Fine Details of the Nodal Electronic Excitations in Bi2_2Sr2_2CaCu2_2O8+δ_{8+\delta}

Very high energy resolution photoemission experiments on high quality samples of optimally doped Bi$_2$Sr$_2$CaCu$_2$O$_{8+\delta}$ show new features in the low-energy electronic excitations. A marked change in the binding energy and temperature dependence of the near-nodal scattering rates is observed near the superconducting transition temperature, $T_C$. The temperature slope of the scattering rate measured at low energy shows a discontinuity at ~$T_C$. In the superconducting state, coherent excitations are found with the scattering rates showing a cubic dependence on frequency and temperature. The superconducting gap has a d-wave magnitude with negligible contribution from higher harmonics. Further, the bi-layer splitting has been found to be finite at the nodal point.Comment: 5 pages, 4 figure

On the Reconstructed Fermi Surface in the Underdoped Cuprates

The Fermi surface topologies of underdoped samples the high-Tc superconductor Bi2212 have been measured with angle resolved photoemission. By examining thermally excited states above the Fermi level, we show that the Fermi surfaces in the pseudogap phase of underdoped samples are actually composed of fully enclosed hole pockets. The spectral weight of these pockets is vanishingly small at the anti-ferromagnetic zone boundary, which creates the illusion of Fermi "arcs" in standard photoemission measurements. The area of the pockets as measured in this study is consistent with the doping level, and hence carrier density, of the samples measured. Furthermore, the shape and area of the pockets is well reproduced by a phenomenological model of the pseudogap phase as a spin liquid.Comment: 4 pages, 4 figures. Submitted to Physics Review Letter

Prosodic phrasing, pitch range, and word order variation in Murrinhpatha

Like many Indigenous Australian languages, Murrinhpatha has flexible word order with no apparent configurational syntax. We analyzed an experimental corpus of Murrinhpatha utterances for associations between different thematic role orders, intonational phrasing patterns and pitch downtrends. We found that initial constituents (Agents or Patients) tend to carry the highest pitch targets (HiF0), followed by patterns of downstep and declination. Sentence-final verbs always have lower Hif0 values than either initial or medial Agents or Patients. Thematic role order does not influence intonational patterns, with the results suggesting that Murrinhpatha has positional prosody, although final nominals can disrupt global pitch downtrends regardless of thematic role

Automating biomedical data science through tree-based pipeline optimization

Over the past decade, data science and machine learning has grown from a mysterious art form to a staple tool across a variety of fields in academia, business, and government. In this paper, we introduce the concept of tree-based pipeline optimization for automating one of the most tedious parts of machine learning---pipeline design. We implement a Tree-based Pipeline Optimization Tool (TPOT) and demonstrate its effectiveness on a series of simulated and real-world genetic data sets. In particular, we show that TPOT can build machine learning pipelines that achieve competitive classification accuracy and discover novel pipeline operators---such as synthetic feature constructors---that significantly improve classification accuracy on these data sets. We also highlight the current challenges to pipeline optimization, such as the tendency to produce pipelines that overfit the data, and suggest future research paths to overcome these challenges. As such, this work represents an early step toward fully automating machine learning pipeline design.Comment: 16 pages, 5 figures, to appear in EvoBIO 2016 proceeding

Predictors of 1-year survival in South African transcatheter aortic valve implant candidates

Background. Transcatheter aortic valve implantation (TAVI) has undergone rapid expansion internationally over the past 15 years. In view of resource constraints in developing countries, a major challenge in applying this technology lies in identifying patients most likely to benefit. The development of a risk prediction model for TAVI has proved elusive, with a reported area under the curve (AUC) of 0.6 - 0.65. The available models were developed in a First-World setting and may not be applicable to South Africa (SA).Objectives. To evaluate novel indicators and to develop a TAVI risk prediction model unique to the SA context. The current work represents the important initial steps of derivation cohort risk model development and internal validation.Methods. Seven-year experience with 244 successive TAVI implants in three centres in Western Cape Province, SA, was used to derive risk parameters. All outcomes are reported in accordance with the Valve Academic Research Consortium definitions. Multiple preprocedural variables were assessed for their impact on 1-year survival using univariate and multivariate models.Results. Factors found not to correlate with 1-year survival included age, renal function and aortic valve gradients. The commonly used surgical risk prediction models (Society of Thoracic Surgeons score and EuroSCORE) showed no correlation with outcomes. Factors found to correlate best with 1-year survival on multivariate analysis were preprocedural body mass index (BMI) (favouring higher BMI), preprocedural left ventricular end-diastolic dimension (LVED) and ejection fraction (EF) (favouring smaller LVED and higher EF), absence of atrial fibrillation, and three novel parameters: independent living, ability to drive a car, and independent food acquisition/cooking. Discriminant analysis of these factors yielded an AUC of 0.8 (95% confidence interval 0.7 - 0.9) to predict 1-year survival, with resubstitution sensitivities and specificities of 72% and 71%, respectively.Conclusions. Apart from existing predictors, we identified three novel risk predictors (independent living, ability to drive a car, and independent food acquisition/cooking) for 1-year survival in TAVI candidates. These novel parameters performed well in this early evaluation, with an AUC for predicting 1-year survival higher than the AUCs for many of the internationally derived parameters. The parameters are inexpensive and easy to obtain at the initial patient visit. If validated prospectively in external cohorts, they may be applicable to other resource-constrained environments.

