Volcanic Eruption in the Nanoworld: Efficient Oxygen Exchange at the Si/SnO2 Interface.

Here, a phenomenon of efficient oxygen exchange between a silicon surface and a thin layer of tin dioxide during chemical vapor deposition is presented, which leads to a unique Sn:SiO2 layer. Under thermodynamic conditions in the temperature range of 725-735 °C, the formation of nanostructures with volcano-like shapes in "active" and "dormant" states are observed. Extensive characterization techniques, such as electron microscopy, X-ray diffraction, synchrotron radiation-based X-ray photoelectron, and X-ray absorption near-edge structure spectroscopy, are applied to study the formation. The mechanism is related to the oxygen retraction between tin(IV) oxide and silicon surface, leading to the thermodynamically unstable tin(II)oxide, which is immediately disproportionate to metallic Sn and SnO2 localized in the SiO2 matrix. The diffusion of metallic tin in the amorphous silicon oxide matrix leads to larger agglomerates of nanoparticles, which is similar to the formation of a magma chamber during the natural volcanic processes followed by magma eruption, which here is associated with the formation of depressions on the surface filled with metallic tin particles. This new effect contributes a new approach to the formation of functional composites but also inspires the development of unique Sn:SiO2 nanostructures for diverse application scenarios, such as thermal energy storage.

Nanostructured Silicon Matrix for Materials Engineering.

Tin-containing layers with different degrees of oxidation are uniformly distributed along the length of silicon nanowires formed by a top-down method by applying metalorganic chemical vapor deposition. The electronic and atomic structure of the obtained layers is investigated by applying nondestructive surface-sensitive X-ray absorption near edge spectroscopy using synchrotron radiation. The results demonstrated, for the first time, a distribution effect of the tin-containing phases in the nanostructured silicon matrix compared to the results obtained for planar structures at the same deposition temperatures. The amount and distribution of tin-containing phases can be effectively varied and controlled by adjusting the geometric parameters (pore diameter and length) of the initial matrix of nanostructured silicon. Due to the occurrence of intense interactions between precursor molecules and decomposition by-products in the nanocapillary, as a consequence of random thermal motion of molecules in the nanocapillary, which leads to additional kinetic energy and formation of reducing agents, resulting in effective reduction of tin-based compounds to a metallic tin state for molecules with the highest penetration depth in the nanostructured silicon matrix. This effect will enable clear control of the phase distributions of functional materials in 3D matrices for a wide range of applications.

Spectromicroscopy Studies of Silicon Nanowires Array Covered by Tin Oxide Layers.

The composition and atomic and electronic structure of a silicon nanowire (SiNW) array coated with tin oxide are studied at the spectromicroscopic level. SiNWs are covered from top to down with a wide bandgap tin oxide layer using a metal-organic chemical vapor deposition technique. Results obtained via scanning electron microscopy and X-ray diffraction showed that tin-oxide nanocrystals, 20 nm in size, form a continuous and highly developed surface with a complex phase composition responsible for the observed electronic structure transformation. The "one spot" combination, containing a chemically sensitive morphology and spectroscopic data, is examined via photoemission electron microscopy in the X-ray absorption near-edge structure spectroscopy (XANES) mode. The observed spectromicroscopy results showed that the entire SiNW surface is covered with a tin(IV) oxide layer and traces of tin(II) oxide and metallic tin phases. The deviation from stoichiometric SnO2 leads to the formation of the density of states sub-band in the atop tin oxide layer bandgap close to the bottom of the SnO2 conduction band. These observations open up the possibility of the precise surface electronic structures estimation using photo-electron microscopy in XANES mode.

Differential Outcomes following Optimization of Simian-Human Immunodeficiency Viruses from Clades AE, B, and C.

