3,644 research outputs found
Statistical inference of the generation probability of T-cell receptors from sequence repertoires
Stochastic rearrangement of germline DNA by VDJ recombination is at the
origin of immune system diversity. This process is implemented via a series of
stochastic molecular events involving gene choices and random nucleotide
insertions between, and deletions from, genes. We use large sequence
repertoires of the variable CDR3 region of human CD4+ T-cell receptor beta
chains to infer the statistical properties of these basic biochemical events.
Since any given CDR3 sequence can be produced in multiple ways, the probability
distribution of hidden recombination events cannot be inferred directly from
the observed sequences; we therefore develop a maximum likelihood inference
method to achieve this end. To separate the properties of the molecular
rearrangement mechanism from the effects of selection, we focus on
non-productive CDR3 sequences in T-cell DNA. We infer the joint distribution of
the various generative events that occur when a new T-cell receptor gene is
created. We find a rich picture of correlation (and absence thereof), providing
insight into the molecular mechanisms involved. The generative event statistics
are consistent between individuals, suggesting a universal biochemical process.
Our distribution predicts the generation probability of any specific CDR3
sequence by the primitive recombination process, allowing us to quantify the
potential diversity of the T-cell repertoire and to understand why some
sequences are shared between individuals. We argue that the use of formal
statistical inference methods, of the kind presented in this paper, will be
essential for quantitative understanding of the generation and evolution of
diversity in the adaptive immune system.Comment: 20 pages, including Appendi
Recommended from our members
Architecture of the Short External Rotator Muscles of the Hip.
BackgroundMuscle architecture, or the arrangement of sarcomeres and fibers within muscles, defines functional capacity. There are limited data that provide an understanding of hip short external rotator muscle architecture. The purpose of this study was thus to characterize the architecture of these small hip muscles.MethodsEight muscles from 10 independent human cadaver hips were used in this study (n = 80 muscles). Architectural measurements were made on pectineus, piriformis, gemelli, obturators, quadratus femoris, and gluteus minimus. Muscle mass, fiber length, sarcomere length, and pennation angle were used to calculate the normalized muscle fiber length, which defines excursion, and physiological cross-sectional area (PCSA), which defines force-producing capacity.ResultsGluteus minimus had the largest PCSA (8.29 cm2) followed by obturator externus (4.54 cm2), whereas superior gemellus had the smallest PCSA (0.68 cm2). Fiber lengths clustered into long (pectineus - 10.38 cm and gluteus minimus - 10.30 cm), moderate (obturator internus - 8.77 cm and externus - 8.04 cm), or short (inferior gemellus - 5.64 and superior gemellus - 4.85). There were no significant differences among muscles in pennation angle which were all nearly zero. When the gemelli and obturators were considered as a single functional unit, their collective PCSA (10.00 cm2) exceeded that of gluteus minimus as a substantial force-producing group.ConclusionsThe key findings are that these muscles have relatively small individual PCSAs, short fiber lengths, and low pennation angles. The large collective PCSA and short fiber lengths of the gemelli and obturators suggest that they primarily play a stabilizing role rather than a joint rotating role
Hole Spin Coherence in a Ge/Si Heterostructure Nanowire
Relaxation and dephasing of hole spins are measured in a gate-defined Ge/Si
nanowire double quantum dot using a fast pulsed-gate method and dispersive
readout. An inhomogeneous dephasing time
exceeds corresponding measurements in III-V semiconductors by more than an
order of magnitude, as expected for predominately nuclear-spin-free materials.
Dephasing is observed to be exponential in time, indicating the presence of a
broadband noise source, rather than Gaussian, previously seen in systems with
nuclear-spin-dominated dephasing.Comment: 15 pages, 4 figure
Antilocalization of Coulomb Blockade in a Ge-Si Nanowire
The distribution of Coulomb blockade peak heights as a function of magnetic
field is investigated experimentally in a Ge-Si nanowire quantum dot. Strong
spin-orbit coupling in this hole-gas system leads to antilocalization of
Coulomb blockade peaks, consistent with theory. In particular, the peak height
distribution has its maximum away from zero at zero magnetic field, with an
average that decreases with increasing field. Magnetoconductance in the
open-wire regime places a bound on the spin-orbit length ( < 20 nm),
consistent with values extracted in the Coulomb blockade regime ( < 25
nm).Comment: Supplementary Information available at http://bit.ly/19pMpd
Atomic layer deposition of ZnS nanotubes
We report on growth of high-aspect-ratio () zinc sulfide
nanotubes with variable, precisely tunable, wall thicknesses and tube diameters
into highly ordered pores of anodic alumina templates by atomic layer
deposition (ALD) at temperatures as low as 75 C. Various
characterization techniques are employed to gain information on the
composition, morphology, and crystal structure of the synthesized samples.
