Subgroup-specific structural variation across 1,000 medulloblastoma genomes

Medulloblastoma, the most common malignant paediatric brain tumour, is currently treated with nonspecific cytotoxic therapies including surgery, whole-brain radiation, and aggressive chemotherapy. As medulloblastoma exhibits marked intertumoural heterogeneity, with at least four distinct molecular variants, previous attempts to identify targets for therapy have been underpowered because of small samples sizes. Here we report somatic copy number aberrations (SCNAs) in 1,087 unique medulloblastomas. SCNAs are common in medulloblastoma, and are predominantly subgroup-enriched. The most common region of focal copy number gain is a tandem duplication of SNCAIP, a gene associated with Parkinson's disease, which is exquisitely restricted to Group 4 alpha. Recurrent translocations of PVT1, including PVT1-MYC and PVT1-NDRG1, that arise through chromothripsis are restricted to Group 3. Numerous targetable SCNAs, including recurrent events targeting TGF-beta signalling in Group 3, and NF-kappa B signalling in Group 4, suggest future avenues for rational, targeted therapy.

Rhodolith Beds Are Major CaCO3 Bio-Factories in the Tropical South West Atlantic

Rhodoliths are nodules of non-geniculate coralline algae that occur in shallow waters (<150 m depth) subjected to episodic disturbance. Rhodolith beds stand with kelp beds, seagrass meadows, and coralline algal reefs as one of the world's four largest macrophyte-dominated benthic communities. Geographic distribution of rhodolith beds is discontinuous, with large concentrations off Japan, Australia and the Gulf of California, as well as in the Mediterranean, North Atlantic, eastern Caribbean and Brazil. Although there are major gaps in terms of seabed habitat mapping, the largest rhodolith beds are purported to occur off Brazil, where these communities are recorded across a wide latitudinal range (2 degrees N - 27 degrees S). To quantify their extent, we carried out an inter-reefal seabed habitat survey on the Abrolhos Shelf (16 degrees 50' - 19 degrees 45'S) off eastern Brazil, and confirmed the most expansive and contiguous rhodolith bed in the world, covering about 20,900 km(2). Distribution, extent, composition and structure of this bed were assessed with side scan sonar, remotely operated vehicles, and SCUBA. The mean rate of CaCO3 production was estimated from in situ growth assays at 1.07 kg m(-2) yr(-1), with a total production rate of 0.025 Gt yr(-1), comparable to those of the world's largest biogenic CaCO3 deposits. These gigantic rhodolith beds, of areal extent equivalent to the Great Barrier Reef, Australia, are a critical, yet poorly understood component of the tropical South Atlantic Ocean. Based on the relatively high vulnerability of coralline algae to ocean acidification, these beds are likely to experience a profound restructuring in the coming decades.

Underlying Event measurements in pp collisions at root s=0.9 and 7 TeV with the ALICE experiment at the LHC

We present measurements of Underlying Event observables in pp collisions at root s = 0 : 9 and 7 TeV. The analysis is performed as a function of the highest charged-particle transverse momentum p(T),L-T in the event. Different regions are defined with respect to the azimuthal direction of the leading (highest transverse momentum) track: Toward, Transverse and Away. The Toward and Away regions collect the fragmentation products of the hardest partonic interaction. The Transverse region is expected to be most sensitive to the Underlying Event activity. The study is performed with charged particles above three different p(T) thresholds: 0.15, 0.5 and 1.0 GeV/c. In the Transverse region we observe an increase in the multiplicity of a factor 2-3 between the lower and higher collision energies, depending on the track p(T) threshold considered. Data are compared to PYTHIA 6.4, PYTHIA 8.1 and PHOJET. On average, all models considered underestimate the multiplicity and summed p(T) in the Transverse region by about 10-30%.

Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV

The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.

