Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease.

Rare coding mutations cause ∼45% of congenital heart disease (CHD). Noncoding mutations that perturb cis-regulatory elements (CREs) likely contribute to the remaining cases, but their identification has been problematic. Using a lentiviral massively parallel reporter assay (lentiMPRA) in human induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs), we functionally evaluated 6,590 noncoding de novo variants (ncDNVs) prioritized from the whole-genome sequencing of 750 CHD trios. A total of 403 ncDNVs substantially affected cardiac CRE activity. A majority increased enhancer activity, often at regions with undetectable reference sequence activity. Of ten DNVs tested by introduction into their native genomic context, four altered the expression of neighboring genes and iPSC-CM transcriptional state. To prioritize future DNVs for functional testing, we used the MPRA data to develop a regression model, EpiCard. Analysis of an independent CHD cohort by EpiCard found enrichment of DNVs. Together, we developed a scalable system to measure the effect of ncDNVs on CRE activity and deployed it to systematically assess the contribution of ncDNVs to CHD.

The unusual gene architecture of polyubiquitin is created by dual-specific splice sites.

BACKGROUND: The removal of introns occurs through the splicing of a 5' splice site (5'ss) with a 3' splice site (3'ss). These two elements are recognized by distinct components of the spliceosome. However, introns in higher eukaryotes contain many matches to the 5' and 3' splice-site motifs that are presumed not to be used. RESULTS: Here, we find that many of these sites can be used. We also find occurrences of the AGGT motif that can function as either a 5'ss or a 3'ss-previously referred to as dual-specific splice sites (DSSs)-within introns. Analysis of the Sequence Read Archive reveals a 3.1-fold enrichment of DSSs relative to expectation, implying synergy between the ability to function as a 5'ss and 3'ss. Despite this suggested mechanistic advantage, DSSs are 2.7- and 4.7-fold underrepresented in annotated 5' and 3' splice sites. A curious exception is the polyubiquitin gene UBC, which contains a tandem array of DSSs that precisely delimit the boundary of each ubiquitin monomer. The resulting isoforms splice stochastically to include a variable number of ubiquitin monomers. We found no evidence of tissue-specific or feedback regulation but note the 8.4-fold enrichment of DSS-spliced introns in tandem repeat genes suggests a driving role in the evolution of genes like UBC. CONCLUSIONS: We find an excess of unannotated splice sites and the utilization of DSSs in tandem repeats supports the role of splicing in gene evolution. These findings enhance our understanding of the diverse and complex nature of the splicing process.

Mechanically Robust and Linearly Sensitive Soft Piezoresistive Pressure Sensor for a Wearable Human-Robot Interaction System.

Soft piezoresistive pressure sensors play an underpinning role in enabling a plethora of future Internet of Things (IoT) applications such as human-robot interaction (HRI) technologies, wearable devices, and metaverse ecosystems. Despite significant attempts to enhance the performance of these sensors, existing sensors still fall short of achieving high strain tolerance and linearity simultaneously. Herein, we present a low-cost, facile, and scalable approach to fabricating a highly strain-tolerant and linearly sensitive soft piezoresistive pressure sensor. Our design utilizes thin nanocracked gold films (NC-GFs) deposited on poly(dimethylsiloxane) (PDMS) as electrodes of the sensor. The large mismatch stress between gold (Au) and PDMS induces the formation of secondary wrinkles along the pyramidal-structured electrode under pressure; these wrinkles function as protuberances on the electrode and enable exceptional linear sensitivity of 4.2 kPa-1 over a wide pressure range. Additionally, our pressure sensor can maintain its performance even after severe mechanical deformations, including repeated stretching up to 30% strain, due to the outstanding strain tolerance of NC-GF. Our sensor's impressive sensing performance and mechanical robustness make it suitable for diverse IoT applications, as demonstrated by its use in wearable pulse monitoring devices and human-robot interaction systems.

Fabrication of practical deformable displays: advances and challenges.

