Spin-dependent Bohm trajectories for hydrogen eigenstates

The Bohm trajectories for several hydrogen atom eigenstates are determined, taking into account the additional momentum term that arises from the Pauli current. Unlike the original Bohmian result, the spin-dependent term yields nonstationary trajectories. The relationship between the trajectories and the standard visualizations of orbitals is discussed. The trajectories for a model problem that simulates a 1s-2p transition in hydrogen are also examined.Comment: 11 pages, 3 figure

The Role of Friction in Compaction and Segregation of Granular Materials

We investigate the role of friction in compaction and segregation of granular materials by combining Edwards' thermodynamic hypothesis with a simple mechanical model and mean-field based geometrical calculations. Systems of single species with large friction coefficients are found to compact less. Binary mixtures of grains differing in frictional properties are found to segregate at high compactivities, in contrary to granular mixtures differing in size, which segregate at low compactivities. A phase diagram for segregation vs. friction coefficients of the two species is generated. Finally, the characteristics of segregation are related directly to the volume fraction without the explicit use of the yet unclear notion of compactivity.Comment: 9 pages, 6 figures, submitted to Phys. Rev.

Chip-Firing and Rotor-Routing on Directed Graphs

We give a rigorous and self-contained survey of the abelian sandpile model and rotor-router model on finite directed graphs, highlighting the connections between them. We present several intriguing open problems.Comment: 34 pages, 11 figures. v2 has additional references, v3 corrects figure 9, v4 corrects several typo

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

Regulation of 5-HT Receptors and the Hypothalamic-Pituitary-Adrenal Axis

Disturbances in the serotonin (5-HT) system is the neurobiological abnormality most consistently associated with suicide. Hyperactivity of the hypothalmic-pituitary-adrenal (HPA) axis is also described in suicide victims. The HPA axis is the classical neuroendocrine system that responds to stress and whose final product, corticosteroids, targets components of the limbic system, particularly the hippocampus. We will review resulsts from animal studies that point to the possibility that many of the 5-HT receptor changes observed in suicide brains may be a result of, or may be worsened by, the HPA overactivity that may be present in some suicide victims. The results of these studies can be summarized as follows: (1) chronic unpredictable stress produces high corticosteroid levels in rats; (2) chronic stress also results in changes in specific 5-HT receptors (increases in cortical 5-HT2A and decreases in hipocampal 5-HT1A and 5-HT1B); (3) chronic antidepressant administration prevents many of the 5-HT receptor changes observed after stress; and (4) chronic antidepressant administration reverses the overactivity of the HPA axis. If indeed 5-HT receptors have a partial role in controlling affective states, then their modulation by corticosteroids provides a potential mechanism by which these hormones may regulate mood. These data may also provide a biological understanding of how stressful events may increase the risk for suicide in vulnerable individuals and may help us elucidate the neurobiological underpinnings of treatment resistance.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73437/1/j.1749-6632.1997.tb52357.x.pd

Driver Fusions and Their Implications in the Development and Treatment of Human Cancers.

Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated fusions in 9,624 tumors across 33 cancer types using multiple fusion calling tools. We identified a total of 25,664 fusions, with a 63% validation rate. Integration of gene expression, copy number, and fusion annotation data revealed that fusions involving oncogenes tend to exhibit increased expression, whereas fusions involving tumor suppressors have the opposite effect. For fusions involving kinases, we found 1,275 with an intact kinase domain, the proportion of which varied significantly across cancer types. Our study suggests that fusions drive the development of 16.5% of cancer cases and function as the sole driver in more than 1% of them. Finally, we identified druggable fusions involving genes such as TMPRSS2, RET, FGFR3, ALK, and ESR1 in 6.0% of cases, and we predicted immunogenic peptides, suggesting that fusions may provide leads for targeted drug and immune therapy

TESS hunt for young and maturing exoplanets (THYME). IV. Three small planets orbiting a 120 Myr old star in the pisces-eridanus stream

Young exoplanets can offer insight into the evolution of planetary atmospheres, compositions, and architectures. We present the discovery of the young planetary system TOI 451 (TIC 257605131, Gaia DR2 4844691297067063424). TOI 451 is a member of the 120 Myr old Pisces-Eridanus stream (Psc-Eri). We confirm membership in the stream with its kinematics, its lithium abundance, and the rotation and UV excesses of both TOI 451 and its wide-binary companion, TOI 451 B (itself likely anM-dwarf binary).We identified three candidate planets transiting in the Transiting Exoplanet Survey Satellite data and followed up the signals with photometry from Spitzer and ground-based telescopes. The system comprises three validated planets at periods of 1.9, 9.2, and 16 days, with radii of 1.9, 3.1, and 4.1 R⊗, respectively. The host star is near-solar mass with V=11.0 and H = 9.3 and displays an infrared excess indicative of a debris disk. The planets offer excellent prospects for transmission spectroscopy with the Hubble Space Telescope and the James Webb Space Telescope, providing the opportunity to study planetary atmospheres that may still be in the process of evolving