Spike sorting for large, dense electrode arrays

Developments in microfabrication technology have enabled the production of neural electrode arrays with hundreds of closely spaced recording sites, and electrodes with thousands of sites are under development. These probes in principle allow the simultaneous recording of very large numbers of neurons. However, use of this technology requires the development of techniques for decoding the spike times of the recorded neurons from the raw data captured from the probes. Here we present a set of tools to solve this problem, implemented in a suite of practical, user-friendly, open-source software. We validate these methods on data from the cortex, hippocampus and thalamus of rat, mouse, macaque and marmoset, demonstrating error rates as low as 5%

Mapping photonic entanglement into and out of a quantum memory

Recent developments of quantum information science critically rely on entanglement, an intriguing aspect of quantum mechanics where parts of a composite system can exhibit correlations stronger than any classical counterpart. In particular, scalable quantum networks require capabilities to create, store, and distribute entanglement among distant matter nodes via photonic channels. Atomic ensembles can play the role of such nodes. So far, in the photon counting regime, heralded entanglement between atomic ensembles has been successfully demonstrated via probabilistic protocols. However, an inherent drawback of this approach is the compromise between the amount of entanglement and its preparation probability, leading intrinsically to low count rate for high entanglement. Here we report a protocol where entanglement between two atomic ensembles is created by coherent mapping of an entangled state of light. By splitting a single-photon and subsequent state transfer, we separate the generation of entanglement and its storage. After a programmable delay, the stored entanglement is mapped back into photonic modes with overall efficiency of 17 %. Improvements of single-photon sources together with our protocol will enable "on demand" entanglement of atomic ensembles, a powerful resource for quantum networking.Comment: 7 pages, and 3 figure

Cavity Induced Interfacing of Atoms and Light

This chapter introduces cavity-based light-matter quantum interfaces, with a single atom or ion in strong coupling to a high-finesse optical cavity. We discuss the deterministic generation of indistinguishable single photons from these systems; the atom-photon entanglement intractably linked to this process; and the information encoding using spatio-temporal modes within these photons. Furthermore, we show how to establish a time-reversal of the aforementioned emission process to use a coupled atom-cavity system as a quantum memory. Along the line, we also discuss the performance and characterisation of cavity photons in elementary linear-optics arrangements with single beam splitters for quantum-homodyne measurements.Comment: to appear as a book chapter in a compilation "Engineering the Atom-Photon Interaction" published by Springer in 2015, edited by A. Predojevic and M. W. Mitchel

Sperm design and variation in the New World blackbirds (Icteridae)

Post-copulatory sexual selection (PCSS) is thought to be one of the evolutionary forces responsible for the rapid and divergent evolution of sperm design. However, whereas in some taxa particular sperm traits are positively associated with PCSS, in other taxa, these relationships are negative, and the causes of these different patterns across taxa are poorly understood. In a comparative study using New World blackbirds (Icteridae), we tested whether sperm design was influenced by the level of PCSS and found significant positive associations with the level of PCSS for all sperm components but head length. Additionally, whereas the absolute length of sperm components increased, their variation declined with the intensity of PCSS, indicating stabilizing selection around an optimal sperm design. Given the diversity of, and strong selection on, sperm design, it seems likely that sperm phenotype may influence sperm velocity within species. However, in contrast to other recent studies of passerine birds, but consistent with several other studies, we found no significant link between sperm design and velocity, using four different species that vary both in sperm design and PCSS. Potential reasons for this discrepancy between studies are discussed

Predictors of return to work following motor vehicle related orthopaedic trauma

© 2016 Murgatroyd et al. Background: Work disability following motor vehicle related orthopaedic trauma is a significant contributor to the burden of injury and disease. Early identification of predictors for return to work (RTW) is essential for developing effective interventions to prevent work disability. The study aim was to determine the predictors (including compensation related factors) of time to RTW following motor vehicle related orthopaedic trauma. Methods: Admitted patients were recruited prospectively from two trauma hospitals with upper and/or lower extremity fractures following a motor vehicle crash. Baseline and follow up data were collected by written questionnaire. For baseline, this occurred in person within 2 weeks of injury. For follow up, this occurred by mail at six, 12 and 24 months. Additional demographic and injury-related information was retrieved from hospital databases. Analysis involved: descriptive statistics; logrank test to detect survival distributions of categorical variables; and Cox proportional hazards regression models for risks of time to RTW using baseline characteristic and compensation related variables (at 6 months). Results: Of 452 study participants 334 (74 %) were working pre-injury: results are based on this subset. Baseline characteristics were mean age 36 years (13.9 Standard Deviation [SD]), 80 % male; 72 % self-assessed very good-excellent pre-injury health, 83 % household income > AU$40,000 (Australian Dollar). Follow up data was available for 233 (70 %), 210 (63 %), and 182 (54 %) participants at six, 12 and 24 months respectively. Significant risks of a longer time to RTW were greater injury severity, as measured by the New Injury Severity Score (NISS) (Hazards Rate Ratio [HRR] = 0.54, 95 % CI 0.35-0.82); and lower occupational skill levels (HRR = 0.53, 95 % CI 0.34-0.83). Significant risks of a shorter time to RTW were: recovery expectations for usual activities within 90 days (HRR = 2.10, 95 % CI 1.49-2.95); full-time pre-injury work hours (HRR = 1.99, 95 % CI 1.26-3.14); and very good self-assessed pre-injury health status (HRR = 1.41, 95 % CI 0.98-2.02). Legal representation (analysed at six months only) was not associated with time to RTW. At each time period, there were 146 (63 %), 149 (71 %), and 137 (76 %) working participants. Conclusions: A longer time to RTW was associated with greater injury severity and lower occupational skill levels; while a shorter time to RTW was associated with recovery expectations for usual activities within 90 days, full-time pre-injury work hours, and very good self-assessed pre-injury health status. Our findings reinforce existing research. There is an opportunity to trial interventions that address potentially modifiable factors. The issues surrounding legal representation are complex and require further research

