Insights into the 3D permeable pore structure within novel monodisperse mesoporous silica nanoparticles by cryogenic electron tomography.

Sintered agglomerate of synthetic mesoporous silica nanoparticles (MSNs) is an architected geomaterial that provides confinement-mediated flow and transport properties of fluids needed for environmental research such as geological subsurface energy storage or carbon capture. The design of those properties can be guided by numerical simulations but is hindered by the lack of method to characterize the permeable pores within MSNs due to pore size. This work uses the advances of an Individual Particle cryogenic transmission Electron Tomography (IPET) technique to obtain detailed 3D morphology of monodispersed MSNs with diameters below 50 nm. The 3D reconstructed density-maps show the diameters of those MSNs vary from 35-46 nm, containing connected intraparticle pores in diameter of 2-20 nm with a mean of 9.2 ± 3 nm, which is comparable to the mean interparticle pore diameters in sintered agglomerate. The characterization of the pore shape and dimensions provides key information for estimating the flow and transport properties of fluids within the sintered agglomerate of those MSNs and for modeling the atomic MSN structures needed for pore-fluid simulations.

Flow Reduction in Pore Networks of Packed Silica Nanoparticles: Insights from Mesoscopic Fluid Models.

A modified many-body dissipative particle dynamics (mDPD) model is rigorously calibrated to achieve realistic fluid-fluid/solid interphase properties and applied for mesoscale flow simulations to elucidate the transport mechanisms of heptane liquid and water, respectively, through pore networks formed by packed silica nanoparticles with a uniform diameter of 30 nm. Two million CPU core hours were used to complete the simulation studies. Results show reduction of permeability by 54-64% in heptane flow and by 88-91% in water flow, respectively, compared to the Kozeny-Carman equation. In these nanopores, a large portion of the fluids are in the near-wall regions and thus not mobile due to the confinement effect, resulting in reduced hydraulic conductivity. Moreover, intense oscillations in the calculated flow velocities also indicate the confinement effect that contests the external driven force to flow. The generic form of Darcy's law is considered valid for flow through homogeneous nanopore networks, while permeability depends collectively on pore size and surface wettability. This fluid-permeability dependency is unique to flow in nanopores. In addition, potential dependence of permeability on pore connectivity is observed when the porosity remains the same in different core specimens.

Pilot-scale grinding and briquetting studies on variable moisture content municipal solid waste bales - Impact on physical properties, chemical composition, and calorific value.

Low bulk density, variable moisture content, and particle size of municipal solid waste (MSW) create feeding, handling, storage, and transportation challenges. In this study, MSW bales were size-reduced in stage-1 and stage-2 hammer mill grinders fitted with 50.8-mm and 6.35-, 12.7-, and 19.05-mm screens. Ground MSW was densified further in a pilot-scale briquette press by varying moisture content in the range of 10-25% wet basis (w.b.). At 40% (w.b.) MSW moisture content, the stage-1 grinder fitted with a 50.4-mm screen took about 136kWh/ton, while the stage-2 grinder fitted with a 19.05-mm screen took about 151kWh/ton. The bulk density of MSW after stage-1 and stage-2 grinding was about 25-50 kg/m3. Unit bulk and tapped density were in the range of 680-850 kg/m3, 478-315 kg/m3, and 346-540 kg/m3 post briquetting, and 591-830 kg/m3, 295-458 kg/m3, and 319-519 kg/m3 post five days of storage at 20 °C. The durability was about 93.40-98.54% post briquetting, and after five days of storage. Increasing the moisture content and screen size decreased density and improved durability. Briquetting energy increased to 120 kWh/ton at a higher moisture content and larger grind size. MSW flow characteristics improved after briquetting. Higher lignin content (≈30%) and calorific value (19-21 MJ/kg) suggest MSW is suitable for thermochemical conversion. Ash content in the MSW was in the 11.9-14.8% range. CT-scan images of the briquettes showed a network of interconnected pores formed due to compression of various MSW fractions.

CD8+ T-cell-Mediated Immunoediting Influences Genomic Evolution and Immune Evasion in Murine Gliomas.

