Citation and peer review of data: moving towards formal data publication

This paper discusses many of the issues associated with formally publishing data in academia, focusing primarily on the structures that need to be put in place for peer review and formal citation of datasets. Data publication is becoming increasingly important to the scientific community, as it will provide a mechanism for those who create data to receive academic credit for their work and will allow the conclusions arising from an analysis to be more readily verifiable, thus promoting transparency in the scientific process. Peer review of data will also provide a mechanism for ensuring the quality of datasets, and we provide suggestions on the types of activities one expects to see in the peer review of data. A simple taxonomy of data publication methodologies is presented and evaluated, and the paper concludes with a discussion of dataset granularity, transience and semantics, along with a recommended human-readable citation syntax

Kinesin Light Chains Are Essential for Axonal Transport in Drosophila

Kinesin is a heterotetramer composed of two 115-kD heavy chains and two 58-kD light chains. The microtubule motor activity of kinesin is performed by the heavy chains, but the functions of the light chains are poorly understood. Mutations were generated in the Drosophila gene Kinesin light chain (Klc), and the phenotypic consequences of loss of Klc function were analyzed at the behavioral and cellular levels. Loss of Klc function results in progressive lethargy, crawling defects, and paralysis followed by death at the end of the second larval instar. Klc mutant axons contain large aggregates of membranous organelles in segmental nerve axons. These aggregates, or organelle jams (Hurd, D.D., and W.M. Saxton. 1996. Genetics. 144: 1075-1085), contain synaptic vesicle precursors as well as organelles that may be transported by kinesin, kinesin-like protein 68D, and cytoplasmic dynein, thus providing evidence that the loss of Klc function blocks multiple pathways of axonal transport. The similarity of the Klc and Khc ((Saxton et al. Cell 64:1093-1102; Hurd, D.D., and W.M. Saxton. 1996. Genetics 144: 1075-1085) mutant phenotypes indicates that KLC is essential for kinesin function, perhaps by tethering KHC to intracellular cargos or by activating the kinesin motor

Teaching and Learning Issues in the Disciplines: Leisure Studies

This report is submitted to the Higher Education Academy (HEA) on behalf of the Leisure Studies Association (LSA). The LSA aims to foster research in Leisure Studies; to promote interest in Leisure Studies and advance education in this field; to encourage debate through publications, and an international journal Leisure Studies; to stimulate the exchange of ideas on contemporary leisure issues; to disseminate knowledge of Leisure Studies to create the conditions for better-informed decisions by policy makers. The LSA is a member society of the Academy of Social Sciences

Imaging geometry through dynamics: the observable representation

For many stochastic processes there is an underlying coordinate space, $V$, with the process moving from point to point in $V$ or on variables (such as spin configurations) defined with respect to $V$. There is a matrix of transition probabilities (whether between points in $V$ or between variables defined on $V$) and we focus on its ``slow'' eigenvectors, those with eigenvalues closest to that of the stationary eigenvector. These eigenvectors are the ``observables,'' and they can be used to recover geometrical features of $V$

Biot-Savart correlations in layered superconductors

We discuss the superconductor to normal phase transition in an infinite-layered type-II superconductor in the limit where the Josephson coupling between layers is negligible. We model each layer as a neutral gas of thermally excited pancake vortices. We assume the dominant interaction between vortices in the same and in different layers is the electromagnetic interaction between the screening currents induced by these vortices. Our main result, obtained by exactly solving the leading order renormalization group flow, is that the phase transition in this model is a Kosterlitz--Thouless transition despite being a three--dimensional system. While the transition itself is driven by the unbinding of two-dimensional pancake vortices, an RG analysis of the low temperature phase and a mean-field theory of the high temperature phase reveal that both phases possess three-dimensional correlations. An experimental consequence of this is that the jump in the measured in-plane superfluid stiffness, which is a universal quantity in 2d Kosterlitz-Thouless theory, will receive a small non--universal correction (of order 1% in Bi$_2$Sr$_2$CaCu$_2$O$_{8+x}$). This overall picture places some claims expressed in the literature on a more secure analytical footing and also resolves some conflicting views.Comment: 16 pages, 2 figures; minor typos corrected, references adde

Normal Breathing Pattern and Arterial Blood Gases in Awake and Sleeping Goats after Near Total Destruction of the Presumed Pre-Bötzinger Complex and the Surrounding Region

