Genomics, bio specimens, and other biological data: Current status and future directions

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146389/1/mp12912_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146389/2/mp12912.pd

Lecture archiving on a larger scale at the University of Michigan and CERN

The ATLAS Collaboratory Project at the University of Michigan has been a leader in the area of collaborative tools since 1999. Its activities include the development of standards, software and hardware tools for lecture archiving, and making recommendations for videoconferencing and remote teaching facilities. Starting in 2006 our group became involved in classroom recordings, and in early 2008 we spawned CARMA, a University-wide recording service. This service uses a new portable recording system that we developed. Capture, archiving and dissemination of rich multimedia content from lectures, tutorials and classes are increasingly widespread activities among universities and research institutes. A growing array of related commercial and open source technologies is becoming available, with several new products introduced in the last couple years. As the result of a new close partnership between U-M and CERN IT, a market survey of these products was conducted and a summary of the results are presented here. It is informing an ambitious effort in 2009 to equip many CERN rooms with automated lecture archiving systems, on a much larger scale than before. This new technology is being integrated with CERN's existing webcast, CDS, and Indico applications.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/85420/1/jpconf10_219_082003.pd

Discriminating Electroweak-ino Parameter Ordering at the LHC and Its Impact on LFV Studies

Current limit on the dark matter relic abundance may suggest that $|\mu|$ should be smaller than prediction in the minimal supergravity scenario (mSUGRA) for moderate $m_0$ and $m_{1/2}$. The electroweak-ino parameter $M_1, M_2$ and $|\mu|$ are then much closer to each other. This can be realized naturally in the non-universal Higgs mass model (NUHM). Since the heaviest neutralino ($\tilde\chi^0_4$) and chargino ($\tilde\chi^\pm_2$) have significant gaugino components, they may appear frequently in the left-handed squark decay and then be detectable at the LHC. In such a case, we showed that the hierarchy of $M_1, M_2$ and $|\mu|$ can be determined. In the light slepton mass scenario with non-vanishing lepton-flavor violation (LFV) in the right-handed sector, NUHM with small $|\mu|$ corresponds to region of parameter space where strong cancellation among leading contributions to $Br(\mu\to e\gamma)$ can occur. We showed that determination of electroweak-ino hierarchy plays a crucial role in resolving cancellation point of $Br(\mu\to e\gamma)$ and determination of LFV parameters. We also discussed test of the universality of the slepton masses at the LHC and the implications to SUSY flavor models.Comment: 34 pages, 16 figure

The ATLAS MDT remote calibration centers

The precision chambers of the ATLAS Muon Spectrometer are built with Monitored Drift Tubes (MDT). The requirement of high accuracy and low systematic error, to achieve a transverse momentum resolution of 10% at 1 TeV, can only be accomplished if the calibrations are known with an accuracy of 20 μm. The relation between the drift path and the measured time (the socalled r-t relation) depends on many parameters (temperature T, hit rate, gas composition, thresholds,...) subject to time variations. The r-t relation has to be measured from the data without the use of an external detector, using the autocalibration technique. This method relies on an iterative procedure applied to the same data sample, starting from a preliminary set of constants. The required precision can be achieved using a large (few thousand) number of non-parallel tracks crossing a region, called calibration region, i.e. the region of the MDT chamber sharing the same r-t relation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/85421/1/jpconf10_219_022028.pd

Separation of a single photon and products of the π0,η,Ks0\pi^0,\eta, K^0_s meson neutral decay channels in the CMS electromagnetic calorimeter using neural network

The artificial neural network approach is used for separation of signals from a single photon $\gamma$ and products of the $\pi^0,\eta, K^0_s$ meson neutral decay channels on the basis of the data from the CMS electromagnetic calorimeter alone. Rejection values for the three types of mesons as a function of single photon selection efficiencies are obtained for two Barrel and one Endcap pseudorapidity regions and initial \Et of 20, 40, 60 and 100 GeV.Comment: 16 pages, uses cernrep.cls style fil

RooStatsCms: a tool for analyses modelling, combination and statistical studies

The RooStatsCms (RSC) software framework allows analysis modelling and combination, statistical studies together with the access to sophisticated graphics routines for results visualisation. The goal of the project is to complement the existing analyses by means of their combination and accurate statistical studies.Comment: Proceedings of the 11th Topical Seminar on Innovative Particle and Radiation Detectors. 4 pages and 5 figure

