Characterizing the Major Structural Variant Alleles of the Human Genome.

In order to provide a comprehensive resource for human structural variants (SVs), we generated long-read sequence data and analyzed SVs for fifteen human genomes. We sequence resolved 99,604 insertions, deletions, and inversions including 2,238 (1.6 Mbp) that are shared among all discovery genomes with an additional 13,053 (6.9 Mbp) present in the majority, indicating minor alleles or errors in the reference. Genotyping in 440 additional genomes confirms the most common SVs in unique euchromatin are now sequence resolved. We report a ninefold SV bias toward the last 5 Mbp of human chromosomes with nearly 55% of all VNTRs (variable number of tandem repeats) mapping to this portion of the genome. We identify SVs affecting coding and noncoding regulatory loci improving annotation and interpretation of functional variation. These data provide the framework to construct a canonical human reference and a resource for developing advanced representations capable of capturing allelic diversity.

Genomic Patterns of De Novo Mutation in Simplex Autism.

To further our understanding of the genetic etiology of autism, we generated and analyzed genome sequence data from 516 idiopathic autism families (2,064 individuals). This resource includes >59 million single-nucleotide variants (SNVs) and 9,212 private copy number variants (CNVs), of which 133,992 and 88 are de novo mutations (DNMs), respectively. We estimate a mutation rate of ∼1.5 × 10-8 SNVs per site per generation with a significantly higher mutation rate in repetitive DNA. Comparing probands and unaffected siblings, we observe several DNM trends. Probands carry more gene-disruptive CNVs and SNVs, resulting in severe missense mutations and mapping to predicted fetal brain promoters and embryonic stem cell enhancers. These differences become more pronounced for autism genes (p = 1.8 × 10-3, OR = 2.2). Patients are more likely to carry multiple coding and noncoding DNMs in different genes, which are enriched for expression in striatal neurons (p = 3 × 10-3), suggesting a path forward for genetically characterizing more complex cases of autism.

Publisher Correction: Nanomagnetic encoding of shape-morphing micromachines.

An Amendment to this paper has been published and can be accessed via a link at the top of the paper.

Nanomagnetic encoding of shape-morphing micromachines.

Shape-morphing systems, which can perform complex tasks through morphological transformations, are of great interest for future applications in minimally invasive medicine1,2, soft robotics3-6, active metamaterials7 and smart surfaces8. With current fabrication methods, shape-morphing configurations have been embedded into structural design by, for example, spatial distribution of heterogeneous materials9-14, which cannot be altered once fabricated. The systems are therefore restricted to a single type of transformation that is predetermined by their geometry. Here we develop a strategy to encode multiple shape-morphing instructions into a micromachine by programming the magnetic configurations of arrays of single-domain nanomagnets on connected panels. This programming is achieved by applying a specific sequence of magnetic fields to nanomagnets with suitably tailored switching fields, and results in specific shape transformations of the customized micromachines under an applied magnetic field. Using this concept, we have built an assembly of modular units that can be programmed to morph into letters of the alphabet, and we have constructed a microscale 'bird' capable of complex behaviours, including 'flapping', 'hovering', 'turning' and 'side-slipping'. This establishes a route for the creation of future intelligent microsystems that are reconfigurable and reprogrammable in situ, and that can therefore adapt to complex situations.

A single touch can provide sufficient mechanical stimulation to trigger Venus flytrap closure.

The carnivorous Venus flytrap catches prey by an ingenious snapping mechanism. Based on work over nearly 200 years, it has become generally accepted that two touches of the trap's sensory hairs within 30 s, each one generating an action potential, are required to trigger closure of the trap. We developed an electromechanical model, which, however, suggests that under certain circumstances one touch is sufficient to generate two action potentials. Using a force-sensing microrobotic system, we precisely quantified the sensory-hair deflection parameters necessary to trigger trap closure and correlated them with the elicited action potentials in vivo. Our results confirm the model's predictions, suggesting that the Venus flytrap may be adapted to a wider range of prey movements than previously assumed.

