Children’s level of word knowledge predicts their exclusion of familiar objects as referents of novel words

When children are learning a novel object label, they tend to exclude as possible referents familiar objects for which they already have a name. In the current study, we wanted to know if children would behave in this same way regardless of how well they knew the name of potential referent objects, specifically, whether they could only comprehend it or they could both comprehend and produce it. Sixty-six monolingual German-speaking 2-, 3-, and 4-year-old children participated in two experimental sessions. In one session the familiar objects were chosen such that their labels were in the children’s productive vocabularies, and in the other session the familiar objects were chosen such that their labels were only in the children’s receptive vocabularies. Results indicated that children at all three ages were more likely to exclude a familiar object as the potential referent of the novel word if they could comprehend and produce its name rather than comprehend its name only. Indeed, level of word knowledge as operationalized in this way was a better predictor than was age. These results are discussed in the context of current theories of word learning by exclusion

Corrigendum: Reduced mu power in response to unusual actions is context-dependent in 1-year-olds

During social interactions infants predict and evaluate other people’s actions. Previous behavioral research found that infants’ imitation of others’ actions depends on these evaluations and is context-dependent: 1-year-olds predominantly imitated an unusual action (turning on a lamp with one’s forehead) when the model’s hands were free compared to when the model’s hands were occupied or restrained. In the present study, we adapted this behavioral paradigm to a neurophysiological study measuring infants’ brain activity while observing usual and unusual actions via electroencephalography. In particular, we measured differences in mu power (6 – 8 Hz) associated with motor activation. In a between-subjects design, 12- to 14-month-old infants watched videos of adult models demonstrating that their hands were either free or restrained. Subsequent test frames showed the models turning on a lamp or a soundbox by using their head or their hand. Results in the hands-free condition revealed that 12- to 14-month-olds displayed a reduction of mu power in frontal regions in response to unusual and thus unexpected actions (head touch) compared to usual and expected actions (hand touch). This may be explained by increased motor activation required for updating prior action predictions in response to unusual actions though alternative explanations in terms of general attention or cognitive control processes may also be considered. In the hands-restrained condition, responses in mu frequency band did not differ between action outcomes. This implies that unusual head-touch actions compared to hand-touch actions do not necessarily evoke a reduction of mu power. Thus, we conclude that reduction of mu frequency power is context-dependent during infants’ action perception. Our results are interpreted in terms of motor system activity measured via changes in mu frequency band as being one important neural mechanism involved in action prediction and evaluation from early on

Transition probabilities for general birth-death processes with applications in ecology, genetics, and evolution

A birth-death process is a continuous-time Markov chain that counts the number of particles in a system over time. In the general process with $n$ current particles, a new particle is born with instantaneous rate $\lambda_n$ and a particle dies with instantaneous rate $\mu_n$. Currently no robust and efficient method exists to evaluate the finite-time transition probabilities in a general birth-death process with arbitrary birth and death rates. In this paper, we first revisit the theory of continued fractions to obtain expressions for the Laplace transforms of these transition probabilities and make explicit an important derivation connecting transition probabilities and continued fractions. We then develop an efficient algorithm for computing these probabilities that analyzes the error associated with approximations in the method. We demonstrate that this error-controlled method agrees with known solutions and outperforms previous approaches to computing these probabilities. Finally, we apply our novel method to several important problems in ecology, evolution, and genetics

Gram-negative and -positive bacteria differentiation in blood culture samples by headspace volatile compound analysis

BACKGROUND: Identification of microorganisms in positive blood cultures still relies on standard techniques such as Gram staining followed by culturing with definite microorganism identification. Alternatively, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry or the analysis of headspace volatile compound (VC) composition produced by cultures can help to differentiate between microorganisms under experimental conditions. This study assessed the efficacy of volatile compound based microorganism differentiation into Gram-negatives and -positives in unselected positive blood culture samples from patients. METHODS: Headspace gas samples of positive blood culture samples were transferred to sterilized, sealed, and evacuated 20 ml glass vials and stored at −30 °C until batch analysis. Headspace gas VC content analysis was carried out via an auto sampler connected to an ion–molecule reaction mass spectrometer (IMR-MS). Measurements covered a mass range from 16 to 135 u including CO(2), H(2), N(2), and O(2). Prediction rules for microorganism identification based on VC composition were derived using a training data set and evaluated using a validation data set within a random split validation procedure. RESULTS: One-hundred-fifty-two aerobic samples growing 27 Gram-negatives, 106 Gram-positives, and 19 fungi and 130 anaerobic samples growing 37 Gram-negatives, 91 Gram-positives, and two fungi were analysed. In anaerobic samples, ten discriminators were identified by the random forest method allowing for bacteria differentiation into Gram-negative and -positive (error rate: 16.7 % in validation data set). For aerobic samples the error rate was not better than random. CONCLUSIONS: In anaerobic blood culture samples of patients IMR-MS based headspace VC composition analysis facilitates bacteria differentiation into Gram-negative and -positive. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s40709-016-0040-0) contains supplementary material, which is available to authorized users

