Diagnostics for SARS-CoV-2 infections.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread to nearly every corner of the globe, causing societal instability. The resultant coronavirus disease 2019 (COVID-19) leads to fever, sore throat, cough, chest and muscle pain, dyspnoea, confusion, anosmia, ageusia and headache. These can progress to life-threatening respiratory insufficiency, also affecting the heart, kidney, liver and nervous systems. The diagnosis of SARS-CoV-2 infection is often confused with that of influenza and seasonal upper respiratory tract viral infections. Due to available treatment strategies and required containments, rapid diagnosis is mandated. This Review brings clarity to the rapidly growing body of available and in-development diagnostic tests, including nanomaterial-based tools. It serves as a resource guide for scientists, physicians, students and the public at large.

A tridomain model for potassium clearance in optic nerve of Necturus.

Complex fluids flow in complex ways in complex structures. Transport of water and various organic and inorganic molecules in the central nervous system are important in a wide range of biological and medical processes. However, the exact driving mechanisms are often not known. In this work, we investigate flows induced by action potentials in an optic nerve as a prototype of the central nervous system. Different from traditional fluid dynamics problems, flows in biological tissues such as the central nervous system are coupled with ion transport. They are driven by osmosis created by concentration gradient of ionic solutions, which in turn influence the transport of ions. Our mathematical model is based on the known structural and biophysical properties of the experimental system used by the Harvard group Orkand et al. Asymptotic analysis and numerical computation show the significant role of water in convective ion transport. The full model (including water) and the electrodiffusion model (excluding water) are compared in detail to reveal an interesting interplay between water and ion transport. In the full model, convection due to water flow dominates inside the glial domain. This water flow in the glia contributes significantly to the spatial buffering of potassium in the extracellular space. Convection in the extracellular domain does not contribute significantly to spatial buffering. Electrodiffusion is the dominant mechanism for flows confined to the extracellular domain.

Gating current noise produced by Brownian models of a voltage sensor.

The activation of voltage-dependent ion channels is associated with the movement of gating charges, which give rise to gating currents. Although gating currents from a single channel are too small to be detected, analysis of the fluctuations of macroscopic gating currents from a population of channels allows a good guess of their magnitude. The analysis of experimental gating current fluctuations, when interpreted in terms of a rate model of channel activation and assuming sufficiently high bandwidth, is in accordance with the presence of a main step along the activation pathway carrying a charge of 2.3-2.4 e0. To give a physical interpretation to these results and to relate them to the known atomic structure of the voltage sensor domain, we used a Brownian model of voltage-dependent gating based on atomic detail structure, that follows the laws of electrodynamics. The model predicts gating currents and gating current fluctuations essentially similar to those experimentally observed. The detailed study of the model output, also performed by making several simplifications aimed at understanding the basic dependencies of the gating current fluctuations, suggests that in real channels the voltage sensor moves along a sequence of intermediate states separated by relatively low (<5 kT) energy barriers. As a consequence, crossings of successive gating charges through the gating pore become very frequent, and the corresponding current shots are often seen to overlap because of the relatively high filtering. Notably, this limited bandwidth effect is at the origin of the relatively high single-step charge experimentally detected.

Maxwell Equations without a Polarization Field, Using a Paradigm from Biophysics.

When forces are applied to matter, the distribution of mass changes. Similarly, when an electric field is applied to matter with charge, the distribution of charge changes. The change in the distribution of charge (when a local electric field is applied) might in general be called the induced charge. When the change in charge is simply related to the applied local electric field, the polarization field P is widely used to describe the induced charge. This approach does not allow electrical measurements (in themselves) to determine the structure of the polarization fields. Many polarization fields will produce the same electrical forces because only the divergence of polarization enters Maxwell's first equation, relating charge and electric forces and field. The curl of any function can be added to a polarization field P without changing the electric field at all. The divergence of the curl is always zero. Additional information is needed to specify the curl and thus the structure of the P field. When the structure of charge changes substantially with the local electric field, the induced charge is a nonlinear and time dependent function of the field and P is not a useful framework to describe either the electrical or structural basis-induced charge. In the nonlinear, time dependent case, models must describe the charge distribution and how it varies as the field changes. One class of models has been used widely in biophysics to describe field dependent charge, i.e., the phenomenon of nonlinear time dependent induced charge, called 'gating current' in the biophysical literature. The operational definition of gating current has worked well in biophysics for fifty years, where it has been found to makes neurons respond sensitively to voltage. Theoretical estimates of polarization computed with this definition fit experimental data. I propose that the operational definition of gating current be used to define voltage and time dependent induced charge, although other definitions may be needed as well, for example if the induced charge is fundamentally current dependent. Gating currents involve substantial changes in structure and so need to be computed from a combination of electrodynamics and mechanics because everything charged interacts with everything charged as well as most things mechanical. It may be useful to separate the classical polarization field as a component of the total induced charge, as it is in biophysics. When nothing is known about polarization, it is necessary to use an approximate representation of polarization with a dielectric constant that is a single real positive number. This approximation allows important results in some cases, e.g., design of integrated circuits in silicon semiconductors, but can be seriously misleading in other cases, e.g., ionic solutions.

