Term-BLAST-like alignment tool for concept recognition in noisy clinical texts.

MOTIVATION: Methods for concept recognition (CR) in clinical texts have largely been tested on abstracts or articles from the medical literature. However, texts from electronic health records (EHRs) frequently contain spelling errors, abbreviations, and other nonstandard ways of representing clinical concepts. RESULTS: Here, we present a method inspired by the BLAST algorithm for biosequence alignment that screens texts for potential matches on the basis of matching k-mer counts and scores candidates based on conformance to typical patterns of spelling errors derived from 2.9 million clinical notes. Our method, the Term-BLAST-like alignment tool (TBLAT) leverages a gold standard corpus for typographical errors to implement a sequence alignment-inspired method for efficient entity linkage. We present a comprehensive experimental comparison of TBLAT with five widely used tools. Experimental results show an increase of 10% in recall on scientific publications and 20% increase in recall on EHR records (when compared against the next best method), hence supporting a significant enhancement of the entity linking task. The method can be used stand-alone or as a complement to existing approaches. AVAILABILITY AND IMPLEMENTATION: Fenominal is a Java library that implements TBLAT for named CR of Human Phenotype Ontology terms and is available at https://github.com/monarch-initiative/fenominal under the GNU General Public License v3.0

Prediction of Anisotropic Single-Dirac-Cones in Bi1−x{}_{1-x}Sbx{}_{x} Thin Films

The electronic band structures of Bi${}_{1-x}$Sb${}_{x}$ thin films can be varied as a function of temperature, pressure, stoichiometry, film thickness and growth orientation. We here show how different anisotropic single-Dirac-cones can be constructed in a Bi${}_{1-x}$Sb${}_{x}$ thin film for different applications or research purposes. For predicting anisotropic single-Dirac-cones, we have developed an iterative-two-dimensional-two-band model to get a consistent inverse-effective-mass-tensor and band-gap, which can be used in a general two-dimensional system that has a non-parabolic dispersion relation as in a Bi${}_{1-x}$Sb${}_{x}$ thin film system

A boron-coated CCD camera for direct detection of Ultracold Neutrons (UCN)

A new boron-coated CCD camera is described for direct detection of ultracold neutrons (UCN) through the capture reactions $^{10}$B (n,$\alpha$0$\gamma$)$^7$Li (6%) and $^{10}$B(n,$\alpha$1$\gamma$)$^7$Li (94%). The experiments, which extend earlier works using a boron-coated ZnS:Ag scintillator, are based on direct detections of the neutron-capture byproducts in silicon. The high position resolution, energy resolution and particle ID performance of a scientific CCD allows for observation and identification of all the byproducts $\alpha$, $^7$Li and $\gamma$ (electron recoils). A signal-to-noise improvement on the order of 10$^4$ over the indirect method has been achieved. Sub-pixel position resolution of a few microns is demonstrated. The technology can also be used to build UCN detectors with an area on the order of 1 m$^2$. The combination of micrometer scale spatial resolution, few electrons ionization thresholds and large area paves the way to new research avenues including quantum physics of UCN and high-resolution neutron imaging and spectroscopy.Comment: 10 pages, 8 figure

Term-BLAST-like alignment tool for concept recognition in noisy clinical texts

Motivation: Methods for concept recognition (CR) in clinical texts have largely been tested on abstracts or articles from the medical literature. However, texts from electronic health records (EHRs) frequently contain spelling errors, abbreviations, and other nonstandard ways of representing clinical concepts. Results: Here, we present a method inspired by the BLAST algorithm for biosequence alignment that screens texts for potential matches on the basis of matching k-mer counts and scores candidates based on conformance to typical patterns of spelling errors derived from 2.9 million clinical notes. Our method, the Term-BLAST-like alignment tool (TBLAT) leverages a gold standard corpus for typographical errors to implement a sequence alignment-inspired method for efficient entity linkage. We present a comprehensive experimental comparison of TBLAT with five widely used tools. Experimental results show an increase of 10% in recall on scientific publications and 20% increase in recall on EHR records (when compared against the next best method), hence supporting a significant enhancement of the entity linking task. The method can be used stand-alone or as a complement to existing approaches. Availability and implementation: Fenominal is a Java library that implements TBLAT for named CR of Human Phenotype Ontology terms and is available at https://github.com/monarch-initiative/fenominal under the GNU General Public License v3.0