Display form factors such as size and shape have been conventionally determined in consideration of usability and portability. The recent trends requiring wearability and convergence of various smart devices demand innovations in display form factors to realize deformability and large screens. Expandable displays that are foldable, multi-foldable, slidable, or rollable have been commercialized or on the edge of product launches. Beyond such two-dimensional (2D) expansion of displays, efforts have been made to develop three dimensional (3D) free-form displays that can be stretched and crumpled for use in realistic tactile sensation, artificial skin for robots, and on-skin or implantable displays. This review article analyzes the current state of the 2D and 3D deformable displays and discusses the technological challenges to be achieved for industrial commercialization.

Multiplexed Single-Nucleus RNA Sequencing Using Lipid-Oligo Barcodes.

This protocol describes a robust pipeline for simultaneously analyzing multiple samples by single-nucleus (sn)RNA-seq. cDNA obtained from each single sample are labeled with the same lipid-coupled oligonucleotide barcode (10X Genomics). Nuclei from as many as 12 individual samples can be pooled together and simultaneously processed for cDNA library construction and subsequent DNA sequencing. While previous protocols using lipid-coupled oligonucleotide barcodes were optimized for analysis of samples consisting of viable cells, this protocol is optimized for analyses of quick-frozen cell samples. The protocol ensures efficient recovery of nuclei both by incorporating high sucrose buffered solutions and by including a tracking dye (trypan blue) during nuclei isolation. The protocol also describes a procedure for removing single nuclei 'artifacts' by removing cell debris prior to single nuclear fractionation. This protocol informs the use of computational tools for filtering poorly labeled nuclei and assigning sample identity using barcode unique molecular identifier (UMI) read counts percentages. The computational pipeline is applicable to either cultured or primary, fresh or frozen cells, regardless of their cell types and species. Overall, this protocol reduces batch effects and experimental costs while enhancing sample comparison. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Labeling cells with lipid oligo barcodes and generating multiplexed single-nucleus RNA-seq libraries Basic Protocol 2: Bioinformatic deconvolution of the multiplexed snRNAseq libraries.

An ancient founder mutation located between ROBO1 and ROBO2 is responsible for increased microtia risk in Amerindigenous populations.

Microtia is a congenital malformation that encompasses mild hypoplasia to complete loss of the external ear, or pinna. Although the contribution of genetic variation and environmental factors to microtia remains elusive, Amerindigenous populations have the highest reported incidence. Here, using both transmission disequilibrium tests and association studies in microtia trios (parents and affected child) and microtia cohorts enrolled in Latin America, we map an ∼10-kb microtia locus (odds ratio = 4.7; P = 6.78e-18) to the intergenic region between Roundabout 1 (ROBO1) and Roundabout 2 (ROBO2) (chr3: 78546526 to 78555137). While alleles at the microtia locus significantly increase the risk of microtia, their penetrance is low (<1%). We demonstrate that the microtia locus contains a polymorphic complex repeat element that is expanded in affected individuals. The locus is located near a chromatin loop region that regulates ROBO1 and ROBO2 expression in induced pluripotent stem cell­derived neural crest cells. Furthermore, we use single nuclear RNA sequencing to demonstrate ROBO1 and ROBO2 expression in both fibroblasts and chondrocytes of the mature human pinna. Because the microtia allele is enriched in Amerindigenous populations and is shared by some East Asian subjects with craniofacial malformations, we propose that both populations share a mutation that arose in a common ancestor prior to the ancient migration of Eurasian populations into the Americas and that the high incidence of microtia among Amerindigenous populations reflects the population bottleneck that occurred during the migration out of Eurasia.

Cactus-Spine-Inspired Sweat-Collecting Patch for Fast and Continuous Monitoring of Sweat.

A sweat sensor is expected to be the most appropriate wearable device for noninvasive healthcare monitoring. However, the practical use of sweat sensors is impeded by irregular and low sweat secretion rates. Here, a sweat-collecting patch that can collect sweat efficiently for fast and continuous healthcare monitoring is demonstrated. The patch uses cactus-spine-inspired wedge-shaped wettability-patterned channels on a hierarchical microstructured/nanostructured surface. The channel shape, in combination with the superhydrophobic/superhydrophilic surface materials, induces a unidirectional Laplace pressure that transports the sweat to the sensing area spontaneously even when the patch is aligned vertically. The patch demonstrates superior sweat-collecting efficiency and reduces the time required to fill the sensing area by transporting sweat almost without leaving it inside the channel. Therefore, a sensor based on the patch responds quickly to biochemicals in sweat, and the patch enables the continuous monitoring of changes in sweat biochemicals according to their changes in the wearer's blood.