On the polarization of ligands by proteins.

Although ligand-binding sites in many proteins contain a high number density of charged side chains that can polarize small organic molecules and influence binding, the magnitude of this effect has not been studied in many systems. Here, we use a quantum mechanics/molecular mechanics (QM/MM) approach, in which the ligand is the QM region, to compute the ligand polarization energy of 286 protein-ligand complexes from the PDBBind Core Set (release 2016). Calculations were performed both with and without implicit solvent based on the domain decomposition Conductor-like Screening Model. We observe that the ligand polarization energy is linearly correlated with the magnitude of the electric field acting on the ligand, the magnitude of the induced dipole moment, and the classical polarization energy. The influence of protein and cation charges on the ligand polarization diminishes with the distance and is below 2 kcal mol-1 at 9 Å and 1 kcal mol-1 at 12 Å. Compared to these embedding field charges, implicit solvent has a relatively minor effect on ligand polarization. Considering both polarization and solvation appears essential to computing negative binding energies in some crystallographic complexes. Solvation, but not polarization, is essential for achieving moderate correlation with experimental binding free energies.

A Bidomain Model for Lens Microcirculation.

There exists a large body of research on the lens of the mammalian eye over the past several decades. The objective of this work is to provide a link between the most recent computational models and some of the pioneering work in the 1970s and 80s. We introduce a general nonelectroneutral model to study the microcirculation in the lens of the eye. It describes the steady-state relationships among ion fluxes, between water flow and electric field inside cells, and in the narrow extracellular spaces between cells in the lens. Using asymptotic analysis, we derive a simplified model based on physiological data and compare our results with those in the literature. We show that our simplified model can be reduced further to the first-generation models, whereas our full model is consistent with the most recent computational models. In addition, our simplified model captures in its equations the main features of the full computational models. Our results serve as a useful link intermediate between the computational models and the first-generation analytical models. Simplified models of this sort may be particularly helpful as the roles of similar osmotic pumps of microcirculation are examined in other tissues with narrow extracellular spaces, such as cardiac and skeletal muscle, liver, kidney, epithelia in general, and the narrow extracellular spaces of the central nervous system, the "brain." Simplified models may reveal the general functional plan of these systems before full computational models become feasible and specific.

Continuum Gating Current Models Computed with Consistent Interactions.

The action potential of nerve and muscle is produced by voltage-sensitive channels that include a specialized device to sense voltage. The voltage sensor depends on the movement of charges in the changing electric field as suggested by Hodgkin and Huxley. Gating currents of the voltage sensor are now known to depend on the movements of positively charged arginines through the hydrophobic plug of a voltage sensor domain. Transient movements of these permanently charged arginines, caused by the change of transmembrane potential V, further drag the S4 segment and induce opening/closing of the ion conduction pore by moving the S4-S5 linker. This moving permanent charge induces capacitive current flow everywhere. Everything interacts with everything else in the voltage sensor and protein, and so it must also happen in its mathematical model. A Poisson-Nernst-Planck (PNP)-steric model of arginines and a mechanical model for the S4 segment are combined using energy variational methods in which all densities and movements of charge satisfy conservation laws, which are expressed as partial differential equations in space and time. The model computes gating current flowing in the baths produced by arginines moving in the voltage sensor. The model also captures the capacitive pile up of ions in the vestibules that link the bulk solution to the hydrophobic plug. Our model reproduces the signature properties of gating current: 1) equality of ON and OFF charge Q in integrals of gating current, 2) saturating voltage dependence in the Q(charge)-voltage curve, and 3) many (but not all) details of the shape of gating current as a function of voltage. Our results agree qualitatively with experiments and can be improved by adding more details of the structure and its correlated movements. The proposed continuum model is a promising tool to explore the dynamics and mechanism of the voltage sensor.

Orbital Exenteration to Manage Infiltrative Sinonasal, Orbital Adnexal, and Cutaneous Malignancies Provides Acceptable Survival Outcomes: An Institutional Review, Literature Review, and Meta-Analysis.

