Improved risk stratification of nasopharyngeal cancer by targeted sequencing of Epstein-Barr virus DNA in post-treatment plasma.

BACKGROUND: Quantitative measurement of plasma Epstein-Barr virus (EBV) DNA by real-time PCR at the end of primary treatment is a robust prognostic marker for nasopharyngeal carcinoma (NPC) patients. However, up to 40% of patients who would later develop disease recurrence had undetectable post-treatment plasma EBV DNA. Targeted sequencing for the entire EBV genome potentially allows a more comprehensive and unbiased detection of plasma EBV DNA and enables the use of other parameters such as fragment size as biomarkers. Hence, we explored if plasma EBV DNA sequencing might allow more accurate prognostication of NPC patients. PATIENTS AND METHODS: Plasma samples collected from 769 patients with stage IIB-IVB NPC at 6-8 weeks after radiotherapy were analysed using targeted sequencing for EBV DNA. RESULTS: The sensitivities of the PCR-based analysis, at a cut-off of any detectable levels of plasma EBV DNA, for prediction of local and distant recurrences were 42.3% and 85.3%, respectively. The sequencing-based analysis (involving quantitation and size profiling) achieved better performance for both local and distant recurrences than PCR. Using a cut-off of the proportion of plasma EBV DNA deduced by sequencing at 0.01%, the sensitivities of the sequencing-based analysis for local and distant recurrences were 88.5% and 97.1%, with the resultant negative predictive values of 99.1% and 99.4%, respectively. Among patients with undetectable EBV DNA on quantitative PCR, sequencing could further define a subgroup that enjoyed superior survival outcomes based on the proportion of plasma EBV DNA, with a 5-year progression-free survival (PFS) approaching 90%. On multivariate analysis, sequencing-based quantitative level of plasma EBV DNA was the independent prognostic factor with the highest hazard ratio for prediction of overall survival and PFS. CONCLUSION: NPC prognostication using post-treatment plasma EBV DNA could be enhanced through sequencing.

Observation of High Transformer Ratio of Shaped Bunch Generated by an Emittance-Exchange Beam Line.

Collinear wakefield acceleration has been long established as a method capable of generating ultrahigh acceleration gradients. Because of the success on this front, recently, more efforts have shifted towards developing methods to raise the transformer ratio (TR). This figure of merit is defined as the ratio of the peak acceleration field behind the drive bunch to the peak deceleration field inside the drive bunch. TR is always less than 2 for temporally symmetric drive bunch distributions and therefore recent efforts have focused on generating asymmetric distributions to overcome this limitation. In this Letter, we report on using the emittance-exchange method to generate a shaped drive bunch to experimentally demonstrate a TR≈5 in a dielectric wakefield accelerator.

Precision Control of the Electron Longitudinal Bunch Shape Using an Emittance-Exchange Beam Line.

We report on the experimental generation of relativistic electron bunches with a tunable longitudinal bunch shape. A longitudinal bunch-shaping (LBS) beam line, consisting of a transverse mask followed by a transverse-to-longitudinal emittance exchange (EEX) beam line, is used to tailor the longitudinal bunch shape (or current profile) of the electron bunch. The mask shapes the bunch's horizontal profile, and the EEX beam line converts it to a corresponding longitudinal profile. The Argonne wakefield accelerator rf photoinjector delivers electron bunches into a LBS beam line to generate a variety of longitudinal bunch shapes. The quality of the longitudinal bunch shape is limited by various perturbations in the exchange process. We develop a simple method, based on the incident slope of the bunch, to significantly suppress the perturbations.

Rotenone and elevated extracellular potassium concentration induce cell-specific fibrillation of α-synuclein in axons of cholinergic enteric neurons in the guinea-pig ileum.