A Biodegradable Magnetic Microrobot Based on Gelatin Methacrylate for Precise Delivery of Stem Cells with Mass Production Capability.

A great deal of research has focused on small-scale robots for biomedical applications and minimally invasive delivery of therapeutics (e.g., cells, drugs, and genes) to a target area. Conventional fabrication methods, such as two-photon polymerization, can be used to build sophisticated micro- and nanorobots, but the long fabrication cycle for a single microrobot has limited its practical use. This study proposes a biodegradable spherical gelatin methacrylate (GelMA) microrobot for mass production in a microfluidic channel. The proposed microrobot is fabricated in a flow-focusing droplet generator by shearing a mixture of GelMA, photoinitiator, and superparamagnetic iron oxide nanoparticles (SPIONs) with a mixture of oil and surfactant. Human nasal turbinate stem cells (hNTSCs) are loaded on the GelMA microrobot, and the hNTSC-loaded microrobot shows precise rolling motion in response to an external rotating magnetic field. The microrobot is enzymatically degraded by collagenase, and released hNTSCs are proliferated and differentiated into neuronal cells. In addition, the feasibility of the GelMA microrobot as a cell therapeutic delivery system is investigated by measuring electrophysiological activity on a multielectrode array. Such a versatile and fully biodegradable microrobot has the potential for targeted stem cell delivery, proliferation, and differentiation for stem cell-based therapy.

Metal-Organic Frameworks in Motion.

During the last two decades, engineering motion with small-scale matter has received much attention in several areas of research, ranging from supramolecular chemistry and colloidal science to robotics and automation. The numerous discoveries and innovative concepts realized in motile micro- and nanostructures have converged in the field of small-scale swimmers. These man-made micro- and nanomachines can move in fluids by transforming different forms of energy to mechanical motion. Recently, metal-organic frameworks (MOFs), which are crystalline coordination polymers with high porosity, have been proposed as key building blocks in several small-scale swimmer designs. These materials possess the required features for motile micro- and nanodevices, such as high cargo-loading capacity, biodegradability, biocompatibility, and stimuli-responsiveness. In this review, we take a journey through the major breakthroughs and milestones realized in the area of MOF-based small-scale swimmers. First, a brief introduction to the field of small-scale swimmers is provided. Next, we review different strategies that have been reported for imparting motion to MOFs. Finally, we emphasize the incorporation of molecular machines into the MOF's architecture as the means to create highly integrated small-scale swimmers. The strategies and developments explored in this review pave the way toward the use of motile MOFs for a variety of applications in the fields of biomedicine, environmental remediation, and on-the-fly chemistry.

National Collegiate Athletic Association Swimmers With Glenohumeral Multidirectional Laxity Have an Increased Glenohumeral Joint Range of Motion Profile.

CONTEXT: Adaptations in glenohumeral joint laxity and range of motion (ROM) are prevalent in competitive swimmers. Increased glenohumeral laxity in swimmers has been found to exist in multiple directions. However, it is unclear if swimmers with multidirectional laxity (MDL) possess altered glenohumeral ROM compared with swimmers without MDL. The purpose of this study was to compare the glenohumeral ROM characteristics of external rotation (ER), internal rotation (IR), total arc of motion (ER + IR), and total arc of motion ratio (ER/IR) between swimmers with MDL and without MDL. Our secondary objective was to investigate the effect of MDL on self-reported pain and function. DESIGN: Observational study. METHODS: Twenty-nine NCAA Division I swimmers (females: 15 and males: 14; age 19.5 [1.2] y; body mass index 23.9 [2.0] km/m2) participated in a preseason physical assessment including measures of glenohumeral ROM and joint laxity. These measures were used to determine the presence or absence of MDL for both shoulders of each participant. Glenohumeral ROM characteristics were compared between shoulders with MDL and shoulders without MDL with independent t tests. Self-reported pain and function scores were recorded biweekly across the season with a modified Kerlan-Jobe Orthopedic Clinic questionnaire. The seasonal average Kerlan-Jobe Orthopedic Clinic questionnaire scores were compared between swimmers with MDL and swimmers without MDL with analysis of variance, with factors of sex and MDL status. RESULTS: Shoulders with MDL possessed increased glenohumeral IR (P < .001; effect size: 0.65) and total arc of motion (P < .004; effect size: 0.45) compared with shoulders without MDL. There were no differences in ER. There was no difference in self-reported pain and function between groups. CONCLUSIONS: Shoulders with MDL possess increased glenohumeral IR and total arc of motion compared with shoulders without MDL. The presence of MDL may not affect self-reported pain and function in competitive swimmers.

