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Characterisation of FAD-family folds using a machine learning approach
Flavin adenine dinucleotide (FAD) and its derivatives play a crucial role in
biological processes. They are major organic cofactors and electron carriers
in both enzymatic activities and biochemical pathways. We have analysed
the relationships between sequence and structure of FAD-containing proteins
using a machine learning approach. Decision trees were generated using the
C4.5 algorithm as a means of automatically generating rules from biological
databases (TOPS, CATH and PDB). These rules were then used as
background knowledge for an ILP system to characterise the four different
classes of FAD-family folds classified in Dym and Eisenberg (2001). These
FAD-family folds are: glutathione reductase (GR), ferredoxin reductase (FR),
p-cresol methylhydroxylase (PCMH) and pyruvate oxidase (PO). Each FADfamily
was characterised by a set of rules. The “knowledge patterns”
generated from this approach are a set of rules containing conserved sequence
motifs, secondary structure sequence elements and folding information.
Every rule was then verified using statistical evaluation on the measured
significance of each rule. We show that this machine learning approach is
capable of learning and discovering interesting patterns from large biological
databases and can generate “knowledge patterns” that characterise the FADcontaining
proteins, and at the same time classify these proteins into four
different families
Anomalous Pressure Dependence of Kadowaki-Woods ratio and Crystal Field Effects in Mixed-valence YbInCu4
The mixed-valence (MV) compound YbInCu4 was investigated by electrical
resistivity and ac specific heat at low temperatures and high pressures. At
atmospheric pressure, its Kadowaki-Woods (KW) ratio, A/\gamma ^2, is 16 times
smaller than the universal value R_{KW}(=1.0 x 10^-5 \mu \Omega cm mol^2 K^2
mJ^-2), but sharply increases to 16.5R_{KW} at 27 kbar. The pressure-induced
change in the KW ratio and deviation from R_{KW} are analyzed in terms of the
change in f-orbital degeneracy N and carrier density n. This analysis is
further supported by a dramatic change in residual resistivity \rho_0 near 25
kbar, where \rho_0 jumps by a factor of 7.Comment: 4pages, 3figure
Presure-Induced Superconducting State of Antiferromagnetic CaFeAs
The antiferromagnet CaFeAs does not become superconducting when
subject to ideal hydrostatic pressure conditions, where crystallographic and
magnetic states also are well defined. By measuring electrical resistivity and
magnetic susceptibility under quasi-hydrostatic pressure, however, we find that
a substantial volume fraction of the sample is superconducting in a narrow
pressure range where collapsed tetragonal and orthorhombic structures coexist.
At higher pressures, the collapsed tetragonal structure is stabilized, with the
boundary between this structure and the phase of coexisting structures strongly
dependent on pressure history. Fluctuations in magnetic degrees of freedom in
the phase of coexisting structures appear to be important for
superconductivity.Comment: revised (6 pages, 5 figures) - includes additional experimental
result
Pressure dependence of upper critical fields in FeSe single crystals
We investigate the pressure dependence of the upper critical fields
({\mu}) for FeSe single crystals with pressure up to 2.57 GPa.
The superconducting (SC) properties show a disparate behavior across a critical
pressure where the pressure-induced antiferromagnetic phase coexists with
superconductivity. The magnetoresistance for and is very
different: for , magnetic field induces and enhances a hump in the
resistivity close to the for pressures higher than 1.2 GPa, while it is
absent for . Since the measured {\mu} for FeSe samples is
smaller than the orbital limited upper critical field ()
estimated by the Werthamer Helfand and Hohenberg (WHH) model, the Maki
parameter ({\alpha}) related to Pauli spin-paramagnetic effects is additionally
considered to describe the temperature dependence of {\mu}().