BACKGROUND: Parkinson's disease is a progressive neurodegenerative disorder that results in the widespread loss of select classes of neurons throughout the nervous system. The pathological hallmarks of Parkinson's disease are Lewy bodies and neurites, of which α-synuclein fibrils are the major component. α-Synuclein aggregation has been reported in the gut of Parkinson's disease patients, even up to a decade before motor symptoms, and similar observations have been made in animal models of disease. However, unlike the central nervous system, the nature of α-synuclein species that form these aggregates and the classes of neurons affected in the gut are unclear. We have previously reported selective expression of α-synuclein in cholinergic neurons in the gut (J Comp Neurol. 2013; 521:657), suggesting they may be particularly vulnerable to degeneration in Parkinson's disease. METHODS: In this study, we used immunohistochemistry to detect α-synuclein oligomers and fibrils via conformation-specific antibodies after rotenone treatment or prolonged exposure to high [K+ ] in ex vivo segments of guinea-pig ileum maintained in organotypic culture. KEY RESULTS: Rotenone and prolonged raising of [K+ ] caused accumulation of α-synuclein fibrils in the axons of cholinergic enteric neurons. This took place in a time- and, in the case of rotenone, concentration-dependent manner. Rotenone also caused selective necrosis, indicated by increased cellular autofluorescence, of cholinergic enteric neurons, labeled by ChAT-immunoreactivity, also in a concentration-dependent manner. CONCLUSIONS & INFERENCES: To our knowledge, this is the first report of rotenone causing selective loss of a neurochemical class in the enteric nervous system. Cholinergic enteric neurons may be particularly susceptible to Lewy pathology and degeneration in Parkinson's disease.

Development and characterization of Rift Valley fever virus-like particles.

Rift Valley fever (RVF) is an acute, febrile zoonotic disease that is caused by the RVF virus (RVFV) and spread by arthropod vectors. RVF is currently prevalent in Africa and the Arabian Peninsula, and causes substantial economic losses. Furthermore, this disease poses a serious threat to animal and human health in regions worldwide, making it a serious public health concern. However, RVFV vaccines for human use are still unavailable, and hence there is an urgent need for novel efficient vaccines against RVFV. Vaccine preparation techniques have become a crucial factor in developing new vaccines. In the current study, the N and G protein genes of RVFV were inserted into the pFastBacDual baculovirus expression vector downstream of the pP10 and pPH promoters. The resultant recombinant vector, pFastBacDual-S-M, was transfected into Sf9 insect cells by lipofection. The recombinant baculovirus, named rBac-N-G, was retrieved and infected into Sf9 insect cells to generate RVFV virus-like particles (VLPs). Using polyclonal antibodies against RVFV proteins in immunofluorescence and western blot analyses, we positively identified the presence of the RVFV proteins in VLP preparations. Sucrose density gradient centrifugation and transmission electron microscopy revealed that the morphology of the RVFV VLPs was consistent with previous reports of RVFV virions. This study describes a technique for efficient production of RVFV VLPs, and has laid the foundation for future VLP-based RVFV vaccines.

Interaction of an Ultrarelativistic Electron Bunch Train with a W-Band Accelerating Structure: High Power and High Gradient.

Electron beam interaction with high frequency structures (beyond microwave regime) has a great impact on future high energy frontier machines. We report on the generation of multimegawatt pulsed rf power at 91 GHz in a planar metallic accelerating structure driven by an ultrarelativistic electron bunch train. This slow-wave wakefield device can also be used for high gradient acceleration of electrons with a stable rf phase and amplitude which are controlled by manipulation of the bunch train. To achieve precise control of the rf pulse properties, a two-beam wakefield interferometry method was developed in which the rf pulse, due to the interference of the wakefields from the two bunches, was measured as a function of bunch separation. Measurements of the energy change of a trailing electron bunch as a function of the bunch separation confirmed the interferometry method.

Experimental demonstration of energy-chirp compensation by a tunable dielectric-based structure.