PURPOSE: Orbital exenteration (OE) is an aggressive operative undertaking that results in a disfiguring and dysfunctional outcome for patients. The purpose of our study was to determine the survival outcome for patients who underwent OE for malignant disease that had invaded the orbit. MATERIALS AND METHODS: We conducted an ambispective cohort study based on a review of the records of 31 consecutive patients who had undergone OE within John Hunter Hospital. The study period was 2006 to 2013. The predictor variables were the demographic, tumor site, and clinicopathologic characteristics that might influence survival. The secondary outcome variable was survival. Descriptive statistics were calculated for the categorical and continuous variables. Kaplan-Meier estimates of the survival distribution were plotted. We also performed a review of published studies and a meta-analysis to investigate the nature of OE performed by various surgical disciplines. RESULTS: Of the 31 patients included in the present study, 24 were men and 7 were women. The mean age was 65 years. Of the 31 cases, 15 were squamous cell carcinoma, 8 were basal cell carcinoma, and 8 were a mixture of other pathologic types. The time to median (50%) survival for all patients was 78.4 months. The 1-year survival rate was 93.4% and the 5-year survival rate was 54.1%. Although not statistically significant, notable differences were found in the interval to death with respect to the identification of perineural invasion, lymphovascular invasion, and histopathologic features. The review of published studies suggested a difference in the histologic features and location of the disorder treated, the extent of OE undertaken, and the method of reconstruction between the ophthalmology and nonophthalmology surgical disciplines. CONCLUSIONS: Although OE results in significant disfigurement and dysfunction, it does provide good survival outcomes, given the extent of disease at presentation, evident in our group of patients. Continuation of the study, with greater numbers of patients, will serve to increase the statistical power of our observations.

Absence of CD59 exacerbates systemic autoimmunity in MRL/lpr mice.

CD59 is a GPI-anchored membrane regulator of complement expressed on blood cells as well as peripheral tissues. It protects host cells from complement injury by inhibiting formation of the membrane attack complex. Recent studies in mice have suggested also a role of CD59 in T cell immune response that was mechanistically independent of complement. In the present study, we investigated the function of CD59 in the MRL/lpr model of murine lupus. We backcrossed the Cd59a knockout (Cd59a(-/-)) mouse onto the MRL/lpr background and compared Cd59a(+/+)-MRL/lpr and Cd59a(-/-)-MRL/lpr littermates for the development of systemic autoimmunity. We found that CD59a deficiency significantly exacerbated the skin disease and lymphoproliferation characteristic of MRL/lpr mice. It also increased autoantibody titers and caused a higher level of proteinuria in male MRL/lpr mice. Bone marrow transfer experiments indicated that CD59a expression on both bone marrow-derived cells and peripheral tissues played a role in lymphoproliferation, whereas the skin disease phenotype is determined mainly by local CD59a expression. Importantly, C3 gene deletion or C5 neutralization with a blocking mAb in Cd59a(-/-)-MRL/lpr mice did not rescue the proautoimmune phenotype associated with CD59a deficiency. These results together suggest that CD59a inhibits systemic autoimmunity in MRL/lpr mice through a complement-independent mechanism.

Malignant transformation of metachronous bilateral Schneiderian inverted papilloma of the lacrimal sac: management considerations and the contentious issue of orbital exenteration.

The authors present an unusual case of malignant transformation of metachronous bilateral Schneiderian inverted papilloma (IP) of the lacrimal sac. Such pathology has been sparingly covered in prior published literature, in particular with little formal discussion surrounding its optimal management. We describe the clinical presentation, course and management in a 35-year-old male with histopathological diagnosis of Squamous cell carcinoma (SCC) arising within IP. He underwent radical surgery, including orbital exenteration and medial maxillectomy. Our patient re-presented with IP in the contralateral side and subsequent malignant transformation to SCC with disseminated disease. Unfortunately he succumbed to disease approximately 20 months following initial surgery. This case raises several important questions with regard to appropriate treatment. In particular, we discuss the various management options with special consideration given to the contentious topic of orbital exenteration in such patients. We emphasise two particular controversial issues, namely, oncological efficacy of orbital preservation and the functional compromise that may result in the preserved eye.

The role of antibodies in inflammatory arthritis.

Inflammatory arthritis presents in a variety of diseases, from rheumatoid arthritis to hepatitis. Antibodies to autoantigens or to microbial constituents are commonly associated with these conditions. In some cases, the antibodies have diagnostic and prognostic relevance. It cannot as yet be determined definitively that any of them mediate joint damage, although the evidence from animal models indicates that this mechanism is likely. The purpose of this article is to give an overview of the spectrum of antibodies found in a variety of inflammatory arthritides. The relevant animal models are also discussed.

