Erratum: Modeling Gel Swelling Equilibrium in the Mean Field: From Explicit to Poisson-Boltzmann Models [Phys. Rev. Lett. 122, 208002 (2019)].

This corrects the article DOI: 10.1103/PhysRevLett.122.208002.

Influence of weak groups on polyelectrolyte mobilities.

The ionization of dissociable groups in weak polyelectrolytes does not occur in a homogenous fashion. Monomer connectivity imposes constraints on the localization of the dissociated (charged) monomers that affect the local electric potential. As a result, the mean bare charge along a weak polyelectrolyte can vary depending on the proximity to topological features (e.g. presence of crosslinks or dangling ends). Using reaction-ensemble Monte-Carlo simulations we calculate the dissociation inhomogeneities for a few selected PE configurations, linear, rod-like, flexible four-arm star, and a star with stiff arms. An ensemble preaverage is used to obtain the annealed bare charge profile for these different polymer configurations. Using molecular dynamics simulations within a Lattice-Boltzman fluid, we investigate how the electrophoretic mobility is affected by the bare charge inhomogeneities arising from the annealed weak polyelectrolytes. Surprisingly, the mobility obtained for the situations corresponding to the predicted charge profile for annealed weak polyelectrolytes are not significantly different than the mobility obtained when all the monomers have an identical charge (under the constraint that the total polyelectrolyte bare charge is the same). This is also true for the stiff rod-like variants where conformational changes induced from the localization of the monomer charges are negligible. In salty solutions, we find that counterions are affected by the electric potential modulations induced by the topological features. Since the counterions crowd in regions where the electric potential caused by the dissociated monomers is highest, they wash-out the bare charge inhomogeneities and contribute to a more uniform effective backbone charge.

Modeling Gel Swelling Equilibrium in the Mean Field: From Explicit to Poisson-Boltzmann Models.

We develop a double mean-field theory for charged macrogels immersed in electrolyte solutions in the spirit of the cell model approach. We first demonstrate that the equilibrium sampling of a single explicit coarse-grained charged polymer in a cell yields accurate predictions of the swelling equilibrium if the geometry is suitably chosen and all pressure contributions have been incorporated accurately. We then replace the explicit flexible chain by a suitably modeled penetrable charged rod that allows us to compute all pressure terms within the Poisson-Boltzmann approximation. This model, albeit computationally cheap, yields excellent predictions of swelling equilibria under varying chain length, polymer charge fraction, and external reservoir salt concentrations when compared to coarse-grained molecular dynamics simulations of charged macrogels. We present an extension of the model to the experimentally relevant cases of pH-sensitive gels.

Simulations of ionization equilibria in weak polyelectrolyte solutions and gels.

This article recapitulates the state of the art regarding simulations of ionization equilibria of weak polyelectrolyte solutions and gels. We start out by reviewing the essential thermodynamics of ionization and show how the weak polyelectrolyte ionization differs from the ionization of simple weak acids and bases. Next, we describe simulation methods for ionization reactions, focusing on two methods: the constant-pH ensemble and the reaction ensemble. After discussing the advantages and limitations of both methods, we review the existing simulation literature. We discuss coarse-grained simulations of weak polyelectrolytes with respect to ionization equilibria, conformational properties, and the effects of salt, both in good and poor solvent conditions. This is followed by a discussion of branched star-like weak polyelectrolytes and weak polyelectrolyte gels. At the end we touch upon the interactions of weak polyelectrolytes with other polymers, surfaces, nanoparticles and proteins. Although proteins are an important class of weak polyelectrolytes, we explicitly exclude simulations of protein ionization equilibria, unless they involve protein-polyelectrolyte interactions. Finally, we try to identify gaps and open problems in the existing simulation literature, and propose challenges for future development.

Langevin dynamcis simulations of driven polymer translocation into a cross-linked gel.

We investigate the dynamics of driving a polyelectrolyte such as DNA through a nanopore and into a cross-linked gel. Placing the gel on the trans-side of the nanopore can increase the translocation time while not negatively affecting the capture rates. Thus, this setup combines the mechanics of gel electrophoresis with nanopore translocation. However, contrary to typical gel electrophoresis scenarios, the effect of the field is localized in the immediate vicinity of the nanopore and becomes negligible inside the gel matrix. Thus, we investigate the process by which a semiflexible polymer can be pushed into a gel matrix via a localized field and we describe how the dynamics of gel penetration depends upon the field intensity, polymer stiffness, and gel pore size. Our simulation results show that a semiflexible polymer enters the gel region with two distinct mechanisms depending upon the ratio between the bending length scale and the gel pore size. In both regimes, the gel fibers cause a net increase in the mean translocation time. Interestingly, the translocation rate is found to be constant (a potentially useful feature for many applications) during the predominant part of the translocation process when the polymer is stiff over a length scale comparable to the gel pore size.