The association between seeking financial compensation and injury recovery following motor vehicle related orthopaedic trauma

© 2016 The Author(s). Background: Motor vehicle related moderate-severe orthopaedic trauma has a major impact on the burden of injury. In Australia, all states and territories provide access to financial compensation following injury in a motor vehicle crash. The aim of this study was to investigate the influence of seeking financial compensation (i.e., making a claim) on injury recovery following motor vehicle related moderate-severe orthopaedic trauma. Methods: Patients admitted with upper/lower extremity fractures after a motor vehicle crash were recruited from two trauma hospitals. Baseline data were collected in person by written questionnaire within two weeks of injury. Follow up data were collected by a mailed written questionnaire at six, 12 and 24 months. Additional (demographic/injury-related) information was collected from hospital databases, all other measures were self-reported. Outcomes were: Short Form-36 Version 2.0 (SF36v2), Physical/Mental Component Scores (PCS/MCS); Post Traumatic Stress Disorder (PTSD) Checklist Civilian Version (PCL-C); and Global Rating of Change (GRC) scale. Analysis involved descriptive statistics and linear mixed models to examine the effect of compensation status on injury recovery over time. Results: There were 452 study participants. Baseline characteristics showed: mean age 40 years (17.1 Standard Deviation [SD]); 75 % male; 74 % worked pre-injury; 67 % in excellent-very good pre-injury health; 56 % sustained serious injuries, Injury Severity Score (ISS) 9-15; 61 % had a low-middle range household income. Overall, after controlling for possible confounders, the compensable group had poorer recovery compared to the non-compensable group for PCS (-2.97 Mean Difference (MD), 95 % CI -4.73, -1.22); MCS (-3.44 MD, 95 % CI -5. 62, -1.26); PCL-C (3.42MD, 95 % CI 0.87, 5.99); and GRC (-0.66MD, 95 % CI -1.15, -0.17). Injury recovery over time for all participants showed: PCS improved from 6-12 and 12-24 months; MCS and GRC improved from 6-12 months; and PCL-C did not significantly improve from 6-12 and 12-24 months. Injury recovery over time continued for compensable and non-compensable groups but compensable participants had poorer scores at each time period, especially MCS and PCL-C. Conclusions: Making a claim was associated with poor injury recovery following motor vehicle related orthopaedic trauma, mainly for mental health. Irrespective of claim status, the majority had poor injury recovery, especially for mental health

Haptoglobin phenotype is not a predictor of recurrence free survival in high-risk primary breast cancer patients

Contains fulltext : 70104tjan-heijnen.pdf (publisher's version ) (Open Access)BACKGROUND: Better breast cancer prognostication may improve selection of patients for adjuvant therapy. We conducted a retrospective follow-up study in which we investigated sera of high-risk primary breast cancer patients, to search for proteins predictive of recurrence free survival. METHODS: Two sample sets of high-risk primary breast cancer patients participating in a randomised national trial investigating the effectiveness of high-dose chemotherapy were analysed. Sera in set I (n = 63) were analysed by surface enhanced laser desorption ionisation time-of-flight mass spectrometry (SELDI-TOF MS) for biomarker finding. Initial results were validated by analysis of sample set II (n = 371), using one-dimensional gel-electrophoresis. RESULTS: In sample set I, the expression of a peak at mass-to-charge ratio 9198 (relative intensity 20), identified as haptoglobin (Hp) alpha-1 chain, was strongly associated with recurrence free survival (global Log-rank test; p = 0.0014). Haptoglobin is present in three distinct phenotypes (Hp 1-1, Hp 2-1, and Hp 2-2), of which only individuals with phenotype Hp 1-1 or Hp 2-1 express the haptoglobin alpha-1 chain. As the expression of the haptoglobin alpha-1 chain, determined by SELDI-TOF MS, corresponds to the phenotype, initial results were validated by haptoglobin phenotyping of the independent sample set II by native one-dimensional gel-electrophoresis. With the Hp 1-1 phenotype as the reference category, the univariate hazard ratio for recurrence was 0.87 (95% CI: 0.56 - 1.34, p = 0.5221) and 1.03 (95% CI: 0.65 - 1.64, p = 0.8966) for the Hp 2-1 and Hp 2-2 phenotypes, respectively, in sample set II. CONCLUSION: In contrast to our initial results, the haptoglobin phenotype was not identified as a predictor of recurrence free survival in high-risk primary breast cancer in our validation set. Our initial observation in the discovery set was probably the result of a type I error (i.e. false positive). This study illustrates the importance of validation in obtaining the true clinical applicability of a potential biomarker

