Adaptive Sentence Boundary Disambiguation

Labeling of sentence boundaries is a necessary prerequisite for many natural language processing tasks, including part-of-speech tagging and sentence alignment. End-of-sentence punctuation marks are ambiguous; to disambiguate them most systems use brittle, special-purpose regular expression grammars and exception rules. As an alternative, we have developed an efficient, trainable algorithm that uses a lexicon with part-of-speech probabilities and a feed-forward neural network. After training for less than one minute, the method correctly labels over 98.5\% of sentence boundaries in a corpus of over 27,000 sentence-boundary marks. We show the method to be efficient and easily adaptable to different text genres, including single-case texts.Comment: This is a Latex version of the previously submitted ps file (formatted as a uuencoded gz-compressed .tar file created by csh script). The software from the work described in this paper is available by contacting [email protected]

Probing the Gamma-Ray Burst Rate with Trigger Simulations of the Swift Burst Alert Telescope

The long gamma-ray burst (GRB) rate is essential for revealing the connection between GRBs, supernovae and stellar evolution. Additionally, the GRB rate at high redshift provides a strong probe of star formation history in the early universe. While hundreds of GRBs are observed by Swift, it remains difficult to determine the intrinsic GRB rate due to the complex trigger algorithm of Swift. Current studies usually approximate the Swift trigger algorithm by a single detection threshold. However, unlike the previously flown GRB instruments, Swift has over 500 trigger criteria based on photon count rate and additional image threshold for localization. To investigate possible systematic biases and explore the intrinsic GRB properties, we developed a program that is capable of simulating all the rate trigger criteria and mimicking the image trigger threshold. We use this program to search for the intrinsic GRB rate. Our simulations show that adopting the complex trigger algorithm of Swift increases the detection rate of dim bursts. As a result, we find that either the GRB rate is much higher than previously expected at large redshift, or the luminosity evolution is non-negligible. We will discuss the best results of the GRB rate in our search, and their impact on the star-formation history.Comment: 6 pages, 3 figures, 7th Huntsville Gamma-Ray Burst Symposium, GRB 2013: paper 35 in eConf Proceedings C130414

Probing the Cosmic Gamma-Ray Burst Rate with Trigger Simulations of the Swift Burst Alert Telescope

The gamma-ray burst (GRB) rate is essential for revealing the connection between GRBs, supernovae and stellar evolution. Additionally, the GRB rate at high redshift provides a strong probe of star formation history in the early universe. While hundreds of GRBs are observed by Swift, it remains difficult to determine the intrinsic GRB rate due to the complex trigger algorithm of Swift. Current studies of the GRB rate usually approximate the Swift trigger algorithm by a single detection threshold. However, unlike the previously flown GRB instruments, Swift has over 500 trigger criteria based on photon count rate and additional image threshold for localization. To investigate possible systematic biases and explore the intrinsic GRB properties, we develop a program that is capable of simulating all the rate trigger criteria and mimicking the image threshold. Our simulations show that adopting the complex trigger algorithm of Swift increases the detection rate of dim bursts. As a result, our simulations suggest bursts need to be dimmer than previously expected to avoid over-producing the number of detections and to match with Swift observations. Moreover, our results indicate that these dim bursts are more likely to be high redshift events than low-luminosity GRBs. This would imply an even higher cosmic GRB rate at large redshifts than previous expectations based on star-formation rate measurements, unless other factors, such as the luminosity evolution, are taken into account. The GRB rate from our best result gives a total number of 4571^{+829}_{-1584} GRBs per year that are beamed toward us in the whole universe. SPECIAL NOTE (2015.05.16): This new version incorporates an erratum. All the GRB rate normalizations ($R_{\rm GRB}(z=0)$) should be a factor of 2 smaller than previously reported. Please refer to the Appendix for more details. We sincerely apologize for the mistake.Comment: 52 pages, 17 figures, published in ApJ 783, 24L (2014). An erratum is included. A typo in Eq. 8 is fixed in this versio

A Theoretical Model for the Mbh−σM_{\rm bh}-\sigma Relation for Supermassive Black Holes in Galaxies

We construct a model for the formation of black holes within galactic bulges. The initial state is a slowly rotating isothermal sphere, characterized by effective transport speed \aeff and rotation rate $\Omega$. The black hole mass is determined when the centrifugal radius of the collapse flow exceeds the capture radius of the central black hole. This model reproduces the observed correlation between black hole masses and galactic velocity dispersions, \mbh \approx 10^8 M_\odot (\sigma/200 \kms)^4, where \sigma = \sqrt{2} \aeff. This model also predicts the ratio \mrat of black hole mass to host mass: \mrat $\approx$ 0.004 (\sigma/200 \kms).Comment: 9 pages, 2 figures, submitted to Astrophysical Journal Letter

