assays were 100 percent specific. Further analysis of 53 samples showed that the virus could be amplified at IgM positive/negative values of up to 4.2, and up to six days after onset of fever. The viral detection rate was inversely proportional to the day of fever onset as well as IgM values.

CONCLUSION

The sensitivity and specificity of the conventional multiplex RT-PCR assay are 98.18 percent and 100 percent, respectively, and for the real-time SYBR Green assay, 99.09 percent and 100 percent, respectively. The melting curve analysis allows all four dengue serotypes to be discriminated based on distinct melting temperature value. The accuracy and speed of this multiplex RTPCR assay makes it a suitable test for the diagnosis of dengue and for epidemiological surveillance.

On the accuracy of Mindlin plate predictions for the frequency-temperature behavior of resonant modes in AT- and SC-cut quartz plates

The frequency spectra of resonant modes in AT- and SC-cut quartz plates and their frequency-temperature behavior were studied using Mindlin first- and third-order plate equations. Both straight-crested wave solutions and two-dimensional plate solutions were studied. The first-order Mindlin plate theory with shear correction factors was previously found to yield inaccurate frequency spectra of the modes in the vicinity of the fundamental thickness-shear frequency. The third-order Mindlin plate equations without correction factors, on the other hand, predict well the frequency spectrum in the same vicinity. In general, the frequency-temperature curves of the fundamental thickness-shear obtained from the first-order Mindlin plate theory are sufficiently different from those of the third-order Mindlin plate theory that they raise concerns. The least accurately predicted mode of vibration is the flexure mode, which results in discrepancies in its frequency-temperature behavior. The accuracy of other modes of vibrations depends on the degree of couplings with the flexure mode. Mindlin first-order plate theory with only the shear correction factors is not sufficiently accurate for high frequency crystal vibrations at the fundamental thickness-shear frequency. Comparison with measured resonant frequencies and frequency-temperature results on an AT-cut quartz plate shows that the third-order plate theory is more accurate than the first-order plate theory; this is especially true for the technically important fundamental thickness shear mode in the AT-cut quartz plate.

Numerical algorithms and results for SC-cut quartz plates vibrating at the third harmonic overtone of thickness shear

Finite element matrix equations, derived from two-dimensional piezoelectric high frequency plate theory are solved to study the vibrational behavior of the third overtone of thickness shear in square and circular SC-cut quartz resonators. The mass-loading and electric effects of electrodes are included. A perturbation method which reduces the memory requirements and computational time significantly is employed to calculate the piezoelectric resonant frequencies. A new storage scheme is introduced which reduces memory requirements for mass matrix by about 90% over that of the envelope storage scheme. Substructure techniques are used in eigenvalue calculation to save storage. Resonant frequency and the mode shapes of the harmonic third overtone thickness shear vibrations for square and circular plates are calculated. A predominant third overtone thickness shear displacement, coupled with the third overtone of thickness stretch and thickness twist, is observed. Weak coupling between the third order thickness shear displacement and the zeroth-, first-, and second-order displacements is noted. The magnitudes of the lower order displacements are found to be about two orders smaller than that of the third overtone thickness shear displacement.

A perturbation method for finite element modeling of piezoelectric vibrations in quartz plate resonators

When the piezoelectric stiffening matrix is added to the mechanical stiffness matrix of a finite element model, its sparse matrix structure is destroyed. A direct consequence of this loss in sparseness is a significant rise in memory and computational time requirements for the model. For weakly coupled piezoelectric materials, the matrix sparseness can be retained by a perturbation method which separates the mechanical eigenvalue solution from its piezoelectric effects. Using this approach, a perturbation and finite element scheme for weakly coupled piezoelectric vibrations in quartz plate resonators has been developed. Finite-element matrix equations were derived specifically for third-overtone thickness-shear, SC-cut quartz plate resonators with electrode platings. High-frequency piezoelectric plate equations were employed in the formulation of the finite element matrix equation. Results from the perturbation method compared well with the direct solution of the piezoelectric finite element equations. This method will result in significant savings in the computer memory and computational time. Resonance and antiresonance frequencies of a certain mode could be calculated easily by using the same eigenpair from the purely mechanical stiffness matrix. Numerical results for straight crested waves in a third overtone SC-cut quartz strip with and without electrodes are presented. The steady-state response to an electrical excitation is calculated.

