Genome sequencing detects a wide range of clinically relevant copy-number variants and other genomic alterations.

PURPOSE: Copy-number variants (CNVs) and other non-single nucleotide variant/indel variant types contribute an important proportion of diagnoses in individuals with suspected genetic disease. This study describes the range of such variants detected by genome sequencing (GS). METHODS: For a pediatric cohort of 1032 participants undergoing clinical GS, we characterize the CNVs and other non-single nucleotide variant/indel variant types that were reported, including aneuploidies, mobile element insertions, and uniparental disomies, and we describe the bioinformatic pipeline used to detect these variants. RESULTS: Together, these genetic alterations accounted for 15.8% of reported variants. Notably, 67.9% of these were deletions, 32.9% of which overlapped a single gene, and many deletions were reported together with a second variant in the same gene in cases of recessive disease. A retrospective medical record review in a subset of this cohort revealed that up to 6 additional genetic tests were ordered in 68% (26/38) of cases, some of which failed to report the CNVs/rare variants reported on GS. CONCLUSION: GS detected a broad range of reported variant types, including CNVs ranging in size from 1 Kb to 46 Mb.

Ultrasound Measurement of the Transverse Abdominis, Internal Oblique, and External Oblique Muscles Associated with Forward Head Posture and Reduced Cranio-Vertebral Angle.

BACKGROUND Abnormal posture can affect the alignment of the cervical spine, which can lead to various physical problems. There are many ways to solve the problem by limiting the area around the neck to restore abnormal neck condition. However, there is a need to look at these problems from an enlarged perspective through the relationship between the cervical spine and trunk. This study aimed to investigate the significance of the thickness of the transverse abdominis, internal oblique, and external oblique muscles in patients with forward head posture and reduced cranio-vertebral angle. MATERIAL AND METHODS We included 24 healthy adult males in their 20s without lower back pain. The cranio-vertebral angle (CVA) in all the subjects was measured with the help of pictures taken in the sagittal plane using a digital camera. The thickness of muscles, including transverse abdominis (TrA), internal oblique (IO), and external oblique (EO), was measured using a diagnostic ultrasound device. Pearson's correlation analysis was used to identify the correlation between the variables measured. RESULTS CVA showed a statistically significant correlation with TrA thickness (r=0.506/p=0.012), and among the abdominal muscles, there was a significant correlation between IO and EO thickness (r=0.663/p=0.000). CONCLUSIONS A reduced CVA due to FHP was significantly associated with reduced TrA thickness. Therefore, increasing the bulk of the abdominal muscles with restoration of the abnormal CVA is a potential treatment approach and requires further study.

Differences in respiratory pressure and pulmonary function among children with spastic diplegic and hemiplegic cerebral palsy in comparison with normal controls.

[Purpose] The purpose of this study was to determine differences in respiratory pressure and pulmonary function among children with spastic diplegic and hemiplegic cerebral palsy (CP) in comparison with children with normal development. [Subjects and Methods] Fourteen children with spastic diplegic CP, 11 children with hemiplegic CP, and 14 children with normal development were recruited. Respiratory pressure was measured and the pulmonary function test (PFT) was performed to evaluate the strength of the respiratory muscles and lung volumetric capacity. [Results] Regarding respiratory pressure, children with spastic diplegic and hemiplegic CP showed significantly lower functions in terms of MIP and MEP compared with children with normal development, although no significant differences were found between children with the two types of CP. In the pulmonary function test, children with spastic diplegic CP showed significantly higher pulmonary function than children with normal development in terms of only FVC and FEV1. [Conclusion] Children with CP showed relatively lower function in terms of respiratory pressure and lung capacity, in comparison with children with normal development. Therefore, respiratory function in children with CP should be carefully evaluated and should receive more attention in a rehabilitation setting.

Effectiveness of motor sequential learning according to practice schedules in healthy adults; distributed practice versus massed practice.