(No) Eternal Inflation and Precision Higgs Physics

Even if nothing but a light Higgs is observed at the LHC, suggesting that the Standard Model is unmodified up to scales far above the weak scale, Higgs physics can yield surprises of fundamental significance for cosmology. As has long been known, the Standard Model vacuum may be metastable for low enough Higgs mass, but a specific value of the decay rate holds special significance: for a very narrow window of parameters, our Universe has not yet decayed but the current inflationary period can not be future eternal. Determining whether we are in this window requires exquisite but achievable experimental precision, with a measurement of the Higgs mass to 0.1 GeV at the LHC, the top mass to 60 MeV at a linear collider, as well as an improved determination of alpha_s by an order of magnitude on the lattice. If the parameters are observed to lie in this special range, particle physics will establish that the future of our Universe is a global big crunch, without harboring pockets of eternal inflation, strongly suggesting that eternal inflation is censored by the fundamental theory. This conclusion could be drawn even more sharply if metastability with the appropriate decay rate is found in the MSSM, where the physics governing the instability can be directly probed at the TeV scale.Comment: 25 pages, 3 figures. v2: updated value of top mass, added references, JHEP published versio

SEQanswers: an open access community for collaboratively decoding genomes

Summary: The affordability of high-throughput sequencing has created an unprecedented surge in the use of genomic data in basic, translational and clinical research. The rapid evolution of sequencing technology, coupled with its broad adoption across biology and medicine, necessitates fast, collaborative interdisciplinary discussion. SEQanswers provides a real-time knowledge-sharing resource to address this need, covering experimental and computational aspects of sequencing and sequence analysis. Developers of popular analysis tools are among the >4000 active members, and ~40 peer-reviewed publications have referenced SEQanswers

From Genotype to Phenotype: Linking Bioinformatics and Medical Informatics Ontologies

A small group of around 40 people came together at the Chancellors Conference Centre in Manchester for the Ontologies Workshop, chaired by Alan Rector and Robert Stevens. The workshop was, rather strangely, spread over 2 half days. In hindsight, this programme worked very well as it gave people the opportunity to chat over a drink on the Saturday evening and share ideas, before launching into the second half on the following day. The participants were from various walks of life, all with a common interest in finding out more about ontologies and promoting collaborations between the medical informatics and bioinformatics ontology communities

Nets, Spray or Both? The Effectiveness of Insecticide-Treated Nets and Indoor Residual Spraying in Reducing Malaria Morbidity and Child Mortality in sub-Saharan Africa.

Malaria control programmes currently face the challenge of maintaining, as well as accelerating, the progress made against malaria with fewer resources and uncertain funding. There is a critical need to determine what combination of malaria interventions confers the greatest protection against malaria morbidity and child mortality under routine conditions. This study assesses intervention effectiveness experienced by children under the age of five exposed to both insecticide-treated nets (ITNs) and indoor residual spraying (IRS), as compared to each intervention alone, based on nationally representative survey data collected from 17 countries in sub-Saharan Africa. Living in households with both ITNs and IRS was associated with a significant risk reduction against parasitaemia in medium and high transmission areas, 53% (95% CI 37% to 67%) and 31% (95% CI 11% to 47%) respectively. For medium transmission areas, an additional 36% (95% CI 7% to 53%) protection was garnered by having both interventions compared with exposure to only ITNs or only IRS. Having both ITNs and IRS was not significantly more protective against parasitaemia than either intervention alone in low and high malaria transmission areas. In rural and urban areas, exposure to both interventions provided significant protection against parasitaemia, 57% (95% CI 48% to 65%) and 39% (95% CI 10% to 61%) respectively; however, this effect was not significantly greater than having a singular intervention. Statistically, risk for all-cause child mortality was not significantly reduced by having both ITNs and IRS, and no additional protectiveness was detected for having dual intervention coverage over a singular intervention. These findings suggest that greater reductions in malaria morbidity and health gains for children may be achieved with ITNs and IRS combined beyond the protection offered by IRS or ITNs alone