PAMELA: An Open-Source Software Package for Calculating Nonlocal Exact Exchange Effects on Electron Gases in Core-Shell Nanowires

We present a new pseudospectral approach for incorporating many-body, nonlocal exact exchange interactions to understand the formation of electron gases in core-shell nanowires. Our approach is efficiently implemented in the open-source software package PAMELA (Pseudospectral Analysis Method with Exchange & Local Approximations) that can calculate electronic energies, densities, wavefunctions, and band-bending diagrams within a self-consistent Schrodinger-Poisson formalism. The implementation of both local and nonlocal electronic effects using pseudospectral methods is key to PAMELA's efficiency, resulting in significantly reduced computational effort compared to finite-element methods. In contrast to the new nonlocal exchange formalism implemented in this work, we find that the simple, conventional Schrodinger-Poisson approaches commonly used in the literature (1) considerably overestimate the number of occupied electron levels, (2) overdelocalize electrons in nanowires, and (3) significantly underestimate the relative energy separation between electronic subbands. In addition, we perform several calculations in the high-doping regime that show a critical tunneling depth exists in these nanosystems where tunneling from the core-shell interface to the nanowire edge becomes the dominant mechanism of electron gas formation. Finally, in order to present a general-purpose set of tools that both experimentalists and theorists can easily use to predict electron gas formation in core-shell nanowires, we document and provide our efficient and user-friendly PAMELA source code that is freely available at http://alum.mit.edu/www/usagiComment: Accepted by AIP Advance

A Linear Classifier Based on Entity Recognition Tools and a Statistical Approach to Method Extraction in the Protein-Protein Interaction Literature

We participated, in the Article Classification and the Interaction Method subtasks (ACT and IMT, respectively) of the Protein-Protein Interaction task of the BioCreative III Challenge. For the ACT, we pursued an extensive testing of available Named Entity Recognition and dictionary tools, and used the most promising ones to extend our Variable Trigonometric Threshold linear classifier. For the IMT, we experimented with a primarily statistical approach, as opposed to employing a deeper natural language processing strategy. Finally, we also studied the benefits of integrating the method extraction approach that we have used for the IMT into the ACT pipeline. For the ACT, our linear article classifier leads to a ranking and classification performance significantly higher than all the reported submissions. For the IMT, our results are comparable to those of other systems, which took very different approaches. For the ACT, we show that the use of named entity recognition tools leads to a substantial improvement in the ranking and classification of articles relevant to protein-protein interaction. Thus, we show that our substantially expanded linear classifier is a very competitive classifier in this domain. Moreover, this classifier produces interpretable surfaces that can be understood as "rules" for human understanding of the classification. In terms of the IMT task, in contrast to other participants, our approach focused on identifying sentences that are likely to bear evidence for the application of a PPI detection method, rather than on classifying a document as relevant to a method. As BioCreative III did not perform an evaluation of the evidence provided by the system, we have conducted a separate assessment; the evaluators agree that our tool is indeed effective in detecting relevant evidence for PPI detection methods.Comment: BMC Bioinformatics. In Pres

A murine model of variant late infantile ceroid lipofuscinosis recapitulates behavioral and pathological phenotypes of human disease.

Neuronal ceroid lipofuscinoses (NCLs; also known collectively as Batten Disease) are a family of autosomal recessive lysosomal storage disorders. Mutations in as many as 13 genes give rise to ∼10 variants of NCL, all with overlapping clinical symptomatology including visual impairment, motor and cognitive dysfunction, seizures, and premature death. Mutations in CLN6 result in both a variant late infantile onset neuronal ceroid lipofuscinosis (vLINCL) as well as an adult-onset form of the disease called Type A Kufs. CLN6 is a non-glycosylated membrane protein of unknown function localized to the endoplasmic reticulum (ER). In this study, we perform a detailed characterization of a naturally occurring Cln6 mutant (Cln6(nclf)) mouse line to validate its utility for translational research. We demonstrate that this Cln6(nclf) mutation leads to deficits in motor coordination, vision, memory, and learning. Pathologically, we demonstrate loss of neurons within specific subregions and lamina of the cortex that correlate to behavioral phenotypes. As in other NCL models, this model displays selective loss of GABAergic interneuron sub-populations in the cortex and the hippocampus with profound, early-onset glial activation. Finally, we demonstrate a novel deficit in memory and learning, including a dramatic reduction in dendritic spine density in the cerebral cortex, which suggests a reduction in synaptic strength following disruption in CLN6. Together, these findings highlight the behavioral and pathological similarities between the Cln6(nclf) mouse model and human NCL patients, validating this model as a reliable format for screening potential therapeutics

Role of angiopoietin-like protein 3 in sugar-induced dyslipidemia in rhesus macaques: suppression by fish oil or RNAi.

