In-Depth Blood Proteome Profiling by Extensive Fractionation and Multiplexed Quantitative Mass Spectrometry.

Blood in the circulatory system carries information of physiological and pathological status of the human body, so blood proteins are often used as biomarkers for diagnosis, prognosis, and therapy. Human blood proteome can be explored by the latest technologies in mass spectrometry (MS), creating an opportunity of discovering new disease biomarkers. The extreme dynamic range of protein concentrations in blood, however, poses a challenge to detect proteins of low abundance, namely, tissue leakage proteins. Here, we describe a strategy to directly analyze undepleted blood samples by extensive liquid chromatography (LC) fractionation and 18-plex tandem-mass-tag (TMT) mass spectrometry. The proteins in blood specimens (e.g., plasma or serum) are isolated by acetone precipitation and digested into peptides. The resulting peptides are TMT-labeled, separated by basic pH reverse-phase (RP) LC into at least 40 fractions, and analyzed by acidic pH RPLC and high-resolution MS/MS, leading to the quantification of ~3000 unique proteins. Further increase of basic pH RPLC fractions and adjustment of the fraction concatenation strategy can enhance the proteomic coverage (up to ~5000 proteins). Finally, the combination of multiple batches of TMT experiments allows the profiling of hundreds of blood samples. This TMT-MS-based method provides a powerful platform for deep proteome profiling of human blood samples.

Moiré pattern of interference dislocations in condensate of indirect excitons.

Interference patterns provide direct measurement of coherent propagation of matter waves in quantum systems. Superfluidity in Bose-Einstein condensates of excitons can enable long-range ballistic exciton propagation and can lead to emerging long-scale interference patterns. Indirect excitons (IXs) are formed by electrons and holes in separated layers. The theory predicts that the reduced IX recombination enables IX superfluid propagation over macroscopic distances. Here, we present dislocation-like phase singularities in interference patterns produced by condensate of IXs. We analyze how exciton vortices and skyrmions should appear in the interference experiments and show that the observed interference dislocations are not associated with these phase defects. We show that the observed interference dislocations originate from the moiré effect in combined interference patterns of propagating condensate matter waves. The interference dislocations are formed by the IX matter waves ballistically propagating over macroscopic distances. The long-range ballistic IX propagation is the evidence for IX condensate superfluidity.

Pancharatnam-Berry phase in condensate of indirect excitons.

The Pancharatnam-Berry phase is a geometric phase acquired over a cycle of parameters in the Hamiltonian governing the evolution of the system. Here, we report on the observation of the Pancharatnam-Berry phase in a condensate of indirect excitons (IXs) in a GaAs-coupled quantum well structure. The Pancharatnam-Berry phase is directly measured by detecting phase shifts of interference fringes in IX interference patterns. Correlations are found between the phase shifts, polarization pattern of IX emission, and onset of IX spontaneous coherence. The evolving Pancharatnam-Berry phase is acquired due to coherent spin precession in IX condensate and is observed with no decay over lengths exceeding 10 µm indicating long-range coherent spin transport.

Deep Profiling of Proteome and Phosphoproteome by Isobaric Labeling, Extensive Liquid Chromatography, and Mass Spectrometry.

Mass spectrometry-based proteomics has experienced an unprecedented advance in comprehensive analysis of proteins and posttranslational modifications, with particular technical progress in liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) and isobaric labeling multiplexing capacity. Here, we introduce a deep proteomics profiling protocol that combines 10-plex tandem mass tag (TMT) labeling with an optimized LC-MS/MS platform to quantitate whole proteome and phosphoproteome. The major steps include protein extraction and digestion, TMT labeling, two-dimensional liquid chromatography, TiO2-mediated phosphopeptide enrichment, high-resolution mass spectrometry, and computational data processing. This protocol routinely leads to confident quantification of more than 10,000 proteins and approximately 30,000 phosphosites in mammalian samples. Quality control steps are implemented for troubleshooting and evaluating experimental variation. Such a multiplexed robust method provides a powerful tool for dissecting proteomic signatures at the systems level in a variety of complex samples, ranging from cell culture, animal tissues to human clinical specimens.

Quantum electronics. Probing Johnson noise and ballistic transport in normal metals with a single-spin qubit.