Embedded Microbubbles for Acoustic Manipulation of Single Cells and Microfluidic Applications.

Acoustically excited microstructures have demonstrated significant potential for small-scale biomedical applications by overcoming major microfluidic limitations. Recently, the application of oscillating microbubbles has demonstrated their superiority over acoustically excited solid structures due to their enhanced acoustic streaming at low input power. However, their limited temporal stability hinders their direct applicability for industrial or clinical purposes. Here, we introduce the embedded microbubble, a novel acoustofluidic design based on the combination of solid structures (poly(dimethylsiloxane)) and microbubbles (air-filled cavity) to combine the benefits of both approaches while minimizing their drawbacks. We investigate the influence of various design parameters and geometrical features through numerical simulations and experimentally evaluate their manipulation capabilities. Finally, we demonstrate the capabilities of our design for microfluidic applications by investigating its mixing performance as well as through the controlled rotational manipulation of individual HeLa cells.

Transcriptional fates of human-specific segmental duplications in brain.

Despite the importance of duplicate genes for evolutionary adaptation, accurate gene annotation is often incomplete, incorrect, or lacking in regions of segmental duplication. We developed an approach combining long-read sequencing and hybridization capture to yield full-length transcript information and confidently distinguish between nearly identical genes/paralogs. We used biotinylated probes to enrich for full-length cDNA from duplicated regions, which were then amplified, size-fractionated, and sequenced using single-molecule, long-read sequencing technology, permitting us to distinguish between highly identical genes by virtue of multiple paralogous sequence variants. We examined 19 gene families as expressed in developing and adult human brain, selected for their high sequence identity (average >99%) and overlap with human-specific segmental duplications (SDs). We characterized the transcriptional differences between related paralogs to better understand the birth-death process of duplicate genes and particularly how the process leads to gene innovation. In 48% of the cases, we find that the expressed duplicates have changed substantially from their ancestral models due to novel sites of transcription initiation, splicing, and polyadenylation, as well as fusion transcripts that connect duplication-derived exons with neighboring genes. We detect unannotated open reading frames in genes currently annotated as pseudogenes, while relegating other duplicates to nonfunctional status. Our method significantly improves gene annotation, specifically defining full-length transcripts, isoforms, and open reading frames for new genes in highly identical SDs. The approach will be more broadly applicable to genes in structurally complex regions of other genomes where the duplication process creates novel genes important for adaptive traits.

Nano-3D-Printed Photochromic Micro-Objects.

Molecular photoswitches that can reversibly change color upon irradiation are promising materials for applications in molecular actuation and photoresponsive materials. However, the fabrication of photochromic devices is limited to conventional approaches such as mold casting and spin-coating, which cannot fabricate complex structures. Reported here is the first photoresist for direct laser writing of photochromic 3D micro-objects via two-photon polymerization. The integration of photochromism into thiol-ene photo-clickable resins enables rapid two-photon laser processing of highly complex microstructures and facile postmodification using a series of donor-acceptor Stenhouse adduct (DASA) photoswitches with different excitation wavelengths. The versatility of thiol-ene photo-click reactions allows fine-tuning of the network structure and physical properties as well as the type and concentration of DASA. When exposed to visible light, these microstructures exhibit excellent photoresponsiveness and undergo reversible color-changing via photoisomerization. It is demonstrated that the fluorescence variations of DASAs can be used as a reporter of photoswitching and thermal recovery, allowing the reading of DASA-containing sub-micrometric structures in 3D. This work delivers a new approach for custom microfabrication of 3D photochromic objects with molecularly engineered color and responsiveness.