Besides practical applications, the ALD-grown tubes could be envisaged as model
systems for the study of a certain class of size-dependent quantum and
classical phenomena.Comment: 1 LaTeX source file, 8 eps figures, and the manuscript in PDF forma
Imaging a 1-electron InAs quantum dot in an InAs/InP nanowire
Nanowire heterostructures define high-quality few-electron quantum dots for
nanoelectronics, spintronics and quantum information processing. We use a
cooled scanning probe microscope (SPM) to image and control an InAs quantum dot
in an InAs/InP nanowire, using the tip as a movable gate. Images of dot
conductance vs. tip position at T = 4.2 K show concentric rings as electrons
are added, starting with the first electron. The SPM can locate a dot along a
nanowire and individually tune its charge, abilities that will be very useful
for the control of coupled nanowire dots
Gate Coupling to Nanoscale Electronics
The realization of single-molecule electronic devices, in which a
nanometer-scale molecule is connected to macroscopic leads, requires the
reproducible production of highly ordered nanoscale gaps in which a molecule of
interest is electrostatically coupled to nearby gate electrodes. Understanding
how the molecule-gate coupling depends on key parameters is crucial for the
development of high-performance devices. Here we directly address this,
presenting two- and three-dimensional finite-element electrostatic simulations
of the electrode geometries formed using emerging fabrication techniques. We
quantify the gate coupling intrinsic to these devices, exploring the roles of
parameters believed to be relevant to such devices. These include the thickness
and nature of the dielectric used, and the gate screening due to different
device geometries. On the single-molecule (~1nm) scale, we find that device
geometry plays a greater role in the gate coupling than the dielectric constant
or the thickness of the insulator. Compared to the typical uniform nanogap
electrode geometry envisioned, we find that non-uniform tapered electrodes
yield a significant three orders of magnitude improvement in gate coupling. We
also find that in the tapered geometry the polarizability of a molecular
channel works to enhance the gate coupling
Influence of Different Strain Rates on the Flow Curve and the Formability of Thin Aluminium and Tinplate Sheets
Due to this high number of produced units and the very thin sheet metals used for beverage
cans, precise production processes with high production volumes are necessary. To save
expenses, while optimising these processes, numerical simulation methods are exploited.
Considering this, it is indispensable to identify the material behaviour as exactly as possible.
In practise, often results of quasi static tensile tests are used, although these are insufficient
for the precise modelling of the material behaviour during can production, since strain rates
of up to 10³ s-1 can occur, here. Therefore, quasi static and high speed tensile test have been
done on specimens featuring the typical materials and thicknesses of semi-finished parts
used for beverage can production. The results were compared with similar materials at
higher sheet metal thicknesses and authenticated by numerical simulation. It was shown that
there is an influence of the strain rate on the material behaviour and it is necessary to
determine material characteristics at strain rates, which are close to the process speed.
Furthermore, the results were classified in their signification for beverage can production
and forming technologies in general
Structural biology with carbon nanotube AFM probes
Carbon nanotubes represent ideal probes for high-resolution structural and chemical imaging of biomolecules with atomic force microscopy. Recent advances in fabrication of carbon nanotube probes with sub-nanometer radii promise to yield unique insights into the structure, dynamics and function of biological macromolecules and complexes
Self-directed growth of AlGaAs core-shell nanowires for visible light applications
Al(0.37)Ga(0.63)As nanowires (NWs) were grown in a molecular beam epitaxy
system on GaAs(111)B substrates. Micro-photoluminescence measurements and
energy dispersive X-ray spectroscopy indicated a core-shell structure and Al
composition gradient along the NW axis, producing a potential minimum for
carrier confinement. The core-shell structure formed during the growth as a
consequence of the different Al and Ga adatom diffusion lengths.Comment: 20 pages, 7 figure
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