Predictive Factors for Subjective Vertigo Following Cochlear Implantation: A Regional Multicenter Cohort Study of 395 Patients.

INTRODUCTION: Cochlear implantation (CI) is generally accepted as having a low rate of postoperative complications, but between 9.3% and 13% of cases experience vertigo postoperatively. This study aimed to examine patient, surgical, and device factors contributing toward the risk of postoperative vertigo. METHODOLOGY: A retrospective review was conducted of adult patients who underwent cochlear implant in a regional area of New South Wales from 2007 to 2018. A total of 395 cochlear implant cases were included in the final study. RESULTS: The overall incidence of vertigo at 3 months of follow-up was 7.1% (n = 28/395). No difference was identified in this study between rates of postoperative vertigo between device factors, including implant make (Cochlear vs. Med-El), electrode shape (perimodiolar vs. straight), and electrode model. No significant difference was found also for surgical factors such as the number of electrode rings inserted, side of implantation, or surgical approach of tympanic ramp (round window insertion vs. cochleostomy).A higher percentage of patients with preoperative vertigo experienced vertigo postoperatively (18.4%, n = 7/38), compared with the population without preoperative vertigo (6.0%, n = 21/352) ( p = 0.005). Patients with previous mastoid surgery also reported a higher rate of postoperative vertigo (20%, n = 9/45) compared with those who had not had mastoid surgery (5.43%, n = 19/350) ( p = 0.006). The mean age of patients experiencing postoperative vertigo was higher than the population without postoperative symptoms (67 vs. 63). CONCLUSION: This study of a large multicenter population outlines that patient factors are more critical than surgical or device factors when considering risk factors for vertigo post-cochlear implant.

Tumor necrosis factor receptor-associated factor 1 influences KRN/I-Ag7 mouse arthritis autoantibody production.

PURPOSE: Recently, genomewide association analysis has revealed that the Tumor Necrosis Factor Receptor-associated factor 1-Complement 5 (TRAF1-C5) containing locus on chromosome 9 was associated with an increased risk for RA. Studies in model systems suggested that either gain- or loss-of-function TRAF1 mutations have immune effects that could plausibly lead to or exacerbate the arthritis phenotype. KRN/I-A(g7) (KxB/N) is a genetic mouse model of inflammatory arthritis. We aimed to assess the impact of TRAF1 deficiency on KRN/I-A(g7) mice. METHODS: We have bred KRN/I-A(g7) mice onto a TRAF1-deficient background and followed cohorts for the spontaneous appearance of arthritis. We have also transferred KxB/N serum to B6.I-A(g7) TRAF1KO recipients. In addition, systemic autoimmunity was induced through cGVH by injecting bm12 splenocytes into TRAF1KO recipient mice. RESULTS: TRAF1-deficient KRN/I-A(g7) mice spontaneously developed severe, progressive arthritis, comparable to that seen in TRAF1-intact KRN/I-A(g7) mice. However, the anti-GPI antibody titer was significantly lower in the former group. Interestingly, the TRAF1KO mice that had background levels of anti-GPI antibodies still showed severe arthritis, although with a brief delay compared to TRAF1 sufficient mice. In addition, TRAF1KO mice were fully susceptible to passive, serum transfer experiments. In another model of autoimmunity, TRAF1KO had no effect on cGVH autoantibodies production; nor was the response to an exogenous antigen impaired. CONCLUSION: The pathogenesis of spontaneous KRN/I-A(g7) arthritis can largely proceed by TRAF1-independent pathways. The production of anti-GPI autoantibody, but not other autoantibody or antibody responses, was markedly impaired by TRAF1 deficiency. The spontaneous arthritis model in KRN mice appears to be much less antibody dependent than previously believed.

Rituximab-treated patients have a poor response to influenza vaccination.

The efficacy of influenza vaccination in patients treated with rituximab is a clinically important question. Rheumatology clinics are populated with patients receiving rituximab for a broad array of disorders. Although several studies have explored the efficacy of other vaccines in rituximab-treated populations, results have been conflicting. We wished to define influenza vaccine efficacy in a rituximab-treated cohort. We examined 17 evaluable subjects treated with rituximab for rheumatologic conditions. T cell subsets, B cells subsets, T cell function, and B cell function were evaluated at specific time points along with hemagglutinination inhibition titers after receiving the standard inactivated influenza vaccine. T cell subset counts were significantly different than controls but did not change with rituximab. B cells depleted in all patients but were in various stages of recovery at the time of vaccination. Influenza vaccine responsiveness was poor overall, with only 16 % of subjects having a four-fold increase in titer. Pre-existing titers were retained throughout the study, however. The ability to respond to the influenza vaccine appeared to be related to the degree of B cell recovery at the time of vaccination. This study emphasizes that antibody responses to vaccine are impaired in subjects treated with rituximab and supports the concept that B cell recovery influences influenza vaccine responsiveness.