[Purpose] The purpose of the current study was to compare the effectiveness of motor sequential learning according to two different types of practice schedules, distributed practice schedule (two 12-hour inter-trial intervals) and massed practice schedule (two 10-minute inter-trial intervals) using a serial reaction time (SRT) task. [Subjects and Methods] Thirty healthy subjects were recruited and then randomly and evenly assigned to either the distributed practice group or the massed practice group. All subjects performed three consecutive sessions of the SRT task following one of the two different types of practice schedules. Distributed practice was scheduled for two 12-hour inter-session intervals including sleeping time, whereas massed practice was administered for two 10-minute inter-session intervals. Response time (RT) and response accuracy (RA) were measured in at pre-test, mid-test, and post-test. [Results] For RT, univariate analysis demonstrated significant main effects in the within-group comparison of the three tests as well as the interaction effect of two groups × three tests, whereas the between-group comparison showed no significant effect. The results for RA showed no significant differences in neither the between-group comparison nor the interaction effect of two groups × three tests, whereas the within-group comparison of the three tests showed a significant main effect. [Conclusion] Distributed practice led to enhancement of motor skill acquisition at the first inter-session interval as well as at the second inter-interval the following day, compared to massed practice. Consequentially, the results of this study suggest that a distributed practice schedule can enhance the effectiveness of motor sequential learning in 1-day learning as well as for two days learning formats compared to massed practice.

The effect of aging on respiratory synergy.

[Purpose] The purpose of this study was to investigate the effect of aging on respiratory synergy, through the comparison of an elderly group and a young group, to help further understanding of postural control in the elderly. [Subjects and Methods] Ten community-dwelling elderly subjects and ten young subjects performed standing under two different respiratory conditions: quiet breathing and apnea. Center of foot pressure displacement and joint angular movements of the head, trunk, pelvis, hips, knees and ankles were measured. [Results] The results of this study showed that the elderly group had a respiratory synergy different from that of the young group. The elderly group in quiet stance used significantly more hip and pelvis movements when compensating for respiratory disturbance than standing with apnea, while the young group used significantly more whole body segments. There were no differences in angular displacements in the quiet stance between the elderly and the young groups. [Conclusion] The elderly group demonstrated a respiratory synergy pattern different from that of the young group. The findings indicate that aging changes the respiratory synergy pattern and this change is not due to decreased functioning of the ankle joint alone.

Prevalence and determinants of pain in the ipsilateral upper limb of stroke patients.

This study investigated the prevalence of pain in the ipsilateral upper-limb in stroke patients. 229 stroke patients (133 men, 96 women; M age = 59.0 yr., SD = 12.4) were assessed with the Pain Behaviors Scales and their motor weakness was measured with the Motricity Index. Results indicated that over 27% of patients experienced pain in at least one joint of the ipsilateral upper limb. Shoulder pain was the most common. Further analysis indicated that the occurrence of pain in the ipsilateral upper limb was higher among women, among patients who used a cane, and among patients with a greater weakness of the affected lower limb.

Differences of respiratory function according to level of the gross motor function classification system in children with cerebral palsy.

[Purpose] The current study was designed to investigate the difference in lung capacity and muscle strengthening related to respiration depending on the level of the Gross Motor Function Classification System (GMFCS) in children with cerebral palsy (CP) through tests of respiratory function and respiratory pressure. [Subjects and Methods] A total of 49 children with CP who were classified as below level III of the GMFCS were recruited for this study. They were divided into three groups (i.e., GMFCS level I, GMFCS level II, and GMFCS level III). All children took the pulmonary function test (PFT) and underwent respiratory pressure testing for assessment of respiratory function in terms of lung capacity and respiratory muscle strength. [Results] The GMFCS level III group showed significantly lower scores for all tests of the PFT (i.e., forced vital capacity (FVC), forced expiratory volume at one second (FEV1), and slow vital capacity (SVC)) and testing for respiratory pressures (maximal inspiratory pressure (MIP) and maximal expiratory pressure (MEP)) compared with the other two groups. The results of post hoc analysis indicated that the GMFCS level III group differed significantly from the other two groups in terms of FVC, FEV1, MIP, and MEP. In addition, a significant difference in SVC was observed between GMFCS level II and III. [Conclusion] Children with CP who had relatively low motor function showed poor pulmonary capacity and respiratory muscle weakness. Therefore, clinical manifestations regarding lung capacity and respiratory muscle will be required in children with CP who demonstrate poor physical activity.