Simian-human immunodeficiency virus (SHIV) infection of rhesus monkeys is an important preclinical model for human immunodeficiency virus type 1 (HIV-1) vaccines, therapeutics, and cure strategies. SHIVs have been optimized by incorporating HIV-1 Env residue 375 mutations that mimic the bulky or hydrophobic residues typically found in simian immunodeficiency virus (SIV) Env to improve rhesus CD4 binding. We applied this strategy to three SHIV challenge stocks (SHIV-SF162p3, SHIV-AE16, and SHIV-325c) and observed three distinct outcomes. We constructed six Env375 variants (M, H, W, Y, F, and S) for each SHIV, and we performed a pool competition study in rhesus monkeys to define the optimal variant for each SHIV prior to generating large-scale challenge stocks. We identified SHIV-SF162p3S/wild type, SHIV-AE16W, and SHIV-325cH as the optimal variants. SHIV-SF162p3S could not be improved, as it already contained the optimal Env375 residue. SHIV-AE16W exhibited a similar replicative capacity to the parental SHIV-AE16 stock. In contrast, SHIV-325cH demonstrated a 2.6-log higher peak and 1.6-log higher setpoint viral loads than the parental SHIV-325c stock. These data demonstrate the diversity of potential outcomes following Env375 modification in SHIVs. Moreover, the clade C SHIV-325cH challenge stock may prove useful for evaluating prophylactic or therapeutic interventions against clade C HIV-1.IMPORTANCE We sought to enhance the infectivity of three SHIV stocks by optimization of a key residue in human immunodeficiency virus type 1 (HIV-1) Env (Env375). We developed the following three new simian-human immunodeficiency virus (SHIV) stocks: SHIV-SF162p3S/wild type, SHIV-AE16W, and SHIV-325cH. SHIV-SF162p3S could not be optimized, SHIV-AE16W proved comparable to the parental virus, and SHIV-325cH demonstrated markedly enhanced replicative capacity compared with the parental virus.

Therapeutic Efficacy of Vectored PGT121 Gene Delivery in HIV-1-Infected Humanized Mice.

Broadly neutralizing antibodies (bNAbs) are being explored for HIV-1 prevention and cure strategies. However, administration of purified bNAbs poses challenges in resource-poor settings, where the HIV-1 disease burden is greatest. In vivo vector-based production of bNAbs represents an alternative strategy. We investigated adenovirus serotype 5 (Ad5) and adeno-associated virus serotype 1 (AAV1) vectors to deliver the HIV-1-specific bNAb PGT121 in wild-type and immunocompromised C57BL/6 mice as well as in HIV-1-infected bone marrow-liver-thymus (BLT) humanized mice. Ad5.PGT121 and AAV1.PGT121 produced functional antibody in vivo Ad5.PGT121 produced PGT121 rapidly within 6 h, whereas AAV1.PGT121 produced detectable PGT121 in serum by 72 h. Serum PGT121 levels were rapidly reduced by the generation of anti-PGT121 antibodies in immunocompetent mice but were durably maintained in immunocompromised mice. In HIV-1-infected BLT humanized mice, Ad5.PGT121 resulted in a greater reduction of viral loads than did AAV1.PGT121. Ad5.PGT121 also led to more-sustained virologic control than purified PGT121 IgG. Ad5.PGT121 afforded more rapid, robust, and durable antiviral efficacy than AAV1.PGT121 and purified PGT121 IgG in HIV-1-infected humanized mice. Further evaluation of vector delivery of HIV-1 bNAbs is warranted, although approaches to prevent the generation of antiantibody responses may also be required.IMPORTANCE Broadly neutralizing antibodies (bNAbs) are being explored for HIV-1 prevention and cure strategies, but delivery of purified antibodies may prove challenging. We investigated adenovirus serotype 5 (Ad5) and adeno-associated virus serotype 1 (AAV1) vectors to deliver the HIV-1-specific bNAb PGT121. Ad5.PGT121 afforded more rapid, robust, and durable antiviral efficacy than AAV1.PGT121 and purified PGT121 IgG in HIV-1-infected humanized mice.

The Ubiquitin Ligase Itch and Ubiquitination Regulate BFRF1-Mediated Nuclear Envelope Modification for Epstein-Barr Virus Maturation.

