Correction: A simple method for analyzing data from a randomized trial with a missing binary outcome

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Identifying genes that contribute most to good classification in microarrays

BACKGROUND: The goal of most microarray studies is either the identification of genes that are most differentially expressed or the creation of a good classification rule. The disadvantage of the former is that it ignores the importance of gene interactions; the disadvantage of the latter is that it often does not provide a sufficient focus for further investigation because many genes may be included by chance. Our strategy is to search for classification rules that perform well with few genes and, if they are found, identify genes that occur relatively frequently under multiple random validation (random splits into training and test samples). RESULTS: We analyzed data from four published studies related to cancer. For classification we used a filter with a nearest centroid rule that is easy to implement and has been previously shown to perform well. To comprehensively measure classification performance we used receiver operating characteristic curves. In the three data sets with good classification performance, the classification rules for 5 genes were only slightly worse than for 20 or 50 genes and somewhat better than for 1 gene. In two of these data sets, one or two genes had relatively high frequencies not noticeable with rules involving 20 or 50 genes: desmin for classifying colon cancer versus normal tissue; and zyxin and secretory granule proteoglycan genes for classifying two types of leukemia. CONCLUSION: Using multiple random validation, investigators should look for classification rules that perform well with few genes and select, for further study, genes with relatively high frequencies of occurrence in these classification rules

Both Corticospinal and Reticulospinal Tracts Control Force of Contraction

The control of contraction strength is a key part of movement control. In primates, both corticospinal and reticulospinal cells provide input to motoneurons. Corticospinal discharge is known to correlate with force, but there are no previous reports of how reticular formation (RF) activity modulates with different contractions. Here we trained two female macaque monkeys (body weight 5.9-6.9kg) to pull a handle which could be loaded with 0.5-6kg weights, and recorded from identified pyramidal tract neurons (PTNs) in primary motor cortex and RF cells during task performance. Population-averaged firing rate increased monotonically with higher force for the RF, but showed a complex profile with little net modulation for PTNs. This reflected a more heterogeneous profile of rate modulation across the PTN population, leading to cancellation in the average. Linear discriminant analysis (LDA) classified the force based on the time course of rate modulation equally well for PTNs and RF cells. Peak firing rate had significant linear correlation with force for 43/92 (46.7%) PTNs and 21/46 (43.5%) RF cells. For almost all (20/21) RF cells the correlation coefficient was positive; similar numbers of PTNs (22 vs 21) had positive vs negative coefficients. Considering the timing of force representation, similar fractions (PTNs: 61.2%; RF cells: 55.5%) commenced coding before the onset of muscle activity. We conclude that both corticospinal and reticulospinal tracts contribute to control of contraction force; the reticulospinal tract seems to specify an overall signal simply related to force, whereas corticospinal cell activity would be better suited for fine-scale adjustments.SIGNIFICANCE STATEMENTFor the first time, we compare coding of force for corticospinal and reticular formation cells in awake behaving monkeys, over a wide range of contraction strengths likely to come close to maximum voluntary contraction. Both cortical and brainstem systems coded similarly well for force, but whereas reticular formation cells carried a simple uniform signal, corticospinal neurons were more heterogenous. This may reflect a role in gross specification of a coordinated movement, versus more fine-grained adjustments around individual joints

Efficient transduction of primary vascular cells by the rare adenovirus serotype 49 vector