Angiopoietin-like protein 3 (ANGPTL3) inhibits lipid clearance and is a promising target for managing cardiovascular disease. Here we investigated the effects of a high-sugar (high-fructose) diet on circulating ANGPTL3 concentrations in rhesus macaques. Plasma ANGPTL3 concentrations increased ∼30% to 40% after 1 and 3 months of a high-fructose diet (both P < 0.001 vs. baseline). During fructose-induced metabolic dysregulation, plasma ANGPTL3 concentrations were positively correlated with circulating indices of insulin resistance [assessed with fasting insulin and the homeostatic model assessment of insulin resistance (HOMA-IR)], hypertriglyceridemia, adiposity (assessed as leptin), and systemic inflammation [C-reactive peptide (CRP)] and negatively correlated with plasma levels of the insulin-sensitizing hormone adropin. Multiple regression analyses identified a strong association between circulating APOC3 and ANGPTL3 concentrations. Higher baseline plasma levels of both ANGPTL3 and APOC3 were associated with an increased risk for fructose-induced insulin resistance. Fish oil previously shown to prevent insulin resistance and hypertriglyceridemia in this model prevented increases of ANGPTL3 without affecting systemic inflammation (increased plasma CRP and interleukin-6 concentrations). ANGPTL3 RNAi lowered plasma concentrations of ANGPTL3, triglycerides (TGs), VLDL-C, APOC3, and APOE. These decreases were consistent with a reduced risk of atherosclerosis. In summary, dietary sugar-induced increases of circulating ANGPTL3 concentrations after metabolic dysregulation correlated positively with leptin levels, HOMA-IR, and dyslipidemia. Targeting ANGPTL3 expression with RNAi inhibited dyslipidemia by lowering plasma TGs, VLDL-C, APOC3, and APOE levels in rhesus macaques

Delusional Infestation:Perspectives from Scottish Dermatologists and a 10-year Case Series from a Single Centre

Perceptions of the clinical management of delusional infestation (DI) were compared with clinical outcomes in this 10-year case series from a single centre in Dundee, UK. An online questionnaire (survey-monkey, a TM brand of online survey available for free for basic use) was sent to Scottish Dermatologists to gauge their opinions and confidence in the management of DI. Also, a retrospective review of medical case notes of patients seen by dermatologists in one institution was undertaken and clinical outcomes were reported by patients’ general practitioners (GP). The survey showed that 61% of responding dermatologists encountered 1–5 cases of DI per year. Twenty-four percent respondees were ‘confident’ in managing patients with DI, 54% were ‘somewhat confident’. Forty-seven patients (62% female, 70% single) were seen over the 10 years; 43% brought a self-collected specimen to clinic, 68% of patients had a psychiatric comorbidity, 23% of patients had primary DI and 11/47 (23%) were seen by a psychiatrist. Clinical outcomes as rated by patients’ GPs were reasonable or good in 2/3 patients. A poor outcome was seen in 12 patients and associated with chronic pain in 50% (p< 0.01) and psychiatric comorbidity in 100% (p < 0.01). We conclude that good outcomes can be achieved in some patients with DI without psychiatric input and without psychoactive treatment

Synthesis of the oxysterol, 24(S), 25-epoxycholesterol, parallels cholesterol production and may protect against cellular accumulation of newly-synthesized cholesterol

AIM: The effects of 24(S),25-epoxycholesterol (24,25EC) on aspects of cholesterol homeostasis is well-documented. When added to cells, 24,25EC decreases cholesterol synthesis and up-regulates cholesterol efflux genes, including ABCA1. Synthesis of 24,25EC occurs in a shunt of the mevalonate pathway which also produces cholesterol. Therefore, 24,25EC synthesis should be subject to the same negative feedback regulation as cholesterol synthesis. To date, no role has been ascribed to 24,25EC in light of the fact that increased accumulation of cholesterol should decrease formation of this oxysterol through feedback inhibition. This leads to the intriguing paradox: why inhibit production of an apparently important regulator of cholesterol homeostasis when it is needed most? METHODS: We used a combination of pharmacological and genetic approaches in Chinese Hamster Ovary cell-lines to investigate this paradox. Endogenous synthesis of 24,25EC was manipulated using partial inhibition of the enzyme, Oxidosqualene Cyclase. Changes in cholesterol and 24,25EC synthesis were determined using metabolic labelling with [1-(14)C]-acetate, thin-layer chromatography and phosphorimaging. Transcriptional effects mediated via SREBP and LXR were analysed by luciferase reporter assays. RESULTS: We showed that cholesterol addition to cells lead to a rapid and preferential inhibition of 24,25EC synthesis. Addition of 24,25EC resulted in parallel inhibition of 24,25EC and cholesterol synthesis. Furthermore, we used a variety of approaches to examine the relationship between cholesterol and 24,25EC synthesis, including cell-lines with different rates of cholesterol synthesis, varying cholesterol synthetic rates by pre-treatment with a statin, or lipoprotein cholesterol loading of macrophages. In all cases, we showed that 24,25EC synthesis faithfully tracked cholesterol synthesis. Moreover, changes in 24,25EC synthesis exerted downstream effects, reducing SREBP transcriptional activity whilst increasing ABCA1 and LXR transcriptional activity. CONCLUSION: Our results show that 24,25EC synthesis parallels cholesterol synthesis, consistent with this oxysterol functioning as a safety valve to protect against the accumulation of newly-synthesised cholesterol (as opposed to exogenously-derived cholesterol). Considering that 24,25EC is capable of being produced in all cholesterogenic cells, we propose that production of 24,25EC may represent a ubiquitous defence mechanism