Interestingly, the {\alpha} value is hardly affected by pressure for ,
while it strongly increases with pressure for . The pressure evolution of
the {\mu}(0)s for the FeSe single crystals is found to be almost
similar to that of (), suggesting that the pressure-induced magnetic
order adversely affects the upper critical fields as well as the SC transition
temperature.Comment: 23 pages, 6 figures, 1 tabl
Effect of magnetic order on the superfluid response of single-crystal ErNiBC: A penetration depth study
We report measurements of the in-plane magnetic penetration depth (T) in single crystals of ErNiBC down to 0.1 K using
a tunnel-diode based, self-inductive technique at 21 MHz. We observe four
features: (1) a slight dip in (T) at the Nel
temperature = 6.0 K, (2) a peak at = 2.3 K, where a weak
ferromagnetic component sets in, (3) another maximum at 0.45 K, and (4) a final
broad drop down to 0.1 K. Converting to superfluid density , we see
that the antiferromagnetic order at 6 K only slightly depresses
superconductivity. We seek to explain some of the above features in the context
of antiferromagnetic superconductors, where competition between the
antiferromagnetic molecular field and spin fluctuation scattering determines
increased or decreased pairbreaking. Superfluid density data show only a slight
decrease in pair density in the vicinity of the 2.3 K feature, thus supporting
other evidences against bulk ferromagnetism in this temperature range.Comment: 15 pages, 5 figure
Disorder in a Quantum Critical Superconductor
In four classes of materials, the layered copper-oxides, organics,
iron-pnictides and heavy-fermion compounds, an unconventional superconducting
state emerges as a magnetic transition is tuned toward absolute zero
temperature, that is, toward a magnetic quantum-critical point (QCP). In most
materials, the QCP is accessed by chemical substitutions or applied pressure.
CeCoIn5 is one of the few materials that are born as a quantum-critical
superconductor and, therefore, offers the opportunity to explore the
consequences of chemical disorder. Cadmium-doped crystals of CeCoIn5 are a
particularly interesting case where Cd substitution induces long-range magnetic
order, as in Zn-doped copper-oxides. Applied pressure globally supresses the
Cd-induced magnetic order and restores bulk superconductivity. Here we show,
however, that local magnetic correlations, whose spatial extent decreases with
applied pressure, persist at the extrapolated QCP. The residual droplets of
impurity-induced magnetic moments prevent the reappearance of conventional
signatures of quantum criticality, but induce a heterogeneous electronic state.
These discoveries show that spin droplets can be a source of electronic
heterogeneity in classes of strongly correlated electron systems and emphasize
the need for caution when interpreting the effects of tuning a correlated
system by chemical substitution.Comment: main text and supplementary informatio
Addressing the Requirements of High‐Sensitivity Single‐Molecule Imaging of Low‐Copy‐Number Proteins in Bacteria
Single‐molecule fluorescence super‐resolution imaging and tracking provide nanometer‐scale information about subcellular protein positions and dynamics. These single‐molecule imaging experiments can be very powerful, but they are best suited to high‐copy number proteins where many measurements can be made sequentially in each cell. We describe artifacts associated with the challenge of imaging a protein expressed in only a few copies per cell. We image live Bacillus subtilis in a fluorescence microscope, and demonstrate that under standard single‐molecule imaging conditions, unlabeled B. subtilis cells display punctate red fluorescent spots indistinguishable from the few PAmCherry fluorescent protein single molecules under investigation. All Bacillus species investigated were strongly affected by this artifact, whereas we did not find a significant number of these background sources in two other species we investigated, Enterococcus faecalis and Escherichia coli. With single‐molecule resolution, we characterize the number, spatial distribution, and intensities of these impurity spots.Bright spots: A single‐molecule‐like fluorescent background signal is reported in Bacillus subtilis cells, and the density and fluorescence intensity of these spots are quantified in several Bacillus species and other Gram‐negative and Gram‐positive organisms.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/144710/1/cphc201600035_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144710/2/cphc201600035.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/144710/3/cphc201600035-sup-0001-misc_information.pd
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