Detecting microsatellite instability by length comparison of microsatellites in the 3' untranslated region with RNA-seq.

Microsatellite instability (MSI), a phenomenon caused by deoxyribonucleic acid (DNA) mismatch repair system deficiencies, is an important biomarker in cancer research and clinical diagnostics. MSI detection often involves next-generation sequencing data, with many studies focusing on DNA. Here, we introduce a novel approach by measuring microsatellite lengths directly from ribonucleic acid sequencing (RNA-seq) data and comparing its distribution to detect MSI. Our findings reveal distinct instability patterns between MSI-high (MSI-H) and microsatellite stable samples, indicating the efficacy of RNA-based MSI detection. Additionally, microsatellites in the 3'-untranslated regions showed the greatest predictive value for MSI detection. Notably, this efficacy extends to detecting MSI-H samples even in tumors not commonly associated with MSI. Our approach highlights the utility of RNA-seq data in MSI detection, facilitating more precise diagnostics through the integration of various biological data.

Pragmatic nationwide master observational trial based on genomic alterations in advanced solid tumors: KOrean Precision Medicine Networking Group Study of MOlecular profiling guided therapy based on genomic alterations in advanced Solid tumors (KOSMOS)-II study protocol KCSG AL-22-09.

BACKGROUND: Next-generation sequencing (NGS) has been introduced to many Korean institutions to support molecular diagnostics in cancer since 2017, when it became eligible for reimbursement by the National Health Insurance Service. However, the uptake of molecularly guided treatment (MGT) based on NGS results has been limited because of stringent regulations regarding prescriptions outside of approved indications, a lack of clinical trial opportunities, and limited access to molecular tumor boards (MTB) at most institutions. The KOSMOS-II study was designed to demonstrate the feasibility and effectiveness of MGT, informed by MTBs, using a nationwide precision medicine platform. METHODS: The KOSMOS-II trial is a large-scale nationwide master observational study. It involves a framework for screening patients with metastatic solid tumors for actionable genetic alterations based on local NGS testing. It recommends MGT through a remote and centralized MTB meeting held biweekly. MGT can include one of the following options: Tier 1, the therapeutic use of investigational drugs targeting genetic alterations such as ALK, EGFR, ERBB2, BRAF, FH, ROS1, and RET, or those with high tumor mutational burden; Tier 2, comprising drugs with approved indications or those permitted for treatment outside of the indications approved by the Health Insurance Review and Assessment Service of Korea; Tier 3, involving clinical trials matching the genetic alterations recommended by the MTB. Given the anticipated proportion of patients receiving MGT in the range of 50% ± 3.25%, this study aims to enroll 1,000 patients. Patients must have progressed to one or more lines of therapy and undergone NGS before enrollment. DISCUSSION: This pragmatic master protocol provides a mass-screening platform for rare genetic alterations and high-quality real-world data. Collateral clinical trials, translational studies, and clinico-genomic databases will contribute to generating evidence for drug repositioning and the development of new biomarkers. TRIAL REGISTRATION: NCT05525858.

Exploring quantitative traits-associated copy number deletions through reanalysis of UK10K consortium whole genome sequencing cohorts.