Neointima formation and vascular remodelling through vascular smooth muscle cell migration and proliferation can limit the long term success of coronary interventions, for example in coronary artery bypass grafting (CABG). Ex vivo gene therapy has the potential to reduce unnecessary cell proliferation and limit neointima formation in vascular pathologies. To date the species C adenovirus serotype 5 (Ad5) has been commonly used for pre-clinical gene therapy, however its suitability is potentially limited by relatively poor tropism for vascular cells and high levels of pre-existing immunity in the population. To avoid these limitations, novel species of adenovirus are being tested; here we investigate the potential of adenovirus 49 (Ad49) for use in gene therapy. Transduction of primary human vascular cells by a range of adenovirus serotypes was assessed; Ad49 demonstrated highest transduction of both vascular smooth muscle and endothelial cells. Gene transfer with Ad49 in vascular smooth muscle and endothelial cells was possible following short exposure times (*lt;1hr) and with low MOI which is clinically relevant. Ex vivo delivery to surplus CABG tissue showed efficient gene transfer with Ad49, consistent with the in vitro findings. Luminal infusion of Ad49GFP into intact CABG samples ex vivo resulted in efficient vessel transduction. In addition, no seroprevelance rates to Ad49 were observed in a Scottish cohort of patients from cardiovascular clinics, thus circumventing issues with pre-existing immunity. Our results show Ad49 has tropism for vascular cells in vitro and ex vivo and demonstrate Ad49 may be an improved vector for local vascular gene therapy compared to current alternatives

Estimating the cumulative risk of false positive cancer screenings

BACKGROUND: When evaluating cancer screening it is important to estimate the cumulative risk of false positives from periodic screening. Because the data typically come from studies in which the number of screenings varies by subject, estimation must take into account dropouts. A previous approach to estimate the probability of at least one false positive in n screenings unrealistically assumed that the probability of dropout does not depend on prior false positives. METHOD: By redefining the random variables, we obviate the unrealistic dropout assumption. We also propose a relatively simple logistic regression and extend estimation to the expected number of false positives in n screenings. RESULTS: We illustrate our methodology using data from women ages 40 to 64 who received up to four annual breast cancer screenings in the Health Insurance Program of Greater New York study, which began in 1963. Covariates were age, time since previous screening, screening number, and whether or not a previous false positive occurred. Defining a false positive as an unnecessary biopsy, the only statistically significant covariate was whether or not a previous false positive occurred. Because the effect of screening number was not statistically significant, extrapolation beyond 4 screenings was reasonable. The estimated mean number of unnecessary biopsies in 10 years per woman screened is .11 with 95% confidence interval of (.10, .12). Defining a false positive as an unnecessary work-up, all the covariates were statistically significant and the estimated mean number of unnecessary work-ups in 4 years per woman screened is .34 with 95% confidence interval (.32, .36). CONCLUSION: Using data from multiple cancer screenings with dropouts, and allowing dropout to depend on previous history of false positives, we propose a logistic regression model to estimate both the probability of at least one false positive and the expected number of false positives associated with n cancer screenings. The methodology can be used for both informed decision making at the individual level, as well as planning of health services

Quantitative acoustic models for superfluid circuits

We experimentally realize a highly tunable superfluid oscillator circuit in a quantum gas of ultracold atoms and develop and verify a simple lumped-element description of this circuit. At low oscillator currents, we demonstrate that the circuit is accurately described as a Helmholtz resonator, a fundamental element of acoustic circuits. At larger currents, the breakdown of the Helmholtz regime is heralded by a turbulent shedding of vortices and density waves. Although a simple phase-slip model offers qualitative insights into the circuit's resistive behavior, our results indicate deviations from the phase-slip model. A full understanding of the dissipation in superfluid circuits will thus require the development of empirical models of the turbulent dynamics in this system, as have been developed for classical acoustic systems.Comment: 12 pages, 9 figure

Changes in descending motor pathway connectivity after corticospinal tract lesion in macaque monkey.