Fingerpad-Inspired Multimodal Electronic Skin for Material Discrimination and Texture Recognition.

Human skin plays a critical role in a person communicating with his or her environment through diverse activities such as touching or deforming an object. Various electronic skin (E-skin) devices have been developed that show functional or geometrical superiority to human skin. However, research into stretchable E-skin that can simultaneously distinguish materials and textures has not been established yet. Here, the first approach to achieving a stretchable multimodal device is reported, that operates on the basis of various electrical properties of piezoelectricity, triboelectricity, and piezoresistivity and that exceeds the capabilities of human tactile perception. The prepared E-skin is composed of a wrinkle-patterned silicon elastomer, hybrid nanomaterials of silver nanowires and zinc oxide nanowires, and a thin elastomeric dielectric layer covering the hybrid nanomaterials, where the dielectric layer exhibits high surface roughness mimicking human fingerprints. This versatile device can identify and distinguish not only mechanical stress from a single stimulus such as pressure, tensile strain, or vibration but also that from a combination of multiple stimuli. With simultaneous sensing and analysis of the integrated stimuli, the approach enables material discrimination and texture recognition for a biomimetic prosthesis when the multifunctional E-skin is applied to a robotic hand.

Differences between proximal and distal M1 occlusions after mechanical thrombectomy.

PURPOSE: Whether M1 occlusions proximal (pM1) and distal (dM1) to the lenticulostriate perforators result in different clinical outcomes after mechanical thrombectomy (MT) is unknown. We retrospectively compared the clinical outcomes and baseline characteristics of patients with these two types of occlusions. METHODS: From March 2010 to May 2019, we performed MT for 141 M1 occlusions, including pM1 occlusions (n = 58) and dM1 occlusions (n = 83). RESULTS: Good clinical outcomes (modified Rankin Scale score 0 to 2) were achieved in 28 out of 58 (48.3%) patients with pM1 occlusions and 46 out of 83 (55.4%) patients with dM1 occlusions without significance (p = 0.493). Cardioembolic occlusions represented 19 out of 58 (32.6%) pM1 occlusions and 53 out of 83 (63.9%) dM1 occlusions, and atherosclerotic occlusions represented 37 out of 58 (63.8%) pM1 occlusions and 27 out of 83 (32.5%) dM1 occlusions, with significance (p = 0.001). Rescue treatments, such as balloon angioplasty or stenting, were needed more for pM1 occlusions than dM1 occlusions (21 out of 58 (36.2%) vs. 8 out of 83 (9.8%), p < 0.001). The multivariable logistic regression analysis demonstrated that the need for rescue treatment was associated with pM1 occlusions (adjusted odds ratio; 3.804, 95% confidence interval; 1.306-11.082, p = 0.014). CONCLUSIONS: In our series, pM1 and dM1 occlusions did not significantly differ in good clinical outcomes. Our study also showed that pM1 occlusions were more strongly associated with atherosclerotic occlusions, while dM1 occlusions were more strongly associated with cardioembolic occlusions, and rescue treatments were needed more often for pM1 occlusions than dM1 occlusions.

User-Interactive Thermotherapeutic Electronic Skin Based on Stretchable Thermochromic Strain Sensor.

User-interactive electronic skin (e-skin) with a distinguishable output has enormous potential for human-machine interfaces and healthcare applications. Despite advances in user-interactive e-skins, advances in visual user-interactive therapeutic e-skins remain rare. Here, a user-interactive thermotherapeutic device is reported that is fabricated by combining thermochromic composites and stretchable strain sensors consisting of strain-responsive silver nanowire networks on surface energy-patterned microwrinkles. Both the color and heat of the device are easily controlled through electrical resistance variation induced by applied mechanical strain. The resulting monolithic device exhibits substantial changes in optical reflectance and temperature with durability, rapid response, high stretchability, and linear sensitivity. The approach enables a low-expertise route to fabricating dynamic interactive thermotherapeutic e-skins that can be used to effectively rehabilitate injured connective tissues as well as to prevent skin burns by simultaneously accommodating stretching, providing heat, and exhibiting a color change.