OBJECTIVES: We performed comprehensive association analyses of common high-confidence gnomAD-reported copy number deletions (CNDs) with 60 quantitative traits from UK10K consortium WGS data. METHODS: The study made use of data generated by the UK10K Consortium. UK10K consortium WGS data consist of TwinsUK (n = 1754, middle-aged females) and ALSPAC (n = 1867, birth to adolescence) cohorts. UK10K consortium called 18,739 CNDs (hg19) with GenomeSTRiP software. After filtering out variants with minor allele frequency < 0.05 or HWE P < 1.0 × 10- 6, 1222 (TwinsUK) and 1211 (ALSPAC) CNDs remained for association analyses with 60 normalized quantitative traits. RESULTS: We identified 23 genome-wide significant associations at 13 loci, among which 2 associations reached experiment-wide significance. We found that two common deletions in chromosome 4, located between WDR1 and ZNF518B (23.3 kb, dbVar ID:nssv15888957, 4:10211262-10,234,569 and 9.8 kb, dbVar ID:nssv15888975, 4:10392422-10,402,191), were associated with uric acid levels (P = 5.23 × 10- 11 and 2.29 × 10- 8, respectively). We also discovered a novel deletion spanning chromosome 18 (823 bp, dbVar ID: nssv15841628, 8:74347187-74,348,010) associated with low HDL cholesterol levels (P = 4.15 × 10- 7). Additionally, we observed two red blood cell traits-associated loci with genome-wide significance, a 13.2 kb deletion in 7q22.1 (nssv15922542) and a 3.7 kb deletion in 12q24.12 (nssv15813226), both of which were located in regions previously reported to be associated with red blood cell traits. Two deletions in 11q11 (nssv15803200 and nssv15802240), where clusters of multiple olfactory receptor genes exist, and a deletion (nssv15929560) upstream to DOCK5 were associated with childhood obesity. Finally, when defining Trait-Associated copy number Deletions (TADs) as CNDs with phenotype associations at sub-threshold significance (P < 10- 3), we identified 157 (97.5%) out of 161 TADs in non-coding regions, with a mean size of 4 kb (range: 209 - 47,942 bp). CONCLUSION: We conducted a reanalysis of the UK10K Whole Genome Sequencing cohort, which led to the identification of multiple high confidence copy number deletions associated with quantitative traits. These deletions have standard dbVar IDs and replicate previous findings, as well as reveal novel loci that require further replication studies.

Metal-free electrocatalytic nanocomposites of poly azovan blue-decorated graphitic carbon nitride for simultaneously sensing paracetamol and 4-aminophenol.

Excessive consumption of paracetamol (PA) and 4-aminophenol (4-AP) can have harmful effects on the human body. This study developed a novel electroanalytical technique that utilizes the nanocomposites of poly azovan blue (PAB)-decorated graphitic carbon nitride (g-C3N4), deposited onto a screen-printed carbon electrode (SPCE), for the concurrent sensing of PA and 4-AP. The fabricated g-C3N4@PAB/SPCE exhibited exceptional synergistic effects, such as a high active electrochemical surface area and excellent electron transfer properties. The electrochemical behavior of g-C3N4@PAB/SPCE for simultaneous PA and 4-AP sensing was evaluated in the linear dynamic ranges of 0.08-75 and 0.05-90 µM, with the detection limits (S/N = 3) of 0.011 and 0.016 µM and sensitivities of 2.974 and 2.857 µA/µM/cm-2 for PA and 4-AP, respectively. Additionally, g-C3N4@PAB/SPCE showed long-term stability, high reproducibility (RSD = 2.17%, n = 4), and superior anti-interference capabilities. Finally, when g-C3N4@PAB/SPCE was tested for simultaneously sensing both PA and 4-AP in tap water and artificial urine models, it exhibited satisfactory recoveries, demonstrating its potential use for various industrial and clinical applications.

Combination of Enhanced Instructions Improve Quality of Bowel Preparation: A Prospective, Colonoscopist-Blinded, Randomized, Controlled Study.