Thermally induced electrical currents, known as Johnson noise, cause fluctuating electric and magnetic fields in proximity to a conductor. These fluctuations are intrinsically related to the conductivity of the metal. We use single-spin qubits associated with nitrogen-vacancy centers in diamond to probe Johnson noise in the vicinity of conductive silver films. Measurements of polycrystalline silver films over a range of distances (20 to 200 nanometers) and temperatures (10 to 300 kelvin) are consistent with the classically expected behavior of the magnetic fluctuations. However, we find that Johnson noise is markedly suppressed next to single-crystal films, indicative of a substantial deviation from Ohm's law at length scales below the electron mean free path. Our results are consistent with a generalized model that accounts for the ballistic motion of electrons in the metal, indicating that under the appropriate conditions, nearby electrodes may be used for controlling nanoscale optoelectronic, atomic, and solid-state quantum systems.

Tetraspanins CD9 and CD151, epidermal growth factor receptor and cyclooxygenase-2 expression predict malignant progression in oral epithelial dysplasia.

BACKGROUND: Prognostic biomarkers aim to improve on the current inadequate method of histological assessment to identify patients with oral epithelial dysplasia at greatest risk of malignant transformation. We aimed to assess the prognostic ability of six protein biomarkers linked to the epidermal growth factor receptor (EGFR) pathway, including three tetraspanins, in a large multicentre oral dysplasia cohort. METHODS: One hundred and forty-eight cases with varying degrees of epithelial dysplasia underwent immunohistochemical assessment for CD9, CD151, CD82, EGFR, Her-2, and COX-2. Scoring was performed independently by two observers. Univariate analyses using both logistic and Cox regression models and a multivariate regression were performed. RESULTS: Malignant progression was significantly greater in those cases with decreased expression of CD9 (P=0.02), and increased expression of CD151 (P=0.02), EGFR (P=0.04), and COX-2 (P=0.003). Histological grade (P=0.0002) and morphology (P=0.03) were also prognostic, whereas smoking and alcohol were not. The optimal combination by backward-variable selection was of histological grade (hazard ratio (HR) 1.64; 95% CI 1.12, 2.40), COX-2 overexpression (HR 1.12; 1.02, 1.24) and CD9 underexpression (HR 0.88; 0.80, 0.97). CD82 and Her-2 demonstrated no prognostic ability. CONCLUSION: This is the first study of the expression and prognostic potential of the tetraspanins in oral dysplasia. A combination of certain biomarkers with clinical factors appeared to improve the accuracy of determining the risk of malignancy in individuals with oral dysplasia. These findings may also offer potential new therapeutic approaches for this condition.

Spin currents in a coherent exciton gas.

We report the observation of spin currents in a coherent gas of indirect excitons. The realized long-range spin currents originate from the formation of a coherent gas of bosonic pairs--a new mechanism to suppress the spin relaxation. The spin currents result in the appearance of a variety of polarization patterns, including helical patterns, four-leaf patterns, spiral patterns, bell patterns, and periodic patterns. We demonstrate control of the spin currents by a magnetic field. We also present a theory of coherent exciton spin transport that describes the observed exciton polarization patterns and indicates the trajectories of the spin currents.

Condensation of excitons in a trap.

Condensation is observed in a gas of indirect excitons confined in an electrostatic trap. Imaging and interferometric measurements detect that excitons condense at the trap bottom and exciton spontaneous coherence emerges with lowering temperature. Below a temperature of about 1 K, the direct signature of Bose-Einstein condensation, the extension of coherence over the entire cloud, is observed.

Spontaneous coherence in a cold exciton gas.

If bosonic particles are cooled down below the temperature of quantum degeneracy, they can spontaneously form a coherent state in which individual matter waves synchronize and combine. Spontaneous coherence of matter waves forms the basis of a number of fundamental phenomena in physics, including superconductivity, superfluidity and Bose-Einstein condensation. Spontaneous coherence is the key characteristic of condensation in momentum space. Excitons--bound pairs of electrons and holes--form a model system to explore the quantum physics of cold bosons in solids. Cold exciton gases can be realized in a system of indirect excitons, which can cool down below the temperature of quantum degeneracy owing to their long lifetimes. Here we report measurements of spontaneous coherence in a gas of indirect excitons. We found that spontaneous coherence of excitons emerges in the region of the macroscopically ordered exciton state and in the region of vortices of linear polarization. The coherence length in these regions is much larger than in a classical gas, indicating a coherent state with a much narrower than classical exciton distribution in momentum space, characteristic of a condensate. A pattern of extended spontaneous coherence is correlated with a pattern of spontaneous polarization, revealing the properties of a multicomponent coherent state. We also observed phase singularities in the coherent exciton gas. All these phenomena emerge when the exciton gas is cooled below a few kelvin.