Recurrent structural variation, clustered sites of selection, and disease risk for the complement factor H (CFH) gene family.

Structural variation and single-nucleotide variation of the complement factor H (CFH) gene family underlie several complex genetic diseases, including age-related macular degeneration (AMD) and atypical hemolytic uremic syndrome (AHUS). To understand its diversity and evolution, we performed high-quality sequencing of this ∼360-kbp locus in six primate lineages, including multiple human haplotypes. Comparative sequence analyses reveal two distinct periods of gene duplication leading to the emergence of four CFH-related (CFHR) gene paralogs (CFHR2 and CFHR4 ∼25-35 Mya and CFHR1 and CFHR3 ∼7-13 Mya). Remarkably, all evolutionary breakpoints share a common ∼4.8-kbp segment corresponding to an ancestral CFHR gene promoter that has expanded independently throughout primate evolution. This segment is recurrently reused and juxtaposed with a donor duplication containing exons 8 and 9 from ancestral CFH, creating four CFHR fusion genes that include lineage-specific members of the gene family. Combined analysis of >5,000 AMD cases and controls identifies a significant burden of a rare missense mutation that clusters at the N terminus of CFH [P = 5.81 × 10-8, odds ratio (OR) = 9.8 (3.67-Infinity)]. A bipolar clustering pattern of rare nonsynonymous mutations in patients with AMD (P < 10-3) and AHUS (P = 0.0079) maps to functional domains that show evidence of positive selection during primate evolution. Our structural variation analysis in >2,400 individuals reveals five recurrent rearrangement breakpoints that show variable frequency among AMD cases and controls. These data suggest a dynamic and recurrent pattern of mutation critical to the emergence of new CFHR genes but also in the predisposition to complex human genetic disease phenotypes.

Anterior Cruciate Ligament Reconstructed Female Athletes Exhibit Relative Muscle Dysfunction After Return to Sport.

We sought to examine the relationship between upper-leg compartmental lean mass, muscle-specific strength, and explosive strength following anterior cruciate ligament reconstruction. Twleve adolescent female athletes with prior anterior cruciate ligament reconstruction were individually-matched by age (16.4±0.9 vs. 16.4±1.0 yrs.), body mass index (23.2±2.1 vs. 23.2±2.7 kg/m2), and sport to 12 female athlete controls. One total-body and 2 lateral-leg dual X-ray absorptiometry scans measured total/segmental body composition. Isokinetic dynamometry measured knee extensor/flexor peak torque. Squat jumps on force platforms measured bilateral peak vertical ground reaction force. Paired t-tests assessed lean mass, peak torque, and force between previously-injured athletes' legs and between previously-injured and control athletes' legs. Previously-injured athletes' involved vs. non-involved leg demonstrated lower total (7.13±0.75 vs. 7.43±0.99 kg; p<0.01) and anterior (1.49±0.27 vs. 1.61±0.23 kg; p<0.01) and posterior (1.90±0.19 vs. 2.02±0.21 kg; p=0.04) upper-leg lean mass. Involved leg peak torque (1.36±0.31; 1.06±0.27; 0.97±0.19 Nm/kg) was lower vs. non-involved leg (1.71±0.36; 1.24±0.33; 1.04±0.15 Nm/kg; p<0.01-0.02) for extension at 60 and 120°/sec and flexion at 60°/sec and vs. controls' 'matched' leg (1.77±0.40 Nm/kg; p=0.01) for extension at 60°/sec. Involved leg force (296±45N) was lower vs. non-involved leg (375±55N; p<0.01) and vs. controls' 'matched' leg (372±88N; p=0.02). One-year post-anterior cruciate ligament reconstruction, adolescent female athletes' involved leg demonstrated relative muscle dysfunction.