UNLABELLED: The cellular endosomal sorting complex required for transport (ESCRT) was recently found to mediate important morphogenesis processes at the nuclear envelope (NE). We previously showed that the Epstein-Barr virus (EBV) BFRF1 protein recruits the ESCRT-associated protein Alix to modulate NE structure and promote EBV nuclear egress. Here, we uncover new cellular factors and mechanisms involved in this process. BFRF1-induced NE vesicles are similar to those observed following EBV reactivation. BFRF1 is ubiquitinated, and elimination of possible ubiquitination by either lysine mutations or fusion of a deubiquitinase hampers NE-derived vesicle formation and virus maturation. While it interacts with multiple Nedd4-like ubiquitin ligases, BFRF1 preferentially binds Itch ligase. We show that Itch associates with Alix and BFRF1 and is required for BFRF1-induced NE vesicle formation. Our data demonstrate that Itch, ubiquitin, and Alix control the BFRF1-mediated modulation of the NE and EBV maturation, uncovering novel regulatory mechanisms of nuclear egress of viral nucleocapsids. IMPORTANCE: The nuclear envelope (NE) of eukaryotic cells not only serves as a transverse scaffold for cellular processes, but also as a natural barrier for most DNA viruses that assemble their nucleocapsids in the nucleus. Previously, we showed that the cellular endosomal sorting complex required for transport (ESCRT) machinery is required for the nuclear egress of EBV. Here, we further report the molecular interplay among viral BFRF1, the ESCRT adaptor Alix, and the ubiquitin ligase Itch. We found that BFRF1-induced NE vesicles are similar to those observed following EBV reactivation. The lysine residues and the ubiquitination of BFRF1 regulate the formation of BFRF1-induced NE-derived vesicles and EBV maturation. During the process, a ubiquitin ligase, Itch, preferably associates with BFRF1 and is required for BFRF1-induced NE vesicle formation. Therefore, our data indicate that Itch, ubiquitin, and Alix control the BFRF1-mediated modulation of the NE, suggesting novel regulatory mechanisms for ESCRT-mediated NE modulation.

The ESCRT machinery is recruited by the viral BFRF1 protein to the nucleus-associated membrane for the maturation of Epstein-Barr Virus.

The cellular endosomal sorting complex required for transport (ESCRT) machinery participates in membrane scission and cytoplasmic budding of many RNA viruses. Here, we found that expression of dominant negative ESCRT proteins caused a blockade of Epstein-Barr virus (EBV) release and retention of viral BFRF1 at the nuclear envelope. The ESCRT adaptor protein Alix was redistributed and partially colocalized with BFRF1 at the nuclear rim of virus replicating cells. Following transient transfection, BFRF1 associated with ESCRT proteins, reorganized the nuclear membrane and induced perinuclear vesicle formation. Multiple domains within BFRF1 mediated vesicle formation and Alix recruitment, whereas both Bro and PRR domains of Alix interacted with BFRF1. Inhibition of ESCRT machinery abolished BFRF1-induced vesicle formation, leading to the accumulation of viral DNA and capsid proteins in the nucleus of EBV-replicating cells. Overall, data here suggest that BFRF1 recruits the ESCRT components to modulate nuclear envelope for the nuclear egress of EBV.

Reductive quenching of photosensitizer [Ru(bpy)3]2+ reveals the inhomogeneous distribution of sites in PAN polymer nanofibers for light-driven redox catalysis.

Integration of molecular photocatalysts into redox-inert polymers constitutes a path towards photocatalytically active, lightweight materials. In particular, electrospun polymer fibers hold potential due to their favorable surface-to-volume ratio and their straightforward fabrication. This study focuses on the polyacrylonitrile (PAN) fibers, into which the prototype photosensitizer (PS) ruthenium tris(bipyridine) [Ru(bpy)3]2+, has been embedded by electrospinning. Studying the interaction between the optically excited [Ru(bpy)3]2+ with a non-redox inert solvent within the nanofibers, we resolve a distribution of microenvironments, which differ by the extent to which the photosensitizer is exposed to the solvent. This results in a non-exponential decay of the complex's emission and pronounced differences in the transient absorption signals.

