88 research outputs found
Routes for breaching and protecting genetic privacy
We are entering the era of ubiquitous genetic information for research,
clinical care, and personal curiosity. Sharing these datasets is vital for
rapid progress in understanding the genetic basis of human diseases. However,
one growing concern is the ability to protect the genetic privacy of the data
originators. Here, we technically map threats to genetic privacy and discuss
potential mitigation strategies for privacy-preserving dissemination of genetic
data.Comment: Draft for comment
Biophysical and electrochemical studies of protein-nucleic acid interactions
This review is devoted to biophysical and electrochemical methods used for studying protein-nucleic acid (NA) interactions. The importance of NA structure and protein-NA recognition for essential cellular processes, such as replication or transcription, is discussed to provide background for description of a range of biophysical chemistry methods that are applied to study a wide scope of protein-DNA and protein-RNA complexes. These techniques employ different detection principles with specific advantages and limitations and are often combined as mutually complementary approaches to provide a complete description of the interactions. Electrochemical methods have proven to be of great utility in such studies because they provide sensitive measurements and can be combined with other approaches that facilitate the protein-NA interactions. Recent applications of electrochemical methods in studies of protein-NA interactions are discussed in detail
WNT signalling in prostate cancer
Genome sequencing and gene expression analyses of prostate tumours have highlighted the potential importance of genetic and epigenetic changes observed in WNT signalling pathway components in prostate tumours-particularly in the development of castration-resistant prostate cancer. WNT signalling is also important in the prostate tumour microenvironment, in which WNT proteins secreted by the tumour stroma promote resistance to therapy, and in prostate cancer stem or progenitor cells, in which WNT-β-catenin signals promote self-renewal or expansion. Preclinical studies have demonstrated the potential of inhibitors that target WNT receptor complexes at the cell membrane or that block the interaction of β-catenin with lymphoid enhancer-binding factor 1 and the androgen receptor, in preventing prostate cancer progression. Some WNT signalling inhibitors are in phase I trials, but they have yet to be tested in patients with prostate cancer
A mathematical and computational review of Hartree-Fock SCF methods in Quantum Chemistry
We present here a review of the fundamental topics of Hartree-Fock theory in
Quantum Chemistry. From the molecular Hamiltonian, using and discussing the
Born-Oppenheimer approximation, we arrive to the Hartree and Hartree-Fock
equations for the electronic problem. Special emphasis is placed in the most
relevant mathematical aspects of the theoretical derivation of the final
equations, as well as in the results regarding the existence and uniqueness of
their solutions. All Hartree-Fock versions with different spin restrictions are
systematically extracted from the general case, thus providing a unifying
framework. Then, the discretization of the one-electron orbitals space is
reviewed and the Roothaan-Hall formalism introduced. This leads to a exposition
of the basic underlying concepts related to the construction and selection of
Gaussian basis sets, focusing in algorithmic efficiency issues. Finally, we
close the review with a section in which the most relevant modern developments
(specially those related to the design of linear-scaling methods) are commented
and linked to the issues discussed. The whole work is intentionally
introductory and rather self-contained, so that it may be useful for non
experts that aim to use quantum chemical methods in interdisciplinary
applications. Moreover, much material that is found scattered in the literature
has been put together here to facilitate comprehension and to serve as a handy
reference.Comment: 64 pages, 3 figures, tMPH2e.cls style file, doublesp, mathbbol and
subeqn package
Acute neck pain caused by pseudogout attack of calcified cervical yellow ligament: a case report
Benchmarking Materials Property Prediction Methods: The Matbench Test Set and Automatminer Reference Algorithm
We present a benchmark test suite and an automated machine learning procedure
for evaluating supervised machine learning (ML) models for predicting
properties of inorganic bulk materials. The test suite, Matbench, is a set of
13 ML tasks that range in size from 312 to 132k samples and contain data from
10 density functional theory-derived and experimental sources. Tasks include
predicting optical, thermal, electronic, thermodynamic, tensile, and elastic
properties given a materials composition and/or crystal structure. The