Quantifying decoherence in continuous variable systems

We present a detailed report on the decoherence of quantum states of continuous variable systems under the action of a quantum optical master equation resulting from the interaction with general Gaussian uncorrelated environments. The rate of decoherence is quantified by relating it to the decay rates of various, complementary measures of the quantum nature of a state, such as the purity, some nonclassicality indicators in phase space and, for two-mode states, entanglement measures and total correlations between the modes. Different sets of physically relevant initial configurations are considered, including one- and two-mode Gaussian states, number states, and coherent superpositions. Our analysis shows that, generally, the use of initially squeezed configurations does not help to preserve the coherence of Gaussian states, whereas it can be effective in protecting coherent superpositions of both number states and Gaussian wave packets.Comment: Review article; 36 pages, 19 figures; typos corrected, references adde

Enhanced Lifetime Of Excitons In Nonepitaxial Au/cds Core/shell Nanocrystals

The ability of metal nanoparticles to capture light through plasmon excitations offers an opportunity for enhancing the optical absorption of plasmon-coupled semiconductor materials via energy transfer. This process, however, requires that the semiconductor component is electrically insulated to prevent a backward charge flow into metal and interfacial states, which causes a premature dissociation of excitons. Here we demonstrate that such an energy exchange can be achieved on the nanoscale by using nonepitaxial Au/CdS core/shell nanocomposites. These materials are fabricated via a multistep cation exchange reaction, which decouples metal and semiconductor phases leading to fewer interfacial defects. Ultrafast transient absorption measurements confirm that the lifetime of excitons in the CdS shell (tau approximate to 300 ps) is much longer than lifetimes of excitons in conventional, reduction-grown Au/CdS heteronanostructures. As a result, the energy of metal nanoparticles can be efficiently utilized by the semiconductor component without undergoing significant nonradiative energy losses, an important property for catalytic or photovoltaic applications. The reduced rate of exciton dissociation in the CdS domain of Au/CdS nanocomposites was attributed to the nonepitaxial nature of Au/CdS interfaces associated with low defect density and a high potential barrier of the interstitial phase

Limitations of rupture forecasting exposed by instantaneously triggered earthquake doublet

Earthquake hazard assessments and rupture forecasts are based on the potential length of seismic rupture and whether or not slip is arrested at fault segment boundaries. Such forecasts do not generally consider that one earthquake can trigger a second large event, near-instantaneously, at distances greater than a few kilometers. Here we present a geodetic and seismological analysis of a magnitude 7.1 intra-continental earthquake that occurred in Pakistan in 1997. We find that the earthquake, rather than a single event as hitherto assumed, was in fact an earthquake doublet: initial rupture on a shallow, blind 2 reverse fault was followed just 19 seconds later by a second rupture on a separate reverse fault 50 km away. Slip on the second fault increased the total seismic moment by half, and doubled both the combined event duration and the area of maximum ground shaking. We infer that static Coulomb stresses at the initiation location of the second earthquake were probably reduced as a result of the first. Instead, we suggest that a dynamic triggering mechanism is likely, although the responsible seismic wave phase is unclear. Our results expose a flaw in earthquake rupture forecasts that disregard cascading, multiple-fault ruptures of this type

Nuclear Organization and Dynamics of 7SK RNA in Regulating Gene Expression

We have identified 7SK RNA to be enriched in nuclear speckles. Knock-down of 7SK results in the mislocalization of nuclear speckle constituents, and the transcriptional up-regulation of a reporter gene locus. 7SK RNA transiently associates with the locus upon transcriptional down-regulation correlating with the displacement of pTEF-b

Evidence for the adaptation of protein pH-dependence to subcellular pH

<p>Abstract</p> <p>Background</p> <p>The availability of genome sequences, and inferred protein coding genes, has led to several proteome-wide studies of isoelectric points. Generally, isoelectric points are distributed following variations on a biomodal theme that originates from the predominant acid and base amino acid sidechain pKas. The relative populations of the peaks in such distributions may correlate with environment, either for a whole organism or for subcellular compartments. There is also a tendency for isoelectric points averaged over a subcellular location to not coincide with the local pH, which could be related to solubility. We now calculate the correlation of other pH-dependent properties, calculated from 3D structure, with subcellular pH.</p> <p>Results</p> <p>For proteins with known structure and subcellular annotation, the predicted pH at which a protein is most stable, averaged over a location, gives a significantly better correlation with subcellular pH than does isoelectric point. This observation relates to the cumulative properties of proteins, since maximal stability for individual proteins follows the bimodal isoelectric point distribution. Histidine residue location underlies the correlation, a conclusion that is tested against a background of proteins randomised with respect to this feature, and for which the observed correlation drops substantially.</p> <p>Conclusion</p> <p>There exists a constraint on protein pH-dependence, in relation to the local pH, that is manifested in the pKa distribution of histidine sub-proteomes. This is discussed in terms of protein stability, pH homeostasis, and fluctuations in proton concentration.</p