SERS-based detection of the antibiotic ceftriaxone in spiked fresh plasma and microdialysate matrix by using silver-functionalized silicon nanowire substrates.

Therapeutic drug monitoring (TDM) is an important tool in precision medicine as it allows estimating pharmacodynamic and pharmacokinetic effects of drugs in clinical settings. An accurate, fast and real-time determination of the drug concentrations in patients ensures fast decision-making processes at the bedside to optimize the clinical treatment. Surface-enhanced Raman spectroscopy (SERS), which is based on the application of metallic nanostructured substrates to amplify the inherent weak Raman signal, is a promising technique in medical research due to its molecular specificity and trace sensitivity accompanied with short detection times. Therefore, we developed a SERS-based detection scheme using silicon nanowires decorated with silver nanoparticles, fabricated by means of top-down etching combined with chemical deposition, to detect the antibiotic ceftriaxone (CRO) in spiked fresh plasma and microdialysis samples. We successfully detected CRO in both matrices with an LOD of 94 µM in protein-depleted fresh plasma and 1.4 µM in microdialysate.

Tin/Tin Oxide Nanostructures: Formation, Application, and Atomic and Electronic Structure Peculiarities.

For a very long period, tin was considered one of the most important metals for humans due to its easy access in nature and abundance of sources. In the past, tin was mainly used to make various utensils and weapons. Today, nanostructured tin and especially its oxide materials have been found to possess many characteristic physical and chemical properties that allow their use as functional materials in various fields such as energy storage, photocatalytic process, gas sensors, and solar cells. This review discusses current methods for the synthesis of Sn/SnO2 composite materials in form of powder or thin film, as well as the application of the most advanced characterization tools based on large-scale synchrotron radiation facilities to study their chemical composition and electronic features. In addition, the applications of Sn/SnO2 composites in various fields are presented in detail.

Antiretroviral therapy reveals triphasic decay of intact SIV genomes and persistence of ancestral variants.

The decay kinetics of HIV-1-infected cells are critical to understand virus persistence. We evaluated the frequency of simian immunodeficiency virus (SIV)-infected cells for 4 years of antiretroviral therapy (ART). The intact proviral DNA assay (IPDA) and an assay for hypermutated proviruses revealed short- and long-term infected cell dynamics in macaques starting ART ∼1 year after infection. Intact SIV genomes in circulating CD4+T cells showed triphasic decay with an initial phase slower than the decay of the plasma virus, a second phase faster than the second phase decay of intact HIV-1, and a stable third phase reached after 1.6-2.9 years. Hypermutated proviruses showed bi- or mono-phasic decay, reflecting different selective pressures. Viruses replicating at ART initiation had mutations conferring antibody escape. With time on ART, viruses with fewer mutations became more prominent, reflecting decay of variants replicating at ART initiation. Collectively, these findings confirm ART efficacy and indicate that cells enter the reservoir throughout untreated infection.

Reduced Inter-Voxel White Matter Integrity in Subjective Cognitive Decline: Diffusion Tensor Imaging With Tract-Based Spatial Statistics Analysis.

Subjective cognitive decline (SCD), a self-reported worsening in cognition concurrent with normal performance on standardized neuropsychological tests, has gained much attention due to its high risks in the development of mild cognitive impairments or Alzheimer's disease. The existing cross-sectional diffusion tensor imaging (DTI) studies in SCD have shown extremely controversial findings. Furthermore, all of these studies investigated diffusion properties within the voxel, such as fractional anisotropy, mean diffusivity, or axial diffusivity (DA). However, it remains unclear whether individuals with SCD demonstrate alterations of diffusion profile between voxels and their neighbors, as indexed by local diffusion homogeneity (LDH). We selected 30 healthy controls (HCs) and 23 SCD subjects to acquire their whole-brain DTI. Diffusion images were compared using the tract-based spatial statistics method. Diffusion indices with significant between-group tract clusters were extracted from each individual for further region-of-interest (ROI)-based comparisons. Our results showed that subjects with SCD demonstrated reduced LDH in the left superior frontal gyrus (SFG) and DA in the right anterior cingulate cortex compared with the HC group. In contrast, the SCD group showed higher LDH values in the left lingual gyrus (LG) compared with the HC group. Notably, LDH in the left SFG was significantly and negatively correlated with LDH in the left LG. In conclusion, white matter (WM) integrity in the left SFG, right ACC, and left LG is altered in SCD, suggesting that individuals with SCD exhibit detectable changes in WM tracts before they demonstrate objective cognitive deficits.