Selection of individual VH genes occurs at the pro-B to pre-B cell transition.

B cells are subjected to selection at multiple checkpoints during their development. The selection of Ab H chains is difficult to study because of the large diversity of the CDR3. To study the selection of individual Ab H chain V region genes (V(H)), we performed CDR3 spectratyping of ∼ 75-300 rearrangements per individual V(H) in C57BL6/J mice. We measured the fraction of rearrangements that were in-frame in B cell DNA. We demonstrate that individual V(H)s have different fractions of in-frame rearrangements (IF fractions) ranging from 10 to 90% and that these IF fractions are reproducible in different mice. For most V(H)s, the IF fraction in pro-B cells approximated 33% and then shifted to the nearly final (mature) B cell value by the cycling pre-B cell stage. The frequency of high in-frame (IF) V(H) usage increased in cycling pre-B cells compared with that in pro-B cells, whereas this did not occur for low IF V(H)s. The IF fraction did not shift as much in BCR-expressing B cells and was minimally affected by L chain usage for most V(H). High IF clan II/III V(H)s share more positively charged CDR2 sequences, whereas high IF clan I J558 CDR2 sequences are diverse. These data indicate that individual V(H)s are subjected to differential selection, that V(H) IF fraction is mainly established through pre-BCR-mediated selection, that it may operate differently in clan I versus II/III V(H)s, and that it has a lasting influence on the Ab repertoire.

Simultaneous cochlear implantation during resection of a cerebellopontine angle meningioma: case report.

Cerebellopontine angle (CPA) meningiomas commonly involve the internal auditory canal (IAC). We report a case of a 68-year-old lady with idiopathic profound bilateral deafness with a meningioma which was discovered on workup for cochlear implantation. We performed simultaneous excision of her CPA and IAC meningioma with insertion of a cochlear implant (CI). She regained functional hearing with marked improvement in quality of life. Intraoperative electrophysiological testing can be used to confirm preservation of the cochlear nerve enabling simultaneous implantation which is preferable for clinical and logistical reasons. This creates an option for hearing rehabilitation at the time of IAC/CPA tumour surgery in appropriate patients.

H-Bonds in Crambin: Coherence in an α-Helix.

We applied coherence analysis-used by engineers to identify linear interactions in stochastic systems-to molecular dynamics simulations of crambin, a thionin storage protein found in Abyssinian cabbage. A key advantage of coherence over other analyses is that it is robust, independent of the properties, or even the existence of probability distributions often relied on in statistical mechanics. For frequencies between 0.391 and 5.08 GHz (corresponding reciprocally to times of 2.56 and 0.197 ns), the displacements of oxygen and nitrogen atoms across α-helix H-bonds are strongly correlated, with a coherence greater than 0.9; the secondary structure causes the H-bonds to effectively act as a spring. Similar coherence behavior is observed for covalent bonds and other noncovalent interactions including H-bonds in ß-sheets and salt bridges. In contrast, arbitrary pairs of atoms that are physically distant have uncorrelated motions and negligible coherence. These results suggest that coherence may be used to objectively identify atomic interactions without subjective thresholds such as H-bond lengths angles and angles. Strong coherence is also observed between the average position of adjacent leaves (groups of atoms) in an α-helix, suggesting that the harmonic analysis of classical molecular dynamics can successfully describe the propagation of allosteric interactions through the structure.

Coupled chemical reactions: Effects of electric field, diffusion, and boundary control.

Chemical reactions involve the movement of charges, and this paper presents a mathematical model for describing chemical reactions in electrolytes. The model is developed using an energy variational method that aligns with classical thermodynamics principles. It encompasses both electrostatics and chemical reactions within consistently defined energetic and dissipative functionals. Furthermore, the energy variation method is extended to account for open systems that involve the input and output of charge and mass. Such open systems have the capability to convert one form of input energy into another form of output energy. In particular, a two-domain model is developed to study a reaction system with self-regulation and internal switching, which plays a vital role in the electron transport chain of mitochondria responsible for ATP generation-a crucial process for sustaining life. Simulations are conducted to explore the influence of electric potential on reaction rates and switching dynamics within the two-domain system. It shows that the electric potential inhibits the oxidation reaction while accelerating the reduction reaction.