1,314 research outputs found
Usage of the Python Programming Language on the CMS Experiment
Being a highly dynamic language and allowing reliable programming with quick turnarounds, Python is a widely used programming language in CMS. Most of the tools used in workflow management and the GRID interface tools are written in this language. Also most of the tools used in the context of release management: integration builds, release building and deploying, as well as performance measurements are in Python. With an interface to the CMS data formats, rapid prototyping of analyses and debugging is an additional use case. Finally in 2008 the CMS experiment switched to using Python as its configuration language. This talk will give an overview of the general usage of Python in the CMS experiment and discuss which features of the language make it well-suited for the existing use cases
Protein-DNA computation by stochastic assembly cascade
The assembly of RecA on single-stranded DNA is measured and interpreted as a
stochastic finite-state machine that is able to discriminate fine differences
between sequences, a basic computational operation. RecA filaments efficiently
scan DNA sequence through a cascade of random nucleation and disassembly events
that is mechanistically similar to the dynamic instability of microtubules.
This iterative cascade is a multistage kinetic proofreading process that
amplifies minute differences, even a single base change. Our measurements
suggest that this stochastic Turing-like machine can compute certain integral
transforms.Comment: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC129313/
http://www.pnas.org/content/99/18/11589.abstrac
Identifying Religious and/or Spiritual Perspectives of Adolescents and Young Adults Receiving Blood and Marrow Transplants: A Prospective Qualitative Study
AbstractThe potential benefits (or detriments) of religious beliefs in adolescent and young adults (AYA) are poorly understood. Moreover, the literature gives little guidance to health care teams or to chaplains about assessing and addressing the spiritual needs of AYA receiving hematopoietic stem cell transplants (HSCT). We used an institutional review boardâapproved, prospective, longitudinal study to explore the use of religion and/or spirituality (R/S) in AYA HSCT recipients and to assess changes in belief during the transplantation experience. We used the qualitative methodology, grounded theory, to gather and analyze data. Twelve AYA recipients were interviewed within 100Â days of receiving HSCT and 6 participants were interviewed 1Â year after HSCT; the other 6 participants died. Results from the first set of interviews identified 5 major themes: using R/S to address questions of âwhy me?â and âwhat will happen to me;â believing God has a reason; using faith practices; and benefitting from spiritual support people. The second set of interviews resulted in 4 major themes: believing God chose me; affirming that my life has a purpose; receiving spiritual encouragement; and experiencing strengthened faith. We learned that AYA patients were utilizing R/S far more than we suspected and that rather than losing faith in the process of HSCT, they reported using R/S to cope with illness and HSCT and to understand their lives as having special purpose. Our data, supported by findings of adult R/S studies, suggest that professionally prepared chaplains should be proactive in asking AYA patients about their understanding and use of faith, and the data can actively help members of the treatment team understand how AYA are using R/S to make meaning, address fear, and inform medical decisions
Somatotopic map and inter- and intra-digit distance in Brodmann area 2 by pressure stimulation
The somatotopic representation of the tactile stimulation on the finger in the brain is an essential part of understanding the human somatosensory system as well as rehabilitation and other clinical therapies. Many studies have used vibrotactile stimulations and reported finger somatotopic representations in the Brodmann area 3 (BA 3). On the contrary, few studies investigated finger somatotopic representation using pressure stimulations. Therefore, the present study aimed to find a comprehensive somatotopic representation (somatotopic map and inter- and intra-digit distance) within BA 2 of humans that could describe tactile stimulations on different joints across the fingers by applying pressure stimulation to three joints-the first (p1), second (p2), and third (p3) joints-of four fingers (index, middle, ring, and little finger). Significant differences were observed in the inter-digit distance between the first joints (p1) of the index and little fingers, and between the third joints (p3) of the index and little fingers. In addition, a significant difference was observed in the intra-digit distance between p1 and p3 of the little finger. This study suggests that a somatotopic map and inter- and intra-digit distance could be found in BA 2 in response to pressure stimulation on finger joints.ope
Au-Ag template stripped pattern for scanning probe investigations of DNA arrays produced by Dip Pen Nanolithography
We report on DNA arrays produced by Dip Pen Nanolithography (DPN) on a novel
Au-Ag micro patterned template stripped surface. DNA arrays have been
investigated by atomic force microscopy (AFM) and scanning tunnelling
microscopy (STM) showing that the patterned template stripped substrate enables
easy retrieval of the DPN-functionalized zone with a standard optical
microscope permitting a multi-instrument and multi-technique local detection
and analysis. Moreover the smooth surface of the Au squares (abput 5-10
angstrom roughness) allows to be sensitive to the hybridization of the