Highly driven polymer translocation from a cylindrical cavity with a finite length.

We present a computer simulation study of polymer translocation in a situation where the chain is initially confined to a closed cylindrical cavity in order to reduce the impact of conformational diversity on the translocation times. In particular, we investigate how the coefficient of variation of the distribution of translocation times can be minimized by optimizing both the volume and the aspect ratio of the cavity. Interestingly, this type of confinement sometimes increases the number and impact of hairpin conformations such that the fluctuations in the translocation process do not follow a power law in time (for instance, these fluctuations can even vary non-monotonically with time). We develop a tension-propagation model for a polymer compressed into such a confining volume and find that its predictions are in good agreement with our simulation results in the experimentally relevant strongly driven limit. Both the theoretical calculations and the simulation data yield a minimum in the coefficient of variation of the distribution of translocation times for a cylindrical cavity with an aspect ratio that makes it similar to a hemisphere. This provides guidance for the design of new devices based on the preconfinement of the target polymer into cavities.

The pleiotropic effects of decanoic acid treatment on mitochondrial function in fibroblasts from patients with complex I deficient Leigh syndrome.

There is growing interest in the use of the ketogenic diet (KD) to treat inherited metabolic diseases including mitochondrial disorders. However, neither the mechanism whereby the diet may be working, nor if it could benefit all patients with mitochondrial disease, is known. This study focusses on decanoic acid (C10), a component of the medium chain triglyceride KD, and a ligand for the nuclear receptor PPAR-γ known to be involved in mitochondrial biogenesis. The effects of C10 were investigated in primary fibroblasts from a cohort of patients with Leigh syndrome (LS) caused by nuclear-encoded defects of respiratory chain complex I, using mitochondrial respiratory chain enzyme assays, gene expression microarray, qPCR and flow cytometry. Treatment with C10 increased citrate synthase activity, a marker of cellular mitochondrial content, in 50 % of fibroblasts obtained from individuals diagnosed with LS in a PPAR-γ-mediated manner. Gene expression analysis and qPCR studies suggested that treating cells with C10 supports fatty acid metabolism, through increasing ACADVL and CPT1 expression, whilst downregulating genes involved in glucose metabolism (PDK3, PDK4). PCK2, involved in blocking glucose metabolism, was upregulated, as was CAT, encoding catalase. Moreover, treatment with C10 also decreased oxidative stress in complex I deficient (rotenone treated) cells. However, since not all cells from subjects with LS appeared to respond to C10, prior cellular testing in vitro could be employed as a means for selecting individuals for subsequent clinical studies involving C10 preparations.

Translocation of a polymer through a nanopore starting from a confining nanotube.

In this manuscript, Langevin Dynamics simulations and Tension-Propagation theory are used to investigate the forced translocation of a polymer from a confining tube through a nanopore situated at one of the tube's ends. The diameter of the tube allows for a control over the polymer conformations: decreasing the tube diameter reduces the number of conformations available to the polymer chain both before and during translocation. As the tube diameter is decreased, the translocation time is observed to increase. Interestingly, while the width of the distribution of translocation times is reduced if the chain starts in a tube, it reaches a maximum for weakly confining tubes. A Tension-Propagation approach is developed for the tube-nanopore setup in the strongly driven limit. Good agreement between the simulations and the theory allows for an exploration of the underlying physical mechanisms, including the calculation of an effective pore friction and the assessing of the impact of monomer crowding on the trans side.

Interfacing solid-state nanopores with gel media to slow DNA translocations.