The influence of time of day on static and dynamic postural control in normal adults.

[Purpose] We attempted to determine whether static and dynamic postural control ability fluctuated depending on the influence of the time of day (9 am, 1 pm, and 5 pm), and at which time point postural balance performance was best in healthy individuals. [Subjects and Methods] Twenty-four healthy subjects participated in this study. The static and dynamic postural balance test was conducted during three sessions (i.e., at 9 am, 1 pm, and 5 pm) with a counterbalanced order for prevention of learning effects. As outcome measurements, AP distance, ML distance, and velocity moment were adopted in the static balance test, and the performance time and total distance were measured in the dynamic balance test. [Results] For the static postural balance test, COP distance was shorter and COP velocity was slower at 9 am compared with those at 1 and 5 pm. In particular, the COP distance at 9 am was statistically different from that at 13 pm. During the dynamic postural balance test, performance time and total distance were influenced by the time of day, as the best performance was observed in the morning. [Conclusion] This study found that static and dynamic postural balance abilities were greatest in the morning and worst at 1 pm. Understanding of the mechanism of the time-of-day effect on postural balance will be helpful for assessment and treatment of postural balance by physical therapists and in making desirable clinical decisions.

Cell-Free Systems for the Production of Glycoproteins.

Cell-free protein synthesis (CFPS), whereby cell lysates are used to produce proteins from a genetic template, has matured as an attractive alternative to standard biomanufacturing modalities due to its high volumetric productivity contained within a distributable platform. Initially, cell-free lysates produced from Escherichia coli, which are both simple to produce and cost-effective for the production of a wide variety of proteins, were unable to produce glycosylated proteins as E. coli lacks native glycosylation machinery. With many important therapeutic proteins possessing asparagine-linked glycans that are critical for structure and function, this gap in CFPS production capabilities was addressed with the development of cell-free expression of glycoproteins (glycoCFE), which uses the supplementation of extracted lipid-linked oligosaccharides and purified oligosaccharyltransferases to enable glycoprotein production in the CFPS reaction environment. In this chapter, we highlight the basic methods for the preparation of reagents for glycoCFE and the protocol for expression and glycosylation of a model protein using a more productive, yet simplified, glycoCFE setup. Beyond this initial protocol, we also highlight how this protocol can be extended to a wide range of alternative glycan structures, oligosaccharyltransferases, and acceptor proteins as well as to a one-pot cell-free glycoprotein synthesis reaction.

Diffusion tensor imaging findings of optic radiation in patients with putaminal hemorrhage.

OBJECTIVES: Little is known about optic radiation (OR) injury in intracerebral hemorrhage (ICH). We attempted to investigate OR injury in patients with ICH by diffusion tensor imaging (DTI). METHODS: Forty-three consecutive patients with putaminal hemorrhage and 40 normal healthy control subjects were recruited. DTI data were acquired at the beginning of rehabilitation (average 34 days after onset). DTI-Studio software was used to reconstruct the OR. Fractional anisotropies (FA) and fiber numbers of the ORs were measured. FA values and fiber numbers of affected ORs were described as abnormal when they were more than 2.5 SD lower than those of normal controls. RESULTS: Thirty (70%) of the 43 patients showed an OR abnormality in the affected hemisphere. In 13 (30%) patients, the affected OR was disrupted or nonreconstructable. On the other hand, of the 20 patients with preserved OR integrity, 14 (33%) had a low FA value and 3 (7%) a low FA and fiber number. The other 13 (30%) of the 43 patients had no abnormal OR findings. CONCLUSION: Seventy percent of patients showed any abnormality of OR in the affected hemisphere on DTI. This result suggests that patients with putaminal hemorrhage are at high risk of OR injury.