PURPOSE: Cancer immunoediting shapes tumor progression by the selection of tumor cell variants that can evade immune recognition. Given the immune evasion and intratumor heterogeneity characteristic of gliomas, we hypothesized that CD8+ T cells mediate immunoediting in these tumors. EXPERIMENTAL DESIGN: We developed retrovirus-induced PDGF+ Pten -/- murine gliomas and evaluated glioma progression and tumor immunogenicity in the absence of CD8+ T cells by depleting this immune cell population. Furthermore, we characterized the genomic alterations present in gliomas that developed in the presence and absence of CD8+ T cells. RESULTS: Upon transplantation, gliomas that developed in the absence of CD8+ T cells engrafted poorly in recipients with intact immunity but engrafted well in those with CD8+ T-cell depletion. In contrast, gliomas that developed under pressure from CD8+ T cells were able to fully engraft in both CD8+ T-cell-depleted mice and immunocompetent mice. Remarkably, gliomas developed in the absence of CD8+ T cells exhibited increased aneuploidy, MAPK pathway signaling, gene fusions, and macrophage/microglial infiltration, and showed a proinflammatory phenotype. MAPK activation correlated with macrophage/microglia recruitment in this model and in the human disease. CONCLUSIONS: Our studies indicate that, in these tumor models, CD8+ T cells influence glioma oncogenic pathways, tumor genotype, and immunogenicity. This suggests immunoediting of immunogenic tumor clones through their negative selection by CD8+ T cells during glioma formation.

A Quantitative Genetic Interaction Map of HIV Infection.

We have developed a platform for quantitative genetic interaction mapping using viral infectivity as a functional readout and constructed a viral host-dependency epistasis map (vE-MAP) of 356 human genes linked to HIV function, comprising >63,000 pairwise genetic perturbations. The vE-MAP provides an expansive view of the genetic dependencies underlying HIV infection and can be used to identify drug targets and study viral mutations. We found that the RNA deadenylase complex, CNOT, is a central player in the vE-MAP and show that knockout of CNOT1, 10, and 11 suppressed HIV infection in primary T cells by upregulating innate immunity pathways. This phenotype was rescued by deletion of IRF7, a transcription factor regulating interferon-stimulated genes, revealing a previously unrecognized host signaling pathway involved in HIV infection. The vE-MAP represents a generic platform that can be used to study the global effects of how different pathogens hijack and rewire the host during infection.

A polyomavirus peptide binds to the capsid VP1 pore and has potent antiviral activity against BK and JC polyomaviruses.

In pursuit of therapeutics for human polyomaviruses, we identified a peptide derived from the BK polyomavirus (BKV) minor structural proteins VP2/3 that is a potent inhibitor of BKV infection with no observable cellular toxicity. The thirteen-residue peptide binds to major structural protein VP1 with single-digit nanomolar affinity. Alanine-scanning of the peptide identified three key residues, substitution of each of which results in ~1000 fold loss of binding affinity with a concomitant reduction in antiviral activity. Structural studies demonstrate specific binding of the peptide to the pore of pentameric VP1. Cell-based assays demonstrate nanomolar inhibition (EC50) of BKV infection and suggest that the peptide acts early in the viral entry pathway. Homologous peptide exhibits similar binding to JC polyomavirus VP1 and inhibits infection with similar potency to BKV in a model cell line. Lastly, these studies validate targeting the VP1 pore as a novel strategy for the development of anti-polyomavirus agents.

Pathologic and Radiologic Correlation of Adult Cystic Lung Disease: A Comprehensive Review.