A re-assessment of the distribution of Virginia\u27s warbler in the Black Hills of South Dakota

Virginia’s Warbler (Oreothlypis virginiae) reaches the northeastern limit of its breeding range in the southern Black Hills of South Dakota, where it is considered a species of conservation concern. This population occurs in pine–juniper–shrub habitat in several canyons in extreme western Custer County. Additional such habitat occurs in the southern Black Hills south and east of the documented breeding populations, but these areas have received few systematic surveys, and whether Virginia’s Warbler occupies them was uncertain. Therefore, to define the species’ distribution in the South Dakota Black Hills more precisely, we surveyed with the aid of broadcast song and reviewed other reports. Virginia’s Warblers occurred in appropriate habitats all along the southwestern front (approximately 30 km total) of the Black Hills in Custer County but did not occur in similar habitat along the southeastern front, approximately 25 km distant. The species’ relative abundance in previously and newly identified pine–juniper–shrub habitats was similar. Virginia’s Warbler occurrence was positively associated with shrub cover (primarily mountain-mahogany, Cercocarpus montanus), pine overstory, and slopes of \u3e15°. Its association with the Spotted Towhee (Pipilo maculatus) was negative, with the Yellow-rumped Warbler (Setophaga coronata) tended toward positive, and with the Dusky Flycatcher (Empidonax oberholseri) was variable (negative along the southwestern front but weakly positive across all sites). These data extend the documented breeding range of Virginia’s Warbler in South Dakota by more than 20 km to the southeast. To clarify conservation priorities for this species at the northeastern limit of its range, future studies should delineate local and landscape-level characteristics of this population’s habitat more precisely and address its source–sink population dynamics

Strength and Ultrasonic Characterization of Metallic Interfaces

In recent years, the process of diffusion bonding has found considerable usage in both the nuclear power and aerospace industries. This process requires the compression of mating surfaces at an elevated temperature for a given time. If optimum conditions of time, temperature, pressure and surface cleanliness are achieved, diffusion of material across the interface will occur, yielding interfacial mechanical properties identical to those of the bulk material. The use of insufficient bonding conditions may result in void formation, precipitation of undesired phases or lack of grain growth across the interface. The consequence will be an interface that is less than fully bonded, which will result in severe degradation of the mechanical properties. Applications of diffusion bonding to nuclear reactor fuel elements, helicopter rotor hubs, jet engine turbine blades, etc., thus make the ability to characterize the strength of these interfaces highly desirable

Evidence of widespread selection on standing variation in Europe at height-associated SNPs.

Strong signatures of positive selection at newly arising genetic variants are well documented in humans(1-8), but this form of selection may not be widespread in recent human evolution(9). Because many human traits are highly polygenic and partly determined by common, ancient genetic variation, an alternative model for rapid genetic adaptation has been proposed: weak selection acting on many pre-existing (standing) genetic variants, or polygenic adaptation(10-12). By studying height, a classic polygenic trait, we demonstrate the first human signature of widespread selection on standing variation. We show that frequencies of alleles associated with increased height, both at known loci and genome wide, are systematically elevated in Northern Europeans compared with Southern Europeans (P < 4.3 × 10(-4)). This pattern mirrors intra-European height differences and is not confounded by ancestry or other ascertainment biases. The systematic frequency differences are consistent with the presence of widespread weak selection (selection coefficients ∼10(-3)-10(-5) per allele) rather than genetic drift alone (P < 10(-15))

Exploring ligand stability in protein crystal structures using binding pose metadynamics

Identification of correct protein-ligand binding poses is important in structure-based drug design and crucial for the evaluation of protein-ligand binding affinity. Protein-ligand coordinates are commonly obtained from crystallography experiments that provide a static model of an ensemble of conformations. Binding pose metadynamics (BPMD) is an enhanced sampling method that allows for an efficient assessment of ligand stability in solution. Ligand poses that are unstable under the bias of the metadynamics simulation are expected to be infrequently occupied in the energy landscape, thus making minimal contributions to the binding affinity. Here, the robustness of the method is studied using crystal structures with ligands known to be incorrectly modeled, as well as 63 structurally diverse crystal structures with ligand fit to electron density from the Twilight database. Results show that BPMD can successfully differentiate compounds whose binding pose is not supported by the electron density from those with well-defined electron density