Inference of CRISPR Edits from Sanger Trace Data.

Efficient and precise genome editing requires a fast, quantitative, and inexpensive assay to assess genotype following editing. Here, we present ICE (Inference of CRISPR Edits), which enables robust analysis of CRISPR edits using Sanger data. ICE proposes potential outcomes for editing with guide RNAs, and then determines which are supported by the data via regression. The ICE algorithm is robust and reproducible, and it can be used to analyze CRISPR experiments within days after transfection. We also confirm that ICE produces accurate estimates of editing outcomes across a variety of benchmarks, and within the context of other existing Sanger analysis tools. The ICE tool is free to use and open source, and offers several improvements over current analysis tools, such as batch analysis and support for a variety of editing conditions. It is available online at ice.synthego.com, and the source code is available at github.com/synthego-open/ice.

Human Sensorimotor Cortex Control of Directly Measured Vocal Tract Movements during Vowel Production.

During speech production, we make vocal tract movements with remarkable precision and speed. Our understanding of how the human brain achieves such proficient control is limited, in part due to the challenge of simultaneously acquiring high-resolution neural recordings and detailed vocal tract measurements. To overcome this challenge, we combined ultrasound and video monitoring of the supralaryngeal articulators (lips, jaw, and tongue) with electrocorticographic recordings from the cortical surface of 4 subjects (3 female, 1 male) to investigate how neural activity in the ventral sensory-motor cortex (vSMC) relates to measured articulator movement kinematics (position, speed, velocity, acceleration) during the production of English vowels. We found that high-gamma activity at many individual vSMC electrodes strongly encoded the kinematics of one or more articulators, but less so for vowel formants and vowel identity. Neural population decoding methods further revealed the structure of kinematic features that distinguish vowels. Encoding of articulator kinematics was sparsely distributed across time and primarily occurred during the time of vowel onset and offset. In contrast, encoding was low during the steady-state portion of the vowel, despite sustained neural activity at some electrodes. Significant representations were found for all kinematic parameters, but speed was the most robust. These findings enabled by direct vocal tract monitoring demonstrate novel insights into the representation of articulatory kinematic parameters encoded in the vSMC during speech production.SIGNIFICANCE STATEMENT Speaking requires precise control and coordination of the vocal tract articulators (lips, jaw, and tongue). Despite the impressive proficiency with which humans move these articulators during speech production, our understanding of how the brain achieves such control is rudimentary, in part because the movements themselves are difficult to observe. By simultaneously measuring speech movements and the neural activity that gives rise to them, we demonstrate how neural activity in sensorimotor cortex produces complex, coordinated movements of the vocal tract.

Methods for Specifying Scientific Data Standards and Modeling Relationships with Applications to Neuroscience.

Neuroscience continues to experience a tremendous growth in data; in terms of the volume and variety of data, the velocity at which data is acquired, and in turn the veracity of data. These challenges are a serious impediment to sharing of data, analyses, and tools within and across labs. Here, we introduce BRAINformat, a novel data standardization framework for the design and management of scientific data formats. The BRAINformat library defines application-independent design concepts and modules that together create a general framework for standardization of scientific data. We describe the formal specification of scientific data standards, which facilitates sharing and verification of data and formats. We introduce the concept of Managed Objects, enabling semantic components of data formats to be specified as self-contained units, supporting modular and reusable design of data format components and file storage. We also introduce the novel concept of Relationship Attributes for modeling and use of semantic relationships between data objects. Based on these concepts we demonstrate the application of our framework to design and implement a standard format for electrophysiology data and show how data standardization and relationship-modeling facilitate data analysis and sharing. The format uses HDF5, enabling portable, scalable, and self-describing data storage and integration with modern high-performance computing for data-driven discovery. The BRAINformat library is open source, easy-to-use, and provides detailed user and developer documentation and is freely available at: https://bitbucket.org/oruebel/brainformat.

High-Resolution, Non-Invasive Imaging of Upper Vocal Tract Articulators Compatible with Human Brain Recordings.

A complete neurobiological understanding of speech motor control requires determination of the relationship between simultaneously recorded neural activity and the kinematics of the lips, jaw, tongue, and larynx. Many speech articulators are internal to the vocal tract, and therefore simultaneously tracking the kinematics of all articulators is nontrivial--especially in the context of human electrophysiology recordings. Here, we describe a noninvasive, multi-modal imaging system to monitor vocal tract kinematics, demonstrate this system in six speakers during production of nine American English vowels, and provide new analysis of such data. Classification and regression analysis revealed considerable variability in the articulator-to-acoustic relationship across speakers. Non-negative matrix factorization extracted basis sets capturing vocal tract shapes allowing for higher vowel classification accuracy than traditional methods. Statistical speech synthesis generated speech from vocal tract measurements, and we demonstrate perceptual identification. We demonstrate the capacity to predict lip kinematics from ventral sensorimotor cortical activity. These results demonstrate a multi-modal system to non-invasively monitor articulator kinematics during speech production, describe novel analytic methods for relating kinematic data to speech acoustics, and provide the first decoding of speech kinematics from electrocorticography. These advances will be critical for understanding the cortical basis of speech production and the creation of vocal prosthetics.

Speech map in the human ventral sensory-motor cortex.

The study of spatial maps of the ventral sensory-motor cortex (vSMC) dates back to the earliest cortical stimulation studies. This review surveys a number of recent and historical reports of the features and function of spatial maps within vSMC towards the human behavior of speaking. Representations of the vocal tract, like other body parts, are arranged in a somatotopic fashion within ventral SMC. This region has unique features and connectivity that may give insight into its specialized function in speech production. New methods allow us to probe further into the functional role of this organization by studying the spatial dynamics of vSMC during natural speaking in humans.