A genome-wide CRISPR activation screen identifies

The genome is pervasively transcribed to produce a vast array of non-coding RNAs (ncRNAs). Long non-coding RNAs (lncRNAs) are transcripts of \u3e200 nucleotides and are best known for their ability to regulate gene expression. Enhancer RNAs (eRNAs) are subclass of lncRNAs that are synthesized from enhancer regions and have also been shown to coordinate gene expression. The biological function and significance of most lncRNAs and eRNAs remain to be determined. Epithelial to mesenchymal transition (EMT) is a ubiquitous cellular process that occurs during cellular migration, homeostasis, fibrosis, and cancer-cell metastasis. EMT- transcription factors, such as SNAI1 induce a complex transcriptional program that coordinates the morphological and molecular changes associated with EMT. Such complex transcriptional programs are often subject to coordination by networks of ncRNAs and thus can be leveraged to identify novel functional ncRNA loci. Here, using a genome-wide CRISPR activation (CRISPRa) screen targeting ~10,000 lncRNA loci we identified ncRNA loci that could either promote or attenuate EMT. We discovered a novel locus that we named SCREEM (SNAI1 cis-regulatory eRNAs expressed in monocytes). The SCREEM locus contained a cluster of eRNAs that when activated using CRISPRa induced expression of the neighboring gene SNAI1, driving concomitant EMT. However, the SCREEM eRNA transcripts themselves appeared dispensable for the induction of SNAI1 expression. Interestingly, the SCREEM eRNAs and SNAI1 were co- expressed in activated monocytes, where the SCREEM locus demarcated a monocyte-specific super-enhancer. These findings suggest a potential role for SNAI1 in monocytes. Exploration of the SCREEM-SNAI axis could reveal novel aspects of monocyte biology

On-the-fly Uniformization of Time-Inhomogeneous Infinite Markov Population Models

This paper presents an on-the-fly uniformization technique for the analysis of time-inhomogeneous Markov population models. This technique is applicable to models with infinite state spaces and unbounded rates, which are, for instance, encountered in the realm of biochemical reaction networks. To deal with the infinite state space, we dynamically maintain a finite subset of the states where most of the probability mass is located. This approach yields an underapproximation of the original, infinite system. We present experimental results to show the applicability of our technique

Single Cell Analysis of Blood Mononuclear Cells Stimulated Through Either LPS or Anti-CD3 and Anti-CD28.

Immune cell activation assays have been widely used for immune monitoring and for understanding disease mechanisms. However, these assays are typically limited in scope. A holistic study of circulating immune cell responses to different activators is lacking. Here we developed a cost-effective high-throughput multiplexed single-cell RNA-seq combined with epitope tagging (CITE-seq) to determine how classic activators of T cells (anti-CD3 coupled with anti-CD28) or monocytes (LPS) alter the cell composition and transcriptional profiles of peripheral blood mononuclear cells (PBMCs) from healthy human donors. Anti-CD3/CD28 treatment activated all classes of lymphocytes either directly (T cells) or indirectly (B and NK cells) but reduced monocyte numbers. Activated T and NK cells expressed senescence and effector molecules, whereas activated B cells transcriptionally resembled autoimmune disease- or age-associated B cells (e.g., CD11c, T-bet). In contrast, LPS specifically targeted monocytes and induced two main states: early activation characterized by the expression of chemoattractants and a later pro-inflammatory state characterized by expression of effector molecules. These data provide a foundation for future immune activation studies with single cell technologies (https://czi-pbmc-cite-seq.jax.org/)

Spectral properties of zero temperature dynamics in a model of a compacting granular column

The compacting of a column of grains has been studied using a one-dimensional Ising model with long range directed interactions in which down and up spins represent orientations of the grain having or not having an associated void. When the column is not shaken (zero 'temperature') the motion becomes highly constrained and under most circumstances we find that the generator of the stochastic dynamics assumes an unusual form: many eigenvalues become degenerate, but the associated multi-dimensional invariant spaces have but a single eigenvector. There is no spectral expansion and a Jordan form must be used. Many properties of the dynamics are established here analytically; some are not. General issues associated with the Jordan form are also taken up.Comment: 34 pages, 4 figures, 3 table

Design and construction of new central and forward muon counters for CDF II

New scintillation counters have been designed and constructed for the CDF upgrade in order to complete the muon coverage of the central CDF detector, and to extend this coverage to larger pseudorapidity. A novel light collection technique using wavelength shifting fibers, together with high quality polystyrene-based scintillator resulted in compact counters with good and stable light collection efficiency over lengths extending up to 320 cm. Their design and construction is described and results of their initial performance are reported.Comment: 20 pages, 15 figure

Looking backward: From Euler to Riemann

We survey the main ideas in the early history of the subjects on which Riemann worked and that led to some of his most important discoveries. The subjects discussed include the theory of functions of a complex variable, elliptic and Abelian integrals, the hypergeometric series, the zeta function, topology, differential geometry, integration, and the notion of space. We shall see that among Riemann's predecessors in all these fields, one name occupies a prominent place, this is Leonhard Euler. The final version of this paper will appear in the book \emph{From Riemann to differential geometry and relativity} (L. Ji, A. Papadopoulos and S. Yamada, ed.) Berlin: Springer, 2017