Response Inhibition Induced in the Stop-signal Task by Transcranial Direct Current Stimulation of the Pre-supplementary Motor Area and Primary Sensoriomotor Cortex.

[Purpose] This study examined whether transcranial direct current stimulation (tDCS) of both the pre-supplementary motor area (pre-SMA) and primary sensoriomotor cortex (M1) alters the response time in response inhibition using the stop-signal task (SST). [Methods] Forty healthy subjects were enrolled in this study. The subjects were randomly tested under the three: the pre-SMA tDCS, M1 tDCS, and Sham tDCS conditions. All subjects performed a SST in two consecutive phases: without or after the delivery of anodal tDCS over one of the target sites (pre-SMA or the M1) and under the Sham tDCS condition. [Results] Our findings demonstrated significant reductions in the stop processing times after the anodal tDCS over pre-SMA, and change response times were significantly greater under the pre-SMA tDCS condition compared to both the M1 tDCS condition and the Sham tDCS condition. There was no significant major effect after delivery of the tDCS for the go processing times observed among the three conditions. [Conclusion] Anodal tDCS of the pre-SMA or M1 during performance of the SST resulted in enhancement of the volitional stop movement in inhibitory control. Our results suggest that when concurrently applied with the SST, tDCS might be a useful adjuvant therapeutic modality for modulation of the response inhibition and its related dynamic behavioral changes between motor execution and suppression.

Differences of the Truncal Expansion and Respiratory Function between Children with Spastic Diplegic and Hemiplegic Cerebral Palsy.

[Purpose] We attempted to determine whether differences of respiratory function could be found in terms of truncal expansion, respiratory muscle strength, and pulmonary function test (PFT) between children with spastic diplegic and hemiplegic cerebral palsy. [Subjects and Methods] We recruited 19 children with spastic diplegic CP (diplegic-CP group) and 10 children with spastic hemiplegic CP (hemiplegic-CP group). For all the children, clinical factors associated with respiratory functions were assessed in terms of truncal expansion (chest and waist expansion), respiratory muscle strength (maximal inspiration and expiration pressures: MIP and MEP), and pulmonary function test (FVC, FEV1, and FEV1/FVC). [Results] Overall, the diplegic-CP group showed lower truncal circumference, respiratory muscle strength, and pulmonary function values than the hemiplegic-CP group. However, in the comparison of the two groups significant differences were only found in waist expansion, MIP, MEP, FVC, and FEV1. [Conclusion] The results of this study indicate that children with diplegic CP have much poorer waist expansion, weaker respiratory muscle, and lower pulmonary function values. These findings will provide valuable information for use in the clinical assessment and treatment of children with spastic CP.

Deficits of Movement Accuracy and Proprioceptive Sense in the Ipsi-lesional Upper Limb of Patients with Hemiparetic Stroke.

[Purpose] Previous studies have reported on motor deficits in the ipsilateral upper limbs (UL) of a damaged brain hemisphere in motor tasks. However, little is known about sensory deficits on the ipsilateral side. Therefore, we investigated whether both motor and sensory function of the ipsilateral UL are affected in patients with stroke. [Subjects and Methods] Fifty patients with unilateral stroke and 40 age- and sex- matched normal subjects participated in this study. Subjects were evaluated on performance of a tracking task for motor function, and by the joint reposition test for integrity of proprioceptive sense in the ipsilateral UL. [Result] The comparison of the stroke group and the control group showed significant differences in performance of the tracking task and the joint reposition test. The accuracy index for the tracking task showed significant correlation with the error score for the joint reposition test in the stroke group. [Conclusion] These results suggest that the ipsilateral UL of stroke patients has impairment in sensory function which is related to proprioceptive sense, along with motor deficits. Therefore, we think that the difficulty stroke patients experience with motor tasks for the ipsilateral UL is induced by diminished integrity of sensorimotor function due to both sensory and motor deficits.