Integrated Pedal System for Data Driven Rehabilitation.

We present a system capable of providing visual feedback for ergometer training, allowing detailed analysis and gamification. The presented solution can easily upgrade any existing ergometer device. The system consists of a set of pedals with embedded sensors, readout electronics and wireless communication modules and a tablet device for interaction with the users, which can be mounted on any ergometer, transforming it into a full analytical assessment tool with interactive training capabilities. The methods to capture the forces and moments applied to the pedal, as well as the pedal's angular position, were validated using reference sensors and high-speed video capture systems. The mean-absolute error (MAE) for load is found to be 18.82 N, 25.35 N, 0.153 Nm for Fx, Fz and Mx respectively and the MAE for the pedal angle is 13.2°. A fully gamified experience of ergometer training has been demonstrated with the presented system to enhance the rehabilitation experience with audio visual feedback, based on measured cycling parameters.

An Intelligent In-Shoe System for Gait Monitoring and Analysis with Optimized Sampling and Real-Time Visualization Capabilities.

The deterioration of gait can be used as a biomarker for ageing and neurological diseases. Continuous gait monitoring and analysis are essential for early deficit detection and personalized rehabilitation. The use of mobile and wearable inertial sensor systems for gait monitoring and analysis have been well explored with promising results in the literature. However, most of these studies focus on technologies for the assessment of gait characteristics, few of them have considered the data acquisition bandwidth of the sensing system. Inadequate sampling frequency will sacrifice signal fidelity, thus leading to an inaccurate estimation especially for spatial gait parameters. In this work, we developed an inertial sensor based in-shoe gait analysis system for real-time gait monitoring and investigated the optimal sampling frequency to capture all the information on walking patterns. An exploratory validation study was performed using an optical motion capture system on four healthy adult subjects, where each person underwent five walking sessions, giving a total of 20 sessions. Percentage mean absolute errors (MAE%) obtained in stride time, stride length, stride velocity, and cadence while walking were 1.19%, 1.68%, 2.08%, and 1.23%, respectively. In addition, an eigenanalysis based graphical descriptor from raw gait cycle signals was proposed as a new gait metric that can be quantified by principal component analysis to differentiate gait patterns, which has great potential to be used as a powerful analytical tool for gait disorder diagnostics.

Laser thermal therapy for epilepsy surgery: current standing and future perspectives.

More than 130-year ago, Sir Victor Horsley delivered a landmark address to the British Medical Association, in which he described successful localization and resection of an epileptogenic focus resulting in seizure freedom for the patient. Several important steps in epilepsy surgery have been achieved since, including resection techniques such as anterior temporal lobectomy and selective amygdalohippocampectomy, both resulting in 70-80% seizure freedom and distinct differences in neuropsychological outcomes. The most recent addition to techniques for epilepsy surgery is minimally invasive thermal therapy. Significant advances in imaging technology and thermal ablation have opened a novel avenue for epilepsy treatment, permitting surgical intervention with seizure-freedom rates approaching the success of traditional methods but with reduced invasiveness, blood loss and duration of postoperative hospital stay. Here, we review recent advances on stereotactic ablation techniques focused on epilepsy surgery. Finally, we present emerging navigation techniques, which allow a higher degree of freedom. The described technologies render precise navigation of the ablation probe to avoid critical structures along the trajectory path and open novel pathways to further minimize invasiveness and improve safety and efficacy. Improve safety and efficacy.

Underpinning transport phenomena for the patterning of biomolecules.