We demonstrate the ability to slow DNA translocations through solid-state nanopores by interfacing the trans side of the membrane with gel media. In this work, we focus on two reptation regimes: when the DNA molecule is flexible on the length scale of a gel pore, and when the DNA behaves as persistent segments in tight gel pores. The first regime is investigated using agarose gels, which produce a very wide distribution of translocation times for 5 kbp dsDNA fragments, spanning over three orders of magnitude. The second regime is attained with polyacrylamide gels, which can maintain a tight spread and produce a shift in the distribution of the translocation times by an order of magnitude for 100 bp dsDNA fragments, if intermolecular crowding on the trans side is avoided. While previous approaches have proven successful at slowing DNA passage, they have generally been detrimental to the S/N, capture rate, or experimental simplicity. These results establish that by controlling the regime of DNA movement exiting a nanopore interfaced with a gel medium, it is possible to address the issue of rapid biomolecule translocations through nanopores-presently one of the largest hurdles facing nanopore-based analysis-without affecting the signal quality or capture efficiency.

The ketogenic diet component decanoic acid increases mitochondrial citrate synthase and complex I activity in neuronal cells.

The Ketogenic diet (KD) is an effective treatment with regards to treating pharmaco-resistant epilepsy. However, there are difficulties around compliance and tolerability. Consequently, there is a need for refined/simpler formulations that could replicate the efficacy of the KD. One of the proposed hypotheses is that the KD increases cellular mitochondrial content which results in elevation of the seizure threshold. Here, we have focussed on the medium-chain triglyceride form of the diet and the observation that plasma octanoic acid (C8) and decanoic acid (C10) levels are elevated in patients on the medium-chain triglyceride KD. Using a neuronal cell line (SH-SY5Y), we demonstrated that 250-µM C10, but not C8, caused, over a 6-day period, a marked increase in the mitochondrial enzyme, citrate synthase along with complex I activity and catalase activity. Increased mitochondrial number was also indicated by electron microscopy. C10 is a reported peroxisome proliferator activator receptor γ agonist, and the use of a peroxisome proliferator activator receptor γ antagonist was shown to prevent the C10-mediated increase in mitochondrial content and catalase. C10 may mimic the mitochondrial proliferation associated with the KD and raises the possibility that formulations based on this fatty acid could replace a more complex diet. We propose that decanoic acid (C10) results in increased mitochondrial number. Our data suggest that this may occur via the activation of the PPARγ receptor and its target genes involved in mitochondrial biogenesis. This finding could be of significant benefit to epilepsy patients who are currently on a strict ketogenic diet. Evidence that C10 on its own can modulate mitochondrial number raises the possibility that a simplified and less stringent C10-based diet could be developed.

Can gel concentration gradients improve two-dimensional DNA displays?

The abrupt reduction in gel electrophoretic mobility that is observed when a dsDNA fragment is partially denatured has recently been predicted to exhibit a dependence upon the gel pore size. Using theoretical modeling, we demonstrate that this dependence can be exploited and used to improve the performance of 2D display of DNA. We report experimental evidence of this dependence and propose a new separation system in which a gel porosity gradient is utilized in a way analogous to temperature or denaturant gradients in traditional 2D display. Such gel porosity gradients can also be used in conjunction with denaturant gradients to improve 2D display results. We test these new ideas by modeling the fragment mobilities and computing the final fragment positions to find optimal 2D separation conditions.

Benzodiazepine dependence and its treatment with low dose flumazenil.

Globally benzodiazepines remain one of the most prescribed medication groups, especially in the primary care setting. With such high levels of prescribing it is not surprising that benzodiazepine dependence is common, cutting across all socioeconomic levels. Despite recognition of the potential for the development of iatrogenic dependence and the lack of any effective treatment, benzodiazepines continue to be widely prescribed in general practice. Conventional dependence management, benzodiazepine tapering, is commonly a protracted process over several weeks or months. It is often associated with significant withdrawal symptoms and craving leading to patient drop out and return to use. Accordingly, there is a worldwide need to find effective pharmacotherapeutic interventions for benzodiazepine dependence. One drug of increasing interest is the GABAA benzodiazepine receptor antagonist/partial agonist, flumazenil. Multiple bolus intravenous infusions of low dose flumazenil used either with or without benzodiazepine tapering can reduce withdrawal sequelae, and/or longer term symptoms in the months following withdrawal. Preliminary data suggest that continuous intravenous or subcutaneous flumazenil infusion for 4 days significantly reduces acute benzodiazepine withdrawal sequelae. The subcutaneous infusion was shown to be tissue compatible so the development of a longer acting (i.e. several weeks) depot flumazenil formulation has been explored. This could be capable of managing both acute and longer term benzodiazepine withdrawal sequelae. Preliminary in vitro water bath and in vivo biocompatibility data in sheep show that such an implant is feasible and so is likely to be used in clinical trials in the near future.