Genomic analyses implicate noncoding de novo variants in congenital heart disease.

A genetic etiology is identified for one-third of patients with congenital heart disease (CHD), with 8% of cases attributable to coding de novo variants (DNVs). To assess the contribution of noncoding DNVs to CHD, we compared genome sequences from 749 CHD probands and their parents with those from 1,611 unaffected trios. Neural network prediction of noncoding DNV transcriptional impact identified a burden of DNVs in individuals with CHD (n = 2,238 DNVs) compared to controls (n = 4,177; P = 8.7 × 10-4). Independent analyses of enhancers showed an excess of DNVs in associated genes (27 genes versus 3.7 expected, P = 1 × 10-5). We observed significant overlap between these transcription-based approaches (odds ratio (OR) = 2.5, 95% confidence interval (CI) 1.1-5.0, P = 5.4 × 10-3). CHD DNVs altered transcription levels in 5 of 31 enhancers assayed. Finally, we observed a DNV burden in RNA-binding-protein regulatory sites (OR = 1.13, 95% CI 1.1-1.2, P = 8.8 × 10-5). Our findings demonstrate an enrichment of potentially disruptive regulatory noncoding DNVs in a fraction of CHD at least as high as that observed for damaging coding DNVs.

Misdiagnosis of ameloblastoma in a patient with clear cell odontogenic carcinoma: a case report.

Clear cell odontogenic carcinoma (CCOC), a rare tumor in the head and neck region, displays comparable properties with other tumors clinically and pathologically. In consequence, an incorrect diagnosis may be established. A 51-year-old male patient who was admitted to the Department of Oral and Maxillofacial Surgery at Pusan National University Dental Hospital was initially diagnosed with ameloblastoma via incisional biopsy. However, the excised mass of the patient was observed to manifest histopathological characteristics of ameloblastic carcinoma. The lesion was ultimately diagnosed as clear cell odontogenic carcinoma by the Department of Oral Pathology of Pusan National Dental University. Therefore, segmental mandibulectomy and bilateral neck dissection were performed, followed by reconstruction with fibula free flap and reconstruction plate. Concomitant chemotherapy radiotherapy was not necessary. The patient has been followed up, and no recurrence has occurred 6 months after surgery.

Widespread intra-dependencies in the removal of introns from human transcripts.

Research into the problem of splice site selection has followed a reductionist approach focused on how individual splice sites are recognized. Early applications of information theory uncovered an inconsistency. Human splice signals do not contain enough information to explain the observed fidelity of splicing. Here, we conclude that introns do not necessarily contain 'missing' information but rather may require definition from neighboring processing events. For example, there are known cases where an intronic mutation disrupts the splicing of not only the local intron but also adjacent introns. We present a genome-wide measurement of the order of splicing within human transcripts. The observed order of splicing cannot be explained by a simple kinetic model. Simulations reveal a bias toward a particular, transcript-specific order of intron removal in human genes. We validate an extreme class of intron that can only splice in a multi-intron context. Special categories of splicing such as exon circularization, first and last intron processing, alternative 5 and 3'ss usage and exon skipping are marked by distinct patterns of ordered intron removal. Excessive intronic length and silencer density tend to delay splicing. Shorter introns that contain enhancers splice early.

Corrigendum: Relationship between disease stage and renal function in bisphosphonate-related osteonecrosis of the jaw.

[This corrects the article on p. 16 in vol. 43, PMID: 28280705.].

Relationship between disease stage and renal function in bisphosphonate-related osteonecrosis of the jaw.