The effects of aging on visuomotor coordination and proprioceptive function in the upper limb.

[Purpose] Sensorimotor processing, including motor performance, is altered during the process of normal aging. Previous studies have investigated tasks requiring complex visuomotor coordination and active joint reposition tests. Therefore, the purpose of this study was to investigate age-related changes in upper limb tasks, such as visuomotor coordination and proprioceptive acuity. [Subjects and Methods] We recruited 20 healthy elderly subjects and 20 healthy young subjects. We evaluated a tracking task for visuomotor function and a joint reposition test for integrity of proprioceptive sense in both hands of the elderly subjects, and compared the results with those of the healthy young subjects. [Results] The accuracy index scores for the tracking task were significantly lower in both the dominant and non-dominant hands of the elderly subjects than those of the young group. In addition, the reposition error score in the joint reposition test was significantly higher in the elderly group than in the young group. [Conclusion] Sensorimotor functions of both the dominant and non-dominant hands showed a decline in the elderly group. This finding suggests that sensorimotor function deteriorates with advancing age.

Scalable, high quality, whole genome sequencing from archived, newborn, dried blood spots.

Universal newborn screening (NBS) is a highly successful public health intervention. Archived dried bloodspots (DBS) collected for NBS represent a rich resource for population genomic studies. To fully harness this resource in such studies, DBS must yield high-quality genomic DNA (gDNA) for whole genome sequencing (WGS). In this pilot study, we hypothesized that gDNA of sufficient quality and quantity for WGS could be extracted from archived DBS up to 20 years old without PCR (Polymerase Chain Reaction) amplification. We describe simple methods for gDNA extraction and WGS library preparation from several types of DBS. We tested these methods in DBS from 25 individuals who had previously undergone diagnostic, clinical WGS and 29 randomly selected DBS cards collected for NBS from the California State Biobank. While gDNA from DBS had significantly less yield than from EDTA blood from the same individuals, it was of sufficient quality and quantity for WGS without PCR. All samples DBS yielded WGS that met quality control metrics for high-confidence variant calling. Twenty-eight variants of various types that had been reported clinically in 19 samples were recapitulated in WGS from DBS. There were no significant effects of age or paper type on WGS quality. Archived DBS appear to be a suitable sample type for WGS in population genomic studies.

Predictability of motor outcome according to the time of diffusion tensor imaging in patients with cerebral infarct.

INTRODUCTION: Predictability of diffusion tensor imaging tractography (DTT) for motor outcome can differ according to the time of DTT. We attempted to compare the predictability for motor outcome according to the time of diffusion tensor imaging (DTI) by analyzing the corticospinal tract (CST) integrity on DTT in patients with corona radiata (CR) infarct. METHODS: Seventy-one consecutive hemiparetic patients with CR infarct were recruited. Motor function of the affected extremities was measured twice: at onset and at 6 months from onset. According to the time of DTI, patients were classified into two groups: the early scanning group (ES group) within 14 days since stroke onset; and the late scanning group (LS group) 15-28 days. Motor outcome was compared with the CST integrity on DTT. RESULTS: Motor prognosis was predicted from scan time of DTI and the CST integrity on DTT in the logistic regression model. According to separate regression analysis, the CST integrity of the late group was found to predict MI score (OR = 14.000, 95% CI = 3.194-61.362, p < 0.05), whereas the CST integrity of the early group was not found to predict MI score. CONCLUSIONS: In terms of both positive and negative predictabilities, we found that predictability of DTT for motor outcome was better in patients who were scanned later (15-28 days after onset) than in patients who were scanned earlier (1-14 days after onset).

Somatotopic location of corticospinal tracts in the internal capsule with MR tractography.