Abrupt neurotoxic destruction of \u3e70% of the pre-Bötzinger complex (preBötzC) in awake goats results in respiratory and cardiac failure (Wenninger JM, Pan LG, Klum L, Leekley T, Bastastic J, Hodges MR, Feroah TR, Davis S, Forster HV. J Appl Physiol 97: 1629–1636, 2004). However, in reduced preparations, rhythmic respiratory activity has been found in other areas of the brain stem (Huang Q, St. John WM. J Appl Physiol 64: 1405–1411, 1988; Janczewski WA, Feldman JL. J Physiol 570: 407–420, 2006; Lieske SP, Thoby-Brisson M, Telgkamo P, Ramierz JM. Nature Neurosci 3: 600–607, 2000; St. John WM, Bledsoe TA. J Appl Physiol 59: 684–690, 1985); thus we hypothesized that, when the preBötzC is destroyed incrementally over weeks, time-dependent plasticity within the respiratory network will result in a respiratory rhythm capable of maintaining normal blood gases. Microtubules were bilaterally implanted into the presumed preBötzC of seven goats. After recovery from surgery, studies were completed to establish baseline values for respiratory parameters. At weekly intervals, increasing volumes (in order 0.5, 1, 5, and 10 μl) of ibotenic acid (IA; 50 mM) were then injected into the preBötzC. All IA injections resulted in an acute tachypnea and dysrhythmia featuring augmented breaths, apneas, and increased breath-to-breath variation in breathing. In studies at night, apneas were nearly all central and occurred in the awake state. Breath-to-breath variation in breathing was greater (P \u3c 0.05) during wakefulness than during non-rapid eye movement sleep. However, one week after the final IA injection, the breathing pattern, breath-to-breath variation, and arterial blood gases and pH were unchanged from baseline, but there was a 20% decrease in respiratory frequency (f) and CO2 sensitivity (P \u3c 0.05), as well as a 40% decrease in the ventilatory response to hypoxia (P \u3c 0.001). In subsequent histological analysis of the presumed preBötzC region of lesioned goats, it was determined that there was a 90 and 92% reduction from control goats in total and neurokinin-1 receptor neurons, respectively. Therefore, it was concluded that 1) the dysrhythmic effects on breathing are state dependent; and 2) after incremental, near total destruction of the presumed preBötzC region, time-dependent plasticity within the respiratory network provides a rhythm capable of sustaining normal arterial blood gases

The Effects of Lesions in the Dorsolateral Pons on the Coordination of Swallowing and Breathing in Awake Goats

The purpose of this retrospective study was to gain insight into the contribution of the dorsolateral pons to the coordination of swallowing and breathing in awake goats. In 4 goats, cannulas were chronically implanted bilaterally through the lateral (LPBN) and medial (MPBN) parabrachial nuclei just dorsal to the Kölliker–Fuse nucleus (KFN). After \u3e2 weeks recovery from this surgery, the goats were studied for 5½ h on a control day, and on separate days after receiving 1 and 10 μl injections of ibotenic acid (IA) separated by 1 week. The frequency of swallows did not change during the control and 1 μl IA studies, but after injection of 10 μl IA, there was a transient 65% increase in frequency of swallows (P \u3c 0.05). Under control conditions swallows occurred throughout the respiratory cycle, where late-E swallows accounted for 67.6% of swallows. The distribution of swallow occurrence throughout the respiratory cycle was unaffected by IA injections. Consistent with the concept that swallowing is dominant over breathing, we found that swallows increased inspiratory (TI) and expiratory (TE) time and decreased tidal volume (VT) of the breath of the swallow (n) and/or the subsequent (n + 1) breath. Injections of 10 μl IA attenuated the normal increases in TI and TE and further attenuated VT of the n breath. Additionally, E and I swallows reset respiratory rhythm, but injection of 1 or 10 μl IA progressively attenuated this resetting, suggesting a decreased dominance over respiratory motor output with increasing IA injections. Post mortem histological analysis revealed about 50% fewer (P \u3c 0.05) neurons remained in the KFN, LPBN, and MPBN in lesioned compared to control goats. We conclude that dorsolateral pontine nuclei have a modulatory role in a hypothesized holarchical neural network regulating swallowing and breathing particularly contributing to the normal dominance of swallowing over breathing in both rhythm and motor pattern generation

Photoproduction of the ω\omega meson on the proton at large momentum transfer

The differential cross section, $d\sigma/dt$ for $\omega$ meson exclusive photoproduction on the proton above the resonance region ($2.6<W<2.9$ GeV) was measured up to a momentum transfer $-t = 5$ GeV$^2$ using the CLAS detector at Jefferson Laboratory. The $\omega$ channel was identified by detecting a proton and $\pi^+$ in the final state and using the missing mass technique. While the low momentum transfer region shows the typical diffractive pattern expected from Pomeron and Reggeon exchange, at large $-t$ the differential cross section has a flat behavior. This feature can be explained by introducing quark interchange processes in addition to the QCD-inspired two-gluon exchange.Comment: 5 pages, 5 figure