856 research outputs found
Effect of energy source fed to sows during late gestation on subsequent neonatal survival, energy stores and colostrum composition
Call number: LD2668 .T4 1986 N48Master of ScienceAnimal Science and Industr
SMaSH: A Benchmarking Toolkit for Human Genome Variant Calling
Motivation: Computational methods are essential to extract actionable
information from raw sequencing data, and to thus fulfill the promise of
next-generation sequencing technology. Unfortunately, computational tools
developed to call variants from human sequencing data disagree on many of their
predictions, and current methods to evaluate accuracy and computational
performance are ad-hoc and incomplete. Agreement on benchmarking variant
calling methods would stimulate development of genomic processing tools and
facilitate communication among researchers.
Results: We propose SMaSH, a benchmarking methodology for evaluating human
genome variant calling algorithms. We generate synthetic datasets, organize and
interpret a wide range of existing benchmarking data for real genomes, and
propose a set of accuracy and computational performance metrics for evaluating
variant calling methods on this benchmarking data. Moreover, we illustrate the
utility of SMaSH to evaluate the performance of some leading single nucleotide
polymorphism (SNP), indel, and structural variant calling algorithms.
Availability: We provide free and open access online to the SMaSH toolkit,
along with detailed documentation, at smash.cs.berkeley.edu
Anodic formation and characterization of nanoporous InP in aqueous KOH electrolytes
The anodic behavior of highly doped (> 1018 cm-3) n-InP in aqueous KOH was investigated. Electrodes anodized in the absence of light in 2- 5 mol dm-3 KOH at a constant potential of 0.5- 0.75 V (SCE), or subjected to linear potential sweeps to potentials in this range, were shown to exhibit the formation of a nanoporous subsurface region. Both linear sweep voltammograms and current-time curves at constant potential showed a characteristic anodic peak, corresponding to formation of the nanoporous region. No porous region was formed during anodization in 1 mol dm-3 KOH. The nanoporous region was examined using transmission electron microscopy and found to have a thickness of some 1- 3 μm depending on the anodization conditions and to be located beneath a thin (typically ∼40 nm), dense, near-surface layer. The pores varied in width from 25 to 75 nm and both the pore width and porous region thickness were found to decrease with increasing KOH concentration. The porosity was approximately 35%. The porous layer structure is shown to form by the localized penetration of surface pits into the InP, and the dense, near-surface layer is consistent with the effect of electron depletion at the surface of the semiconductor
A mechanistic study of anodic formation of porous InP
When porous InP is anodically formed in KOH electrolytes, a thin layer ~40
nm in thickness, close to the surface, appears to be unmodified. We have
investigated the earlier stages of the anodic formation of porous InP in 5
mol dm-3 KOH. TEM clearly shows individual porous domains which
appear triangular in cross-section and square in plan view. The crosssections
also show that the domains are separated from the surface by a ~40
nm thick, dense InP layer. It is concluded that the porous domains have a
square-based pyramidal shape and that each one develops from an individual
surface pit which forms a channel through this near-surface layer. We
suggest that the pyramidal structure arises as a result of preferential pore
propagation along the directions. AFM measurements show that the
density of surface pits increases with time. Each of these pits acts as a
source for a pyramidal porous domain, and these domains eventually form a
continuous porous layer. This implies that the development of porous
domains beneath the surface is also progressive in nature. Evidence for this
was seen in plan view TEM images. Merging of domains continues to
occur at potentials more anodic than the peak potential, where the current is
observed to decrease. When the domains grow, the current density increases
correspondingly. Eventually, domains meet, the interface between the
porous and bulk InP becomes relatively flat and its total effective surface
area decreases resulting in a decrease in the current density. Quantitative
models of this process are being developed
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