Electrostatic conveyer for excitons.

We report on the study of indirect excitons in moving lattices-conveyers created by a set of ac voltages applied to the electrodes on the sample surface. The wavelength of this moving lattice is set by the electrode periodicity, the amplitude is controlled by the applied voltage, and the velocity is controlled by the ac frequency. We found the dynamical localization-delocalization transition for excitons in the conveyers and determined its dependence on exciton density and conveyer amplitude and velocity.

All-optical excitonic transistor.

We demonstrate experimental proof of principle for all-optical excitonic transistors where light controls light by using excitons as an intermediate medium. The principle of operation of all-optical excitonic transistors is based on the control of exciton fluxes by light.

Age-related changes in ac-impedance spectroscopy studies of normal human dentine: further investigations.

One of the age-related changes occurring in dentine structure is the formation of peritubular dentine on the inner walls of dentinal tubules leading to complete closure of tubules. Ac-impedance is safe, fast and non-invasive technique. In the last decade, the popularity of the technique has increased in dental research. Several investigators have used the technique to detect tooth cracks and caries. The results of in vitro studies showed that ac-impedance technique was more advanced for caries detection than visual and radiographic methods. However, other studies demonstrated that the accuracy of impedance measurements can be affected by many factors such as remineralization after tooth eruption. A study has been published on effect of age on impedance measurements by the authors for two age groups by employing ac-impedance spectroscopy. Therefore, the aim of this study was to demonstrate the importance of this technique by conducting further investigations on dentine samples of wider age groups. Dentine samples were prepared from extracted sound third molars of known patient age. The ac-impedance measurements were carried out over a wide range of frequency. After performing all electrical measurements, dentine samples were examined under SEM to correlate the electrical measurements with their structure. Impedance measurements showed that there were differences in impedance between young and old dentine. One-way ANOVA of the means of resistance and capacitance for all age groups (20, 25, 30, 40 and 50 years old dentine) revealed a significant difference (ANOVA, P < 0.0001) as a function of age. Applying Tukey's post hoc test, to the same data showed that this difference was due to the 50 years old dentine for resistance and was due to the 40 and 50 years old dentine for capacitance which were statistically different to all other groups. SEM investigation of dentine samples showed that young dentine is characterized by open dentinal tubules distributed all over the sample while in old dentine most dentinal tubules were occluded by peritubular dentine. It is believed that this peritubular deposition is responsible for differences in impedance measurements. In spite of increasing use of electrical techniques to understand electrical properties of teeth, it is clear from this study that local structural variations have a marked influence.

Trapping indirect excitons in a GaAs quantum-well structure with a diamond-shaped electrostatic trap.

We report on the principle and realization of a new trap for excitons--the diamond electrostatic trap--which uses a single electrode to create a confining potential for excitons. We also create elevated diamond traps which permit evaporative cooling of the exciton gas. We observe the collection of excitons towards the trap center with increasing exciton density. This effect is due to screening of disorder in the trap by the excitons. As a result, the diamond trap behaves as a smooth parabolic potential which realizes a cold and dense exciton gas at the trap center.

Indirect excitons in elevated traps.

We report on the study of indirect excitons in elevated traps. The transition from a normal to elevated trap results in the appearance of narrow lines in the emission spectrum. The density, temperature, and voltage dependences indicate that these lines correspond to the emission of individual states of indirect excitons in a disorder potential in the elevated trap.

Switching first-line disease-modifying therapy after failure: impact on the course of relapsing-remitting multiple sclerosis.