A tunable energy-chirp compensator was used to remove a correlated energy chirp from the 60-MeV beam at the Brookhaven National Laboratory Accelerator Test Facility. The compensator operates through the interaction of the wakefield of the electron bunch with itself and consists of a planar structure comprised of two alumina bars with copper-plated backs separated by an adjustable beam aperture. By changing the gap size, the correlated energy chirp of the electron bunch was completely removed. Calculations show that this device, properly scaled to account for the electron bunch charge and length, can be used to remove residual correlated energy spread at the end of the linacs used for free-electron lasers. The experimental results are shown to be in good agreement with numerical simulations. Application of this technique can significantly simplify linac design and improve free-electron lasers performance.

Subpicosecond bunch train production for a tunable mJ level THz source.

A strong energy modulation in an electron bunch passing through a dielectric-lined waveguide was recently demonstrated in Antipov et al., Phys. Rev. Lett. 108, 144801 (2012). In this Letter, we demonstrate a successful conversion of this energy modulation into a beam density modulation, and the formation of a series of microbunches with a subpicosecond periodicity by means of magnetic optics (chicane). A strong coherent transition radiation signal produced by the microbunches is obtained and the tunability of its carrier frequency in the 0.68-0.9 THz range by regulating the energy chirp in the incoming electron bunch is demonstrated using infrared interferometry. A tabletop, compact, tunable, and narrowband source of intense THz radiation based on this technology is proposed.

Increased SUMO-1 expression in the unilateral rotenone-lesioned mouse model of Parkinson's disease.

Parkinson's disease (PD) is a neurodegenerative disease resulting from progressive loss of dopaminergic nigrostriatal neurons. α-Synuclein protein conformational changes, resulting in cytotoxic/aggregated proteins, have been linked to PD pathogenesis. We investigated a unilateral rotenone-lesioned mouse PD model. Unilateral lesion of the medial forebrain bundle for two groups of male C57 black mice (n=5); adult (6-12 months) group and aged (1.75-2 years) group, was via stereotactic rotenone injection. After 2 weeks post-lesion, phenotypic Parkinsonian symptoms, resting tremor, postural instability, left-handed bias, ipsiversive rotation and bradykinesia were observed and were more severe in the aged group. We investigated protein expression profiles of the post-translational modifier, SUMO-1, and α-synuclein between the treated and control hemisphere, and between adult and aged groups. Western analysis of the brain homogenates indicated that there were statistically significant (p<0.05) increases in several specific molecular weight species (ranging 12-190 kDa) of both SUMO-1 (0.75-4.3-fold increased) and α-synuclein (1.6-19-fold increase) in the lesioned compared to un-lesioned hemisphere, with the adult mice showing proportionately greater increases in SUMO-1 than the aged group.

Detection of anti-Trichinella antibodies in serum of experimentally-infected swine by immunochromatographic strip.

An immunochromatographic strip method, developed with the excretory-secretory antigens from muscle larvae (ML) of Trichinella spiralis labeled with colloidal gold, was used for the detection of anti-Trichinella antibodies in serum of experimentally-infected swine. Sera from swine infected with 200, 2000 and 20,000 infective ML were collected at different days post infection (dpi) and used to evaluate the method. The strip method was shown able to detect anti-Trichinella antibodies by 35 dpi, 28 dpi and 21 dpi for the three different infection doses, respectively, and closely correlated with the results of an ELISA test. The strip method is rapid and easy to perform and is suggested as an acceptable alternative for clinical laboratories lacking specialized equipment, and for field diagnosis of trichinellosis.

Surface-emission studies in a high-field RF gun based on measurements of field emission and Schottky-enabled photoemission.

We report on investigations into the fundamental surface emission parameters, the geometric field enhancement factor (ß) and the work function (φ), by making both field emission and Schottky-enabled photoemission measurements. The measurements were performed on a copper surface in the Tsinghua University S-band RF gun in two separate experiments. Fitting our data to the models for each experiment indicate that the traditionally assumed high value of ß(≈50-500) does not provide a plausible explanation of the data, but incorporating a low value of φ at some sites does. In addition, direct measurements of the surface conducted after the experiment show that ß is on the order of a few, consistent with our understanding of the electron emission measurements. Thus we conclude that the dominant source of electron emission in high gradient RF cavities is due to low φ sites, as opposed to the conventionally assumed high ß sites. The origin of low φ at these sites is unclear and should be the subject of further investigation.