Persistence of viral RNA in lymph nodes in ART-suppressed SIV/SHIV-infected Rhesus Macaques.

The establishment of a long-lived viral reservoir is the key obstacle for achieving an HIV-1 cure. However, the anatomic, virologic, and immunologic features of the viral reservoir in tissues during antiretroviral therapy (ART) remain poorly understood. Here we present a comprehensive necroscopic analysis of the SIV/SHIV viral reservoir in multiple lymphoid and non-lymphoid tissues from SIV/SHIV-infected rhesus macaques suppressed with ART for one year. Viral DNA is observed broadly in multiple tissues and is comparable in animals that had initiated ART at week 1 or week 52 of infection. In contrast, viral RNA is restricted primarily to lymph nodes. Ongoing viral RNA transcription is not the result of unsuppressed viral replication, as single-genome amplification and subsequent phylogenetic analysis do not show evidence of viral evolution. Gag-specific CD8+ T cell responses are predominantly observed in secondary lymphoid organs in animals chronically infected prior to ART and these responses are dominated by CD69+ populations. Overall, we observe that the viral reservoir in rhesus macaques is widely distributed across multiple tissue sites and that lymphoid tissues act as a site of persistent viral RNA transcription under conditions of long-term ART suppression.

Origin of rebound virus in chronically SIV-infected Rhesus monkeys following treatment discontinuation.

Viral rebound following antiretroviral therapy (ART) discontinuation in HIV-1-infected individuals is believed to originate from a small pool of CD4+ T cells harboring replication-competent provirus. However, the origin and nature of the rebound virus has remained unclear. Recent studies have suggested that rebound virus does not originate directly from individual latent proviruses but rather from recombination events involving multiple proviruses. Here we evaluate the origin of rebound virus in 16 ART-suppressed, chronically SIV-infected rhesus monkeys following ART discontinuation. We sequence viral RNA and viral DNA in these animals prior to ART initiation, during ART suppression, and following viral rebound, and we compare rebound viral RNA after ART discontinuation with near full-length viral DNA from peripheral blood and lymph node mononuclear cells (PBMC and LNMC) during ART suppression. Sequences of initial rebound viruses closely match viral DNA sequences in PBMC and LNMC during ART suppression. Recombinant viruses are rare in the initial rebound virus populations but arise quickly within 2-4 weeks after viral rebound. These data suggest that intact proviral DNA in PBMC and LNMC during ART suppression is likely the direct origin of viral rebound in chronically SIV-infected rhesus monkeys following ART discontinuation.

The Landscape of Persistent Viral Genomes in ART-Treated SIV, SHIV, and HIV-2 Infections.

Evaluation of HIV cure strategies is complicated by defective proviruses that persist in ART-treated patients but are irrelevant to cure. Non-human primates (NHP) are essential for testing cure strategies. However, the persisting proviral landscape in ART-treated NHPs is uncharacterized. Here, we describe viral genomes persisting in ART-treated, simian immunodeficiency virus (SIV)-infected NHPs, simian-human immunodeficiency virus (SHIV)-infected NHPs, and humans infected with HIV-2, an SIV-related virus. The landscapes of persisting SIV, SHIV, and HIV-2 genomes are also dominated by defective sequences. However, there was a significantly higher fraction of intact SIV proviral genomes compared to ART-treated HIV-1 or HIV-2 infected humans. Compared to humans with HIV-1, SIV-infected NHPs had more hypermutated genomes, a relative paucity of clonal SIV sequences, and a lower frequency of deleted genomes. Finally, we report an assay for measuring intact SIV genomes which may have value in cure research.