The presence of pulmonary parenchymal cysts on computed tomography (CT) imaging presents a significant diagnostic challenge. The diverse range of possible etiologies can usually be differentiated based on the clinical setting and radiologic features. In fact, the advent of high-resolution CT has facilitated making a diagnosis solely on analysis of CT image patterns, thus averting the need for a biopsy. While it is possible to make a fairly specific diagnosis during early stages of disease evolution by its characteristic radiological presentation, distinct features may progress to temporally converge into relatively nonspecific radiologic presentations sometimes necessitating histological examination to make a diagnosis. The aim of this review study is to provide both the pathologist and the radiologist with an overview of the diseases most commonly associated with cystic lung lesions primarily in adults by illustration and description of pathologic and radiologic features of each entity. Brief descriptions and characteristic radiologic features of the various disease entities are included and illustrative examples are provided for the common majority of them. In this article, we also classify pulmonary cystic disease with an emphasis on the pathophysiology behind cyst formation in an attempt to elucidate the characteristics of similar cystic appearances seen in various disease entities.

Single dose GLP toxicity and biodistribution study of a conditionally replicative adenovirus vector, CRAd-S-pk7, administered by intracerebral injection to Syrian hamsters.

BACKGROUND: CRAd-S-pk7 is a conditionally replicative oncolytic adenoviral vector that contains a survivin promoter and a pk7 fiber modification that confer tumor-specific transcriptional targeting and preferential replication in glioma while sparing the surrounding normal brain parenchyma. METHODS: This IND-enabling study performed under GLP conditions evaluated the toxicity and biodistribution of CRAd-S-pk7 administered as a single intracerebral dose to Syrian hamsters, a permissive model of adenoviral replication. Two hundred and forty animals were stereotactically administered either vehicle (n = 60) or CRAd-S-pk7 at 2.5 × 10(7), 2.5 × 10(8), or 2.5 × 10(9) viral particles (vp)/animal (each n = 60) on day 1. The animals were closely monitored for toxicology evaluation, assessment of viral distribution, and immunogenicity of CRAd-S-pk7. RESULTS: Changes in hematology, clinical chemistry, and coagulation parameters were minor and transient, and consistent with the inflammatory changes observed microscopically. These changes were considered to be of little toxicological significance. The vector remained localized primarily in the brain and to some degree in the tissues at the incision site. Low levels of vector DNA were detected in other tissues in a few animals suggesting systemic circulation of the virus. Viral DNA was detected in brains of hamsters for up to 62 days. However, microscopic changes and virus-related toxicity to the central nervous system were considered minor and decreased in incidence and severity over time. Such changes are not uncommon in studies using adenoviral vectors. CONCLUSION: This study provides safety and toxicology data justifying a clinical trial of CRAd-S-pk7 loaded in FDA-approved HB1.F3.CD neural stem cell carriers administered at the tumor resection bed in humans with recurrent malignant glioma.

Plexiform fibromyxoma with cotyledon-like serosal growth: A case report of a rare gastric tumor and review of the literature.

Plexiform fibromyxoma is a rare, benign mesenchymal neoplasm that predilects the gastric antrum and has potential for misdiagnosis as a gastrointestinal stromal tumor (GIST). The histology of the tumor is characterized by interwoven fascicular growth of cytologically bland spindled cells within a variably myxoid stroma. The current study reports the clinicopathological and immunohistochemical findings of a plexiform fibromyxoma resected from a 28-year-old Vietnamese female. The patient presented with acute, severe abdominal pain and worsening anemia. The initial fine-needle aspiration and needle core biopsy of the gastric antral mass led to an initial diagnosis of GIST. The subsequent distal partial gastrectomy revealed a 5.5-cm transmural antral mass that ulcerated the overlying mucosa and grew as variably elongated, myxoedematous, polypoid (cotyledon-like) excrescences from the serosal surface. Microscopically, the tumor demonstrated plexiform and multinodular growth of cytologically bland spindled cells proliferating in an abundant myxocollagenous stroma with a prominent capillary network. Tumor cells immunohistochemically expressed smooth muscle actin and CD10, but did not express CD117, Discovered on GIST-1 or nuclear ß-catenin. Follow-up evaluation 23 months post surgery revealed no evidence of residual tumor. A review the cases of this rare entity reported in the English language literature is also provided.

Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity.