Evaluation of the current knowledge limitations in breast cancer research: a gap analysis

BACKGROUND A gap analysis was conducted to determine which areas of breast cancer research, if targeted by researchers and funding bodies, could produce the greatest impact on patients. METHODS Fifty-six Breast Cancer Campaign grant holders and prominent UK breast cancer researchers participated in a gap analysis of current breast cancer research. Before, during and following the meeting, groups in seven key research areas participated in cycles of presentation, literature review and discussion. Summary papers were prepared by each group and collated into this position paper highlighting the research gaps, with recommendations for action. RESULTS Gaps were identified in all seven themes. General barriers to progress were lack of financial and practical resources, and poor collaboration between disciplines. Critical gaps in each theme included: (1) genetics (knowledge of genetic changes, their effects and interactions); (2) initiation of breast cancer (how developmental signalling pathways cause ductal elongation and branching at the cellular level and influence stem cell dynamics, and how their disruption initiates tumour formation); (3) progression of breast cancer (deciphering the intracellular and extracellular regulators of early progression, tumour growth, angiogenesis and metastasis); (4) therapies and targets (understanding who develops advanced disease); (5) disease markers (incorporating intelligent trial design into all studies to ensure new treatments are tested in patient groups stratified using biomarkers); (6) prevention (strategies to prevent oestrogen-receptor negative tumours and the long-term effects of chemoprevention for oestrogen-receptor positive tumours); (7) psychosocial aspects of cancer (the use of appropriate psychosocial interventions, and the personal impact of all stages of the disease among patients from a range of ethnic and demographic backgrounds). CONCLUSION Through recommendations to address these gaps with future research, the long-term benefits to patients will include: better estimation of risk in families with breast cancer and strategies to reduce risk; better prediction of drug response and patient prognosis; improved tailoring of treatments to patient subgroups and development of new therapeutic approaches; earlier initiation of treatment; more effective use of resources for screening populations; and an enhanced experience for people with or at risk of breast cancer and their families. The challenge to funding bodies and researchers in all disciplines is to focus on these gaps and to drive advances in knowledge into improvements in patient care

The Quantum Internet

Quantum networks offer a unifying set of opportunities and challenges across exciting intellectual and technical frontiers, including for quantum computation, communication, and metrology. The realization of quantum networks composed of many nodes and channels requires new scientific capabilities for the generation and characterization of quantum coherence and entanglement. Fundamental to this endeavor are quantum interconnects that convert quantum states from one physical system to those of another in a reversible fashion. Such quantum connectivity for networks can be achieved by optical interactions of single photons and atoms, thereby enabling entanglement distribution and quantum teleportation between nodes.Comment: 15 pages, 6 figures Higher resolution versions of the figures can be downloaded from the following link: http://www.its.caltech.edu/~hjkimble/QNet-figures-high-resolutio

Measurement of the inclusive and dijet cross-sections of b-jets in pp collisions at sqrt(s) = 7 TeV with the ATLAS detector

The inclusive and dijet production cross-sections have been measured for jets containing b-hadrons (b-jets) in proton-proton collisions at a centre-of-mass energy of sqrt(s) = 7 TeV, using the ATLAS detector at the LHC. The measurements use data corresponding to an integrated luminosity of 34 pb^-1. The b-jets are identified using either a lifetime-based method, where secondary decay vertices of b-hadrons in jets are reconstructed using information from the tracking detectors, or a muon-based method where the presence of a muon is used to identify semileptonic decays of b-hadrons inside jets. The inclusive b-jet cross-section is measured as a function of transverse momentum in the range 20 < pT < 400 GeV and rapidity in the range |y| < 2.1. The bbbar-dijet cross-section is measured as a function of the dijet invariant mass in the range 110 < m_jj < 760 GeV, the azimuthal angle difference between the two jets and the angular variable chi in two dijet mass regions. The results are compared with next-to-leading-order QCD predictions. Good agreement is observed between the measured cross-sections and the predictions obtained using POWHEG + Pythia. MC@NLO + Herwig shows good agreement with the measured bbbar-dijet cross-section. However, it does not reproduce the measured inclusive cross-section well, particularly for central b-jets with large transverse momenta.Comment: 10 pages plus author list (21 pages total), 8 figures, 1 table, final version published in European Physical Journal