Adaptive Monotone Shrinkage for Regression

We develop an adaptive monotone shrinkage estimator for regression models with the following characteristics: i) dense coefficients with small but important effects; ii) a priori ordering that indicates the probable predictive importance of the features. We capture both properties with an empirical Bayes estimator that shrinks coefficients monotonically with respect to their anticipated importance. This estimator can be rapidly computed using a version of Pool-Adjacent-Violators algorithm. We show that the proposed monotone shrinkage approach is competitive with the class of all Bayesian estimators that share the prior information. We further observe that the estimator also minimizes Stein's unbiased risk estimate. Along with our key result that the estimator mimics the oracle Bayes rule under an order assumption, we also prove that the estimator is robust. Even without the order assumption, our estimator mimics the best performance of a large family of estimators that includes the least squares estimator, constant-$\lambda$ ridge estimator, James-Stein estimator, etc. All the theoretical results are non-asymptotic. Simulation results and data analysis from a model for text processing are provided to support the theory.Comment: Appearing in Uncertainty in Artificial Intelligence (UAI) 201

Gray-matter volume, midbrain dopamine D2/D3 receptors and drug craving in methamphetamine users.

Dysfunction of the mesocorticolimbic system has a critical role in clinical features of addiction. Despite evidence suggesting that midbrain dopamine receptors influence amphetamine-induced dopamine release and that dopamine is involved in methamphetamine-induced neurotoxicity, associations between dopamine receptors and gray-matter volume have been unexplored in methamphetamine users. Here we used magnetic resonance imaging and [(18)F]fallypride positron emission tomography, respectively, to measure gray-matter volume (in 58 methamphetamine users) and dopamine D2/D3 receptor availability (binding potential relative to nondisplaceable uptake of the radiotracer, BPnd) (in 31 methamphetamine users and 37 control participants). Relationships between these measures and self-reported drug craving were examined. Although no difference in midbrain D2/D3 BPnd was detected between methamphetamine and control groups, midbrain D2/D3 BPnd was positively correlated with gray-matter volume in the striatum, prefrontal cortex, insula, hippocampus and temporal cortex in methamphetamine users, but not in control participants (group-by-midbrain D2/D3 BPnd interaction, P<0.05 corrected for multiple comparisons). Craving for methamphetamine was negatively associated with gray-matter volume in the insula, prefrontal cortex, amygdala, temporal cortex, occipital cortex, cerebellum and thalamus (P<0.05 corrected for multiple comparisons). A relationship between midbrain D2/D3 BPnd and methamphetamine craving was not detected. Lower midbrain D2/D3 BPnd may increase vulnerability to deficits in gray-matter volume in mesocorticolimbic circuitry in methamphetamine users, possibly reflecting greater dopamine-induced toxicity. Identifying factors that influence prefrontal and limbic volume, such as midbrain BPnd, may be important for understanding the basis of drug craving, a key factor in the maintenance of substance-use disorders

Trunk motion visual feedback during walking improves dynamic balance in older adults: Assessor blinded randomized controlled trial.

BACKGROUND: Virtual reality and augmented feedback have become more prevalent as training methods to improve balance. Few reports exist on the benefits of providing trunk motion visual feedback (VFB) during treadmill walking, and most of those reports only describe within session changes. RESEARCH QUESTION: To determine whether trunk motion VFB treadmill walking would improve over-ground balance for older adults with self-reported balance problems. METHODS: 40 adults (75.8 years (SD 6.5)) with self-reported balance difficulties or a history of falling were randomized to a control or experimental group. Everyone walked on a treadmill at a comfortable speed 3×/week for 4 weeks in 2 min bouts separated by a seated rest. The control group was instructed to look at a stationary bulls-eye target while the experimental group also saw a moving cursor superimposed on the stationary bulls-eye that represented VFB of their walking trunk motion. The experimental group was instructed to keep the cursor in the center of the bulls-eye. Somatosensory (monofilaments and joint position testing) and vestibular function (canal specific clinical head impulses) was evaluated prior to intervention. Balance and mobility were tested before and after the intervention using Berg Balance Test, BESTest, mini-BESTest, and Six Minute Walk. RESULTS: There were no significant differences between groups before the intervention. The experimental group significantly improved on the BESTest (p = 0.031) and the mini-BEST (p = 0.019). The control group did not improve significantly on any measure. Individuals with more profound sensory impairments had a larger improvement on dynamic balance subtests of the BESTest. SIGNIFICANCE: Older adults with self-reported balance problems improve their dynamic balance after training using trunk motion VFB treadmill walking. Individuals with worse sensory function may benefit more from trunk motion VFB during walking than individuals with intact sensory function

