Alien Registration- Mailman, Hanley A. (Pittsfield, Somerset County)

https://digitalmaine.com/alien_docs/6603/thumbnail.jp

First-principles investigation of spin polarized conductance in atomic carbon wire

We analyze spin-dependent energetics and conductance for one dimensional (1D) atomic carbon wires consisting of terminal magnetic (Co) and interior nonmagnetic (C) atoms sandwiched between gold electrodes, obtained employing first-principles gradient corrected density functional theory and Landauer's formalism for conductance. Wires containing an even number of interior carbon atoms are found to be acetylenic with sigma-pi bonding patterns, while cumulene structures are seen in wires containing odd number of interior carbon atoms, as a result of strong pi-conjugation. Ground states of carbon wires containing up to 13 C atoms are found to have anti-parallel spin configurations of the two terminal Co atoms, while the 14 C wire has a parallel Co spin configuration in the ground state. The stability of the anti-ferromagnetic state in the wires is ascribed to a super-exchange effect. For the cumulenic wires this effect is constant for all wire lengths. For the acetylenic wires, the super-exchange effect diminishes as the wire length increases, going to zero for the atomic wire containing 14 carbon atoms. Conductance calculations at the zero bias limit show spin-valve behavior, with the parallel Co spin configuration state giving higher conductance than the corresponding anti-parallel state, and a non-monotonic variation of conductance with the length of the wires for both spin configurations.Comment: revtex, 6 pages, 5 figure

Appetite, energy intake, and PYY3-36 responses to energy-matched continuous exercise and submaximal high-intensity exercise.

High-intensity intermittent exercise induces physiological adaptations similar to energy-matched continuous exercise, but the comparative appetite and energy balance responses are unknown. Twelve healthy males (mean ± SD: age, 22 ± 3 years; body mass index, 23.7 ± 3.0 kg·m(-2); maximum oxygen uptake, 52.4 ± 7.1 mL·kg(-1)·min(-1)) completed three 8 h trials (control, steady-state exercise (SSE), high-intensity intermittent exercise (HIIE)) separated by 1 week. Trials commenced upon completion of a standardized breakfast. Exercise was performed from hour 2 to hour 3. In SSE, 60 min of cycling at 59.5% ± 1.6% of maximum oxygen uptake was performed. In HIIE, ten 4-min cycling intervals were completed at 85.8% ± 4.0% of maximum oxygen uptake, with a 2-min rest between each interval. A standardized lunch and an ad libitum afternoon meal were provided at hours 3.75 and 7, respectively. Appetite ratings and peptide YY3-36 concentrations were measured throughout each trial. Appetite was acutely suppressed during exercise, but more so during HIIE (p < 0.05). Peptide YY3-36 concentrations increased significantly upon cessation of exercise in SSE (p = 0.002), but were highest in the hours after exercise in HIIE (p = 0.05). Exercise energy expenditure was not different between HIIE and SSE (p = 0.649), but perceived exertion was higher in HIIE (p < 0.0005). Ad libitum energy intake did not differ between trials (p = 0.833). Therefore, relative energy intake (energy intake minus the net energy expenditure of exercise) was lower in the SSE and HIIE trials than in the control trial (control, 4759 ± 1268 kJ; SSE, 2362 ± 1224 kJ; HIIE, 2523 ± 1402 kJ; p < 0.0005). An acute bout of energy-matched continuous exercise and HIIE were equally effective at inducing an energy deficit without stimulating compensatory increases in appetite

Constraints and vibrations in static packings of ellipsoidal particles

We numerically investigate the mechanical properties of static packings of ellipsoidal particles in 2D and 3D over a range of aspect ratio and compression $\Delta \phi$. While amorphous packings of spherical particles at jamming onset ($\Delta \phi=0$) are isostatic and possess the minimum contact number $z_{\rm iso}$ required for them to be collectively jammed, amorphous packings of ellipsoidal particles generally possess fewer contacts than expected for collective jamming ($z < z_{\rm iso}$) from naive counting arguments, which assume that all contacts give rise to linearly independent constraints on interparticle separations. To understand this behavior, we decompose the dynamical matrix $M=H-S$ for static packings of ellipsoidal particles into two important components: the stiffness $H$ and stress $S$ matrices. We find that the stiffness matrix possesses $N(z_{\rm iso} - z)$ eigenmodes ${\hat e}_0$ with zero eigenvalues even at finite compression, where $N$ is the number of particles. In addition, these modes ${\hat e}_0$ are nearly eigenvectors of the dynamical matrix with eigenvalues that scale as $\Delta \phi$, and thus finite compression stabilizes packings of ellipsoidal particles. At jamming onset, the harmonic response of static packings of ellipsoidal particles vanishes, and the total potential energy scales as $\delta^4$ for perturbations by amplitude $\delta$ along these `quartic' modes, ${\hat e}_0$. These findings illustrate the significant differences between static packings of spherical and ellipsoidal particles.Comment: 18 pages, 21 figure

