On the t-Term Rank of a Matrix

For t a positive integer, the t-term rank of a (0,1)-matrix A is defined to be the largest number of 1s in A with at most one 1 in each column and at most t 1s in each row. Thus the 1-term rank is the ordinary term rank. We generalize some basic results for the term rank to the t-term rank, including a formula for the maximum term rank over a nonempty class of (0,1)-matrices with the the same row sum and column sum vectors. We also show the surprising result that in such a class there exists a matrix which realizes all of the maximum terms ranks between 1 and t.Comment: 18 page

Profound effect of profiling platform and normalization strategy on detection of differentially expressed microRNAs

Adequate normalization minimizes the effects of systematic technical variations and is a prerequisite for getting meaningful biological changes. However, there is inconsistency about miRNA normalization performances and recommendations. Thus, we investigated the impact of seven different normalization methods (reference gene index, global geometric mean, quantile, invariant selection, loess, loessM, and generalized procrustes analysis) on intra- and inter-platform performance of two distinct and commonly used miRNA profiling platforms. We included data from miRNA profiling analyses derived from a hybridization-based platform (Agilent Technologies) and an RT-qPCR platform (Applied Biosystems). Furthermore, we validated a subset of miRNAs by individual RT-qPCR assays. Our analyses incorporated data from the effect of differentiation and tumor necrosis factor alpha treatment on primary human skeletal muscle cells and a murine skeletal muscle cell line. Distinct normalization methods differed in their impact on (i) standard deviations, (ii) the area under the receiver operating characteristic (ROC) curve, (iii) the similarity of differential expression. Loess, loessM, and quantile analysis were most effective in minimizing standard deviations on the Agilent and TLDA platform. Moreover, loess, loessM, invariant selection and generalized procrustes analysis increased the area under the ROC curve, a measure for the statistical performance of a test. The Jaccard index revealed that inter-platform concordance of differential expression tended to be increased by loess, loessM, quantile, and GPA normalization of AGL and TLDA data as well as RGI normalization of TLDA data. We recommend the application of loess, or loessM, and GPA normalization for miRNA Agilent arrays and qPCR cards as these normalization approaches showed to (i) effectively reduce standard deviations, (ii) increase sensitivity and accuracy of differential miRNA expression detection as well as (iii) increase inter-platform concordance. Results showed the successful adoption of loessM and generalized procrustes analysis to one-color miRNA profiling experiments

Cyclic Matching Sequencibility of Graphs

We define the cyclic matching sequencibility of a graph to be the largest integer $d$ such that there exists a cyclic ordering of its edges so that every $d$ consecutive edges in the cyclic ordering form a matching. We show that the cyclic matching sequencibility of $K_{2m}$ and $K_{2m+1}$ equal $m-1$

A model of non-linear interactions between cortical top-down and horizontal connections explains the attentional gating of collinear facilitation

AbstractPast physiological and psychophysical experiments have shown that attention can modulate the effects of contextual information appearing outside the classical receptive field of a cortical neuron. Specifically, it has been suggested that attention, operating via cortical feedback connections, gates the effects of long-range horizontal connections underlying collinear facilitation in cortical area V1. This article proposes a novel mechanism, based on the computations performed within the dendrites of cortical pyramidal cells, that can account for these observations. Furthermore, it is shown that the top-down gating signal into V1 can result from a process of biased competition occurring in extrastriate cortex. A model based on these two assumptions is used to replicate the results of physiological and psychophysical experiments on collinear facilitation and attentional modulation

Laser spectroscopy and cooling of Yb+ ions on a deep-UV transition

We perform laser spectroscopy of Yb+ ions on the 4f14 6s 2S_{1/2} - 4f13 5d 6s 3D[3/2]_{1/2} transition at 297 nm. The frequency measurements for 170Yb+, 172Yb+, 174Yb+, and 176Yb+ reveal the specific mass shift as well as the field shifts. In addition, we demonstrate laser cooling of Yb+ ions using this transition and show that light at 297 nm can be used as the second step in the photoionization of neutral Yb atoms

A model of partial reference frame transforms through pooling of gain-modulated responses

In multimodal integration and sensorimotor transformation areas of the posterior parietal cortex (PPC), neural responses often appear encoded in spatial reference frames that are intermediate to the in-trinsic sensory reference frames, for example, eye-centered for visual or head-centered for auditory stimulation. Many sensory responses in these areas are also modulated by direction of gaze. We demonstrate that certain types of mixed-frame responses can be generated by pooling gain-modulated responses—similar to how complex cells in the visual cortex are thought to pool the responses of simple cells. The proposed model simulates 2 types of mixed-frame responses observed in the PPC: in particular, sensory responses that shift differentially with gaze in horizontal and verti-cal dimensions and sensory responses that shift differentially for different start and end points along a single dimension of gaze. We distinguish these 2 types of mixed-frame responses from a third type in which sensory responses shift a partial yet approximately equal amount with each gaze shift. We argue that the empirical data on mixed-frame responses may be caused by multiple mechan-isms, and we adapt existing reference-frame measures to dis-tinguish between the different types. Finally, we discuss how mixed-frame responses may be revealing of the local organization of presynaptic responses