CARDS: A Collaborative Community Model for Faculty Development or an Institutional Case Study of Writing Program Administration

The structure of writing programs evolves to account for the transformation of composition studies. Online and dual credit programs necessitate a need to adjust prior practices initially geared towards face-to-face pedagogy; however, several challenges surface in online and dual credit writing programs. The most prevalent is that these online courses are primarily staffed by non-tenured faculty, including adjuncts who do not have a physical presence on campus. The faculty dynamic presents many challenges when attempting to garner participation in collaborations. In recent years, the Writing Program Administrator (WPA) at a regional public university noticed a need to improve faculty morale, satisfaction, and participation, especially with the emergence of online programs. Through a national survey and selective interviews of current faculty at the university, we determined that the answer lies in the structure of the program. The Writing Program Administrator has several models to choose from, but we will argue that the collaborative community model is most conducive to addressing and enhancing faculty morale, satisfaction, and participation in first-year writing programs

Striatal dopamine D1-type receptor availability: no difference from control but association with cortical thickness in methamphetamine users.

Chronic methamphetamine use poses potentially devastating consequences for directly affected individuals and for society. Lower dopamine D2-type receptor availability has been observed in striata of methamphetamine users as compared with controls, but an analogous comparison of D1-type receptors has been conducted only on post-mortem material, with no differences in methamphetamine users from controls in the caudate nucleus and putamen and higher D1-receptor density in the nucleus accumbens. Released from neurons when methamphetamine is self-administered, dopamine binds to both D1- and D2-type receptors in the striatum, with downstream effects on cortical activity. Thus, both receptor subtypes may contribute to methamphetamine-induced alterations in cortical morphology and behavior. In this study, 21 methamphetamine-dependent subjects and 23 healthy controls participated in positron emission tomography and structural magnetic resonance imaging for assessment of striatal D1- and D2-type receptor availability and cortical gray-matter thickness, respectively. Although D2-type receptor availability (BPnd) was lower in the methamphetamine group, as shown previously, the groups did not differ in D1-type BPnd. In the methamphetamine group, mean cortical gray-matter thickness was negatively associated with cumulative methamphetamine use and craving for the drug. Striatal D1-type but not D2-type BPnd was negatively associated with global mean cortical gray-matter thickness in the methamphetamine group, but no association was found between gray-matter thickness and BPnd for either dopamine receptor subtype in the control group. These results suggest a role of striatal D1-type receptors in cortical adaptation to chronic methamphetamine use

Cavity-induced slow gain recovery in pump-probe experiments of quantum cascade lasers

We show that the Fabry-P´erot cavity dynamics of quantum cascade lasers (QCLs) play an important role in the gain recovery observed in a pump-probe experiment. Due to the residual pump power in the cavity after the pump pulse is reflected from the facet, the probed gain recovers at a slower rate

Performance analysis of a parallel, multi-node pipeline for DNA sequencing

Post-sequencing DNA analysis typically consists of read mapping followed by variant calling and is very time-consuming, even on a multi-core machine. Recently, we proposed Halvade, a parallel, multi-node implementation of a DNA sequencing pipeline according to the GATK Best Practices recommendations. The MapReduce programming model is used to distribute the workload among different workers. In this paper, we study the impact of different hardware configurations on the performance of Halvade. Benchmarks indicate that especially the lack of good multithreading capabilities in the existing tools (BWA, SAMtools, Picard, GATK) cause suboptimal scaling behavior. We demonstrate that it is possible to circumvent this bottleneck by using multiprocessing on high-memory machines rather than using multithreading. Using a 15-node cluster with 360 CPU cores in total, this results in a runtime of 1 h 31 min. Compared to a single-threaded runtime of similar to 12 days, this corresponds to an overall parallel efficiency of 53%