Experimental observation of energy modulation in electron beams passing through terahertz dielectric wakefield structures.

We report the observation of a strong wakefield induced energy modulation in an energy-chirped electron bunch passing through a dielectric-lined waveguide. This modulation can be effectively converted into a spatial modulation forming microbunches with a periodicity of 0.5-1 ps and, hence, capable of driving coherent terahertz radiation. The experimental results agree well with theoretical predictions.

Antiviral effect of a selective COX-2 inhibitor on H5N1 infection in vitro.

A selective cyclooxygenase-2 (COX-2) inhibitor has been previously shown to suppress the hyper-induced pro-inflammatory responses in H5N1 infected primary human cells. Here, we demonstrate that COX-2 inhibitors suppress H5N1 virus replication in human macrophages suggesting that H5N1 virus replication (more so than seasonal H1N1 virus) is dependent on activation of COX-2 dependent signaling pathways in host cells. COX-2 and its downstream signaling pathways deserve detailed investigation as a novel therapeutic target for treatment of H5N1 disease.

Experimental demonstration of wakefield acceleration in a tunable dielectric loaded accelerating structure.

We report on a collinear wakefield experiment using the first tunable dielectric loaded accelerating structure. By introducing an extra layer of nonlinear ferroelectric, which has a dielectric constant sensitive to temperature and dc bias, the frequency of a dielectric loaded accelerating structure can be tuned. During the experiment, the energy of a witness bunch at a fixed delay with respect to the drive beam was measured while the temperature of the structure was scanned over a 50 °C range. The energy change corresponded to a change of more than half of the nominal structure wavelength.

Emittance-exchange-based high harmonic generation scheme for a short-wavelength free electron laser.

Generation of short-wavelength radiation by a free-electron laser using up-frequency conversion of an electron bunch density modulation is currently an area of active research. We propose a new scheme for producing the longitudinal electron bunch density modulation similar to the recently proposed echo-enabled harmonic generation but based on an emittance exchange beam line and a multislit mask. Beam line analysis and start-to-end simulation are presented.

Association of metallothionein-III with oligodendroglial cytoplasmic inclusions in multiple system atrophy.

Multiple system atrophy (MSA) is an adult-onset neurodegenerative disease characterised by Parkinsonian and autonomic symptoms and by widespread intracytoplasmic inclusion bodies in oligodendrocytes. These glial cytoplasmic inclusions (GCIs) are comprised of 9-10 nm filaments rich in the protein alpha-synuclein, also found in neuronal inclusion bodies associated with Parkinson's disease. Metallothioneins (MTs) are a class of low-molecular weight (6-7 kDa), cysteine-rich metal-binding proteins the expression of which is induced by heavy metals, glucocorticoids, cytokines and oxidative stress. Recent studies have shown a role for the ubiquitously expressed MT-I/II isoforms in the brain following a variety of stresses, whereas, the function of the brain-specific MT isoform, MT-III, is less clear. MT-III and MT-I/II immunostaining of post-mortem tissue in MSA and normal control human brains showed that the number of MT-III-positive cells is significantly increased in MSA in visual cortex, whereas MT-I/II isoforms showed no significant difference in the distribution of immunopositive cells in MSA compared to normal tissue. GCIs were immunopositive for MT-III, but were immunonegative for the MT-I/II isoforms. Immunofluorescence double labelling showed the co-localisation of alpha-synuclein and MT-III in GCIs in MSA tissue. In isolated GCIs, transmission electron microscopy demonstrated MT-III immunogold labelling of the amorphous material surrounding alpha-synuclein filaments in GCIs. High-molecular weight MT-III species in addition to MT-III monomer were detected in GCIs by Western analysis of the detergent-solubilised proteins of purified GCIs. These results show that MT-III, but not MT-I/II, is a specific component of GCIs, present in abnormal aggregated forms external to the alpha-synuclein filaments.

