Non-invasive MRI quantification of cerebrospinal fluid dynamics in amyotrophic lateral sclerosis patients.

BACKGROUND: Developing novel therapeutic agents to treat amyotrophic lateral sclerosis (ALS) has been difficult due to multifactorial pathophysiologic processes at work. Intrathecal drug administration shows promise due to close proximity of cerebrospinal fluid (CSF) to affected tissues. Development of effective intrathecal pharmaceuticals will rely on accurate models of how drugs are dispersed in the CSF. Therefore, a method to quantify these dynamics and a characterization of differences across disease states is needed. METHODS: Complete intrathecal 3D CSF geometry and CSF flow velocities at six axial locations in the spinal canal were collected by T2-weighted and phase-contrast MRI, respectively. Scans were completed for eight people with ALS and ten healthy controls. Manual segmentation of the spinal subarachnoid space was performed and coupled with an interpolated model of CSF flow within the spinal canal. Geometric and hydrodynamic parameters were then generated at 1 mm slice intervals along the entire spine. Temporal analysis of the waveform spectral content and feature points was also completed. RESULTS: Comparison of ALS and control groups revealed a reduction in CSF flow magnitude and increased flow propagation velocities in the ALS cohort. Other differences in spectral harmonic content and geometric comparisons may support an overall decrease in intrathecal compliance in the ALS group. Notably, there was a high degree of variability between cases, with one ALS patient displaying nearly zero CSF flow along the entire spinal canal. CONCLUSION: While our sample size limits statistical confidence about the differences observed in this study, it was possible to measure and quantify inter-individual and cohort variability in a non-invasive manner. Our study also shows the potential for MRI based measurements of CSF geometry and flow to provide information about the hydrodynamic environment of the spinal subarachnoid space. These dynamics may be studied further to understand the behavior of CSF solute transport in healthy and diseased states

Whole Genome Shotgun Sequencing Detects Greater Lichen Fungal Diversity Than Amplicon-Based Methods in Environmental Samples

In this study we demonstrate the utility of whole genome shotgun (WGS) metagenomics in study organisms with small genomes to improve upon amplicon-based estimates of biodiversity and microbial diversity in environmental samples for the purpose of understanding ecological and evolutionary processes. We generated a database of full-length and near-full-length ribosomal DNA sequence complexes from 273 lichenized fungal species and used this database to facilitate fungal species identification in the southern Appalachian Mountains using low coverage WGS at higher resolution and without the biases of amplicon-based approaches. Using this new database and methods herein developed, we detected between 2.8 and 11 times as many species from lichen fungal propagules by aligning reads from WGS-sequenced environmental samples compared to a traditional amplicon-based approach. We then conducted complete taxonomic diversity inventories of the lichens in each one-hectare plot to assess overlap between standing taxonomic diversity and diversity detected based on propagules present in environmental samples (i.e., the &ldquo;potential&rdquo; of diversity). From the environmental samples, we detected 94 species not observed in organism-level sampling in these ecosystems with high confidence using both WGS and amplicon-based methods. This study highlights the utility of WGS sequence-based approaches in detecting hidden species diversity and demonstrates that amplicon-based methods likely miss important components of fungal diversity. We suggest that the adoption of this method will not only improve understanding of biotic constraints on the distributions of biodiversity but will also help to inform important environmental policy.</p

Azimuthal Angle Correlations for Rapidity Separated Hadron Pairs in d+Au Collisions at sqrt(s_NN) = 200 GeV

We report on two-particle azimuthal angle correlations between charged hadrons at forward/backward (deuteron/gold going direction) rapidity and charged hadrons at mid-rapidity in deuteron-gold (d+Au) and proton-proton (p+p) collisions at sqrt(s_NN) = 200 GeV. Jet structures are observed in the correlations which we quantify in terms of the conditional yield and angular width of away side partners. The kinematic region studied here samples partons in the gold nucleus carrying nucleon momentum fraction x~0.1 to x~0.01. Within this range, we find no x dependence of the jet structure in d+Au collisions.Comment: 330 authors, 6 pages text, 4 figures, no tables. Submitted to Phys. Rev. Lett. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Centrality dependence of charged hadron production in deuteron+gold and nucleon+gold collisions at sqrt(s_NN)=200 GeV