HIV-1 encodes the accessory protein Vif, which hijacks a host Cullin-RING ubiquitin ligase (CRL) complex as well as the non-canonical cofactor CBFß, to antagonize APOBEC3 antiviral proteins. Non-canonical cofactor recruitment to CRL complexes by viral factors, to date, has only been attributed to HIV-1 Vif. To further study this phenomenon, we employed a comparative approach combining proteomic, biochemical, structural, and virological techniques to investigate Vif complexes across the lentivirus genus, including primate (HIV-1 and simian immunodeficiency virus macaque [SIVmac]) and non-primate (FIV, BIV, and MVV) viruses. We find that CBFß is completely dispensable for the activity of non-primate lentiviral Vif proteins. Furthermore, we find that BIV Vif requires no cofactor and that MVV Vif requires a novel cofactor, cyclophilin A (CYPA), for stable CRL complex formation and anti-APOBEC3 activity. We propose modular conservation of Vif complexes allows for potential exaptation of functions through the acquisition of non-CRL-associated host cofactors while preserving anti-APOBEC3 activity.

Sarcomatoid (spindle cell) carcinoma of the pancreas: A case report and review of the literature.

Sarcomatoid (spindle cell) carcinoma of the pancreas is a rare, high-grade epithelial malignancy composed predominantly or exclusively of spindle cells demonstrating evidence of epithelial derivation, but no features indicative of a specific line of mesenchymal differentiation. The current study presents the case of an 85-year-old Caucasian male with a tumor mass in the body of the pancreas. The individual subsequently underwent a distal pancreatectomy, splenectomy and partial gastrectomy. Microscopic examination of the 3.3-cm mass located in the body of the pancreas revealed a small, but high-grade, adenocarcinomatous component that blended imperceptibly with malignant spindle cells. No light microscopic or immunohistochemical evidence of specific mesenchymal differentiation was identified, and the spindle cells, as in the case of the carcinoma, were diffusely keratin-positive. Sarcomatoid (spindle cell) carcinoma defined in this way rarely presents in the pancreas, with, to the best of our knowledge, only six cases reported in the English literature.

Microstructural characterization of next generation nuclear graphites.

This article reports the microstructural characteristics of various petroleum and pitch based nuclear graphites (IG-110, NBG-18, and PCEA) that are of interest to the next generation nuclear plant program. Bright-field transmission electron microscopy imaging was used to identify and understand the different features constituting the microstructure of nuclear graphite such as the filler particles, microcracks, binder phase, rosette-shaped quinoline insoluble (QI) particles, chaotic structures, and turbostratic graphite phase. The dimensions of microcracks were found to vary from a few nanometers to tens of microns. Furthermore, the microcracks were found to be filled with amorphous carbon of unknown origin. The pitch coke based graphite (NBG-18) was found to contain higher concentration of binder phase constituting QI particles as well as chaotic structures. The turbostratic graphite, present in all of the grades, was identified through their elliptical diffraction patterns. The difference in the microstructure has been analyzed in view of their processing conditions.

Vif hijacks CBF-ß to degrade APOBEC3G and promote HIV-1 infection.

Restriction factors, such as the retroviral complementary DNA deaminase APOBEC3G, are cellular proteins that dominantly block virus replication. The AIDS virus, human immunodeficiency virus type 1 (HIV-1), produces the accessory factor Vif, which counteracts the host's antiviral defence by hijacking a ubiquitin ligase complex, containing CUL5, ELOC, ELOB and a RING-box protein, and targeting APOBEC3G for degradation. Here we reveal, using an affinity tag/purification mass spectrometry approach, that Vif additionally recruits the transcription cofactor CBF-ß to this ubiquitin ligase complex. CBF-ß, which normally functions in concert with RUNX DNA binding proteins, allows the reconstitution of a recombinant six-protein assembly that elicits specific polyubiquitination activity with APOBEC3G, but not the related deaminase APOBEC3A. Using RNA knockdown and genetic complementation studies, we also demonstrate that CBF-ß is required for Vif-mediated degradation of APOBEC3G and therefore for preserving HIV-1 infectivity. Finally, simian immunodeficiency virus (SIV) Vif also binds to and requires CBF-ß to degrade rhesus macaque APOBEC3G, indicating functional conservation. Methods of disrupting the CBF-ß-Vif interaction might enable HIV-1 restriction and provide a supplement to current antiviral therapies that primarily target viral proteins.