Monitoring retention in care: using multiple laboratory tests as an indicator for HIV medical care.

Retention in care is an important strategy for HIV prevention. Unfortunately, surveillance systems were not designed to capture face-to-face visits with HIV health care providers to assess retention in care. Instead, HIV-related laboratory tests are used as a surrogate measure. This study estimated the sensitivity (90%) and specificity (28%) of two HIV-related laboratory tests separated by at least 90 days for two face-to-face visits among people receiving HIV-related health care in Oregon. Overall accuracy of the surrogate was good but slightly overestimated the proportion of people living with HIV/AIDS actually retained in care.

Oregon patients with HIV infection who experience delayed diagnosis.

This project sought to understand factors contributing to the delayed diagnosis of HIV in the state of Oregon, USA in order to increase timely testing and diagnosis. People unaware of their positive HIV status account for a disproportionate number of transmissions of HIV, making delayed diagnosis a profound public health concern. We interviewed a sample of 17 adults, diverse in age, reported risk behaviors and sexual orientation, who were identified as being diagnosed late, about their experiences with testing and diagnosis. We defined delayed diagnosis as a diagnosis of AIDS within 12 months of the first positive HIV test. We conducted thematic analysis using NVivo® software for data management. Three overarching themes emerged: risk perception, missed opportunities for diagnosis, routine testing and the role of the medical community. Definitions of these themes, corresponding sub-themes, and illustrious quotations provide an informative description of characteristics of late testers, factors contributing to delayed diagnosis, and potential points of intervention to increase regular and timely testing. We conclude that routine HIV screening as part of regular medical care might significantly reduce the number of delayed diagnoses and minimize the stigma of testing by normalizing it as part of routine medical care. Earlier diagnosis of HIV will result in better outcomes for individual patients and lower rates of HIV transmission by unknowing individuals.

Gel electrophoresis of DNA partially denatured at the ends: what are the dominant conformations?

Gel electrophoresis of a partially denatured dsDNA fragment is studied using Langevin Dynamics computer simulations. For simplicity, the denatured ssDNA sections are placed at the ends of the fragment in a symmetrical fashion. A squid-like conformation is found to sometimes cause the fragment to completely block in the gel. In fact, this conformation is the principal cause of the steep reduction in mobility observed in the simulations. As the field is increased, it is found that the occurrence of this conformation dominates the migration dynamics. Although the squid conformation seems to be more stable at high fields, the field can eventually force the fragments to thread through the gel pores regardless. We qualitatively explore the behavior of this squid-like conformation across a range of fields and degrees of denaturation, and we discuss the relevance of our findings for TGGE.

Efficacy of Using Intermittent Theta Burst Stimulation to Treat Negative Symptoms in Patients with Schizophrenia-A Systematic Review and Meta-Analysis.

Negative symptoms in schizophrenia impose a significant burden with limited effective pharmacological treatment options. Recent trials have shown preliminary evidence for the efficacy of using intermittent theta burst stimulation (iTBS) in treating negative symptoms in schizophrenia. We aim to systematically review the current evidence of iTBS in the treatment of the negative symptoms of schizophrenia as an augmentation therapy. The study protocol was developed and registered on Prospero (registration ID: 323381). MEDLINE, EMBASE, Web of Science (Scopus), PsycINFO and Wan Fang databases were searched for sham-controlled, randomized trials of iTBS among patients with schizophrenia. The mean difference in major outcome assessments for negative symptoms was calculated. The quality of evidence was assessed using the Cochrane Risk of Bias Tool (version 1) and the GRADE system. Moreover, 12 studies including a total of 637 participants were included. Compared to sham treatment, the pooled analysis was in favor of iTBS treatment for negative symptoms (mean weight effect size: 0.59, p = 0.03) but not for positive symptoms (mean weight effect size: 0.01, p = 0.91) and depressive symptoms (mean weight effect size: 0.35, p = 0.16). A significant treatment effect was also observed on the iTBS target site left dorsal prefrontal cortex (mean weight effect size: 0.86, p = 0.007) and for stimulation with 80% motor threshold (mean weight effect size: 0.86, p = 0.02). Thus, our synthesized data support iTBS as a potential treatment for negative symptoms among patients with schizophrenia. However, the long-term efficacy and safety issues of iTBS in a larger population have yet to be examined.

