No concurrent correlations between parental mental state talk and toddlers' language abilities.

Mental State Talk (MST) is utterances describing invisible mental aspects. The first aim of this study was to investigate the characteristics of Parental MST and Child MST and their concurrent association in a Swedish population, and the second aim was to relate these MST measures to the children's general language abilities. Seventy-seven dyads of parents and their 25-month-old toddlers participated. MST was assessed by videotaping the dyads during free-play sessions in a laboratory and general language abilities were based on parental reports. Forty-nine toddlers did not produce MST, while all parents used MST. Child MST was positively associated with vocabulary and grammar. Parental MST was not associated with Child MST nor the children's general language abilities. In exploratory analyses, Parental MST referred to another than the child was positively correlated with vocabulary and grammar. Further studies are needed to confirm these findings and continue studying MST in different linguistic contexts.

The Natural Language Environment of 9-Month-Old Infants in Sweden and Concurrent Association With Early Language Development.

The language environment is important for the development of early communication and language. In the current study, we describe the natural home language environment of 9-month-old infants in Sweden and its concurrent association with language development. Eighty-eight families took part in the study. The home language environment was measured using the Language ENvironment Analysis (LENA) system, and language development was assessed using Swedish Early Communicative Development Inventory (SECDI), a parent questionnaire. LENA measures showed dramatic variation between individuals but were comparable to and showed overlapping variance with previous studies conducted in English-speaking households. Nonetheless, there were significantly more infant vocalizations and conversational turns in the present study than in one previous study. Adult word count correlated significantly and positively with infants' Use of gestures and the subscale of that section Communicative gestures. These together with another four non-significant associations formed a consistent overall pattern that suggested a link between infants' language environment and language development. Although the direction of causality cannot be determined from the current data, future studies should examine children longitudinally to assess the directionality or the bidirectionality of the reported associations between infant's language environment and language development.

Procedural memory in infancy: Evidence from implicit sequence learning in an eye-tracking paradigm.

Procedural memory underpins the learning of skills and habits. It is often tested in children and adults with sequence learning on the serial reaction time (SRT) task, which involves manual motor control. However, due to infants' slowly developing control of motor actions, most procedures that require motor control cannot be examined in infancy. Here, we investigated procedural memory using an SRT task adapted for infants. During the task, images appeared at one of three locations on a screen, with the location order following a five-item recurring sequence. Three blocks of recurring sequences were followed by a random-order fourth block and finally another block of recurring sequences. Eye movement data were collected for infants (n = 35) and adults (n = 31). Reaction time was indexed by calculating the saccade latencies for orienting to each image as it appeared. The entire protocol took less than 3 min. Sequence learning in the SRT task can be operationalized as an increase in latencies in the random block as compared with the preceding and following sequence blocks. This pattern was observed in both the infants and adults. This study is the first to report learning in an SRT task in infants as young as 9  months. This SRT protocol is a promising procedure for measuring procedural memory in infants.

Identifying in-trans process associated genes in breast cancer by integrated analysis of copy number and expression data.

Genomic copy number alterations are common in cancer. Finding the genes causally implicated in oncogenesis is challenging because the gain or loss of a chromosomal region may affect a few key driver genes and many passengers. Integrative analyses have opened new vistas for addressing this issue. One approach is to identify genes with frequent copy number alterations and corresponding changes in expression. Several methods also analyse effects of transcriptional changes on known pathways. Here, we propose a method that analyses in-cis correlated genes for evidence of in-trans association to biological processes, with no bias towards processes of a particular type or function. The method aims to identify cis-regulated genes for which the expression correlation to other genes provides further evidence of a network-perturbing role in cancer. The proposed unsupervised approach involves a sequence of statistical tests to systematically narrow down the list of relevant genes, based on integrative analysis of copy number and gene expression data. A novel adjustment method handles confounding effects of co-occurring copy number aberrations, potentially a large source of false positives in such studies. Applying the method to whole-genome copy number and expression data from 100 primary breast carcinomas, 6373 genes were identified as commonly aberrant, 578 were highly in-cis correlated, and 56 were in addition associated in-trans to biological processes. Among these in-trans process associated and cis-correlated (iPAC) genes, 28% have previously been reported as breast cancer associated, and 64% as cancer associated. By combining statistical evidence from three separate subanalyses that focus respectively on copy number, gene expression and the combination of the two, the proposed method identifies several known and novel cancer driver candidates. Validation in an independent data set supports the conclusion that the method identifies genes implicated in cancer.

Identification of fusion genes in breast cancer by paired-end RNA-sequencing.

BACKGROUND: Until recently, chromosomal translocations and fusion genes have been an underappreciated class of mutations in solid tumors. Next-generation sequencing technologies provide an opportunity for systematic characterization of cancer cell transcriptomes, including the discovery of expressed fusion genes resulting from underlying genomic rearrangements. RESULTS: We applied paired-end RNA-seq to identify 24 novel and 3 previously known fusion genes in breast cancer cells. Supported by an improved bioinformatic approach, we had a 95% success rate of validating gene fusions initially detected by RNA-seq. Fusion partner genes were found to contribute promoters (5' UTR), coding sequences and 3' UTRs. Most fusion genes were associated with copy number transitions and were particularly common in high-level DNA amplifications. This suggests that fusion events may contribute to the selective advantage provided by DNA amplifications and deletions. Some of the fusion partner genes, such as GSDMB in the TATDN1-GSDMB fusion and IKZF3 in the VAPB-IKZF3 fusion, were only detected as a fusion transcript, indicating activation of a dormant gene by the fusion event. A number of fusion gene partners have either been previously observed in oncogenic gene fusions, mostly in leukemias, or otherwise reported to be oncogenic. RNA interference-mediated knock-down of the VAPB-IKZF3 fusion gene indicated that it may be necessary for cancer cell growth and survival. CONCLUSIONS: In summary, using RNA-sequencing and improved bioinformatic stratification, we have discovered a number of novel fusion genes in breast cancer, and identified VAPB-IKZF3 as a potential fusion gene with importance for the growth and survival of breast cancer cells.