Monitoring and prevalence rates of metabolic syndrome in military veterans with serious mental illness.

BACKGROUND: Cardiovascular disease is the leading cause of mortality among patients with serious mental illness (SMI) and the prevalence of metabolic syndrome--a constellation of cardiovascular risk factors--is significantly higher in these patients than in the general population. Metabolic monitoring among patients using second generation antipsychotics (SGAs)--a risk factor for metabolic syndrome--has been shown to be inadequate despite the release of several guidelines. However, patients with SMI have several factors independent of medication use that predispose them to a higher prevalence of metabolic syndrome. Our study therefore examines monitoring and prevalence of metabolic syndrome in patients with SMI, including those not using SGAs. METHODS AND FINDINGS: We retrospectively identified all patients treated at a Veterans Affairs Medical Center with diagnoses of schizophrenia, schizoaffective disorder or bipolar disorder during 2005-2006 and obtained demographic and clinical data. Incomplete monitoring of metabolic syndrome was defined as being unable to determine the status of at least one of the syndrome components. Of the 1,401 patients included (bipolar disorder: 822; schizophrenia: 222; and schizoaffective disorder: 357), 21.4% were incompletely monitored. Only 54.8% of patients who were not prescribed SGAs and did not have previous diagnoses of hypertension or hypercholesterolemia were monitored for all metabolic syndrome components compared to 92.4% of patients who had all three of these characteristics. Among patients monitored for metabolic syndrome completely, age-adjusted prevalence of the syndrome was 48.4%, with no significant difference between the three psychiatric groups. CONCLUSIONS: Only one half of patients with SMI not using SGAs or previously diagnosed with hypertension and hypercholesterolemia were completely monitored for metabolic syndrome components compared to greater than 90% of those with these characteristics. With the high prevalence of metabolic syndrome seen in this population, there appears to be a need to intensify efforts to reduce this monitoring gap.

Purification and characterization of HIV-human protein complexes.

To fully understand how pathogens infect their host and hijack key biological processes, systematic mapping of intra-pathogenic and pathogen-host protein-protein interactions (PPIs) is crucial. Due to the relatively small size of viral genomes (usually around 10-100 proteins), generation of comprehensive host-virus PPI maps using different experimental platforms, including affinity tag purification-mass spectrometry (AP-MS) and yeast two-hybrid (Y2H) approaches, can be achieved. Global maps such as these provide unbiased insight into the molecular mechanisms of viral entry, replication and assembly. However, to date, only two-hybrid methodology has been used in a systematic fashion to characterize viral-host protein-protein interactions, although a deluge of data exists in databases that manually curate from the literature individual host-pathogen PPIs. We will summarize this work and also describe an AP-MS platform that can be used to characterize viral-human protein complexes and discuss its application for the HIV genome.

The evolution of a high copy gene array in Arabidopsis.

Local gene duplication is a prominent mechanism of gene copy number expansion. Elucidating the mechanisms by which local duplicates arise is necessary in understanding the evolution of genomes and their host organisms. Chromosome one of Arabidopsis thaliana contains an 81-gene array subdivided into 27 triplet units (t-units), with each t-unit containing three pre-transfer RNA genes. We utilized phylogenetic tree reconstructions and comparative genomics to order the events leading to the array's formation, and propose a model using unequal crossing-over as the primary mechanism of array formation. The model is supported by additional phylogenetic information from intergenic spacer sequences separating each t-unit, comparative analysis to an orthologous array of 12 t-units in the sister taxa Arabidopsis lyrata, and additional modeling using a stochastic simulation of orthologous array divergence. Lastly, comparative phylogenetic analysis demonstrates that the two orthologous t-unit arrays undergo concerted evolution within each taxa and are likely fluctuating in copy number under neutral evolutionary drift. These findings hold larger implications for future research concerning gene and genome evolution.