Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups

Ependymal tumors across age groups are currently classified and graded solely by histopathology. It is, however, commonly accepted that this classification scheme has limited clinical utility based on its lack of reproducibility in predicting patients' outcome. We aimed at establishing a uniform molecular classification using DNA methylation profiling. Nine molecular subgroups were identified in a large cohort of 500 tumors, 3 in each anatomical compartment of the CNS, spine, posterior fossa, supratentorial. Two supratentorial subgroups are characterized by prototypic fusion genes involving RELA and YAP1, respectively. Regarding clinical associations, the molecular classification proposed herein outperforms the current histopathological classification and thus might serve as a basis for the next World Health Organization classification of CNS tumors.

Abstract 3094: Epigenetic classification of ependymal brain tumors across age groups

Since it has become evident that histopathological grading of ependymoma according to the WHO classification of CNS tumors is not capable of accurately classifying patients into meaningful strata, a broadly accepted molecular classification scheme with prognostic significance is desperately needed. In recent years, ependymomas were classified into molecular subgroups based on transcriptomic alterations. In tumors localized within the posterior fossa, two distinct biological entities of ependymoma were delineated by several studies (designated posterior fossa A and posterior fossa B), which show striking differences in genetic characteristics and clinical outcome. A similar consensus for supratentorial and spinal ependymoma is lacking.

We studied genome-wide DNA methylation (Illumina HumanMethylation450 (450k) array) in 180 primary ependymal tumors (80 with corresponding gene expression profiling data generated by Affymetrix 133plus2.0 arrays), including ependymomas (posterior fossa, supratentorial, spinal), subependymomas (SE), myxopapillary ependymoma (MPE), pineal parenchymal tumors of intermediate differentiation (PPTID), and papillary tumors of the pineal region (PTPR). We performed hierarchical clustering to identify robust molecular subgroups. Independent gene expression profiling datasets from previously published ependymoma studies (Johnson et al.; Wani et al.; Witt et al.) were used as validation cohorts.

DNA methylation data showed that ependymal brain tumors can be classified into eight molecular subgroups. Notably, MPE, SE, PPTID and PTPR tumors formed robust distinct clusters, as did posterior fossa Group A and Group B ependymomas. Supratentorial ependymomas can be classified into two principle molecular subgroups, one of which displays a dismal prognosis, and comprises predominantly children and infants, and is associated with highly recurrent gene fusion. Notably, a significant number of ependymomas previously classified by histology as WHO Grade II/III look like SE by methylation, and also have extremely good survival.

In summary, using genome-wide DNA methylation and transcriptome analysis we could decipher robust molecular subgroups of ependymal brain tumors including supratentorial ependymoma. Diagnoses of tumors with challenging histopathological features can now be supported by this technology. Hence, this approach offers the possibility to replace the unambiguous histological grading system that is currently in use with a robust molecular classification that readily distinguishes biologically, genetically, and clinically meaningful subgroups of ependymal brain tumors.

Citation Format: Hendrik Witt, Martin Sill, Khalida Wani, Steve Mack, David Capper, Stephanie Heim, Pascal Johann, Sally Lambert, Marina Rhyzova, Volker Hovestadt, Theophilos Tzaridis, Kristian Pajtler, Sebastian Bender, Till Milde, Paul A. Northcott, Andreas E. Kulozik, Olaf Witt, Peter Lichter, V Peter Collins, Andreas von Deimling, Marcel Kool, Michael D. Taylor, Martin Hasselblatt, David TW Jones, Andrey Korshunov, Ken Aldape, Stefan Pfister. Epigenetic classification of ependymal brain tumors across age groups. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3094. doi:10.1158/1538-7445.AM2014-3094

Absolute pulse energy measurements of soft x-rays at the Linac Coherent Light Source

This paper reports novel measurements of x-ray optical radiation on an absolute scale from the intense and ultra-short radiation generated in the soft x-ray regime of a free electron laser. We give a brief description of the detection principle for radiation measurements which was specifically adapted for this photon energy range. We present data characterizing the soft x-ray instrument at the Linac Coherent Light Source (LCLS) with respect to the radiant power output and transmission by using an absolute detector temporarily placed at the downstream end of the instrument. This provides an estimation of the reflectivity of all x-ray optical elements in the beamline and provides the absolute photon number per bandwidth per pulse. This parameter is important for many experiments that need to understand the trade-offs between high energy resolution and high flux, such as experiments focused on studying materials via resonant processes. Furthermore, the results are compared with the LCLS diagnostic gas detectors to test the limits of linearity, and observations are reported on radiation contamination from spontaneous undulator radiation and higher harmonic content.