Differential localization of GABAA receptor subunits within the substantia nigra of the human brain: an immunohistochemical study.

Gamma-aminobutyric acid(A) (GABA(A)) receptors (GABA(A)R) are inhibitory heteropentameric chloride ion channels comprising a variety of subunits and are localized at postsynaptic sites within the central nervous system. In this study we present the first detailed immunohistochemical investigation on the regional, cellular, and subcellular localisation of alpha(1), alpha(2), alpha(3), beta(2,3), and gamma(2) subunits of the GABA(A)R in the human substantia nigra (SN). The SN comprises two major regions, the SN pars compacta (SNc) consisting of dopaminergic projection neurons, and the SN pars reticulata (SNr) consisting of GABAergic parvalbumin-positive projection neurons. The results of our single- and double-labeling studies demonstrate that in the SNr GABA(A) receptors contain alpha(1), alpha(3), beta(2,3), and gamma(2) subunits and are localized in a weblike network over the cell soma, dendrites, and spines of SNr parvalbumin-positive nonpigmented neurons. By contrast, GABA(A)Rs on the SNc dopaminergic pigmented neurons contain predominantly alpha(3) and gamma(2) subunits; however there is GABA(A)R heterogeneity in the SNc, with a small subpopulation (6.5%) of pigmented SNc neurons additionally containing alpha(1) and beta(2,3) GABA(A)R subunits. Also, in the SNr, parvalbumin-positive terminals are adjacent to GABA(A)R on the soma and proximal dendrites of SNr neurons, whereas linear arrangements of substance P-positive terminals are adjacent to GABA(A) receptors on all regions of the dendritic tree. These results show marked GABA(A)R subunit hetereogeneity in the SN, suggesting that GABA exerts quite different effects on pars compacta and pars reticulata neurons in the human SN via GABA(A) receptors of different subunit configurations.

Observation of enhanced transformer ratio in collinear wakefield acceleration.

One approach to future high energy particle accelerators is based on the wakefield principle: a leading high-charge drive bunch is used to excite fields in an accelerating structure or plasma that in turn accelerates a trailing low-charge witness bunch. The transformer ratio R is defined as the ratio of the maximum energy gain of the witness bunch to the maximum energy loss of the drive bunch. In general, R<2 for this configuration. A number of techniques have been proposed to overcome the transformer ratio limitation. We report here the first experimental study of the ramped bunch train (RBT) technique in a dielectric based accelerating structure. A single drive bunch was replaced by two bunches with charge ratio of 1:2.5 and a separation of 10.5 wavelengths of the fundamental mode. An average measured transformer ratio enhancement by a factor of 1.31 over the single drive bunch case was obtained.

Alpha-synuclein is upregulated in neurones in response to chronic oxidative stress and is associated with neuroprotection.

Chronic oxidative stress has been linked to the neurodegenerative changes characteristic of Parkinson's disease, particularly alpha-synuclein accumulation and aggregation. However, it remains contentious whether these alpha-synuclein changes are cytotoxic or neuroprotective. The current study utilised long-term primary neural culture techniques with antioxidant free media to study the cellular response to chronic oxidative stress. Cells maintained in antioxidant free media were exquisitely more vulnerable to acute exposure to hydrogen peroxide, yet exposure of up to 10 days in antioxidant free media did not lead to morphological alterations in neurones or glia. However, a subpopulation of neurones demonstrated a significant increase in the level of alpha-synuclein expressed within the cell body and at synaptic sites. This subset of neurones was also more resistant to apoptotic changes following exposure to antioxidant free media relative to other neurones. These data indicate that increased alpha-synuclein content is associated with neuroprotection from relatively low levels of oxidative stress.