BACKGROUND: Options for non-responders to relapsing-remitting multiple sclerosis (RRMS) first-line disease-modifying therapies (DMT) are limited. We explored whether switching first-line DMT is effective. METHODS: Patients with RRMS who first received interferon-beta (IFNB) or glatiramer acetate (GA) were classified in three categories: DMT change because of suboptimal response, DMT change because of other reasons, and no DMT change during follow-up. Outcomes included annualized relapse rate (ARR) and relapse-free proportions. RESULTS: We identified 597 patients who initiated first-line DMT. For patients who did not change DMT (n = 240), pre-DMT and on-DMT median ARR were 0.50 and 0 (P < 0.0001). At 24 months, 76% (95%CI = 69-81%) of patients who did not change DMT were relapse-free. Of the 155 who switched because of suboptimal response, 101 switched to another first-line DMT. Median ARR pre-DMT, on first DMT and second DMT were: 0.50, 0.55, and 0.25 for switchers from IFNB to GA (IFNB/GA, n = 12) (pre-DMT versus first DMT: P = 0.92; first versus second DMT: P = 0.31); 0.90, 0.50, and 0 for switchers from GA to IFNB (GA/IFNB, n = 18; P = 0.19; P = 0.01); 0.50, 0.68, and 0 for switchers from an IFNB to another IFNB (IFNB/IFNB', n = 71; P = 0.34; P = 0.02). Estimated relapse-free proportion after 24 months of treatment was 42% (95%CI=15-66%) during the period on IFNB versus 53% (95%CI = 17-80%) on GA for IFNB/GA (P = 0.21); 12% (95%CI = 0-40%) on GA versus 87% (95%CI = 59-97%) on IFNB for GA/IFNB (P = 0.001); and 41% (95%CI = 29-52%) on initial IFNB versus 67% (95%CI = 53-79%) on subsequent IFNB for IFNB/IFNB' (P = 0.0001). CONCLUSIONS: Switching first-line DMT in patients with RRMS failing initial therapy may be effective in many cases.

Predictors of the location of multiple sclerosis relapse.

BACKGROUND: While clinical relapses are the defining feature of relapsing-remitting multiple sclerosis (RRMS), their characteristics vary widely from patient to patient. This study sought to identify predictors of MS relapse location. Based on the current literature, two potential predictors were identified: treatment with interferon beta (IFNB) and location of previous relapse. METHODS: Patients with RRMS were identified from the UCSF MS Center database who underwent at least 3 months of treatment with IFNB or glatiramer acetate (GA). The relapse immediately preceding the initiation of treatment (pretreatment relapse) and the first relapse occurring after the initiation of treatment (on-treatment relapse) were coded as affecting the spinal cord (SC), optic nerve (ON), brainstem/cerebellum (BC) or cerebrum. Logistic regression was performed to identify independent predictors of on-treatment relapse location. RESULTS: The 134 IFNB and 56 GA patients did not differ in gender, race, age at symptom onset (30.3 years) or disease duration at the start of treatment (5.7 years). Patients with pretreatment SC relapses had increased odds of having on-treatment SC compared with non-SC relapses (OR 2.31, p = 0.013); the same tendency for localisation occurred with BC (OR 3.05, p = 0.013) and ON (OR 3.63, p = 0.011) relapses. Additionally, patients who relapsed on treatment had a higher SC (but not ON or BC) relapse risk when they were receiving IFNB compared with GA (OR 2.05, p = 0.041), independent of pretreatment relapse location. CONCLUSION: These results show a tendency for patients to have localised exacerbations, which could be mediated by genetic or immunological factors. In addition, and to be confirmed in subsequent studies, IFNB treatment may influence SC relapse risk.

Exciton optoelectronic transistor.

We demonstrate experimental proof of principle for an optoelectronic transistor based on the modulation of exciton flux via gate voltage. The exciton optoelectronic transistor (EXOT) implements electronic operation on photons by using excitons as intermediate media; the intensity of light emitted at the optical output is proportional to the intensity of light at the optical input and is controlled electronically by the gate. We demonstrate a contrast ratio of 30 between an on state and an off state of the EXOT and its operation at speeds greater than 1 GHz. Our studies also demonstrate high-speed control of both the flux and the potential energy of excitons on a time scale much shorter than the exciton lifetime.

Paediatric granular cell tumour of the larynx: case report of laser resection with frozen section.

Granular cell tumours of the larynx are a very rare cause of persistent hoarse or husky voice in children. We report the case of a 13-year-old girl who presented with a three-year history of progressively huskier voice. We discuss the presentation, location and diagnosis of the tumour. In addition, we present a method of surgical treatment of the tumour, involving the hitherto unreported technique of laser excision and frozen section of the lesion.

Vascularisation of Norian CRS bone cement and its replacement by autologous bone when used for orbital reconstruction.

Various bone cements based on calcium phosphate have been used as adjuncts for repairing both the craniofacial and axial skeleton. Ideally these materials should provide initial strength and contour for the reconstruction, and be replaced over time by physiological absorption and bony deposition. Although there is evidence from animal models to support this, opportunities for human studies are rare. Here we offer clinical and histological evidence of this process.