Damage to the corticospinal tract is a leading cause of motor disability, for example in stroke or spinal cord injury. Some function usually recovers, but whether plasticity of undamaged ipsilaterally descending corticospinal axons and/or brainstem pathways such as the reticulospinal tract contributes to recovery is unknown. Here, we examined the connectivity in these pathways to motor neurons after recovery from corticospinal lesions. Extensive unilateral lesions of the medullary corticospinal fibres in the pyramidal tract were made in three adult macaque monkeys. After an initial contralateral flaccid paralysis, motor function rapidly recovered, after which all animals were capable of climbing and supporting their weight by gripping the cage bars with the contralesional hand. In one animal where experimental testing was carried out, there was (as expected) no recovery of fine independent finger movements. Around 6 months post-lesion, intracellular recordings were made from 167 motor neurons innervating hand and forearm muscles. Synaptic responses evoked by stimulating the unlesioned ipsilateral pyramidal tract and the medial longitudinal fasciculus were recorded and compared with control responses in 207 motor neurons from six unlesioned animals. Input from the ipsilateral pyramidal tract was rare and weak in both lesioned and control animals, suggesting a limited role for this pathway in functional recovery. In contrast, mono- and disynaptic excitatory post-synaptic potentials elicited from the medial longitudinal fasciculus significantly increased in average size after recovery, but only in motor neurons innervating forearm flexor and intrinsic hand muscles, not in forearm extensor motor neurons. We conclude that reticulospinal systems sub-serve some of the functional recovery after corticospinal lesions. The imbalanced strengthening of connections to flexor, but not extensor, motor neurons mirrors the extensor weakness and flexor spasm which in neurological experience is a common limitation to recovery in stroke survivors

Contrast and lustre:a model that accounts for eleven different forms of contrast discrimination in binocular vision

Our goal here is a more complete understanding of how information about luminance contrast is encoded and used by the binocular visual system. In two-interval forced-choice experiments we assessed observers' ability to discriminate changes in contrast that could be an increase or decrease of contrast in one or both eyes, or an increase in one eye coupled with a decrease in the other (termed IncDec). The base or pedestal contrasts were either in-phase or out-of-phase in the two eyes. The opposed changes in the IncDec condition did not cancel each other out, implying that along with binocular summation, information is also available from mechanisms that do not sum the two eyes' inputs. These might be monocular mechanisms. With a binocular pedestal, monocular increments of contrast were much easier to see than monocular decrements. These findings suggest that there are separate binocular (B) and monocular (L,R) channels, but only the largest of the three responses, max(L,B,R), is available to perception and decision. Results from contrast discrimination and contrast matching tasks were described very accurately by this model. Stimuli, data, and model responses can all be visualized in a common binocular contrast space, allowing a more direct comparison between models and data. Some results with out-of-phase pedestals were not accounted for by the max model of contrast coding, but were well explained by an extended model in which gratings of opposite polarity create the sensation of lustre. Observers can discriminate changes in lustre alongside changes in contrast

Selecting patients for randomized trials: a systematic approach based on risk group

BACKGROUND: A key aspect of randomized trial design is the choice of risk group. Some trials include patients from the entire at-risk population, others accrue only patients deemed to be at increased risk. We present a simple statistical approach for choosing between these approaches. The method is easily adapted to determine which of several competing definitions of high risk is optimal. METHOD: We treat eligibility criteria for a trial, such as a smoking history, as a prediction rule associated with a certain sensitivity (the number of patients who have the event and who are classified as high risk divided by the total number patients who have an event) and specificity (the number of patients who do not have an event and who do not meet criteria for high risk divided by the total number of patients who do not have an event). We then derive simple formulae to determine the proportion of patients receiving intervention, and the proportion who experience an event, where either all patients or only those at high risk are treated. We assume that the relative risk associated with intervention is the same over all choices of risk group. The proportion of events and interventions are combined using a net benefit approach and net benefit compared between strategies. RESULTS: We applied our method to design a trial of adjuvant therapy after prostatectomy. We were able to demonstrate that treating a high risk group was superior to treating all patients; choose the optimal definition of high risk; test the robustness of our results by sensitivity analysis. Our results had a ready clinical interpretation that could immediately aid trial design. CONCLUSION: The choice of risk group in randomized trials is usually based on rather informal methods. Our simple method demonstrates that this decision can be informed by simple statistical analyses