reference algorithm, Automatminer, is a highly-extensible, fully-automated ML
pipeline for predicting materials properties from materials primitives (such as
composition and crystal structure) without user intervention or hyperparameter
tuning. We test Automatminer on the Matbench test suite and compare its
predictive power with state-of-the-art crystal graph neural networks and a
traditional descriptor-based Random Forest model. We find Automatminer achieves
the best performance on 8 of 13 tasks in the benchmark. We also show our test
suite is capable of exposing predictive advantages of each algorithm - namely,
that crystal graph methods appear to outperform traditional machine learning
methods given ~10^4 or greater data points. The pre-processed, ready-to-use
Matbench tasks and the Automatminer source code are open source and available
online (http://hackingmaterials.lbl.gov/automatminer/). We encourage evaluating
new materials ML algorithms on the MatBench benchmark and comparing them
against the latest version of Automatminer.Comment: Main text, supplemental inf
Thalamic Activation Modulates the Responses of Neurons in Rat Primary Auditory Cortex: An In Vivo Intracellular Recording Study
Auditory cortical plasticity can be induced through various approaches. The medial geniculate body (MGB) of the auditory thalamus gates the ascending auditory inputs to the cortex. The thalamocortical system has been proposed to play a critical role in the responses of the auditory cortex (AC). In the present study, we investigated the cellular mechanism of the cortical activity, adopting an in vivo intracellular recording technique, recording from the primary auditory cortex (AI) while presenting an acoustic stimulus to the rat and electrically stimulating its MGB. We found that low-frequency stimuli enhanced the amplitudes of sound-evoked excitatory postsynaptic potentials (EPSPs) in AI neurons, whereas high-frequency stimuli depressed these auditory responses. The degree of this modulation depended on the intensities of the train stimuli as well as the intervals between the electrical stimulations and their paired sound stimulations. These findings may have implications regarding the basic mechanisms of MGB activation of auditory cortical plasticity and cortical signal processing
Biomechanical considerations in the pathogenesis of osteoarthritis of the knee
Osteoarthritis is the most common joint disease and a major cause of disability. The knee is the large joint most affected. While chronological age is the single most important risk factor of osteoarthritis, the pathogenesis of knee osteoarthritis in the young patient is predominantly related to an unfavorable biomechanical environment at the joint. This results in mechanical demand that exceeds the ability of a joint to repair and maintain itself, predisposing the articular cartilage to premature degeneration. This review examines the available basic science, preclinical and clinical evidence regarding several such unfavorable biomechanical conditions about the knee: malalignment, loss of meniscal tissue, cartilage defects and joint instability or laxity
The one dimensional Kondo lattice model at partial band filling
The Kondo lattice model introduced in 1977 describes a lattice of localized
magnetic moments interacting with a sea of conduction electrons. It is one of
the most important canonical models in the study of a class of rare earth
compounds, called heavy fermion systems, and as such has been studied
intensively by a wide variety of techniques for more than a quarter of a
century. This review focuses on the one dimensional case at partial band
filling, in which the number of conduction electrons is less than the number of
localized moments. The theoretical understanding, based on the bosonized
solution, of the conventional Kondo lattice model is presented in great detail.
This review divides naturally into two parts, the first relating to the
description of the formalism, and the second to its application. After an
all-inclusive description of the bosonization technique, the bosonized form of
the Kondo lattice hamiltonian is constructed in detail. Next the
double-exchange ordering, Kondo singlet formation, the RKKY interaction and
spin polaron formation are described comprehensively. An in-depth analysis of
the phase diagram follows, with special emphasis on the destruction of the
ferromagnetic phase by spin-flip disorder scattering, and of recent numerical
results. The results are shown to hold for both antiferromagnetic and
ferromagnetic Kondo lattice. The general exposition is pedagogic in tone.Comment: Review, 258 pages, 19 figure
Community ecology of the metazoan parasites of white croaker, Micropogonias furnieri (Osteichthyes: Sciaenidae), from the coastal zone of the State of Rio de Janeiro, Brazil
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