Cortisol reactions to a social evaluative paradigm in 5- and 6-year-old children

The goal of the present study was to develop a stress paradigm to elicit cortisol secretory responses in a group of 5- and 6-year-old children as a whole. To this end, we tested a paradigm containing elements of social evaluative threat, unpredictability and uncontrollability, and with a duration of 20 min. The Children's Reactions to Evaluation Stress Test is composed of three short tasks that children have to perform in front of a judge. The tasks are rigged so as to provoke (partial) failure in the child's performance. Participants were 42 children (M = 68.0 months, SD = 4.3). Six saliva samples were taken during the testing session to obtain cortisol measurements of baseline concentrations, stress reactivity, and recovery. Our findings showed that this paradigm was effective in provoking a significant increase in salivary cortisol concentration in the group as a whole, with no effects of possible confounders (child's sex, age or school, parental educational level, time of testing, sex of experimenter, and sex of judge). The mean cortisol concentration increase for the group was 127.5% (SD = 190.9); 61% of the children could be classified as reactors (mean increase of 214%, SD = 201.5), and 39% as non-reactors (mean decrease of 7.8%, SD = 16.8). To our knowledge, this is the first study in this age group that shows a significant cortisol response for the group as a whole to a standardized laboratory paradigm. As such, this paradigm is a promising tool to be used in future research on early life interactions between physiology and psychology.

Learning Disability Liaison Nursing Services in south-east Scotland: a mixed-methods impact and outcome study

BACKGROUND

There have been significant concerns about the care and treatment of people with intellectual disabilities (ID) when attending general hospitals, which have led to inquiries that highlight service and systems failures. One response has been the development of Learning Disability Liaison Nursing (LDLN) Services across the UK that aim to ensure that additional, specialist support is available for patients, their carers and general healthcare professionals.

METHODS

A mixed-methods study to investigate the impact of LDLN Services across four Scottish NHS boards was undertaken. In total, 323 referrals made over 18 months were analysed along with qualitative data drawn from interviews and focus groups with a sample of 85 participants including patients with ID (n = 5), carers (n = 16), primary care healthcare professionals (n = 39) and general hospital professionals (n = 19) and learning disability liaison nurses (n = 6).

RESULTS

The referral patterns to the four liaison nursing services closely matched the known health needs of adults with ID, with common admissions being due to neurological, respiratory and gastrointestinal issues. The LDLN role was seen to be complex and impacted on three key areas: (i) clinical patient care; (ii) education and practice development; and (iii) strategic organisational developments. Specific patient outcomes were linked to issues relating to capacity and consent to treatment, fostering person-centred adjustments to care, augmenting communication and the liaison nurses acting as positive role models and ambassadors for people with ID.

CONCLUSIONS

The LDLN Services were valued by stakeholders by achieving person-centred outcomes. With their expert knowledge and skills, the liaison nurses had an important role in developing effective systems and processes within general hospital settings. The outcomes highlight the importance of supporting and promoting LDLN Services and the challenges in delivering the multifaceted elements of the role. There is a need to take account of the complex and multidimensional nature of the LDLN role and the possible tensions between achieving clinical outcomes, education and practice developments and organisational strategic initiatives.

Tuberculosis, incarceration, and HIV at a crossroads in Guyana

OBJECTIVES

The objective of this study was to describe the sociodemographic and clinical characteristics of patients dually infected with HIV and tuberculosis (TB) in Guyana.

METHODS

The data for this study were obtained as part of a related project conducted to determine the prevalence of diabetes mellitus among TB patients in Guyana. From April to June 2006, a convenience sample of 100 patients was selected from those attending three TB clinics in Guyana and a structured questionnaire was used to collect relevant sociodemographic and risk factor data. The sociodemographic and clinical data of HIV-negative and HIV-positive patients with pulmonary TB were compared. Logistic regression was conducted to determine independent relationships between sociodemographic and clinical features.