Neural Stem Cell Grafts and the Influence of Apolipoprotein E in a Mouse Model of Global Ischaemia

Neural stem cell (NSC) transplantation is a promising therapy for the treatment of brain damage. Although the “proof of principle” for NSC transplantation therapy has been demonstrated in a variety of animal models of brain injury (stroke, traumatic brain injury, ageing) and in a clinical setting (Parkinson’s disease), the mechanisms by which grafted stem cells survive, migrate and differentiate in host brain are yet to be elucidated. Initial studies have demonstrated that, after transplantation of the MHP36 neural stem cell line in a focal ischaemia model, the lipid transport protein apolipoprotein E (apoE) is upregulated and co-localised to differentiated cells in parallel with functional recovery. ApoE has been shown to have a critical role in the response to brain injury and repair processes. Furthermore, in humans, three different forms of apoE exist (E2, E3, E4 encoded by the alleles e2, e3, e4) and each of these has a different ability to promote repair, with the E4 form associated with an impaired capacity. This thesis tests the hypothesis that apoE is critical in stem cell integration and investigates whether this effect is APOE genotype dependent, in a mouse model of global cerebral ischaemia. This model was chosen as it produces diffuse selective neuronal damage in the striatum and hippocampus, which also occurs in other conditions such as ageing and Alzheimer’s disease. The studies described in this thesis were designed to test the hypothesis and are outlined as follows: I. Characterisation of neural stem cell grafts in a mouse model of global ischaemia In order to investigate the potential influence of apoE on stem cell grafts, it was first essential to characterise stem cells grafts in mouse brain. Thus, the initial aim of the thesis was to characterise MHP36 grafts in a mouse model of ischaemic neuronal injury. The effect of cyclosporin A (CsA) immunosuppression was also investigated. C57Bl/6J mice underwent an episode of transient global ischaemia induced by bilateral common carotid artery occlusion. Three days following ischaemia, mice received a unilateral striatal graft of fluorescently labelled MHP36 neural stem cells or vehicle; the mice also received CsA or saline. The mice were terminated at either XVII 1 or 4 weeks post-transplantation. This study determined that MHP36 grafts survived and migrated robustly in host ischaemic brain at both 1 week and 4 weeks post-transplantation. Grafted MHP36 cells differentiated into neurons and were able to reduce the extent of ischaemic neuronal damage. An acute host inflammatory response was evoked following MHP36 grafting, but this decreased dramatically by 4 weeks post-transplantation. CsA immunosuppression did not affect MHP36 survival and migration or reduce the host inflammatory response. The successful transplantation and characterisation of MHP36 grafts in mouse brain allowed for future investigation into the genetic factors underlying stem cell graft integration via the use of apoE transgenic mice. II. Influence of apoE on neural stem cell grafts in a mouse model of global ischaemia The aim of this study was to investigate whether endogenous apoE influenced MHP36 survival, migration and differentiation and then to determine potential signalling pathways that may be involved. ApoE deficient mice on a C57Bl/6J background (APOE-KO) and control wildtype C57Bl/6J (WT) mice were subjected to an episode of transient global ischaemia, as in Experiment 1. Two weeks following ischaemia, all mice received unilateral striatal and hippocampal grafts of MHP36 cells. All mice received CsA immunosuppression. Mice were terminated 4 weeks post-transplantation. MHP36 survival and migration was significantly increased in WT as compared to APOE-KO mice. In addition, neuronal differentiation was significantly increased in WT as compared to APOE-KO mice. Increased astrocytic differentiation was observed in the hippocampus, but not striatum of WT as compared to APOE-KO mice. Measurement of the levels of signalling proteins associated with cell survival, extracellular signal-regulated kinase (ERKs) and c-Jun amino-terminal kinase (JNKs) and their phosphorylated forms (pERK and pJNK), indicated selective alterations in JNK with no change in ERK in APOE-KO as compared to WT mice, suggesting that JNK may underlie the apoE effects in stem cell integration. This study demonstrated that apoE strongly influences the survival, migration and differentiation of grafted MHP36 cells and provides initial evidence for the signalling pathways involved. XVIII III. Influence of APOE genotype on neural stem cell grafts in a mouse model of global ischaemia Following the demonstration that endogenous mouse apoE has a critical role in MHP36 graft survival, migration and differentiation, this study sought to investigate whether these effects are influenced by human APOE genotype. Transgenic mice expressing human APOE-e3 or e4, (on an APOE-KO background) and a control group of APOE-KO mice underwent transient global ischaemia and two weeks later MHP36 cells were transplanted unilaterally into the striatum and hippocampus. 1 week after grafting the mice were started on a series of tests for motor balance and coordination using the rotarod, and taken for histology 4 weeks post-transplantation. MHP36 graft survival was significantly improved in APOE-e3 mice compared to APOE-KO and APOE-e4 mice. However, the migration and differentiation of MHP36 cells and motor performance of grafted mice were similar in all three APOE groups, indicating a comparable fate and functional activity within a 4 week survival time. Thus the data indicate that APOE genotype may influence cell survival with minimal effect on stem cell migration and differentiation. The data presented in this thesis demonstrate that endogenous apoE strongly influences MHP36 graft survival, migration and differentiation. Although there was minimal evidence that human APOE genotype influences cell migration and differentiation, stem cell survival was markedly improved in a human APOE-e3 allelic environment, which may affect the effectiveness of stem cells in APOE-e4 individuals