Thickness-shear mode shapes and mass-frequency influence surface of a circular and electroded AT-cut quartz resonator

Finite-element solutions for the fundamental thickness shear mode and the second-anharmonic overtone of a circular, 1.87-MHz AT-cut quartz plate with no electrodes are presented and compared with previously obtained results for a rectangular plate of similar properties. The edge flexural mode in circular plates, a vibration mode not seen in the rectangular plate is also presented. A 5-MHz circular and electroded AT-cut quartz plate is studied. A portion of the frequency spectrum is constructed in the neighborhood of the fundamental thickness-shear mode. A convergence study is also presented for the electroded 5-MHz plate. A new two-dimensional (2-D) technique for visualizing the vibration mode solutions is presented. This method departs substantially from the three-dimensional (3-D) ;wire-frame' plots presented in the previous analysis. The 2-D images can be manipulated to produce nodal line diagrams and can be color coded to illustrate mode shapes and energy trapping phenomenon. A contour plot of the mass-frequency influence surface for the plated 5-MHz resonator is presented. The mass-frequency influence surface is defined as a surface giving the frequency change due to a small localized mass applied to the resonator surface.

Mass-frequency influence surface, mode shapes, and frequency spectrum of a rectangular AT-cut quartz plate

The mass-frequency influence surface and frequency spectrum of a rectangular AT-cut quartz plate are studied. The mass-frequency influence surface is defined as a surface giving the frequency change due to a small localized mass applied on the plate surface. Finite-element solutions of R.D. Mindlin's (1963) two-dimensional plate equations for thickness-shear, thickness-twist, and flexural vibrations are given. Spectrum splicing, and an efficient eigenvalue solver using the C. Lanczos (1950) algorithm are incorporated into the finite-element program. A convergence study of the fundamental thickness-shear mode and its first symmetric, anharmonic overtone is performed for finite-element meshes of increasing fineness. As a general rule, more than two elements must span any half-wave in the plate or spurious mode shapes will be obtained. Two-dimensional (2D) mode shapes and frequency spectrum of a rectangular AT-cut plate in the region of the fundamental thickness-shear frequency are presented. The mass-frequency influence surface for a 5-MHz rectangular, AT-cut plate with patch electrodes is obtained by calculating the frequency change due to a small mass layer moving over the plate surface. The frequency change is proportional to the ratio of mass loading to mass of plate per unit area and is confined mostly within the electrode area, where the magnitude is on the order 10(8) Hz/g.

Modeling resonator frequency fluctuations induced by adsorbing and desorbing surface molecules

Resonator frequency fluctuations due to adsorption and desorption of molecules on plate electrodes are studied using the principle of mass-loading effects of adsorbed molecules. The study is based on a 525 MHz, AT-cut quartz resonator enclosed in a small crystal holder. Equations relating the surface adsorption rates of the crystal holder to pressure were derived and found to be quadratic polynomial functions of the adsorption rates. Calculations based on these equations show that a contaminant gas with a higher desorption energy creates larger changes in pressure when the temperature is varied. The function describing the frequency fluctuations due to any one contaminant site is a continuous-time Markov chain. Kolmogorov equations and an autocorrelation function for the Markov chain are derived. The autocorrelation and spectral density function of resonator frequency fluctuations are derived. The spectral density of frequency fluctuations at 1 Hz is studied as a function of pressure, temperature, and desorption energy of molecules. The noise levels for a contaminant gas with one type of molecules are found to be lower for lower desorption energies, and higher at lower pressures.

Resonator surface contamination-a cause of frequency fluctuations?

The mass loading effects of adsorbing and desorbing contaminant molecules on the magnitude and characteristics of frequency fluctuations in a thickness-shear resonator are studied. The study is motivated by the observation that the frequency of a thickness-shear resonator is determined predominantly by such mechanical parameters as the thickness of the resonator, elastic stiffnesses, mass loading of the electrodes, and energy trapping. An equation was derived relating the spectral density of frequency fluctuations to: (1) rates of adsorption and desorption of one species of contaminant molecules; (2) mass per unit area of a monolayer of molecules: (3) frequency constant; (4) thickness of resonator; and (5) number of molecular sites on one resonator surface. The induced phase noises were found to be significant in very-high-frequency resonators and are not simple functions of the percentage of area contaminated. The spectral density of frequency fluctuations was inversely proportional to the fourth power of the thickness if other parameters were held constant.

Characteristics of a Lagrangian, high-frequency plate element for the static temperature behavior of low-frequency quartz resonators

Finite-element matrix equations based on the Lagrangian, first-order, incremental plate equations of motion superposed on homogeneous thermal strains were formulated using virtual work principles. A program for an isoparametric, four-node quadrilateral element was written and applied to the study of the frequency-temperature (FT) behavior of flexure-mode quartz resonators. The lumped-mass and consistent-mass matrices were found to yield practically the same FT curves. For simple prismatic resonators, two schemes, reduced/selective integration and incompatible modes, produced relatively similar FT curves. The incompatible modes scheme yielded better results for resonators of more complex shapes, such as the tuning fork. It is concluded that the six-degree-of-freedom per node element is needed for the analysis of the FT behavior of a fully anisotropic flexure-mode resonator.