Prevention of SIVmac251 reservoir seeding in rhesus monkeys by early antiretroviral therapy.

The precise time when the viral reservoir is seeded during acute HIV-1 infection remains unclear. We previously demonstrated that the viral reservoir was seeded by day 3 following SIVmac251 infection in rhesus monkeys. Here we report the impact of initiating ART on day 0 (6 h), 1, 2, or 3 following intrarectal SIVmac251 infection in 20 rhesus monkeys (N = 5/group). After 6 months of daily suppressive ART, antiretroviral drugs were discontinued, and viral rebound was monitored. 0% (0 of 5), 20% (1 of 5), 60% (3 of 5), and 100% (5 of 5) of animals that initiated ART on days 0 (6 h), 1, 2, or 3, respectively, showed viral rebound following ART discontinuation and correlated with integrated viral DNA in lymph node CD4+ T cells. These data demonstrate that the viral reservoir is seeded within the first few days of infection and that early ART initiation limits the viral reservoir.

Protection against a mixed SHIV challenge by a broadly neutralizing antibody cocktail.

HIV-1 sequence diversity presents a major challenge for the clinical development of broadly neutralizing antibodies (bNAbs) for both therapy and prevention. Sequence variation in critical bNAb epitopes has been observed in most HIV-1-infected individuals and can lead to viral escape after bNAb monotherapy in humans. We show that viral sequence diversity can limit both the therapeutic and prophylactic efficacy of bNAbs in rhesus monkeys. We first demonstrate that monotherapy with the V3 glycan-dependent antibody 10-1074, but not PGT121, results in rapid selection of preexisting viral variants containing N332/S334 escape mutations and loss of therapeutic efficacy in simian-HIV (SHIV)-SF162P3-infected rhesus monkeys. We then show that the V3 glycan-dependent antibody PGT121 alone and the V2 glycan-dependent antibody PGDM1400 alone both fail to protect against a mixed challenge with SHIV-SF162P3 and SHIV-325c. In contrast, the combination of both bNAbs provides 100% protection against this mixed SHIV challenge. These data reveal that single bNAbs efficiently select resistant viruses from a diverse challenge swarm to establish infection, demonstrating the importance of bNAb cocktails for HIV-1 prevention.

Left ventricular myocardium segmentation on delayed phase of multi-detector row computed tomography.

RATIONALE AND OBJECTIVES: Advanced ischemic heart disease is usually accompanied by left ventricular (LV) myocardial volume loss and an abnormal enhancing pattern on delayed phase of multi-detector row computed tomography (MDCT). To assist radiologists and physicians in estimating the LV myocardial volume on delayed phase, this paper proposes an adaptive segmentation method for contouring the myocardial region in the delayed-phase MDCT and for computing the volume. MATERIALS AND METHODS: The proposed method uses an anisotropic diffusion filter as a preprocessing procedure to enhance contrast and reduce specks in MDCT imaging. This work picks the middle of mid-ventricular level image slices as the lead slice. The proposed method develops two contouring modes to sketch the myocardium contour on the lead slice. By establishing the obtained contours as the initial contours, the region-growing method is employed to identify the contour of the myocardial region for each slice. The convex-hull finding algorithm is then used to refine the extracted contour. Finally, the width properties of the myocardial region and the morphological operators are used to obtain the entire LV myocardial volume. RESULTS: Twenty-seven healthy patients who had no symptoms of ischemic heart disease are examined to evaluate the performance of the proposed method. Compared with manual contours delineated by two experienced experts, the contouring results using computer simulation reveal that the proposed method reliably identifies contours similar to those obtained using manual sketching. CONCLUSION: The proposed method provides robust contouring for the LV myocardium on delayed-phase MDCT. The potential role of this technique may substantially reduce the time required to sketch manually a precise contour with high stability.