What drives the seasonality of photosynthesis across the Amazon basin? A cross-site analysis of eddy flux tower measurements from the Brasil flux network

We investigated the seasonal patterns of Amazonian forest photosynthetic activity, and the effects thereon of variations in climate and land-use, by integrating data from a network of ground-based eddy flux towers in Brazil established as part of the ‘Large-Scale Biosphere Atmosphere Experiment in Amazonia’ project. We found that degree of water limitation, as indicated by the seasonality of the ratio of sensible to latent heat flux (Bowen ratio) predicts seasonal patterns of photosynthesis. In equatorial Amazonian forests (5◦ N–5◦ S), water limitation is absent, and photosynthetic fluxes (or gross ecosystem productivity, GEP) exhibit high or increasing levels of photosynthetic activity as the dry season progresses, likely a consequence of allocation to growth of new leaves. In contrast, forests along the southern flank of the Amazon, pastures converted from forest, and mixed forest-grass savanna, exhibit dry-season declines in GEP, consistent with increasing degrees of water limitation. Although previous work showed tropical ecosystem evapotranspiration (ET) is driven by incoming radiation, GEP observations reported here surprisingly show no or negative relationships with photosynthetically active radiation (PAR). Instead, GEP fluxes largely followed the phenology of canopy photosynthetic capacity (Pc), with only deviations from this primary pattern driven by variations in PAR. Estimates of leaf flush at three

Structural modification of DNA--a therapeutic option in SLE?

Systemic lupus erythematosus (SLE) is an autoimmune disease that affects multiple organs, with glomerulonephritis representing a frequent and serious manifestation. SLE is characterized by the presence of various autoantibodies, including anti-DNA antibodies that occur in approximately 70% of patients with SLE and which contribute to disease pathogenesis. Consequently, immunosuppressive therapies are applied in the treatment of SLE to reduce autoantibody levels. However, increasing evidence suggests that DNA--especially double--stranded DNA-constitutes an important pathogenic factor that is able to activate inflammatory responses by itself in autoimmune diseases. Therefore, modifying the structure of DNA to reduce its pathogenicity might be a more targeted approach for the treatment of SLE than immunosuppression. This article presents information in support of this strategy, and discusses the potential methods of DNA structure manipulation--in light of data obtained from mouse models of SLE--including topoisomerase I inhibition, administration of DNase I, or modification of histones using heparin or histone deacetylase inhibitors.

A Double-Blind Randomized Controlled Trial (RCT) of Titanium-13Zirconium versus Titanium Grade IV Small-Diameter Bone Level Implants in Edentulous Mandibles - Results from a 1-Year Observation Period

Background: The use of endosseous dental implants has become common practice for the rehabilitation of edentulous patients, and a two-implant overdenture has been recommended as the standard of care. The use of small-diameter implants may extend treatment options and reduce the necessity for bone augmentation. However, the mechanical strength of titanium is limited, so titanium alloys with greater tensile and fatigue strength may be preferable. Purpose: This randomized, controlled, double-blind, multicenter study investigated in a split-mouth model whether small-diameter implants made from Titanium-13Zirconium alloy (TiZr, Roxolid™) perform at least as well as Titanium Grade IV implants. Methods and Materials: Patients with an edentulous mandible received one TiZr and one Ti Grade IV small-diameter bone level implant (3.3 mm, SLActive®) in the interforaminal region. The site distribution was randomized and double-blinded. Outcome measures included change in radiological peri-implant bone level from surgery to 12 months post-insertion (primary), implant survival, success, soft tissue conditions, and safety (secondary). Results: Of 91 treated patients, 87 were available for the 12-month follow-up. Peri-implant bone level change (-0.3 ± 0.5 mm vs -0.3 ± 0.6 mm), plaque, and sulcus bleeding indices were not significantly different between TiZr and Ti Grade IV implants. Implant survival rates were 98.9 percent and 97.8 percent, success rates were 96.6 percent and 94.4 percent, respectively. Nineteen minor and no serious adverse events were related to the study devices. Conclusion: This study confirms that TiZr small-diameter bone level implants provide at least the same outcomes after 12 months as Ti Grade IV bone level implants. The improved mechanical properties of TiZr implants may extend implant therapy to more challenging clinical situations.