BACKGROUND: Appropriate bowel preparation is highly important for the efficacy of colonoscopy; however, up to one-third of patients do not accomplish adequate bowel preparation. OBJECTIVE: We investigated the impact of the combination of enhanced instruction on the quality of bowel preparation and its impact on clinically relevant outcomes. DESIGN: This was a colonoscopist-blinded, prospective, randomized trial. SETTINGS: All patients received regular instructions for bowel preparation. Patients were randomly assigned to the control, telephone reeducation, and combined enhanced instruction groups. PATIENTS: Outpatients aged 19 to 75 years scheduled to undergo colonoscopy were included. MAIN OUTCOME MEASURES: The main outcome was adequate bowel preparation rate. RESULTS: A total of 311 patients were randomly assigned to the combined enhanced instruction (n = 104), telephone reeducation (n = 101), and control groups (n = 106). An intention-to-treat analysis showed that the adequate bowel preparation rate was higher in the combined enhanced instruction group than in the telephone reeducation and control groups (92.3% vs 82.2% vs 76.4%, p = 0.007). The rate of compliance with the instructions was significantly higher in the combined enhanced instruction group than in the telephone reeducation and control groups. Method of education was associated with proper bowel preparation (adjusted OR 17.46; p < 0.001 for combined enhanced instruction relative to control). LIMITATIONS: This was a single-center study conducted in Korea. CONCLUSIONS: Combined enhanced instruction as an adjunct to regular instructions much improved the quality of bowel preparation and patients' adherence to the preparation instructions. The combined enhanced instruction method could be the best option for bowel preparation instruction. See Video Abstract at http://links.lww.com/DCR/B673. LA COMBINACIN DE INSTRUCCIONES MEJORADAS, INCREMENTA LA CALIDAD DE LA PREPARACIN INTESTINAL ESTUDIO PROSPECTIVO, CONTROLADO, ALEATORIO Y CIEGO PARA EL COLONOSCOPISTA: ANTECEDENTES:La preparación adecuada del intestino es muy importante para la eficacia de la colonoscopia; sin embargo, hasta un tercio de los pacientes no logran buenos resutlados.OBJETIVO:Investigar el impacto de la combinación de instrucciónes claras en la calidad de la preparación intestinal y su impacto en los resultados clínicos.DISEÑO:Trabajo aleatorio, prospectivo y ciego para el colonoscopista.AJUSTES:Los pacientes recibieron instrucciones periódicas para la preparación intestinal. Fueron asignados aleatoriamente al grupo control, educación telefónica y de instrucción mejoradas.PACIENTES:Se incluyeron pacientes ambulatorios de 19 a 75 años programados para ser sometidos a colonoscopia.PRINCIPALES MEDIDAS DE RESULTADO:El principal resultado fue una adecuada preparación intestinal.RESULTADOS:Un total de 311 pacientes fueron asignados al azar a la instrucción mejorada combinada (n = 104), reeducación telefónica (n = 101) y grupo de control (n = 106). El análisis estadístico mostró que la tasa de preparación intestinal adecuada fue mayor en el grupo combinado de instrucción mejorada que en los grupos de reeducación telefónica y control (92,3% vs 82,2% vs 76,4%, p = 0,007). La tasa de cumplimiento de las instrucciones fue significativamente mayor en el grupo de instrucción mejorada combinada que en los otros. El método de educación se asoció con una preparación intestinal adecuada (razón de posibilidades ajustada de 17,46; p <0,001 para la instrucción mejorada combinada en relación con el control.LIMITACIONES:Estudio en un solo centro realizado en Corea.CONCLUSIONES:La instrucción mejorada combinada como complemento de las instrucciones regulares mejoró mucho la calidad de la preparación intestinal y la adherencia de los pacientes a las instrucciones de preparación. El método de instrucción mejorado combinado podría ser la mejor opción para la instrucción de preparación intestinal. Consulte Video Resumen en http://links.lww.com/DCR/B673.

rs2671655 single nucleotide polymorphism modulates the risk for gastric cancer in Helicobacter pylori-infected individuals: a genome-wide association study in the Korean population.

OBJECTIVE: To identify genetic variations which is associated with gastric cancer (GC) risk according to Helicobacter pylori infection. METHODS: This study incorporated 527 GC patients and 441 controls from a cohort at Seoul National University Bundang Hospital. The associations between GC risk and single nucleotide polymorphisms were calculated, stratified by H. pylori status, adjusting for age, sex, and smoking. mRNA expression from non-cancerous gastric mucosae was evaluated using reverse transcription quantitative polymerase chain reaction. RESULTS: In the entire cohort, genome-wide association study showed no significant variants reached the genome-wide significance level. In the H. pylori-positive group, rs2671655 (chr17:47,468,020;hg19, GH17J049387 enhancer region) was identified at a genome-wide significance level, which was more pronounced in diffuse type GC. There was no significant variant in the H. pylori-negative group, indicating the effect modification of rs2671655 by H. pylori. Among the target genes of GH17J049387 enhancer (PHB1, ZNF652 and SPOP), PHB1 mRNA was expressed more in cases than in controls, who were not affected by H. pylori. By contrast, an increase in ZNF652 and SPOP in GC was observed only in the H. pylori-negative group (P < 0.05). Mediation analysis showed that PHB1 (P = 0.0238) and SPOP (P = 0.0328) mediated the effect of rs2671655 on GC risk. The polygenic risk score was associated with the number of rs2671655 risk alleles only in the H. pylori-positive group (P = 0.0112). CONCLUSION: After H. pylori infection, rs2671655 may increase GC risk, especially in diffuse-type GC, by regulating the expression of several genes that consequently modify susceptibility to GC.