DistiLD Database: diseases and traits in linkage disequilibrium blocks

Genome-wide association studies (GWAS) have identified thousands of single nucleotide polymorphisms (SNPs) associated with the risk of hundreds of diseases. However, there is currently no database that enables non-specialists to answer the following simple questions: which SNPs associated with diseases are in linkage disequilibrium (LD) with a gene of interest? Which chromosomal regions have been associated with a given disease, and which are the potentially causal genes in each region? To answer these questions, we use data from the HapMap Project to partition each chromosome into so-called LD blocks, so that SNPs in LD with each other are preferentially in the same block, whereas SNPs not in LD are in different blocks. By projecting SNPs and genes onto LD blocks, the DistiLD database aims to increase usage of existing GWAS results by making it easy to query and visualize disease-associated SNPs and genes in their chromosomal context. The database is available at http://distild.jensenlab.org/

Quantifying single nucleotide variant detection sensitivity in exome sequencing

BACKGROUND: The targeted capture and sequencing of genomic regions has rapidly demonstrated its utility in genetic studies. Inherent in this technology is considerable heterogeneity of target coverage and this is expected to systematically impact our sensitivity to detect genuine polymorphisms. To fully interpret the polymorphisms identified in a genetic study it is often essential to both detect polymorphisms and to understand where and with what probability real polymorphisms may have been missed. RESULTS: Using down-sampling of 30 deeply sequenced exomes and a set of gold-standard single nucleotide variant (SNV) genotype calls for each sample, we developed an empirical model relating the read depth at a polymorphic site to the probability of calling the correct genotype at that site. We find that measured sensitivity in SNV detection is substantially worse than that predicted from the naive expectation of sampling from a binomial. This calibrated model allows us to produce single nucleotide resolution SNV sensitivity estimates which can be merged to give summary sensitivity measures for any arbitrary partition of the target sequences (nucleotide, exon, gene, pathway, exome). These metrics are directly comparable between platforms and can be combined between samples to give “power estimates” for an entire study. We estimate a local read depth of 13X is required to detect the alleles and genotype of a heterozygous SNV 95% of the time, but only 3X for a homozygous SNV. At a mean on-target read depth of 20X, commonly used for rare disease exome sequencing studies, we predict 5–15% of heterozygous and 1–4% of homozygous SNVs in the targeted regions will be missed. CONCLUSIONS: Non-reference alleles in the heterozygote state have a high chance of being missed when commonly applied read coverage thresholds are used despite the widely held assumption that there is good polymorphism detection at these coverage levels. Such alleles are likely to be of functional importance in population based studies of rare diseases, somatic mutations in cancer and explaining the “missing heritability” of quantitative traits

PolymiRTS Database 2.0: linking polymorphisms in microRNA target sites with human diseases and complex traits

The polymorphism in microRNA target site (PolymiRTS) database aims to identify single-nucleotide polymorphisms (SNPs) that affect miRNA targeting in human and mouse. These polymorphisms can disrupt the regulation of gene expression by miRNAs and are candidate genetic variants responsible for transcriptional and phenotypic variation. The database is therefore organized to provide links between SNPs in miRNA target sites, cis-acting expression quantitative trait loci (eQTLs), and the results of genome-wide association studies (GWAS) of human diseases. Here, we describe new features that have been integrated in the PolymiRTS database, including: (i) polymiRTSs in genes associated with human diseases and traits in GWAS, (ii) polymorphisms in target sites that have been supported by a variety of experimental methods and (iii) polymorphisms in miRNA seed regions. A large number of newly identified microRNAs and SNPs, recently published mouse phenotypes, and human and mouse eQTLs have also been integrated into the database. The PolymiRTS database is available at http://compbio.uthsc.edu/miRSNP/

Differential involvement of striato- and cerebello-thalamo-cortical pathways in tremor- and akinetic/rigid-predominant Parkinson's disease

Parkinson's disease (PD) presents clinically with varying degrees of resting tremor, rigidity, and bradykinesia. For decades, striatal-thalamo-cortical (STC) dysfunction has been implied in bradykinesia and rigidity, but does not explain resting tremor in PD. To understand the roles of cerebello-thalamo-cortical (CTC) and STC circuits in the pathophysiology of the heterogeneous clinical presentation of PD, we collected functional magnetic resonance imaging (fMRI) data from 17 right-handed PD patients [nine tremor predominant (PDT) and eight akinetic-rigidity predominant (PDAR)] and 14 right-handed Controls while they performed internally-guided (IG) sequential finger tapping tasks. The percentage of voxels activated in regions constituting the STC and CTC [divided as cerebellar hemisphere-thalamo-cortical (CHTC) and vermis-thalamo-cortical (CVTC)] circuits was calculated. Multivariate analysis of variance compared the activation patterns of these circuits between study groups. Compared to Controls, both PDAR and PDT subjects displayed an overall increase in the percentage of voxels activated in both STC and CTC circuits. These increases reached statistical significance in contralateral STC and CTC circuits for PDT subjects, and in contralateral CTC pathways for PDAR subjects. Comparison of PDAR and PDT subjects revealed significant differences in ipsilateral STC (p=0.005) and CTC (p=0.043 for CHTC and p=0.003 for CVTC) circuits. These data support the differential involvement of STC and CTC circuits in PD subtypes, and help explain the heterogeneous presentation of PD symptoms. These findings underscore the importance of integrating CTC circuits in understanding PD and other disorders of the basal ganglia