What’s so bad about scientism?

In their attempt to defend philosophy from accusations of uselessness made by prominent scientists, such as Stephen Hawking, some philosophers respond with the charge of ‘scientism.’ This charge makes endorsing a scientistic stance, a mistake by definition. For this reason, it begs the question against these critics of philosophy, or anyone who is inclined to endorse a scientistic stance, and turns the scientism debate into a verbal dispute. In this paper, I propose a different definition of scientism, and thus a new way of looking at the scientism debate. Those philosophers who seek to defend philosophy against accusations of uselessness would do philosophy a much better service, I submit, if they were to engage with the definition of scientism put forth in this paper, rather than simply make it analytic that scientism is a mistake

ALFRED: an allele frequency resource for research and teaching

ALFRED (http://alfred.med.yale.edu) is a free, web accessible, curated compilation of allele frequency data on DNA sequence polymorphisms in anthropologically defined human populations. Currently, ALFRED has allele frequency tables on over 663 400 polymorphic sites; 170 of them have frequency tables for more than 100 different population samples. In ALFRED, a population may have multiple samples with each ‘sample’ consisting of many individuals on which an allele frequency is based. There are 3566 population samples from 710 different populations with allele frequency tables on at least one polymorphism. Fifty of those population samples have allele frequency data for over 650 000 polymorphisms. Records also have active links to relevant resources (dbSNP, PharmGKB, OMIM, Ethnologue, etc.). The flexible search options and data display and download capabilities available through the web interface allow easy access to the large quantity of high-quality data in ALFRED

Electronic Structure of the Cuprate Superconducting and Pseudogap Phases from Spectroscopic Imaging STM

We survey the use of spectroscopic imaging STM to probe the electronic structure of underdoped cuprates. Two distinct classes of electronic states are observed in both the d-wave superconducting (dSC) and the pseudogap (PG) phases. The first class consists of the dispersive Bogoliubov quasiparticle excitations of a homogeneous d-wave superconductor, existing below a lower energy scale E=Delta0. We find that the Bogoliubov quasiparticle interference signatures of delocalized Cooper pairing are restricted to a k-space arc which terminates near the lines connecting k=\pm(pi/a0,0) to k=\pm(pi/a0). This arc shrinks continuously with decreasing hole density such that Luttinger's theorem could be satisfied if it represents the front side of a hole-pocket which is bounded behind by the lines between k=\pm(pi/a0,0) and k=\pm(0,pi/a0). In both phases the only broken symmetries detected for the |E|<Delta0 states are those of a d-wave superconductor. The second class of states occurs proximate to the pseudogap energy scale E=Delta1. Here the non-dispersive electronic structure breaks the expected 90o-rotational symmetry of electronic structure within each unit cell, at least down to 180o-rotational symmetry. This Q=0 electronic symmetry breaking was first detected as an electronic inequivalence at the two oxygen sites within each unit cell by using a measure of nematic (C2) symmetry. Incommensurate non-dispersive conductance modulations, locally breaking both rotational and translational symmetries, coexist with this intra-unit-cell electronic symmetry breaking at E=Delta1. Their characteristic wavevector Q is determined by the k-space points where Bogoliubov quasiparticle interference terminates and therefore changes continuously with doping. The distinct broken electronic symmetry states (Q=0 and finite Q) coexisting at E~Delta1 are found to be indistinguishable in the dSC and PG phases.Comment: 32 pages with 10 figure