Preference for geometric patterns early in life as a risk factor for autism.

CONTEXT: Early identification efforts are essential for the early treatment of the symptoms of autism but can only occur if robust risk factors are found. Children with autism often engage in repetitive behaviors and anecdotally prefer to visually examine geometric repetition, such as the moving blade of a fan or the spinning of a car wheel. The extent to which a preference for looking at geometric repetition is an early risk factor for autism has yet to be examined. OBJECTIVES: To determine if toddlers with an autism spectrum disorder (ASD) aged 14 to 42 months prefer to visually examine dynamic geometric images more than social images and to determine if visual fixation patterns can correctly classify a toddler as having an ASD. DESIGN: Toddlers were presented with a 1-minute movie depicting moving geometric patterns on 1 side of a video monitor and children in high action, such as dancing or doing yoga, on the other. Using this preferential looking paradigm, total fixation duration and the number of saccades within each movie type were examined using eye tracking technology. SETTING: University of California, San Diego Autism Center of Excellence. PARTICIPANTS: One hundred ten toddlers participated in final analyses (37 with an ASD, 22 with developmental delay, and 51 typical developing toddlers). MAIN OUTCOME MEASURE: Total fixation time within the geometric patterns or social images and the number of saccades were compared between diagnostic groups. RESULTS: Overall, toddlers with an ASD as young as 14 months spent significantly more time fixating on dynamic geometric images than other diagnostic groups. If a toddler spent more than 69% of his or her time fixating on geometric patterns, then the positive predictive value for accurately classifying that toddler as having an ASD was 100%. CONCLUSION: A preference for geometric patterns early in life may be a novel and easily detectable early signature of infants and toddlers at risk for autism.

Reconstructing Dryopteris "semicristata" (Dryopteridaceae): Molecular profiles of tetraploids verify their undiscovered diploid ancestor.

PREMISE OF THE STUDY: Discovering missing ancestors is essential to understanding the evolutionary history of biodiversity on Earth. Evidence from extinct species can provide links for reconstructing intricate patterns of reticulate relationships among extant descendents. When fossils are unavailable and other evidence yields competing hypotheses to explain species ancestry, data from proteins and DNA can help resolve conflicts and generate novel perspectives. The identity of a parent shared by two tetraploid species in the cosmopolitan fern genus Dryopteris has remained elusive for more than 50 years. Based on available data, four hypotheses were developed previously, each providing a different resolution to this uncertainty. • METHODS: New molecular evidence from studies of isozymes and restriction site analysis of chloroplast DNA tested the competing hypotheses about the diploid ancestors of these two extant Dryopteris polyploids. • KEY RESULTS: The results falsify two of the hypotheses, resolve the uncertainty in the third, and support the fourth. • CONCLUSIONS: Our data validate the prior existence of Dryopteris "semicristata," which was proposed 38 years ago as a diploid progenitor of the allotetraploids D. cristata and D. carthusiana but has never been collected. After developing a phylogeny using the new molecular data, we describe a plausible morphology for D. "semicristata" by extrapolating likely character states from related extant species.

A molecular phylogeny of scaly tree ferns (Cyatheaceae).

Tree ferns recently were identified as the closest sister group to the hyperdiverse clade of ferns, the polypods. Although most of the 600 species of tree ferns are arborescent, the group encompasses a wide range of morphological variability, from diminutive members to the giant scaly tree ferns, Cyatheaceae. This well-known family comprises most of the tree fern diversity (∼500 species) and is widespread in tropical, subtropical, and south temperate regions of the world. Here we investigate the phylogenetic relationships of scaly tree ferns based on DNA sequence data from five plastid regions (rbcL, rbcL-accD IGS, rbcL-atpB IGS, trnG-trnR, and trnL-trnF). A basal dichotomy resolves Sphaeropteris as sister to all other taxa and scale features support these two clades: Sphaeropteris has conform scales, whereas all other taxa have marginate scales. The marginate-scaled clade consists of a basal trichotomy, with the three groups here termed (1) Cyathea (including Cnemidaria, Hymenophyllopsis, Trichipteris), (2) Alsophila sensu stricto, and (3) Gymnosphaera (previously recognized as a section within Alsophila) + A. capensis. Scaly tree ferns display a wide range of indusial structures, and although indusium shape is homoplastic it does contain useful phylogenetic information that supports some of the larger clades recognised.

Tree ferns: monophyletic groups and their relationships as revealed by four protein-coding plastid loci.

Tree ferns are a well-established clade within leptosporangiate ferns. Most of the 600 species (in seven families and 13 genera) are arborescent, but considerable morphological variability exists, spanning the giant scaly tree ferns (Cyatheaceae), the low, erect plants (Plagiogyriaceae), and the diminutive endemics of the Guayana Highlands (Hymenophyllopsidaceae). In this study, we investigate phylogenetic relationships within tree ferns based on analyses of four protein-coding, plastid loci (atpA, atpB, rbcL, and rps4). Our results reveal four well-supported clades, with genera of Dicksoniaceae (sensu ) interspersed among them: (A) (Loxomataceae, (Culcita, Plagiogyriaceae)), (B) (Calochlaena, (Dicksonia, Lophosoriaceae)), (C) Cibotium, and (D) Cyatheaceae, with Hymenophyllopsidaceae nested within. How these four groups are related to one other, to Thyrsopteris, or to Metaxyaceae is weakly supported. Our results show that Dicksoniaceae and Cyatheaceae, as currently recognised, are not monophyletic and new circumscriptions for these families are needed.