Predictability of biomass burning in response to climate changes

Climate is an important control on biomass burning, but the sensitivity of fire to changes in temperature and moisture balance has not been quantified. We analyze sedimentary charcoal records to show that the changes in fire regime over the past 21,000 yrs are predictable from changes in regional climates. Analyses of paleo- fire data show that fire increases monotonically with changes in temperature and peaks at intermediate moisture levels, and that temperature is quantitatively the most important driver of changes in biomass burning over the past 21,000 yrs. Given that a similar relationship between climate drivers and fire emerges from analyses of the interannual variability in biomass burning shown by remote-sensing observations of month-by-month burnt area between 1996 and 2008, our results signal a serious cause for concern in the face of continuing global warming.

THE ROLE OF AN EXPLICIT CAUSAL FRAMEWORK IN AFFECTED SIB PAIR DESIGNS WITH COVARIATES

The affected sib/relative pair (ASP/ARP) design is often used with covariates to find genes that can cause a disease in pathways other than through those covariates. However, such "covariates" can themselves have genetic determinants, and the validity of existing methods has so far only been argued under implicit assumptions. We propose an explicit causal formulation of the problem using potential outcomes and principal stratification. The general role of this formulation is to identify and separate the meaning of the different assumptions that can provide valid causal inference in linkage analysis. This separation helps to (a) develop better methods under explicit assumptions, and (b) show the different ways in which these assumptions can fail, which is necessary for developing further specific designs to test these assumptions and confirm or improve the inference. Using this formulation in the specific problem above, we show that, when the "covariate" (e.g., addiction to smoking) also has genetic determinants, then existing methods, including those previously thought as valid, can declare linkage between the disease and marker loci even when no such linkage exists. We also introduce design strategies to address the problem.

A MULTILEVEL MODEL TO ADDRESS BATCH EFFECTS IN COPY NUMBER ESTIMATION USING SNP ARRAYS

Submicroscopic changes in chromosomal DNA copy number dosage are common and have been implicated in many heritable diseases and cancers. Recent high-throughput technologies have a resolution that permits the detection of segmental changes in DNA copy number that span thousands of basepairs across the genome. Genome-wide association studies (GWAS) may simultaneously screen for copy number-phenotype and SNP-phenotype associations as part of the analytic strategy. However, genome-wide array analyses are particularly susceptible to batch effects as the logistics of preparing DNA and processing thousands of arrays often involves multiple laboratories and technicians, or changes over calendar time to the reagents and laboratory equipment. Failure to adjust for batch effects can lead to incorrect inference and requires inefficient post-hoc quality control procedures that exclude regions that are associated with batch. Our work extends previous model-based approaches for copy number estimation by explicitly modeling batch effects and using shrinkage to improve locus-specific estimates of copy number uncertainty. Key features of this approach include the use of diallelic genotype calls from experimental data to estimate batch- and locus-specific parameters of background and signal without the requirement of training data. We illustrate these ideas using a study of bipolar disease and a study of chromosome 21 trisomy. The former has batch effects that dominate much of the observed variation in quantile-normalized intensities, while the latter illustrates the robustness of our approach to datasets where as many as 25% of the samples have altered copy number. Locus-specific estimates of copy number can be plotted on the copy-number scale to investigate mosaicism and guide the choice of appropriate downstream approaches for smoothing the copy number as a function of physical position. The software is open source and implemented in the R package CRLMM available at Bioconductor (http:www.bioconductor.org).

