Single-molecule correlated chemical probing of RNA.

Complex higher-order RNA structures play critical roles in all facets of gene expression; however, the through-space interaction networks that define tertiary structures and govern sampling of multiple conformations are poorly understood. Here we describe single-molecule RNA structure analysis in which multiple sites of chemical modification are identified in single RNA strands by massively parallel sequencing and then analyzed for correlated and clustered interactions. The strategy thus identifies RNA interaction groups by mutational profiling (RING-MaP) and makes possible two expansive applications. First, we identify through-space interactions, create 3D models for RNAs spanning 80-265 nucleotides, and characterize broad classes of intramolecular interactions that stabilize RNA. Second, we distinguish distinct conformations in solution ensembles and reveal previously undetected hidden states and large-scale structural reconfigurations that occur in unfolded RNAs relative to native states. RING-MaP single-molecule nucleic acid structure interrogation enables concise and facile analysis of the global architectures and multiple conformations that govern function in RNA.

Activity of somatosensory-responsive neurons in high subdivisions of SI cortex during locomotion.

Responses of neurons in the primary somatosensory cortex during movements are poorly understood, even during such simple tasks as walking on a flat surface. In this study, we analyzed spike discharges of neurons in the rostral bank of the ansate sulcus (areas 1-2) in 2 cats while the cats walked on a flat surface or on a horizontal ladder, a complex task requiring accurate stepping. All neurons (n = 82) that had receptive fields (RFs) on the contralateral forelimb exhibited frequency modulation of their activity that was phase locked to the stride cycle during simple locomotion. Neurons with proximal RFs (upper arm/shoulder) and pyramidal tract-projecting neurons (PTNs) with fast-conducting axons tended to fire at peak rates in the middle of the swing phase, whereas neurons with RFs on the distal limb (wrist/paw) and slow-conducting PTNs typically showed peak firing at the transition between swing and stance phases. Eleven of 12 neurons with tactile RFs on the volar forepaw began firing toward the end of swing, with peak activity occurring at the moment of foot contact with floor, thereby preceding the evoked sensory volley from touch receptors. Requirement to step accurately on the ladder affected 91% of the neurons, suggesting their involvement in control of accuracy of stepping. During both tasks, neurons exhibited a wide variety of spike distributions within the stride cycle, suggesting that, during either simple or ladder locomotion, they represent the cycling somatosensory events in their activity both predictively before and reflectively after these events take place.

QuShape: rapid, accurate, and best-practices quantification of nucleic acid probing information, resolved by capillary electrophoresis.

Chemical probing of RNA and DNA structure is a widely used and highly informative approach for examining nucleic acid structure and for evaluating interactions with protein and small-molecule ligands. Use of capillary electrophoresis to analyze chemical probing experiments yields hundreds of nucleotides of information per experiment and can be performed on automated instruments. Extraction of the information from capillary electrophoresis electropherograms is a computationally intensive multistep analytical process, and no current software provides rapid, automated, and accurate data analysis. To overcome this bottleneck, we developed a platform-independent, user-friendly software package, QuShape, that yields quantitatively accurate nucleotide reactivity information with minimal user supervision. QuShape incorporates newly developed algorithms for signal decay correction, alignment of time-varying signals within and across capillaries and relative to the RNA nucleotide sequence, and signal scaling across channels or experiments. An analysis-by-reference option enables multiple, related experiments to be fully analyzed in minutes. We illustrate the usefulness and robustness of QuShape by analysis of RNA SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) experiments.

Principles for understanding the accuracy of SHAPE-directed RNA structure modeling.

Accurate RNA structure modeling is an important, incompletely solved, challenge. Single-nucleotide resolution SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension) yields an experimental measurement of local nucleotide flexibility that can be incorporated as pseudo-free energy change constraints to direct secondary structure predictions. Prior work from our laboratory has emphasized both the overall accuracy of this approach and the need for nuanced interpretation of modeled structures. Recent studies by Das and colleagues [Kladwang, W., et al. (2011) Biochemistry 50, 8049; Nat. Chem. 3, 954], focused on analyzing six small RNAs, yielded poorer RNA secondary structure predictions than expected on the basis of prior benchmarking efforts. To understand the features that led to these divergent results, we re-examined four RNAs yielding the poorest results in this recent work: tRNA(Phe), the adenine and cyclic-di-GMP riboswitches, and 5S rRNA. Most of the errors reported by Das and colleagues reflected nonstandard experiment and data processing choices, and selective scoring rules. For two RNAs, tRNA(Phe) and the adenine riboswitch, secondary structure predictions are nearly perfect if no experimental information is included but were rendered inaccurate by the SHAPE data of Das and colleagues. When best practices were used, single-sequence SHAPE-directed secondary structure modeling recovered ~93% of individual base pairs and >90% of helices in the four RNAs, essentially indistinguishable from the results of the mutate-and-map approach with the exception of a single helix in the 5S rRNA. The field of experimentally directed RNA secondary structure prediction is entering a phase focused on the most difficult prediction challenges. We outline five constructive principles for guiding this field forward.

Neocortical layer 4 as a pluripotent function linearizer.

A highly effective kernel-based strategy used in machine learning is to transform the input space into a new "feature" space where nonlinear problems become linear and more readily solvable with efficient linear techniques. We propose that a similar "problem-linearization" strategy is used by the neocortical input layer 4 to reduce the difficulty of learning nonlinear relations between the afferent inputs to a cortical column and its to-be-learned upper layer outputs. The key to this strategy is the presence of broadly tuned feed-forward inhibition in layer 4: it turns local layer 4 domains into functional analogs of radial basis function networks, which are known for their universal function approximation capabilities. With the use of a computational model of layer 4 with feed-forward inhibition and Hebbian afferent connections, self-organized on natural images to closely match structural and functional properties of layer 4 of the cat primary visual cortex, we show that such layer-4-like networks have a strong intrinsic tendency to perform input transforms that automatically linearize a broad repertoire of potential nonlinear functions over the afferent inputs. This capacity for pluripotent function linearization, which is highly robust to variations in network parameters, suggests that layer 4 might contribute importantly to sensory information processing as a pluripotent function linearizer, performing such a transform of afferent inputs to a cortical column that makes it possible for neurons in the upper layers of the column to learn and perform their complex functions using primarily linear operations.

Area 3a neuron response to skin nociceptor afferent drive.

Area 3a neurons are identified that respond weakly or not at all to skin contact with a 25-38 degrees C probe, but vigorously to skin contact with the probe at > or =49 degrees C. Maximal rate of spike firing associated with 1- to 7-s contact at > or =49 degrees C occurs 1-2 s after probe removal from the skin. The activity evoked by 5-s contact with the probe at 51 degrees C remains above-background for approximately 20 s after probe retraction. After 1-s contact at 55-56 degrees C activity remains above-background for approximately 4 s. Magnitude of spike firing associated with 5-s contact increases linearly as probe temperature is increased from 49-51 degrees C. Intradermal capsaicin injection elicits a larger (approximately 2.5x) and longer-lasting (100x) increase in area 3a neuron firing rate than 5-s contact at 51 degrees C. Area 3a neurons exhibit enhanced or novel responsivity to 25-38 degrees C contact for a prolonged time after intradermal injection of capsaicin or alpha, beta methylene adenosine triphosphate. Their 1) delayed and persisting increase in spike firing in response to contact at > or =49 degrees C, 2) vigorous and prolonged response to intradermal capsaicin, and 3) enhanced and frequently novel response to 25-38 degrees C contact following intradermal algogen injection or noxious skin heating suggest that the area 3a neurons identified in this study contribute to second pain and mechanical hyperalgesia/allodynia.

Methodological Problems With Online Concussion Testing.

Reaction time testing is widely used in online computerized concussion assessments, and most concussion studies utilizing the metric have demonstrated varying degrees of difference between concussed and non-concussed individuals. The problem with most of these online concussion assessments is that they predominantly rely on consumer grade technology. Typical administration of these reaction time tests involves presenting a visual stimulus on a computer monitor and prompting the test subject to respond as quickly as possible via keypad or computer mouse. However, inherent delays and variabilities are introduced to the reaction time measure by both computer and associated operating systems that the concussion assessment tool is installed on. The authors hypothesized systems that are typically used to collect concussion reaction time data would demonstrate significant errors in reaction time measurements. To remove human bias, a series of experiments was conducted robotically to assess timing errors introduced by reaction time tests under four different conditions. In the first condition, a visual reaction time test was conducted by flashing a visual stimulus on a computer monitor. Detection was via photodiode and mechanical response was delivered via computer mouse. The second condition employed a mobile device for the visual stimulus, and the mechanical response was delivered to the mobile device's touchscreen. The third condition simulated a tactile reaction time test, and mechanical response was delivered via computer mouse. The fourth condition also simulated a tactile reaction time test, but response was delivered to a dedicated device designed to store the interval between stimulus delivery and response, thus bypassing any problems hypothesized to be introduced by computer and/or computer software. There were significant differences in the range of responses recorded from the four different conditions with the reaction time collected from visual stimulus on a mobile device being the worst and the device with dedicated hardware designed for the task being the best. The results suggest that some of the commonly used visual tasks on consumer grade computers could be (and have been) introducing significant errors for reaction time testing and that dedicated hardware designed for the reaction time task is needed to minimize testing errors.

Contributions of Nociresponsive Area 3a to Normal and Abnormal Somatosensory Perception.

Traditionally, cytoarchitectonic area 3a of primary somatosensory cortex (SI) has been regarded as a proprioceptive relay to motor cortex. However, neuronal spike-train recordings and optical intrinsic signal imaging, obtained from nonhuman sensorimotor cortex, show that neuronal activity in some of the cortical columns in area 3a can be readily triggered by a C-nociceptor afferent drive. These findings indicate that area 3a is a critical link in cerebral cortical encoding of secondary/slow pain. Also, area 3a contributes to abnormal pain processing in the presence of activity-dependent reversal of gamma-aminobutyric acid A receptor-mediated inhibition. Accordingly, abnormal processing within area 3a may contribute mechanistically to generation of clinical pain conditions. PERSPECTIVE: Optical imaging and neurophysiological mapping of area 3a of SI has revealed substantial driving from unmyelinated cutaneous nociceptors, complementing input to areas 3b and 1 of SI from myelinated nociceptors and non-nociceptors. These and related findings force a reconsideration of mechanisms for SI processing of pain.

Quantification of Mild Traumatic Brain Injury via Cortical Metrics: Analytical Methods.

Mild traumatic brain injuries are difficult to diagnose or assess with commonly used diagnostic methods. However, the functional state of cerebral cortical networks can be rapidly and effectively probed by measuring tactile-based sensory percepts (called cortical metrics), which are designed to exercise various components of cortical machinery. In this study, such cortical metrics were obtained from 52 college students before and after they experienced sports-related concussions by delivering vibrotactile stimuli to the index and middle fingertips. Performance on four of the sensory test protocols is described: reaction time, amplitude discrimination, temporal order judgment, and duration discrimination. The collected test performance data were analyzed using methods of uni- and multivariate statistics, receiver operated characteristic (ROC) curves, and discriminant analysis. While individual cortical metrics vary extensively in their ability to discriminate between control and concussed subjects, their combined discriminative performance greatly exceeds that of any individual metric, achieving cross-validated 93.0% sensitivity, 92.3% specificity, 93.0% positive predictive value, and 92.3% negative predictive value. The cortical metrics vector can be used to track an individual's recovery from concussion. The study thus establishes that cortical metrics can be used effectively as a quantitative indicator of central nervous system health status.

Clinical Utility and Analysis of the Run-Roll-Aim Task: Informing Return-to-Duty Readiness Decisions in Active-Duty Service Members.

INTRODUCTION: The Assessment of Military Multitasking Performance (AMMP1) consists of six dual-task and multitask military-relevant performance-based assessments which were developed to provide assistance in making return-to-duty decisions after concussion or mild traumatic brain injury (mTBI.) The Run-Roll-Aim (RRA) task, one component of the AMMP, was developed to target vulnerabilities following mTBI including attention, visual function, dynamic stability, rapid transition, and vestibular function. One aim of this study was to assess the known-group and construct validity of the RRA, and additionally to further explore reliability limitations reported previously. MATERIALS AND METHODS: A cross-sectional study consisting of 84 Active Duty service members in two groups (healthy control - HC and individuals experiencing persistent mTBI symptoms) completed neurocognitive tests and the RRA. The RRA task requires a high level of mobility and resembles military training activities in a maneuver that includes combat rolls, fast transitions, obstacle avoidance, and visual search. Observational and inertial sensor data were compared between groups and performance across four trial times was compared within groups. Correlations between RRA results and neurocognitive test scores were analyzed. RESULTS: Simple observational measures (time, errors) did not differ between groups. Spectral power analysis of the inertial sensor data showed significant differences in motor performance between groups. Within group one-way ANOVAs showed that in HC trial 1, time was significantly different than trials 2,3 and 4 (F(3,47) = 4.60, p < 0.01, Tukey HSD p < 0.05) while the mTBI group showed no significant difference in time between trials. During testing individuals with mTBI were less likely to complete the multiple test trials or required additional rest between trials than HCs (χ2 = 10.78, p < 0.01). Small but significant correlations were seen with two neurocognitive tests of attention and RRA performance time. CONCLUSION: While observational scores were not sensitive to group differences, inertial sensor data showed motor performance on the forward run, combat roll, and backward run differed significantly between groups. The RRA task appeared challenging and provoked symptoms in the mTBI group, causing 8 of 33 mTBI participants to stop the task or require additional rest between trials while none of the HC participants had to stop. Individuals with mTBI demonstrated slower learning of the complex motor sequence compared to HCs who had significant improvement after one trial of RRA. Complex novel training maneuvers like RRA may aid clinicians in informing return to duty decisions.

A newly identified nociresponsive region in the transitional zone (TZ) in rat sensorimotor cortex.

The primary somatosensory cortex (S1) comprises a number of functionally distinct regions, reflecting the diversity of somatosensory receptor submodalities innervating the body. In particular, two spatially and functionally distinct nociceptive regions have been described in primate S1 (Vierck et al., 2013; Whitsel et al., 2019). One region is located mostly in Brodmann cytoarchitectonic area 1, where a subset of neurons exhibit functional characteristics associated with myelinated Aδ nociceptors and perception of 1st/sharp, discriminative pain. The second region is located at the transition between S1 and primary motor cortex (M1) in area 3a, where neurons exhibit functional characteristics associated with unmyelinated C nociceptors and perception of 2nd/slow, burning pain. To test the hypothesis that in rats the transitional zone (TZ) - which is a dysgranular region at the transition between M1 and S1 - is the functional equivalent of the nociresponsive region of area 3a in primates, extracellular spike discharge activity was recorded from TZ neurons in rats under general isoflurane anesthesia. Thermonoxious stimuli were applied by lowering the contralateral forepaw or hindpaw into a 48-51 °C heated water bath for 5-10 s. Neurons in TZ were found to be minimally affected by non-noxious somatosensory stimuli, but highly responsive to thermonoxious skin stimuli in a slow temporal summation manner closely resembling that of nociresponsive neurons in primate area 3a. Selective inactivation of TZ by topical lidocaine application suppressed or delayed the nociceptive withdrawal reflex, suggesting that TZ exerts a tonic facilitatory influence over spinal cord neurons producing this reflex. In conclusion, TZ appears to be a rat homolog of the nociresponsive part of monkey area 3a. A possibility is considered that this region might be primarily engaged in autonomic aspects of nociception.

Effects of stimulus-driven synchronization on sensory perception.

BACKGROUND: A subject's ability to differentiate the loci of two points on the skin depends on the stimulus-evoked pericolumnar lateral inhibitory interactions which increase the spatial contrast between regions of SI cortex that are activated by stimulus-evoked afferent drive. Nevertheless, there is very little known about the impact that neuronal interactions - such as those evoked by mechanical skin stimuli that project to and coordinate synchronized activity in adjacent and/or near-adjacent cortical columns - could have on sensory information processing. METHODS: The temporal order judgment (TOJ) and temporal discriminative threshold (TDT) of 20 healthy adult subjects were assessed both in the absence and presence of concurrent conditions of tactile stimulation. These measures were obtained across a number of paired sites - two unilateral and one bilateral - and several conditions of adapting stimuli were delivered both prior to and concurrently with the TOJ and TDT tasks. The pairs of conditioning stimuli were synchronized and periodic, synchronized and non-periodic, or asynchronous and non-periodic. RESULTS: In the absence of any additional stimuli, TOJ and TDT results obtained from the study were comparable across a number of pairs of stimulus sites - unilateral as well as bilateral. In the presence of a 25 Hz conditioning sinusoidal stimulus which was delivered both before, concurrently and after the TOJ task, there was a significant change in the TOJ measured when the two stimuli were located unilaterally on digits 2 and 3. However, in the presence of the same 25 Hz conditioning stimulus, the TOJ obtained when the two stimuli were delivered bilaterally was not impacted. TDT measures were not impacted to the same degree by the concurrent stimuli that were delivered to the unilateral or bilateral stimulus sites. This led to the speculation that the impact that the conditioning stimuli - which were sinusoidal, periodic and synchronous - had on TOJ measures was due to the synchronization of adjacent cortical ensembles in somatosensory cortex, and that the synchronization of these cortical ensembles could have been responsible for the degradation in temporal order judgment. In order to more directly test this hypothesis, the synchronized 25 Hz conditioning stimuli that were delivered during the initial TOJ test were replaced with asynchronous non-periodic 25 Hz conditioning stimuli, and these asynchronous conditioning stimuli did not impact the TOJ measures. CONCLUSION: The results give support to the theory that synchronization of cortical ensembles in SI could significantly impact the topography of temporal perception, and these findings are speculated to be linked mechanistically to previously reported co-activation plasticity studies. Additionally, the impact that such synchronizing conditioning stimuli have on TOJ - which can be measured relatively quickly - could provide an effective means to assess the functional connectivity of neurologically compromised subject populations.

Activation of cat SII cortex by flutter stimulation of contralateral vs. ipsilateral forepaws.

A distinguishing feature of SII cortex is that it receives substantial input from skin mechanoreceptors located on both sides of the body. It remains uncertain, however, if integration of bilateral inputs occurs mainly in those regions of SII that represent near-midline body regions or also occurs to a significant extent in those regions of SII that represent the distal extremities. This issue was addressed using extracellular microelectrode recordings in cat SII in combination with the method of optical intrinsic signal (OIS) imaging. Stimulation of the central pad of either the contra- or ipsilateral forepaw with a 25-Hz sinusoidal vertical skin displacement ("skin flutter") stimulus evoked a prominent OIS response ("activation") in an extensive anteroposterior sector of SII. In the anteriorly located SII region that yielded the maximal OIS response to stimulation of the contralateral central pad, neurons consistently possessed receptive fields that included the stimulated skin site. This "forepaw" SII region also exhibited significant although 75% weaker OIS activation in response to stimulation of the ipsilateral central pad. Stimulation of the central pads of either contra- or ipsilateral forepaws also evoked OIS activation in the posteriorly located 'hindlimb' region of SII--defined as the SII region comprised of neurons with receptive fields on the contralateral hindlimb. The OIS response to ipsilateral central pad stimulation was strongest in the posterior SII region that borders the suprasylvian fringe--a region in which neurons have very large, and frequently bilateral, cutaneous receptive fields. The results indicate that widespread regions within cat SII receive cutaneous inputs from the ipsilateral distal forelimb. It is suggested that the functional role of these ipsilateral inputs may be different in different SII regions.

Neurosensory Assessments of Concussion.

The purpose of this research was to determine if cortical metrics-a unique set of sensory-based assessment tools-could be used to characterize and differentiate concussed individuals from nonconcussed individuals. Cortical metrics take advantage of the somatotopic relationship between skin and cortex, and the protocols are designed to evoke interactions between adjacent cortical regions to investigate fundamental mechanisms that mediate cortical-cortical interactions. Student athletes, aged 18 to 22 years, were recruited into the study through an athletic training center that made determinations of postconcussion return-to-play status. Sensory-based performance tasks utilizing vibrotactile stimuli applied to tips of the index and middle fingers were administered to test an individual's amplitude discrimination, temporal order judgment, and duration discrimination capacity in the presence and absence of illusion-inducing conditioning stimuli. Comparison of the performances in the presence and absence of conditioning stimuli demonstrated differences between concussed and nonconcussed individuals. Additionally, mathematically combining results from the measures yields a unique central nervous system (CNS) profile that describes an individual's information processing capacity. A comparison was made of CNS profiles of concussed vs. nonconcussed individuals and demonstrated with 99% confidence that the two populations are statistically distinct. The study established solid proof-of-concept that cortical metrics have significant potential as a quantitative biomarker of CNS status.

Stimulus-dependent spatial patterns of response in SI cortex.

BACKGROUND: Recently we reported that vibrotactile flutter stimulation of a skin locus at different amplitudes evokes an optical response confined to the same local region of the primary somatosensory cortex (SI), where its overall magnitude varies proportionally to the flutter amplitude. In this report, we characterize the impact of the flutter amplitude on the spatial patterns of activity evoked within the responding SI region. RESULTS: In order to characterize the spatial pattern of activity within the responding SI region, images of the flutter-evoked SI optical response were segmented and analyzed with spatial frequency analysis. The analysis revealed that: (1) dominant spatial frequencies in the optical intrinsic signal emerge within the responding SI region within 3-5 sec of stimulus onset; (2) the stimulus-evoked activity is spatially organized in a form of several roughly parallel, anterior-posteriorly extended waves, spaced 0.4-0.5 mm apart; (3) the waves themselves exhibit spatial periodicities along their long axis; and (4) depending on the flutter stimulus amplitude, these periodicities can range from fine 0.15 mm "ripples" at 50 microm amplitude to well-developed 0.5 mm fluctuations at the amplitude of 400 microm. CONCLUSION: The observed spatiointensive fractionation on a sub-macrocolumnar scale of the SI response to skin stimulation might be the product of local competitive interactions within the stimulus-activated SI region and may be a feature that could yield novel insights into the functional interactions that take place in SI cortex.

Amplitude-dependency of response of SI cortex to flutter stimulation.

BACKGROUND: It is established that increasing the amplitude of a flutter stimulus increases its perceived intensity. Although many studies have examined this phenomenon with regard to the responding afferent population, the way in which the intensity of a stimulus is coded in primary somatosensory cortex (SI) remains unclear. RESULTS: Optical intrinsic signal (OIS) imaging was used to study the evoked responses in SI of anesthetized squirrel monkeys by 25 Hz sinusoidal vertical skin displacement stimulation. Stimuli were 10 sec duration with a 50 sec inter-stimulus interval. Stimulus amplitude ranged from 50 to 400 microns and different amplitudes were interleaved. Control levels of activity were measured in the absence of stimulation, and used to compare with activation levels evoked by the different stimulus amplitudes. Stimulation of a discrete skin site on the forelimb evoked a prominent increase in absorbance within the forelimb representational region in cytoarchitectonic areas 3b and 1 of the contralateral hemisphere. An increase in stimulus amplitude led to a proportional increase in the magnitude of the absorbance increase in this region of areas 3b and 1 while surrounding cortex underwent a decrease in absorbance. Correlation maps revealed that as stimulus amplitude is increased, the spatial extent of the activated region in SI remains relatively constant, and the activity within this region increases progressively. Additionally, as stimulus amplitude is increased to suprathreshold levels, activity in the surround of the activated SI territory decreases, suggesting an increase in inhibition of neuronal activity within these regions. CONCLUSION: Increasing the amplitude of a flutter stimulus leads to a proportional increase in absorbance within the forelimb representational region of SI. This most likely reflects an increase in the firing rate of neurons in this region of SI. The relatively constant spatial extent of this stimulus-evoked increase in absorbance suggests that an increase in the amplitude of a 25 Hz skin stimulus does not evoke a larger area of SI neuronal activation due to an amplitude-dependent lateral inhibitory effect that spatially funnels the responding SI neuronal population.

Percept of the duration of a vibrotactile stimulus is altered by changing its amplitude.

There have been numerous studies conducted on time perception. However, very few of these have involved tactile stimuli to assess a subject's capacity for duration discrimination. Previous optical imaging studies in non-human primates demonstrated that increasing the duration of a vibrotactile stimulus resulted in a consistently longer and more well defined evoked SI cortical response. Additionally, and perhaps more interestingly, increasing the amplitude of a vibrotactile stimulus not only evoked a larger magnitude optical intrinsic signal (OIS), but the return to baseline of the evoked response was much longer in duration for larger amplitude stimuli. This led the authors to hypothesize that the magnitude of a vibrotactile stimulus could influence the perception of its duration. In order to test this hypothesis, subjects were asked to compare two sets of vibrotactile stimuli. When vibrotactile stimuli differed only in duration, subjects typically had a difference limen (DL) of approximately 13%, and this followed Weber's Law for standards between 500 and 1500 ms, as increasing the value of the standard yielded a proportional increase in DL. However, the percept of duration was impacted by variations in amplitude of the vibrotactile stimuli. Specifically, increasing the amplitude of the standard stimulus had the effect of increasing the DL, while increasing the amplitude of the test stimulus had the effect of decreasing the DL. A pilot study, conducted on individuals who were concussed, found that increasing the amplitude of the standard did not have an impact on the DL of this group of individuals. Since this effect did not parallel what was predicted from the optical imaging findings in somatosensory cortex of non-human primates, the authors suggest that this particular measure or observation could be sensitive to neuroinflammation and that neuron-glial interactions, impacted by concussion, could have the effect of ignoring, or not integrating, the increased amplitude.

Empiricist word learning.

At first, Bloom's theory appears inimical to empiricism, since he credits very young children with highly sophisticated cognitive resources (e.g., a theory of mind and a belief that real kinds have essences), and he also attacks the empiricist's favoured learning theory, namely, associationism. We suggest that, on the contrary, the empiricist can embrace much of what Bloom says.

SHAPE analysis of small RNAs and riboswitches.

We describe structural analysis of small RNAs by SHAPE chemical probing. RNAs are treated with 1-methyl-7-nitroisatoic anhydride, a reagent that detects local nucleotide flexibility; and N-methylisatoic anhydride and 1-methyl-6-nitroisatoic anhydride, reagents which together detect higher-order and noncanonical interactions. Chemical adducts are quantified as stops during reverse transcriptase-mediated primer extension. Probing information can be used to infer conformational changes and ligand binding and to develop highly accurate models of RNA secondary structures.

Attenuated Glial K(+) Clearance Contributes to Long-Term Synaptic Potentiation Via Depolarizing GABA in Dorsal Horn Neurons of Rat Spinal Cord.

It has been reported that long-term enhancement of superficial dorsal horn (DHs) excitatory synaptic transmission underlies central sensitization, secondary hyperalgesia, and persistent pain. We tested whether impaired clearance of K(+) and glutamate by glia in DHs may contribute to initiation and maintenance of the CNS pain circuit and sensorimotor abnormalities. Transient exposure of the spinal cord slice to fluorocitrate (FC) is shown to be accompanied by a protracted decrease of the DHs optical response to repetitive electrical stimulation of the ipsilateral dorsal root, and by a similarly protracted increase in the postsynaptic response of the DHs like LTP. It also is shown that LTPFC does not occur in the presence of APV, and becomes progressively smaller as [K(+)]o in the perfusion solution decreased from 3.0 mM to 0.0 mM. Interestingly LTPFC is reduced by bath application of Bic. Whole-cell patch recordings were carried out to evaluate the effects of FC on the response of DHs neurons to puffer-applied GABA. The observations reveal that transient exposure to FC is reliably accompanied by a prolonged (>1 hr) depolarizing shift of the equilibrium potential for the DHs neuron transmembrane ionic currents evoked by GABA. Considered collectively, the findings demonstrate that LTPFC involves (1) elevation of [K(+)]o in the DHs, (2) NMDAR activation, and (3) conversion of the effect of GABA on DHs neurons from inhibition to excitation. It is proposed that a transient impairment of astrocyte energy production can trigger the cascade of dorsal horn mechanisms that underlies hyperalgesia and persistent pain.