oligonucleotide array with label-free target DNA. Our Au-Ag substrates,
combining the retrieving capabilities of the patterned surface with the
smoothness of the template stripped technique, are candidates for the
investigation of DPN nanostructures and for the development of label free
detection methods for DNA nanoarrays based on the use of scanning probes.Comment: Langmuir (accepted
Comprehensive characterization of molecular interactions based on nanomechanics
Molecular interaction is a key concept in our understanding of the biological mechanisms of life. Two physical properties change when one molecular partner binds to another. Firstly, the masses combine and secondly, the structure of at least one binding partner is altered, mechanically transducing the binding into subsequent biological reactions. Here we present a nanomechanical micro-array technique for bio-medical research, which not only monitors the binding of effector molecules to their target but also the subsequent effect on a biological system in vitro. This label-free and real-time method directly and simultaneously tracks mass and nanomechanical changes at the sensor interface using micro-cantilever technology. To prove the concept we measured lipid vesicle (approximately 748*10(6) Da) adsorption on the sensor interface followed by subsequent binding of the bee venom peptide melittin (2840 Da) to the vesicles. The results show the high dynamic range of the instrument and that measuring the mass and structural changes simultaneously allow a comprehensive discussion of molecular interactions
Single-molecule studies of the stringency factors and rates governing the polymerization of RecA on double-stranded DNA
RecA is a key protein in homologous recombination. During recombination, one single-stranded DNA (ssDNA) bound to site I in RecA exchanges WatsonâCrick pairing with a sequence-matched ssDNA that was part of a double-stranded DNA molecule (dsDNA) bound to site II in RecA. After strand exchange, heteroduplex dsDNA is bound to site I. In vivo, direct polymerization of RecA on dsDNA through site I does not occur, though it does in vitro. The mechanisms underlying the difference have been unclear. We use single-molecule experiments to decouple the two steps involved in polymerization: nucleation and elongation. We find that elongation is governed by a fundamental clock that is insensitive to force and RecA concentration from 0.2 and 6âÂľM, though rates depend on ionic conditions. Thus, we can probe nucleation site stability by creating nucleation sites at high force and then measuring elongation as a function of applied force. We find that in the presence of ATP hydrolysis a minimum force is required for polymerization. The minimum force decreases with increasing RecA or ATP concentrations. We propose that force reduces the off-rate for nucleation site binding and that nucleation site stability is the stringency factor that prevents in vivo polymerization
Search for the standard model Higgs boson in the H to ZZ to 2l 2nu channel in pp collisions at sqrt(s) = 7 TeV
A search for the standard model Higgs boson in the H to ZZ to 2l 2nu decay
channel, where l = e or mu, in pp collisions at a center-of-mass energy of 7
TeV is presented. The data were collected at the LHC, with the CMS detector,
and correspond to an integrated luminosity of 4.6 inverse femtobarns. No
significant excess is observed above the background expectation, and upper
limits are set on the Higgs boson production cross section. The presence of the
standard model Higgs boson with a mass in the 270-440 GeV range is excluded at
95% confidence level.Comment: Submitted to JHE
Measurement of the t t-bar production cross section in the dilepton channel in pp collisions at sqrt(s) = 7 TeV
The t t-bar production cross section (sigma[t t-bar]) is measured in
proton-proton collisions at sqrt(s) = 7 TeV in data collected by the CMS
experiment, corresponding to an integrated luminosity of 2.3 inverse
femtobarns. The measurement is performed in events with two leptons (electrons
or muons) in the final state, at least two jets identified as jets originating
from b quarks, and the presence of an imbalance in transverse momentum. The
measured value of sigma[t t-bar] for a top-quark mass of 172.5 GeV is 161.9 +/-
2.5 (stat.) +5.1/-5.0 (syst.) +/- 3.6(lumi.) pb, consistent with the prediction
of the standard model.Comment: Replaced with published version. Included journal reference and DO
Combined search for the quarks of a sequential fourth generation
Results are presented from a search for a fourth generation of quarks
produced singly or in pairs in a data set corresponding to an integrated
luminosity of 5 inverse femtobarns recorded by the CMS experiment at the LHC in
2011. A novel strategy has been developed for a combined search for quarks of
the up and down type in decay channels with at least one isolated muon or
electron. Limits on the mass of the fourth-generation quarks and the relevant
Cabibbo-Kobayashi-Maskawa matrix elements are derived in the context of a
simple extension of the standard model with a sequential fourth generation of
fermions. The existence of mass-degenerate fourth-generation quarks with masses
below 685 GeV is excluded at 95% confidence level for minimal off-diagonal
mixing between the third- and the fourth-generation quarks. With a mass
difference of 25 GeV between the quark masses, the obtained limit on the masses
of the fourth-generation quarks shifts by about +/- 20 GeV. These results
significantly reduce the allowed parameter space for a fourth generation of
fermions.Comment: Replaced with published version. Added journal reference and DO
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