Regulation of endothelial cell cytoskeletal reorganization by a secreted frizzled-related protein-1 and frizzled 4- and frizzled 7-dependent pathway: role in neovessel formation

Consistent with findings of Wnt pathway members involved in vascular cells, a role for Wnt/Frizzled signaling has recently emerged in vascular cell development. Among the few Wnt family members implicated in vessel formation in adult, Wnt7b and Frizzled 4 have been shown as involved in vessel formation in the lung and in the retina, respectively. Our previous work has shown a role for secreted Frizzled-related protein-1 (sFRP-1), a proposed Wnt signaling inhibitor, in neovascularization after an ischemic event and demonstrated its role as a potent angiogenic factor. However the mechanisms involved have not been investigated. Here, we show that sFRP-1 treatment increases endothelial cell spreading on extracellular matrix as revealed by actin stress fiber reorganization in an integrin-dependent manner. We demonstrate that sFRP-1 can interact with Wnt receptors Frizzled 4 and 7 on endothelial cells to transduce downstream to cellular machineries requiring Rac-1 activity in cooperation with GSK-3beta. sFRP-1 overexpression in endothelium specifically reversed the inactivation of GSK-3 beta and increased neovascularization in ischemia-induced angiogenesis in mouse hindlimb. This study illustrates a regulated pathway by sFRP-1 involving GSK-3beta and Rac-1 in endothelial cell cytoskeletal reorganization and in neovessel formation.

Biomimetic Coatings and Their Biological Functionalization

The biomimetic coating technique can be used to deposit layers of calcium phosphate (CaP) on medical devices to improve their osteoconductivity and osseointegration.The inorganic layer generated is akin to mineralized bone matrix and can be degraded as such. The biomimetic coating technique involves the nucleation and growth of bone-like crystals on a pretreated substrate by immersing it in a supersaturated solution of CaP under physiological conditions of temperature (37°C) and pH (7.4). The method, originally developed by Kokubo and his co-workers in 1990, has since undergone improvement and refinement by several groups of investigators. Biomimetic coatings are valuable in that they can serve as a vehicle for the slow, sustained release of osteogenic agents at the site of implantation. This attribute is rendered possible by the near-physiological conditions under which these coatings are prepared, which permits the incorporation of bioactive agents into the inorganic crystal latticework rather than their superficial adsorption on preformed layers. In addition, the biomimetic coating technique can be applied to implants of an organic as well as of a metallic nature and to those with irregular surface geometries, which is not possible using conventional methodologies.

Firing Up the Crucible with Senator Lee Metcalf & Governor Forrest Anderson -- Judge Gordon Bennett in “The Crucible of Change”