RESULTS

One hundred TB patients were considered for enrolment in the study, but since the HIV status was known for only 77 persons, these were included in the analysis. Thirty-one of the 77 (40.3%) were HIV-positive. Seventy-two of the 77 (93.5%) patients had pulmonary TB, 28 of whom were HIV-positive; the other five had extrapulmonary TB, three of whom were dually infected. Several social factors and clinical manifestations including incarceration at the time of TB diagnosis (p=0.01), cigarette smoking (p=0.05), homelessness (p=0.07), chest pain (p=0.001), hemoptysis (p=0.02), cough (p=0.08), and being acid-fast bacillus (AFB) sputum smear-positive (p=0.06) were associated with HIV-negative pulmonary TB. In the logistic regression model, HIV-negative TB patients demonstrated higher frequencies of complaints of chest pain (odds ratio (OR) 34.48, 95% confidence interval (CI) 4.35-250) and were more likely to be AFB sputum smear-positive (OR 11.97, 95% CI 1.91-74.76) than HIV-positive TB patients.

CONCLUSIONS

Guyana is faced with a particularly high burden of HIV infection among TB patients. Given the impact of HIV on the clinical presentation of TB, physicians managing HIV patients should demonstrate a high level of suspicion for TB among these patients. Incarceration is a strong correlate of TB, overall.

Spin-seebeck effect: a phonon driven spin distribution

Here we report on measurements of the spin-Seebeck effect in GaMnAs over an extended temperature range alongside the thermal conductivity, specific heat, magnetization, and thermoelectric power. The amplitude of the spin-Seebeck effect in GaMnAs scales with the thermal conductivity of the GaAs substrate and the phonon-drag contribution to the thermoelectric power of the GaMnAs, demonstrating that phonons drive the spin redistribution. A phenomenological model involving phonon-magnon drag explains the spatial and temperature dependence of the measured spin distribution.

Early clinical experience of the safety and effectiveness of Hemospray in achieving hemostasis in patients with acute peptic ulcer bleeding

BACKGROUND AND STUDY AIMS

Endoscopic therapy of upper gastrointestinal bleeding remains challenging with conventional endoscopic devices. Use of Hemospray, where a nanopowder with clotting abilities is sprayed onto the bleeding site, had been highly effective for management of arterial bleeding in a heparizined animal model. The safety and effectiveness of Hemospray for hemostasis of active peptic ulcer bleeding in humans was evaluated.

PATIENTS AND METHODS

In a prospective, single-arm, pilot clinical study, consecutive adults with confirmed peptic ulcer bleeding (Forrest score Ia or Ib), who had all given informed consent to participation, underwent upper gastrointestinal endoscopy and application of Hemospray within 24 hours of hospital admission once hemodynamically stable. Up to two applications of Hemospray, not exceeding a total of 150 g were allowed. Bleeding recurrence was monitored post procedurally, by second-look endoscopy (72 hours post treatment), and by phone at 30 days. Rate of hemostasis, recurrent bleeding, mortality, need for surgical intervention, and treatment-related complications were assessed.

RESULTS

20 patients were recruited (18 men, 2 women; mean age 60.2 years). Acute hemostasis was achieved in 95 % (19 / 20) of patients; 1 patient had a pseudoaneurysm requiring arterial embolization. Bleeding recurred in 2 patients within 72 hours (shown by hemoglobin drop); neither had active bleeding identified at the 72-hour endoscopy. No mortality, major adverse events, or treatment- or procedure-related serious adverse events were reported during 30-day follow-up.

CONCLUSION

These pilot results indicate that Hemospray is safe in humans. Hemospray was effective in achieving acute hemostasis in active peptic ulcer bleeding.

Morphology of femtosecond laser modification of bulk dielectrics

Using 3D Finite-Difference-Time-Domain simulations, we study the morphology of the laser-created damage inside fused silica. Among the competing effects limiting the intensity in the dielectric, we find the most important is the pulse defocusing by the plasma lens, partially balanced by the Kerr effect. Less important are collisional energy dissipation and laser depletion by multi-photon absorption. We also found that the profile of generated plasma is asymmetrical in the transverse cross-section, with the plasma extended along the direction perpendicular to the laser polarization.