We demonstrated the exact location of the somatotopic area of the corticospinal tract in the internal capsule. Ten healthy subjects participated in this study. We used the imaging technique that combines functional magnetic resonance imaging and diffusion tensor tractography. In order to reduce erroneous elements while image processing, we used the probabilistic tracking algorithm and brain normalization method. Our results showed that hand fibers were located anteromedial to foot fibers, and the separation angle between them was 45.00-78.69°. In conclusion, we confirmed the relative location of hand and foot fibers and the separation angle in the internal capsule. These data are useful information for neuroscience researchers.

The prevalence of central poststroke pain according to the integrity of the spino-thalamo-cortical pathway.

OBJECTIVES: Little is known about the prevalence of central poststroke pain (CPSP) according to the integrity of the spino-thalamo-cortical pathway (STP). Using diffusion tensor tractography, we investigated the prevalence of CPSP according to the integrity of the STP in patients with intracerebral hemorrhage. METHODS: We recruited 52 consecutive chronic patients and 10 normal control subjects. Patients were classified into two groups according to preservation of the integrity of the STP. Each group was divided into two subgroups according to the presence of CPSP. RESULTS: The preserved group included 34 patients [CPSP subgroup, 16 (47%) patients; non-CPSP subgroup, 18 (53%) patients], and 18 patients were enrolled into the disrupted group [CPSP subgroup, 3 (17%) patients; non-CPSP subgroup, 15 (83%) patients]. The fractional anisotropy and mean diffusivity values of the CPSP and non-CPSP subgroups of the preserved group were decreased and increased when compared with those of the control group, respectively (p < 0.05). CONCLUSIONS: We found that the prevalence of CPSP in patients with partial injury of the STP was higher than that of patients with complete injury of the STP. Partial injury of the STP appears to be more vulnerable to development of CPSP than complete injury of the STP in patients with intracerebral hemorrhage.

A universal glycoenzyme biosynthesis pipeline that enables efficient cell-free remodeling of glycans.

The ability to reconstitute natural glycosylation pathways or prototype entirely new ones from scratch is hampered by the limited availability of functional glycoenzymes, many of which are membrane proteins that fail to express in heterologous hosts. Here, we describe a strategy for topologically converting membrane-bound glycosyltransferases (GTs) into water soluble biocatalysts, which are expressed at high levels in the cytoplasm of living cells with retention of biological activity. We demonstrate the universality of the approach through facile production of 98 difficult-to-express GTs, predominantly of human origin, across several commonly used expression platforms. Using a subset of these water-soluble enzymes, we perform structural remodeling of both free and protein-linked glycans including those found on the monoclonal antibody therapeutic trastuzumab. Overall, our strategy for rationally redesigning GTs provides an effective and versatile biosynthetic route to large quantities of diverse, enzymatically active GTs, which should find use in structure-function studies as well as in biochemical and biomedical applications involving complex glycomolecules.

All-Solution-Processed Van der Waals Heterostructures for Wafer-Scale Electronics.

2D van der Waals (vdW) materials have been considered as potential building blocks for use in fundamental elements of electronic and optoelectronic devices, such as electrodes, channels, and dielectrics, because of their diverse and remarkable electrical properties. Furthermore, two or more building blocks of different electronic types can be stacked vertically to generate vdW heterostructures with desired electrical behaviors. However, such fundamental approaches cannot directly be applied practically because of issues such as precise alignment/positioning and large-quantity material production. Here, these limitations are overcome and wafer-scale vdW heterostructures are demonstrated by exploiting the lateral and vertical assembly of solution-processed 2D vdW materials. The high exfoliation yield of the molecular intercalation-assisted approach enables the production of micrometer-sized nanosheets in large quantities and its lateral assembly in a wafer-scale via vdW interactions. Subsequently, the laterally assembled vdW thin-films are vertically assembled to demonstrate various electronic device applications, such as transistors and photodetectors. Furthermore, multidimensional vdW heterostructures are demonstrated by integrating 1D carbon nanotubes as a p-type semiconductor to fabricate p-n diodes and complementary logic gates. Finally, electronic devices are fabricated via inkjet printing as a lithography-free manner based on the stable nanomaterial dispersions.