During the lead-up to Montana second progressive era, Lee Metcalf and Forrest Anderson, along with others, kept the progressive flame lit in Montana. Metcalf’s political history is replete with close electoral wins because of his commitment to progressive ideals when the times were not always politically favorable for that. As State Legislator, MT Supreme Court Justice, Congressman and eventually as US Senator, Lee won races by as little as 55 votes because he stuck to his guns as a progressive. In Forrest Anderson’s career as a County Attorney, State Legislator, MT Supreme Court Justice and 12 years as MT Attorney General he was respected as a pragmatic practitioner of politics. But during that entire career leading up to his election as Governor, Forrest Anderson was also a stalwart supporter of the progressive agenda exemplified by FDR and the New Deal, which brought folks out of the Great Depression that was brought on by the bad policies of the GOP and big business. As MT’s second progressive period began in 1965, the first important election was Senator Metcalf’s successful re-election battle in 1966 with the sitting MT Governor, Tim Babcock. And the progressive express was really ignited by the election of Forrest Anderson as Governor in 1968 after 16 years of Republican Governors in MT. Gordon Bennett played a rather unique role, being a confidant of Metcalf and Anderson, both who respected his wide and varied experience, his intellect, and his roots in progressivism beginning with his formative years in the Red Corner of NE Montana. Working with Senator Metcalf and his team, including Brit Englund, Vic Reinemer, Peggy McLaughlin, Betty Davis and Jack Condon among others, Bennett helped shape the progressive message both in Washington DC and MT. Progressive labor and farm organizations, part of the progressive coalition, benefitted from Bennett’s advice and counsel and aided the Senator in his career including the huge challenge of having a sitting popular governor run against him for the Senate in 1966. Metcalf’s noted intern program produced a cadre of progressive leaders in Montana over the years. Most notably, Ron Richards transitioned from Metcalf Intern to Executive Secretary of the Montana Democratic Party (MDP) and assisted, along with Bennett, in the 1966 Metcalf-Babcock race in a big way. As Executive Secretary Richards was critical to the success of the MDP as a platform for Forrest Anderson’s general election run and win in 1968. After Forrest’s gubernatorial election, Richards became Executive Assistant (now called Chief of Staff) for Governor Anderson and also for Governor Thomas Judge. The Metcalf progressive strain, exemplified by many including Richards and Bennett, permeated Democratic politics during the second progressive era. So, too, did the coalition that supported Metcalf and his policies. The progressivism of the period of “In the Crucible of Change” was fired up by Lee Metcalf, Forrest Anderson and their supporters and coalitions, and Gordon Bennett was in the center of all of that, helping fire up the crucible, setting the stage for many policy advancements in both Washington DC and Montana. Gordon Bennett’s important role in the 1966 re-election of Senator Lee Metcalf and the 1968 election of Governor Forrest Anderson, as well as his wide experience in government and politics of that time allows him to provide us with an insider’s personal perspective of those races and other events at the beginning of the period of progressive change being documented “In the Crucible of Change,” as well as his personal insights into the larger political/policy picture of Montana. Gordon Bennett, a major and formative player “In the Crucible of Change,” was born in the far northeast town of Scobey, MT in 1922. He attended school in Scobey through the eighth grade and graduated from Helena High School. After attending Carroll College for two years, he received his BA in economics from Carleton College in Northfield, MN. During a brief stint on the east coast, his daily reading of the New York Times (“best newspaper in the world at that time … and now”) inspired him to pursue a career in journalism. He received his MA in Journalism from the University of Missouri and entered the field. As a reporter for the Great Falls Tribune under the ownership and management of the Warden Family, he observed and competed with the rigid control of Montana’s press by the Anaconda Company (the Great Falls Tribune was the only large newspaper in Montana NOT owned by ACM). Following his intellectual curiosity and his philosophical bend, he attended a number of Farm-Labor Institutes which he credits with motivating him to pursue solutions to economic and social woes through the law. In 1956, at the age of 34, he received his Juris Doctorate degree from the Georgetown University Law Center in Washington, DC. Bennett’s varied career included eighteen years as a farmer, four years in the US Army during WWII (1942-46), two years as Assistant MT Attorney General (1957-59) with Forrest Anderson, three years in private practice in Glasgow (1959-61), two years as Associate Solicitor in the Department of Interior in Washington, DC (1961-62), and private law practice in Helena from 1962 to 1969. While in Helena he was an unsuccessful candidate for the Montana Supreme Court (1962) and cemented his previous relationships with Attorney General Forrest Anderson and US Senator Lee Metcalf. Bennett modestly refuses to accept the title of Campaign Manager for either Lee Metcalf (1966 re-election over the challenger, MT Republican Governor Tim Babcock) or Forrest Anderson (his 1968 election as Governor), saying that “they ran their campaigns … we were only there to help.” But he has been generally recognized as having filled that critical role in both of those critical elections. After Governor Anderson’s election in 1968, Bennett was appointed Director of the MT Unemployment Compensation Commission, a position from where he could be a close advisor and confidant of the new Governor. In 1971, Governor Anderson appointed him Judge in the most important jurisdiction in Montana, the 1st Judicial District in Helena, a position he held for seventeen years (1971-88). Upon stepping down from his judgeship, for twenty years (1988-2008) he was a law instructor, mediator and arbitrator. He currently resides in Helena with his wife, Norma Tirrell, former newspaper reporter and researcher/writer. Bennett has two adult children and four grandchildren.