Glial cells are functionally impaired in juvenile neuronal ceroid lipofuscinosis and detrimental to neurons.

The neuronal ceroid lipofuscinoses (NCLs or Batten disease) are a group of inherited, fatal neurodegenerative disorders of childhood. In these disorders, glial (microglial and astrocyte) activation typically occurs early in disease progression and predicts where neuron loss subsequently occurs. We have found that in the most common juvenile form of NCL (CLN3 disease or JNCL) this glial response is less pronounced in both mouse models and human autopsy material, with the morphological transformation of both astrocytes and microglia severely attenuated or delayed. To investigate their properties, we isolated glia and neurons from Cln3-deficient mice and studied their basic biology in culture. Upon stimulation, both Cln3-deficient astrocytes and microglia also showed an attenuated ability to transform morphologically, and an altered protein secretion profile. These defects were more pronounced in astrocytes, including the reduced secretion of a range of neuroprotective factors, mitogens, chemokines and cytokines, in addition to impaired calcium signalling and glutamate clearance. Cln3-deficient neurons also displayed an abnormal organization of their neurites. Most importantly, using a co-culture system, Cln3-deficient astrocytes and microglia had a negative impact on the survival and morphology of both Cln3-deficient and wildtype neurons, but these effects were largely reversed by growing mutant neurons with healthy glia. These data provide evidence that CLN3 disease astrocytes are functionally compromised. Together with microglia, they may play an active role in neuron loss in this disorder and can be considered as potential targets for therapeutic interventions

Demonstrating Photon Ring Existence with Single-Baseline Polarimetry

Images of supermassive black hole accretion flows contain features of both curved spacetime and plasma structure. Inferring properties of the spacetime from images requires modeling the plasma properties, and vice versa. The Event Horizon Telescope Collaboration has imaged near-horizon millimeter emission from both Messier 87* (M87*) and Sagittarius A* (Sgr A*) with very-long-baseline interferometry (VLBI) and has found a preference for magnetically arrested disk (MAD) accretion in each case. MAD accretion enables spacetime measurements through future observations of the photon ring, the image feature composed of near-orbiting photons. The ordered fields and relatively weak Faraday rotation of MADs yield rotationally symmetric polarization when viewed at modest inclination. In this letter, we utilize this symmetry along with parallel transport symmetries to construct a gain-robust interferometric quantity that detects the transition between the weakly lensed accretion flow image and the strongly lensed photon ring. We predict a shift in polarimetric phases on long baselines and demonstrate that the photon rings in M87* and Sgr A* can be unambiguously detected {with sensitive, long-baseline measurements. For M87* we find that photon ring detection in snapshot observations requires $\sim1$ mJy sensitivity on $>15$ G$\lambda$ baselines at 230 GHz and above, which could be achieved with space-VLBI or higher-frequency ground-based VLBI. For Sgr A*, we find that interstellar scattering inhibits photon ring detectability at 230 GHz, but $\sim10$ mJy sensitivity on $>12$ G$\lambda$ baselines at 345 GHz is sufficient, which is accessible from the ground. For both sources, these sensitivity requirements may be relaxed by repeated observations and averaging.Comment: 14 pages, 7 figures, Accepted to ApJ