We present transverse momentum (p_T) spectra of charged hadrons measured in deuteron-gold and nucleon-gold collisions at \sqrts = 200 GeV for four centrality classes. Nucleon-gold collisions were selected by tagging events in which a spectator nucleon was observed in one of two forward rapidity detectors. The spectra and yields were investigated as a function of the number of binary nucleon-nucleon collisions, \nu, suffered by deuteron nucleons. A comparison of charged particle yields to those in p+p collisions show that the yield per nucleon-nucleon collision saturates with \nu for high momentum particles. We also present the charged hadron to neutral pion ratios as a function of p_T.Comment: 330 authors, 15 pages text, 16 figures, 3 tables. Submitted to Phys. Rev. Lett. v2 has minor changes to reflect revisions during review process. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

System Size and Energy Dependence of Jet-Induced Hadron Pair Correlation Shapes in Cu+Cu and Au+Au Collisions at sqrt(s_NN) = 200 and 62.4 GeV

We present azimuthal angle correlations of intermediate transverse momentum (1-4 GeV/c) hadrons from {dijets} in Cu+Cu and Au+Au collisions at sqrt(s_NN) = 62.4 and 200 GeV. The away-side dijet induced azimuthal correlation is broadened, non-Gaussian, and peaked away from \Delta\phi=\pi in central and semi-central collisions in all the systems. The broadening and peak location are found to depend upon the number of participants in the collision, but not on the collision energy or beam nuclei. These results are consistent with sound or shock wave models, but pose challenges to Cherenkov gluon radiation models.Comment: 464 authors from 60 institutions, 6 pages, 3 figures, 2 tables. Submitted to Physical Review Letters. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Nuclear Modification Factors for Hadrons At Forward and Backward Rapidities in Deuteron-Gold Collisions at sqrt(s_NN) = 200 GeV

We report on charged hadron production in deuteron-gold reactions at sqrt(s_NN) = 200 GeV. Our measurements in the deuteron-direction cover 1.4 < eta < 2.2, referred to as forward rapidity, and in the gold-direction -2.0 < eta < -1.4, referred to as backward rapidity, and a transverse momentum range p_T = 0.5-4.0 GeV/c. We compare the relative yields for different deuteron-gold collision centrality classes. We observe a suppression relative to binary collision scaling at forward rapidity, sensitive to low momentum fraction (x) partons in the gold nucleus, and an enhancement at backward rapidity, sensitive to high momentum fraction partons in the gold nucleus.Comment: 330 authors, 6 pages text, 4 figures, REVTeX4. Published in Physical Review Letters. Minor changes over previous version in response to referee and editor comments, plus updating of references. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are publicly available at http://www.phenix.bnl.gov/papers.htm

High-pT pi^zero Production with Respect to the Reaction Plane in Au + Au Collisions at sqrt(s_NN) = 200 GeV

Measurements of the azimuthal anisotropy of high-\pT neutral pion neutral pion production in Au+Au collisions at sqrt(s_NN) = 200 GeV by the PHENIX experiment are presented. The data included in this paper were collected during the 2004 RHIC running period and represent approximately an order of magnitude increase in the number of analyzed events relative to previously published results. Azimuthal angle distributions of pi^0s detected in the PHENIX electromagnetic calorimeters are measured relative to the reaction plane determined event-by-event using the forward and backward beam-beam counters. Amplitudes of the second Fourier component (v_2) of the angular distributions are presented as a function of pi^0 transverse momentum p_T for different bins in collision centrality. Measured reaction plane dependent pi^0 yields are used to determine the azimuthal dependence of the pi^0 suppression as a function of p_T, R_AA (Delta phi,p_T). A jet-quenching motivated geometric analysis is presented that attempts to simultaneously describe the centrality dependence and reaction plane angle dependence of the pi^0 suppression in terms of the path lengths of hypothetical parent partons in the medium. This set of results allows for a detailed examination of the influence of geometry in the collision region, and of the interplay between collective flow and jet-quenching effects along the azimuthal axis.Comment: 344 authors, 35 pages text, RevTeX-4, 24 figures, 8 tables. Submitted to Physical Review