Observation of the spin-Seebeck effect in a ferromagnetic semiconductor

Reducing the heat generated in traditional electronics is a chief motivation for the development of spin-based electronics, called spintronics. Spin-based transistors that do not strictly rely on the raising or lowering of electrostatic barriers can overcome scaling limits in charge-based transistors. Spin transport in semiconductors might also lead to dissipation-less information transfer with pure spin currents. Despite these thermodynamic advantages, little experimental literature exists on the thermal aspects of spin transport in solids. A recent and surprising exception was the discovery of the spin-Seebeck effect, reported as a measurement of a redistribution of spins along the length of a sample of permalloy (NiFe) induced by a temperature gradient. This macroscopic spatial distribution of spins is, surprisingly, many orders of magnitude larger than the spin diffusion length, which has generated strong interest in the thermal aspects of spin transport. Here, the spin-Seebeck effect is observed in a ferromagnetic semiconductor, GaMnAs, which allows flexible design of the magnetization directions, a larger spin polarization, and measurements across the magnetic phase transition. This effect is observed even in the absence of longitudinal charge transport. The spatial distribution of spin currents is maintained across electrical breaks, highlighting the local nature of this thermally driven effect.

Oscillatory spin polarization and magneto-optical Kerr effect in Fe₃O₄ thin films on GaAs(001)

The spin dependent properties of epitaxial Fe₃O₄ thin films on GaAs(001) are studied by the ferromagnetic proximity polarization (FPP) effect and magneto-optical Kerr effect (MOKE). Both FPP and MOKE show oscillations with respect to Fe₃O₄ film thickness, and the oscillations are large enough to induce repeated sign reversals. We attribute the oscillatory behavior to spin-polarized quantum well states forming in the Fe₃O₄ film. Quantum confinement of the t(2g) states near the Fermi level provides an explanation for the similar thickness dependences of the FPP and MOKE oscillations.

Spin control of drifting electrons using local nuclear polarization in ferromagnet-semiconductor heterostructures

We demonstrate methods to locally control the spin rotation of moving electrons in a GaAs channel. The Larmor frequency of optically injected spins is modulated when the spins are dragged through a region of spin-polarized nuclei created at a MnAs/GaAs interface. The effective field created by the nuclei is controlled either optically or electrically using the ferromagnetic proximity polarization effect. Spin rotation is also tuned by controlling the carrier traverse time through the polarized region. We demonstrate coherent spin rotations of 5π   rad during transport.

[Demographic distribution and prevalence of overactive bladder in Venezuela]

OBJECTIVE

There is a lack of information regarding overactive bladder (OAB) in South America. Our aim in this study was to estimate the prevalence of overactive bladder (OAB) in Venezuela based on the 2002 International Continence Society (ICS) consensus criteria and also to verify its demographic distribution in this country.

SUBJECTS AND METHODS

We performed a multicentric prospective evaluation of patients from 2003 to 2007 in different cities in Venezuela. A number 3.407 adults (M:38%, F:62%) between 18 and 75 years of age (mean age 54 years) completed a physician guided questionnaire (V8) of urinary symptoms, bladder function, diet, general habits and general medical condition. Statistical procedures were carried out using software based on R programming for computational statistics.

RESULTS

The overall prevalence of OAB in Venezuela was determined as 21%. Female were more affected as compared to male (25.6% vs. 13.7% in men, p < 0.005) OAB was detected at early age (18 yrs) maintaining higher prevalence in women (M: 9%, F: 14%). In the studied cohort OAB shows its highest prevalence between the subgroup of 65 to 69 years of age. In all statistical tests the level of significance was defined as p < 0.005, with a confidence interval of 95%.

CONCLUSION

The OAB-V8 questionnaire aids to clearly identify patients with OAB symptoms. The overall prevalence of OAB in Venezuela is 21%. It is present in both genders, predominantly women and can be detected at early age.