Dual Targeting of EGFR and MTOR Pathways Inhibits Glioblastoma Growth by Modulating the Tumor Microenvironment.

Glioblastoma's (GBM) aggressive growth is driven by redundant activation of a myriad of signaling pathways and genomic alterations in tyrosine kinase receptors, such as epidermal growth factor receptor (EGFR), which is altered in over 50% of cases. Single agents targeting EGFR have not proven effective against GBM. In this study, we aimed to identify an effective anti-tumor regimen using pharmacogenomic testing of patient-derived GBM samples, in culture and in vivo. High-throughput pharmacological screens of ten EGFR-driven GBM samples identified the combination of erlotinib (EGFRi) and MLN0128 (a mammalian target of rapamycin inhibitor, or MTORi) as the most effective at inhibiting tumor cell viability. The anti-tumor activity of erlonitib+MLN0128 was synergistic and produced inhibition of the p-EGFR, mitogen-activated protein kinase (MAPK), and Phosphoinositide 3-kinase (PI3K) pathways in culture. Using an orthotopic murine model of GBM, we show that erlotinib+MLN0128 inhibited tumor growth in vivo and significantly prolonged the survival of tumor-bearing mice. Expression profiling of tumor tissues from treated mice revealed a unique gene signature induced by erlotinib+MLN0128, consisting of downregulation of immunosuppressive chemokines in the tumor microenvironment, including C-C motif chemokine ligand 2 (CCL2) and periostin. Lower periostin levels resulted in the inhibition of Iba1+ (tumor-promoting) macrophage infiltration of GBM xenografts. Taken together, our results demonstrate that pharmacological co-targeting of EGFR and MTOR using clinically available drugs represents an effective treatment paradigm for EGFR-driven GBMs, acting both by inhibiting tumor cell growth and modulating the immune tumor microenvironment.

Electrophoretic mobility of partially denatured DNA in a gel: qualitative and semiquantitative differences between bubbles and split ends.

Partially melted DNA is known to exhibit an abrupt decrease of electrophoretic mobility in a gel. Although this is the main phenomenon exploited in TGGE/DGGE (temperature gradient gel electrophoresis/denaturing gradient gel electrophoresis), not much is known about the physical processes responsible for the blocking. While there is a commonly used formula for the reduced mobility based on the theory of branched polymers, it does not discriminate between denatured domains bounded on one (split end) or two sides (bubble). To better understand how the blocking occurs in both of these cases, a coarse-grained model of DNA gel electrophoresis is simulated using Langevin Dynamics. The simulations reveal that the low-field mobility is much more sensitive to denatured domains located at the ends of a DNA fragment. A denatured domain occurring at the center of a fragment indeed reduces the mobility, but at a much lower rate.

The NPH-II helicase displays efficient DNA x RNA helicase activity and a pronounced purine sequence bias.

The superfamily 2 vaccinia viral helicase nucleoside triphosphate phosphohydrolase-II (NPH-II) exhibits robust RNA helicase activity but typically displays little activity on DNA substrates. NPH-II is thus believed to make primary contacts with backbone residues of an RNA substrate. We report an unusual nucleobase bias, previously unreported in any superfamily 1 or 2 helicase, whereby purines are heavily preferred as components of both RNA and DNA tracking strands. The observed sequence bias allows NPH-II to efficiently unwind a DNA x RNA hybrid containing a purine-rich DNA track derived from the 3'-untranslated region of an early vaccinia gene. These results provide insight into potential biological functions of NPH-II and the role of sequence in targeting NPH-II to appropriate substrates. Furthermore, they demonstrate that in addition to backbone contacts, nucleotide bases play an important role in modulating the behavior of NPH-II. They also establish that processive helicase enzymes can display sequence selectivity.

Efficacy of Etanercept in the Treatment of Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis.

It has been suggested that the use of etanercept for treatment of Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) might provide improved mortality benefit and decreased skin healing times. This retrospective study compared the use of single-dose subcutaneous etanercept to intravenous immunoglobulin (IVIG) and supportive care alone. Thirteen patients were treated with a single dose (50 mg) of subcutaneous etanercept. Results of this study support the use of etanercept as a potentially beneficial agent in the treatment of SJS/TEN.