Surface-based assays are increasingly being used in biology and medicine, which in turn demand increasing quantitation and reproducibility. This translates into more stringent requirements on the patterning of biological entities on surfaces (also referred to as biopatterning). This tutorial focuses on mass transport in the context of existing and emerging biopatterning technologies. We here develop a step-by-step analysis of how analyte transport affects surface kinetics, and of the advantages and limitations this entails in major categories of patterning methods, including evaporating sessile droplets, laminar flows in microfluidics or electrochemistry. Understanding these concepts is key to obtaining the desired pattern uniformity, coverage, analyte usage or processing time, and equally applicable to surface assays. A representative technological review accompanies each section, highlighting the technical progress enabled by transport control in e.g. microcontact printing, inkjet printing, dip-pen nanolithography and microfluidic probes. We believe this tutorial will serve researchers to better understand available patterning methods/principles, optimize conditions and to help design protocols/assays. By highlighting fundamental challenges and available approaches, we wish to trigger the development of new surface patterning methods and assays.

Kinematics Governing Mechanotransduction in the Sensory Hair of the Venus flytrap.

Insects fall prey to the Venus flytrap (Dionaea muscipula) when they touch the sensory hairs located on the flytrap lobes, causing sudden trap closure. The mechanical stimulus imparted by the touch produces an electrical response in the sensory cells of the trigger hair. These cells are found in a constriction near the hair base, where a notch appears around the hair's periphery. There are mechanosensitive ion channels (MSCs) in the sensory cells that open due to a change in membrane tension; however, the kinematics behind this process is unclear. In this study, we investigate how the stimulus acts on the sensory cells by building a multi-scale hair model, using morphometric data obtained from µ-CT scans. We simulated a single-touch stimulus and evaluated the resulting cell wall stretch. Interestingly, the model showed that high stretch values are diverted away from the notch periphery and, instead, localized in the interior regions of the cell wall. We repeated our simulations for different cell shape variants to elucidate how the morphology influences the location of these high-stretch regions. Our results suggest that there is likely a higher mechanotransduction activity in these 'hotspots', which may provide new insights into the arrangement and functioning of MSCs in the flytrap.

Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA.

We performed whole-genome sequencing (WGS) of 208 genomes from 53 families affected by simplex autism. For the majority of these families, no copy-number variant (CNV) or candidate de novo gene-disruptive single-nucleotide variant (SNV) had been detected by microarray or whole-exome sequencing (WES). We integrated multiple CNV and SNV analyses and extensive experimental validation to identify additional candidate mutations in eight families. We report that compared to control individuals, probands showed a significant (p = 0.03) enrichment of de novo and private disruptive mutations within fetal CNS DNase I hypersensitive sites (i.e., putative regulatory regions). This effect was only observed within 50 kb of genes that have been previously associated with autism risk, including genes where dosage sensitivity has already been established by recurrent disruptive de novo protein-coding mutations (ARID1B, SCN2A, NR3C2, PRKCA, and DSCAM). In addition, we provide evidence of gene-disruptive CNVs (in DISC1, WNT7A, RBFOX1, and MBD5), as well as smaller de novo CNVs and exon-specific SNVs missed by exome sequencing in neurodevelopmental genes (e.g., CANX, SAE1, and PIK3CA). Our results suggest that the detection of smaller, often multiple CNVs affecting putative regulatory elements might help explain additional risk of simplex autism.

Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region.

Recurrent rearrangements of Chromosome 8p23.1 are associated with congenital heart defects and developmental delay. The complexity of this region has led to inconsistencies in the current reference assembly, confounding studies of genetic variation. Using comparative sequence-based approaches, we generated a high-quality 6.3-Mbp alternate reference assembly of an inverted Chromosome 8p23.1 haplotype. Comparison with nonhuman primates reveals a 746-kbp duplicative transposition and two separate inversion events that arose in the last million years of human evolution. The breakpoints associated with these rearrangements map to an ape-specific interchromosomal core duplicon that clusters at sites of evolutionary inversion (P = 7.8 × 10-5). Refinement of microdeletion breakpoints identifies a subgroup of patients that map to the same interchromosomal core involved in the evolutionary formation of the duplication blocks. Our results define a higher-order genomic instability element that has shaped the structure of specific chromosomes during primate evolution contributing to rearrangements associated with inversion and disease.