OBJECTIVES: Bisphosphonate is the primary cause of bisphosphonate-related osteonecrosis of the jaw (BRONJ). Bisphosphonates are eliminated from the human body by the kidneys. It is anticipated that bisphosphonate levels in the body will increase if the kidney is in a weak state or if there is systemic disease that affects kidney function. The aim of this study was to analyze the relevance of renal function in the severity of BRONJ. MATERIALS AND METHODS: Ninety-three patients diagnosed with BRONJ in Pusan National University Dental Hospital from January 2012 to December 2014 were included in this study. All patients underwent a clinical exam, radiographs, and serologic lab test, including urine analysis. The patient's medical history was also taken, including the type of bisphosphonate drug, the duration of administration and drug holiday, route of administration, and other systemic diseases. In accordance with the guidelines of the 2009 position paper of American Association of Oral and Maxillofacial Surgeons, the BRONJ stage was divided into 4 groups, from stage 0 to 3, according to the severity of disease. IBM SPSS Statistics version 21.0 (IBM Co., USA) was used to perform regression analysis with a 0.05% significance level. RESULTS: BRONJ stage and renal factor (estimated glomerular filtration rate) showed a moderate statistically significant correlation. In the group with higher BRONJ stage, the creatinine level was higher, but the increase was not statistically significant. Other factors showed no significant correlation with BRONJ stage. There was a high statistically significant correlation between BRONJ stage and 'responder group' and 'non-responder group,' but there was no significant difference with the 'worsened group.' In addition, the age of the patients was a relative factor with BRONJ stage. CONCLUSION: With older age and lower renal function, BRONJ is more severe, and there may be a decrease in patient response to treatment.

Hyaluronated nanoparticles with pH- and enzyme-responsive drug release properties.

In this study, we report the development of a novel pH-responsive nanoparticle composed of hyaluronic acid (HA) grafted with functional 3-diethylaminopropyl (DEAP) groups (HA-g-DEAP). The pH-responsive nanoparticles were fabricated by a self-assembled arrangement of a hydrophilic block (HA) and a hydrophobic block (non-protonated DEAP) of HA-g-DEAP at pH 7.4. HA-g-DEAP was prepared by a simple conjugation of the carboxylic acid groups of HA and the free amine groups of DEAP. The HA-g-DEAP nanoparticles displayed pH-dependent changes in their physicochemical properties. We observed nanoparticle destabilization because of the protonation of DEAP when the pH of the solution decreased to 5.0. This phenomenon resulted in the release of the encapsulated content (model drug, doxorubicin: DOX) from the nanoparticle core. In addition, the degradation of HA by hyaluronidase (Hyal) significantly accelerated the DOX release rate, which may allow for increased drug release in diseased cells with acidic endosomal pH (∼pH 5.0) in the presence of Hyal. Overall, a significant improvement in the drug release rate was evident when this nanoparticle system was stimulated by both an acidic pH and specific enzymes.

Effect of La2O3 addition on interface chemistry between 4YSZ top layer and Ni based alloy bond coat in thermal barrier coating by EB PVD.

The effect of a 5 mol% La2O3 addition on the forming behavior and compositional variation at interface between a 4 mol% Yttria (Y2O3) stabilized ZrO2 (4YSZ) top coat and bond coat (NiCrAlY) as a thermal barrier coating (TBC) has been investigated. Top coats were deposited by electron beam physical vapor deposition (EB PVD) onto a super alloy (Ni-Cr-Co-Al) substrate without pre-oxidation of the bond coat. Top coats are found to consist of dense columnar grains with a thin interdiffusion layer between metallic bond coats. In the as-received 4YSZ coating, a thin interdiffusion zone at the interface between the top and bond coats was found to consist of a Ni-Zr intermetallic compound with a reduced quantity of Y, Al or O elements. On the other hand, in the case of an interdiffusion area of 5 mol% La2O3-added 4YSZ coating, it was found that the complicated composition and structure with La-added YSZ and Ni-Al rich compounds separately. The thermal conductivity of 5 mol% La2O3-added 4YSZ coating (- 1.6 W/m x k at 1100 degrees C) was lower than a 4YSZ coating (- 3.2 W/m x k at 1100 degrees C) alone.

Embelin inhibits growth and induces apoptosis through the suppression of Akt/mTOR/S6K1 signaling cascades.

BACKGROUND: Akt/mTOR/S6K1 signaling cascades play an important role both in the survival and proliferation of tumor cells. METHODS: In the present study, we investigated the effects of embelin (EB), identified primarily from the Embelia ribes plant, on the Akt/mTOR/S6K1 activation, associated gene products, cellular proliferation, and apoptosis in human prostate cancer cells. RESULTS: EB exerted significant cytotoxic and suppressive effects on Akt and mTOR activation against androgen-independent PC-3 cells as compared to androgen-dependent LNCaP cells. Moreover, EB suppressed the constitutive activation of Akt/mTOR/S6K1 signaling cascade, which correlated with the induction of apoptosis as characterized by accumulation of cells in subG1 phase, positive Annexin V binding, down-regulation of anti-apoptotic (Bcl-2, Bcl-xL, survivin, IAP-1, and IAP-2) and proliferative (cyclin D1) proteins, activation of caspase-3, and cleavage of PARP. We also observed that EB can significantly enhance the apoptotic effects of a specific pharmacological Akt inhibitor when used in combination and also caused broad inhibition of all the three kinases in Akt/mTOR/S6K1 signaling axis in PC-3 cells. CONCLUSIONS: EB inhibits multiple signaling cascades involved in tumorigenesis and can be used as a potential therapeutic candidate for both the prevention and treatment of prostate cancer.

Changes in sensitization rate to weed allergens in children with increased weeds pollen counts in Seoul metropolitan area.

The prevalence of allergic diseases in children has increased for several decades. We evaluated the correlation between pollen count of weeds and their sensitization rate in Seoul, 1997-2009. Airborne particles carrying allergens were collected daily from 3 stations around Seoul. Skin prick tests to pollen were performed on children with allergic diseases. Ragweed pollen gradually increased between 1999 and 2005, decreased after 2005 and plateaued until 2009 (peak counts, 67 in 2003, 145 in 2005 and 83 grains/m(3)/day in 2007). Japanese hop pollen increased between 2002 and 2009 (peak counts, 212 in 2006 and 492 grains/m(3)/day in 2009). Sensitization rates to weed pollen, especially ragweed and Japanese hop in children with allergic diseases, increased annually (ragweed, 2.2% in 2000 and 2.8% in 2002; Japanese hop, 1.4% in 2000 and 1.9% in 2002). The age for sensitization to pollen gradually became younger since 2000 (4 to 6 yr of age, 3.5% in 1997 and 6.2% in 2009; 7 to 9 yr of age, 4.2% in 1997 and 6.4% in 2009). In conclusion, sensitization rates for weed pollens increase in Korean children given increasing pollen counts of ragweed and Japanese hop.

The revised edition of korean calendar for allergenic pollens.

The old calendar of pollens did not reflect current pollen distribution and concentrations that can be influenced by changes of weather and environment of each region in South Korea. A new pollen calendar of allergenic pollens was made based on the data on pollen concentrations obtained in eight regions nationwide between 1997 and 2009. The distribution of pollen was assessed every day at 8 areas (Seoul, Guri, Busan, Daegu, Jeonju, Kwangju, Kangneung, and Jeju) for 12 years between July 1, 1997 and June 30, 2009. Pollens were collected by using Burkard 7-day sampler (Burkard Manufacturing Co Ltd, UK). Pollens which were stained with Calberla's fuchsin staining solution were identified and counted. Pine became the highest pollen in May, and the pollen concentrations of oak and birch also became high. Ragweed appeared in the middle of August and showed the highest pollen concentration in the middles of September. Japanese hop showed a high concentration between the middle of August and the end of September, and mugwort appeared in the middles of August and its concentration increased up until early September. In Kangneung, birch appeared earlier, pine showed a higher pollen concentration than in the other areas. In Daegu, Oriental thuja and alder produced a large concentration of pollens. Pine produced a large concentration of pollens between the middle of April and the end of May. Weeds showed higher concentrations in September and mugwort appeared earlier than ragweed. In Busan the time of flowering is relatively early, and alder and Oriental thuja appeared earliest among all areas. In Kwangju, Oriental thuja and hazelnut appeared in early February. Japanese cedar showed the highest pollen concentration in March in Jeju. In conclusion, update information on pollen calendar in South Korea should be provided for allergic patients through the website to manage and prevent the pollinosis.