Emergence of the persistent spin helix in semiconductor quantum wells

According to Noether's theorem, for every symmetry in nature there is a corresponding conservation law. For example, invariance with respect to spatial translation corresponds to conservation of momentum. In another well-known example, invariance with respect to rotation of the electron's spin, or SU(2) symmetry, leads to conservation of spin polarization. For electrons in a solid, this symmetry is ordinarily broken by spin-orbit coupling, allowing spin angular momentum to flow to orbital angular momentum. However, it has recently been predicted that SU(2) can be achieved in a two-dimensional electron gas, despite the presence of spin-orbit coupling. The corresponding conserved quantities include the amplitude and phase of a helical spin density wave termed the 'persistent spin helix'. SU(2) is realized, in principle, when the strengths of two dominant spin-orbit interactions, the Rashba (strength parameterized by alpha) and linear Dresselhaus (beta(1)) interactions, are equal. This symmetry is predicted to be robust against all forms of spin-independent scattering, including electron-electron interactions, but is broken by the cubic Dresselhaus term (beta(3)) and spin-dependent scattering. When these terms are negligible, the distance over which spin information can propagate is predicted to diverge as alpha approaches beta(1). Here we report experimental observation of the emergence of the persistent spin helix in GaAs quantum wells by independently tuning alpha and beta(1). Using transient spin-grating spectroscopy, we find a spin-lifetime enhancement of two orders of magnitude near the symmetry point. Excellent quantitative agreement with theory across a wide range of sample parameters allows us to obtain an absolute measure of all relevant spin-orbit terms, identifying beta(3) as the main SU(2)-violating term in our samples. The tunable suppression of spin relaxation demonstrated in this work is well suited for application to spintronics.

A comprehensive view of the structure and expression of the ependymoma genome at presentation and relapse

2073

Background: Although pediatric and adult ependymomas are associated with significant mortality and morbidity, little is known about the biology of these tumors. To identify underlying genetic alterations and cellular pathways that drive this disease, we conducted a genomic study of 200 adult and pediatric ependymomas. Methods: Using 500k single nucleotide polymorphism arrays, U133 Affymetrix gene and microRNA (miRNA) expression microarrays, and appropriate bioinformatics, we characterized 56 supratentorial (ST), 104 posterior fossa (PF), and 40 spinal (SP) ependymomas. Real-Time polymerase chain reaction and fluorescence in situ hybridization validated observed genetic events. Results: Gene expression profiles segregated tumors by site and identified disease subgroups within each anatomical region (4 ST, 4 PF, 1 SP). miRNA expression profiles identified these same subgroups, indicating that they are biologically distinct. Subgroup-specific gene expression profiles were dictated partly by developmental regulatory genes and partly by large chromosomal gains (eg. 1q, 5p, 16p) and losses (eg. 9p, 22q). Integrated genetic and expression mapping revealed key candidate tumor suppressor (TSG) and onco- genes, likely drivers of these large alterations. While large chromosomal changes occurred more frequently in SP tumors (p < 0.0001), ST tumors averaged more focal changes (n = 13.2) than PF (n = 6.2) or SP tumors (n = 3.0) (p < 0.0001). A total of 29 and 33 non-random focal amplifications and deletions, respectively, encompassing 402 known genes and miRNA clusters, were validated, of which 80 displayed copy number driven expression. These genetic alterations targeted specific cellular functions (e.g., cell adhesion, cell-cycle, neuronal development) and pathways (e.g., NOTCH, EPHRIN, TP53). Our cohort also included five sample sets consisting of primary tumor and at least two corresponding relapses. Genomic analysis of these tumors identified large chromosomal alterations as well as focal gains and losses associated with disease relapse. Conclusions: We present a highly comprehensive view of the ependymoma genome, including 80 previously unrecognized candidate TSG and oncogenes that may afford diagnostic and therapeutic targets.

No significant financial relationships to disclose.

Inversion of ferromagnetic proximity polarization by MgO interlayers

We investigate the spin-dependent reflection properties in Fe/MgO/GaAs heterostructures by optical pump-probe measurement of the ferromagnetic proximity polarization (FPP). As a function of MgO thickness, the FPP is initially enhanced (<2.0 A) and then exhibits an unexpected sign reversal at approximately 5.0 A. The identification of two competing thresholds in the intensity dependence of FPP and the observation of FPP sign reversal in Fe/Mg/GaAs suggest that the inversion of FPP is related to an interfacial bonding effect.