Jet Structure from Dihadron Correlations in d+Au collisions at sqrt(s_NN) = 200 GeV

Dihadron correlations at high transverse momentum in d+Au collisions at sqrt(s_NN) = 200 GeV at midrapidity are measured by the PHENIX experiment at the Relativistic Heavy Ion Collider (RHIC). From these correlations we extract several structural characteristics of jets; the root-mean-squared (RMS) transverse momentum of fragmenting hadrons with respect to the jet sqrt(), the mean sine-squared angle between the scattered partons , and the number of particles produced within the dijet that are associated with a high-p_T particle (dN/dx_E distributions). We observe that the fragmentation characteristics of jets in d+Au collisions are very similar to those in p+p collisions and that there is also little dependence on the centrality of the d+Au collision. This is consistent with the nuclear medium having little influence on the fragmentation process. Furthermore, there is no statistically significant increase in the value of from p+p to d+Au collisions. This constrains the amount of multiple scattering that partons undergo in the cold nuclear medium before and after a hard-collision.Comment: 330 authors, 30 pages text, RevTeX4, 42 figures, 20 tables. Submitted to Physical Review C. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm

Transverse-energy distributions at midrapidity in pp++pp, dd++Au, and Au++Au collisions at sNN=62.4\sqrt{s_{_{NN}}}=62.4--200~GeV and implications for particle-production models

Measurements of the midrapidity transverse energy distribution, d\Et/d\eta, are presented for $p$$+$$p$, $d$$+$Au, and Au$+$Au collisions at $\sqrt{s_{_{NN}}}=200$ GeV and additionally for Au$+$Au collisions at $\sqrt{s_{_{NN}}}=62.4$ and 130 GeV. The d\Et/d\eta distributions are first compared with the number of nucleon participants $N_{\rm part}$, number of binary collisions $N_{\rm coll}$, and number of constituent-quark participants $N_{qp}$ calculated from a Glauber model based on the nuclear geometry. For Au$+$Au, \mean{d\Et/d\eta}/N_{\rm part} increases with $N_{\rm part}$, while \mean{d\Et/d\eta}/N_{qp} is approximately constant for all three energies. This indicates that the two component ansatz, $dE_{T}/d\eta \propto (1-x) N_{\rm part}/2 + x N_{\rm coll}$, which has been used to represent $E_T$ distributions, is simply a proxy for $N_{qp}$, and that the $N_{\rm coll}$ term does not represent a hard-scattering component in $E_T$ distributions. The $dE_{T}/d\eta$ distributions of Au$+$Au and $d$$+$Au are then calculated from the measured $p$$+$$p$ $E_T$ distribution using two models that both reproduce the Au$+$Au data. However, while the number-of-constituent-quark-participant model agrees well with the $d$$+$Au data, the additive-quark model does not.Comment: 391 authors, 24 pages, 19 figures, and 15 Tables. Submitted to Phys. Rev. C. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are publicly available at http://www.phenix.bnl.gov/papers.htm

Transverse momentum and centrality dependence of dihadron correlations in Au+Au collisions at sqrt(s_NN)=200 GeV: Jet-quenching and the response of partonic matter

Azimuthal angle \Delta\phi correlations are presented for charged hadrons from dijets for 0.4 < p_T < 10 GeV/c in Au+Au collisions at sqrt(s_NN) = 200 GeV. With increasing p_T, the away-side distribution evolves from a broad to a concave shape, then to a convex shape. Comparisons to p+p data suggest that the away-side can be divided into a partially suppressed "head" region centered at Delta\phi ~ \pi, and an enhanced "shoulder" region centered at Delta\phi ~ \pi +/- 1.1. The p_T spectrum for the "head" region softens toward central collisions, consistent with the onset of jet quenching. The spectral slope for the "shoulder" region is independent of centrality and trigger p_T, which offers constraints on energy transport mechanisms and suggests that the "shoulder" region contains the medium response to energetic jets.Comment: 420 authors from 58 institutions, 6 pages, 4 figures. Submitted to Physical Review Letters. Plain text data tables for the points plotted in figures for this and previous PHENIX publications are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm