Visual adaptation to convexity in macaque area V4

Aftereffects are perceptual illusions caused by visual adaptation to one or more stimulus attribute, such as orientation, motion, or shape. Neurophysiological studies seeking to understand the basis of visual adaptation have observed firing rate reduction and changes in tuning of stimulus-selective neurons following periods of prolonged visual stimulation. In the domain of shape, recent psychophysical work has shown that adaptation to a convex pattern induces a subsequently seen rectangle to appear slightly concave. In the present study, we investigate the possible contribution of V4 neurons of rhesus monkeys, which are thought to be involved in the coding of convexity, to shape-specific adaptation. Visually responsive neurons were monitored during the brief presentation of simple shapes varying in their convexity level. Each test presentation was preceded by either a blank period or several seconds of adaptation to a convex or concave stimulus, presented in two different sizes. Adaptation consistently shifted the tuning of neurons away from the convex or concave adapter, including shifting response to the neutral rectangle in the direction of the opposite convexity. This repulsive shift resembled the known perceptual distortion associated with adaptation to such stimuli. In addition, adaptation caused a nonspecific response decrease, as well as a specific decrease for repeated stimuli. The latter effects were observed whether or not the adapting and test stimuli matched closely in their size. Taken together, these results provide evidence for shape-specific adaptation of neurons in area V4, which may contribute to the perception of the convexity aftereffect

Startle response probability and amplitude may be independently modulated by affective foreground stimulation as acoustic probe intensity decreases

The magnitude of the eyeblink reflex to an acoustic startle probe is reliable potentiated to highly arousing unpleasant foreground stimuli and inhibited to highly arousing pleasant foreground stimuli across all probe intensity levels. The present study examined the response magnitude findings of Cuthbert, Bradley, and Lang (1996) as response amplitude and probability. Medium arousal pleasant pictures produced larger blink amplitude responses than unpleasant pictures of the same arousal level to 80 and 95, but not 105 dB acoustic startle probes. This effect was opposite for high arousal pictures at all intensity levels. Response probability means decreased from pleasant to unpleasant across all arousal levels to 80 dB probes. The current study provides insight into the differential activation of response amplitude and probability to affective foreground stimulation at lower acoustic stimulus intensities and possible implications for mechanisms involved in the orienting and defensive responses

Solution of the Quasispecies Model for an Arbitrary Gene Network

In this paper, we study the equilibrium behavior of Eigen's quasispecies equations for an arbitrary gene network. We consider a genome consisting of $N$ genes, so that each gene sequence $\sigma$ may be written as $\sigma = \sigma_1 \sigma_2 ... \sigma_N$. We assume a single fitness peak (SFP) model for each gene, so that gene $i$ has some ``master'' sequence $\sigma_{i, 0}$ for which it is functioning. The fitness landscape is then determined by which genes in the genome are functioning, and which are not. The equilibrium behavior of this model may be solved in the limit of infinite sequence length. The central result is that, instead of a single error catastrophe, the model exhibits a series of localization to delocalization transitions, which we term an ``error cascade.'' As the mutation rate is increased, the selective advantage for maintaining functional copies of certain genes in the network disappears, and the population distribution delocalizes over the corresponding sequence spaces. The network goes through a series of such transitions, as more and more genes become inactivated, until eventually delocalization occurs over the entire genome space, resulting in a final error catastrophe. This model provides a criterion for determining the conditions under which certain genes in a genome will lose functionality due to genetic drift. It also provides insight into the response of gene networks to mutagens. In particular, it suggests an approach for determining the relative importance of various genes to the fitness of an organism, in a more accurate manner than the standard ``deletion set'' method. The results in this paper also have implications for mutational robustness and what C.O. Wilke termed ``survival of the flattest.''Comment: 29 pages, 5 figures, to be submitted to Physical Review

RnaseIII and T4 Polynucleotide Kinase Sequence Biases and Solutions During RNA-Seq Library Construction

Background: RNA-seq is a next generation sequencing method with a wide range of applications including single nucleotide polymorphism (SNP) detection, splice junction identification, and gene expression level measurement. However, the RNA-seq sequence data can be biased during library constructions resulting in incorrect data for SNP, splice junction, and gene expression studies. Here, we developed new library preparation methods to limit such biases. Results: A whole transcriptome library prepared for the SOLiD system displayed numerous read duplications (pile-ups) and gaps in known exons. The pile-ups and gaps of the whole transcriptome library caused a loss of SNP and splice junction information and reduced the quality of gene expression results. Further, we found clear sequence biases for both 5' and 3' end reads in the whole transcriptome library. To remove this bias, RNaseIII fragmentation was replaced with heat fragmentation. For adaptor ligation, T4 Polynucleotide Kinase (T4PNK) was used following heat fragmentation. However, its kinase and phosphatase activities introduced additional sequence biases. To minimize them, we used OptiKinase before T4PNK. Our study further revealed the specific target sequences of RNaseIII and T4PNK. Conclusions: Our results suggest that the heat fragmentation removed the RNaseIII sequence bias and significantly reduced the pile-ups and gaps. OptiKinase minimized the T4PNK sequence biases and removed most of the remaining pile-ups and gaps, thus maximizing the quality of RNA-seq data.National Institute on Alcohol Abuse and Alcoholism (NIAAA) AA12404, AA019382, AA020926, AA016648National Institutes of Health (NIH) R01 GM088344Waggoner Center for Alcohol and Addiction Researc

The Error and Repair Catastrophes: A Two-Dimensional Phase Diagram in the Quasispecies Model

This paper develops a two gene, single fitness peak model for determining the equilibrium distribution of genotypes in a unicellular population which is capable of genetic damage repair. The first gene, denoted by $\sigma_{via}$, yields a viable organism with first order growth rate constant $k > 1$ if it is equal to some target ``master'' sequence $\sigma_{via, 0}$. The second gene, denoted by $\sigma_{rep}$, yields an organism capable of genetic repair if it is equal to some target ``master'' sequence $\sigma_{rep, 0}$. This model is analytically solvable in the limit of infinite sequence length, and gives an equilibrium distribution which depends on \mu \equiv L\eps , the product of sequence length and per base pair replication error probability, and \eps_r , the probability of repair failure per base pair. The equilibrium distribution is shown to exist in one of three possible ``phases.'' In the first phase, the population is localized about the viability and repairing master sequences. As \eps_r exceeds the fraction of deleterious mutations, the population undergoes a ``repair'' catastrophe, in which the equilibrium distribution is still localized about the viability master sequence, but is spread ergodically over the sequence subspace defined by the repair gene. Below the repair catastrophe, the distribution undergoes the error catastrophe when $\mu$ exceeds \ln k/\eps_r , while above the repair catastrophe, the distribution undergoes the error catastrophe when $\mu$ exceeds $\ln k/f_{del}$, where $f_{del}$ denotes the fraction of deleterious mutations.Comment: 14 pages, 3 figures. Submitted to Physical Review

Exploring differential effects of an intervention on historical inquiry tasks: a qualitative analysis of 12th-grade students’ progress

Multiple-documents-based (inquiry) tasks are often used to examine historical thinking, as they require students to apply discipline-specific ways of reasoning and writing. Intervention studies using such tasks have often relied on principles from cognitive apprenticeship to make these discipline-specific heuristics explicit to students. While several studies have found positive results, they offer little insight into how and where exactly students’ progress on historical thinking manifests itself, nor into the differential effects of the intervention. Building on essay data gathered during an intervention study on students’ historical inquiry skills, this study explores differential effects of the intervention according to students’ initial historical inquiry ability. To this end, a purposeful sample of students was selected for whom the intervention was particularly effective. The qualitative analysis of students’ essay tasks (pretest and posttest) revealed remarkable differences between students with high and low pretest scores. Although both groups made progress on all aspects of the essay task, they differed in terms of where and how this progress manifested itself: at posttest, students with a high initial score outperformed others in evaluating sources and rebuttals. This study offers insight into patterns of progress in students’ historical inquiry skills which can inform differentiation in instructional practices

Specific disruption of hippocampal mossy fiber synapses in a mouse model of familial Alzheimer's disease.

The earliest stages of Alzheimer's disease (AD) are characterized by deficits in memory and cognition indicating hippocampal pathology. While it is now recognized that synapse dysfunction precedes the hallmark pathological findings of AD, it is unclear if specific hippocampal synapses are particularly vulnerable. Since the mossy fiber (MF) synapse between dentate gyrus (DG) and CA3 regions underlies critical functions disrupted in AD, we utilized serial block-face electron microscopy (SBEM) to analyze MF microcircuitry in a mouse model of familial Alzheimer's disease (FAD). FAD mutant MF terminal complexes were severely disrupted compared to control - they were smaller, contacted fewer postsynaptic spines and had greater numbers of presynaptic filopodial processes. Multi-headed CA3 dendritic spines in the FAD mutant condition were reduced in complexity and had significantly smaller sites of synaptic contact. Significantly, there was no change in the volume of classical dendritic spines at neighboring inputs to CA3 neurons suggesting input-specific defects in the early course of AD related pathology. These data indicate a specific vulnerability of the DG-CA3 network in AD pathogenesis and demonstrate the utility of SBEM to assess circuit specific alterations in mouse models of human disease

Detection of transcranial alternating current stimulation aftereffects is improved by considering the individual electric field strength and self-rated sleepiness

Non-invasive electrical stimulation methods, such as transcranial alternating current stimulation (tACS), are increasingly used in human neuroscience research and offer potential new avenues to treat neurological and psychiatric disorders. However, their often variable effects have also raised concerns in the scientific and clinical communities. This study aims to investigate the influence of subject-specific factors on the alpha tACS-induced aftereffect on the alpha amplitude (measured with electroencephalography, EEG) as well as on the connectivity strength between nodes of the default mode network (DMN) [measured with functional magnetic resonance imaging (fMRI)]. As subject-specific factors we considered the individual electrical field (EFIELD) strength at target regions in the brain, the frequency mismatch between applied stimulation and individual alpha frequency (IAF) and as a covariate, subject's changes in mental state, i.e., sleepiness. Eighteen subjects participated in a tACS and a sham session conducted on different days. Each session consisted of three runs (pre/stimulation/). tACS was applied during the second run at each subject's individual alpha frequency (IAF), applying 1 mA peak-to-peak intensity for 7 min, using an occipital bihemispheric montage. In every run, subjects watched a video designed to increase in-scanner compliance. To investigate the aftereffect of tACS on EEG alpha amplitude and on DMN connectivity strength, EEG data were recorded simultaneously with fMRI data. Self-rated sleepiness was documented using a questionnaire. Conventional statistics (ANOVA) did not show a significant aftereffect of tACS on the alpha amplitude compared to sham stimulation. Including individual EFIELD strengths and self-rated sleepiness scores in a multiple linear regression model, significant tACS-induced aftereffects were observed. However, the subject-wise mismatch between tACS frequency and IAF had no contribution to our model. Neither standard nor extended statistical methods confirmed a tACS-induced aftereffect on DMN functional connectivity. Our results show that it is possible and necessary to disentangle alpha amplitude changes due to intrinsic mechanisms and to external manipulation using tACS on the alpha amplitude that might otherwise be overlooked. Our results suggest that EFIELD is really the most significant factor that explains the alpha amplitude modulation during a tACS session. This knowledge helps to understand the variability of the tACS-induced aftereffects