Multiplicative Gain Modulation Arises Through Unsupervised Learning in a Predictive Coding Model of Cortical Function

The combination of two or more population-coded signals in a neural model of pre-dictive coding can give rise to multiplicative gain modulation in the response properties of individual neurons. Synaptic weights generating these multiplicative response properties can be learned using an unsupervised, Hebbian, learning rule. The behaviour of the model is compared to empirical data on gaze-dependent gain modulation of cortical cells, and found to be in good agreement with a range of physiological observations. Furthermore, it is demonstrated that the model can learn to represent a set of basis functions. The current paper thus connects an often-observed neurophysiological phenomenon and important neu-rocomputational principle (gain modulation) with an influential theory of brain operation (predictive coding).

Eastern Beringia and beyond: Late Wisconsinan and Holocene landscape dynamics along the Yukon Coastal Plain, Canada

Terrestrial permafrost archives along the Yukon Coastal Plain (northwest Canada) have recorded landscape development and environmental change since the Late Wisconsinan at the interface of unglaciated Beringia (i.e. Komakuk Beach) and the northwestern limit of the Laurentide Ice Sheet (i.e. Herschel Island). The objective of this paper is to compare the late glacial and Holocene landscape development on both sides of the former ice margin based on permafrost sequences and ground ice. Analyses at these sites involved a multi-proxy approach including: sedimentology, cryostratigraphy, palaeoecology of ostracods, stable water isotopes in ground ice, hydrochemistry, and AMS radiocarbon and infrared stimulated luminescence (IRSL) dating. AMS and IRSL age determinations yielded full glacial ages at Komakuk Beach that is the northeastern limit of ice-free Beringia. Herschel Island to the east marks the Late Wisconsinan limit of the northwest Laurentide Ice Sheet and is composed of ice-thrust sediments containing plant detritus as young as 16.2 cal ka BP that might provide a maximum age on ice arrival. Late Wisconsinan ice wedges with sediment-rich fillings on Herschel Island are depleted in heavy oxygen isotopes (mean δ18O of −29.1‰); this, together with low dexcess values, indicates colder-than-modern winter temperatures and probably reduced snow depths. Grain-size distribution and fossil ostracod assemblages indicate that deglaciation of the Herschel Island icethrust moraine was accompanied by alluvial, proluvial, and eolian sedimentation on the adjacent unglaciated Yukon Coastal Plain until ~11 cal ka BP during a period of low glacio-eustatic sea level. The late glacial–Holocene transition was marked by higher-than-modern summer temperatures leading to permafrost degradation that began no later than 11.2 cal ka BP and caused a regional thaw unconformity. Cryostructures and ice wedges were truncated while organic matter was incorporated and soluble ions were leached in the thaw zone. Thermokarst activity led to the formation of ice-wedge casts and deposition of thermokarst lake sediments. These were subsequently covered by rapidly accumulating peat during the early Holocene Thermal Maximum. A rising permafrost table, reduced peat accumulation, and extensive ice-wedge growth resulted from climate cooling starting in the middle Holocene until the late 20th century. The reconstruction of palaeolandscape dynamics on the Yukon Coastal Plain and the eastern Beringian edge contributes to unraveling the linkages between ice sheet, ocean, and permafrost that have existed since the Late Wisconsinan

Effects of live-bait shrimp trawling on seagrass beds and fish bycatch in Tampa Bay, Florida

The use of live shrimp for bait in recreational fishing has resulted in a controversial fishery for shrimp in Florida. In this fishery, night collections are conducted over seagrass beds with roller beam trawls to capture live shrimp, primarily pink shrimp, Penaeus duorarum. These shrimp are culled from the catch on sorting tables and placed in onboard aerated “live” wells. Beds of turtlegrass, Thalassia testudinum, a species that has highest growth rates and biomass during summer and lowest during the winter (Fonseca et al., 1996) are predominant areas for live-bait shrimp trawling (Tabb and Kenny, 1969). Our study objectives were 1) to determine effects of a roller beam trawl on turtlegrass biomass and morphometrics during intensive (up to 18 trawls over a turtlegrass bed), short-term (3-hour duration) use and 2) to examine the mortality of bycatch finfish following capture by a trawl