Graphitic carbon-encapsulated V2O5 nanocomposites as a superb photocatalyst for crystal violet degradation.

To materialize the excellent photocatalyst for crystal violet dye-degradation, the graphitic carbon-encapsulated vanadium pentoxide (GC-V2O5) nanocomposites were synthesized through the simple sonication method by using the green tea waste-derived GC nanoflakes and the sonochemically synthesized V2O5 nanorods. The nanocomposites were confirmed to comprise an aggregated morphology, in which the orthorhombic V2O5 nanorods were well anchored with the intertwingled GC nanoflakes. Owing to the encapsulation of defective V2O5 by conductive GC, the GC-V2O5 nanocomposites exhibited the enhanced photocatalytic dye-degradation efficiency up to 98.4% within 105 min. Namely, the encapsulated GC nanosheets might compensate the native defects (i.e., charge traps) on the V2O5 surface; hence, the charge transport could be enhanced during the dye-degradation process while the photocarrier recombination could be suppressed. The results suggest the conducting layer-encapsulated semiconducting oxide nanocomposites (e.g., GC-V2O5) to be of good use for future green environmental technology, particularly, as a superb photocatalyst for dye degradation.

Significant Mendelian genetic contribution to pediatric mild-to-moderate hearing loss and its comprehensive diagnostic approach.

PURPOSE: Timely diagnosis and identification of etiology of pediatric mild-to-moderate sensorineural hearing loss (SNHL) are both medically and socioeconomically important. However, the exact etiologic spectrum remains uncertain. We aimed to establish a genetic etiological spectrum, including copy-number variations (CNVs) and efficient genetic testing pipeline, of this defect. METHODS: A cohort of prospectively recruited pediatric patients with mild-to-moderate nonsyndromic SNHL from 2014 through 2018 (n = 110) was established. Exome sequencing, multiplex ligation-dependent probe amplification (MLPA), and nested customized polymerase chain reaction (PCR) for exclusion of a pseudogene, STRCP, from a subset (n = 83) of the cohort, were performed. Semen analysis was also performed to determine infertility (n = 2). RESULTS: Genetic etiology was confirmed in nearly two-thirds (52/83 = 62.7%) of subjects, with STRC-related deafness (n = 29, 34.9%) being the most prevalent, followed by MPZL2-related deafness (n = 9, 10.8%). This strikingly high proportion of Mendelian genetic contribution was due particularly to the frequent detection of CNVs involving STRC in one-third (27/83) of our subjects. We also questioned the association of homozygous continuous gene deletion of STRC and CATSPER2 with deafness-infertility syndrome (MIM61102). CONCLUSION: Approximately two-thirds of sporadic pediatric mild-to-moderate SNHL have a clear Mendelian genetic etiology, and one-third is associated with CNVs involving STRC. Based on this, we propose a new guideline for molecular diagnosis of these children.

Transformation of Pathology Reports Into the Common Data Model With Oncology Module: Use Case for Colon Cancer.

BACKGROUND: Common data models (CDMs) help standardize electronic health record data and facilitate outcome analysis for observational and longitudinal research. An analysis of pathology reports is required to establish fundamental information infrastructure for data-driven colon cancer research. The Observational Medical Outcomes Partnership (OMOP) CDM is used in distributed research networks for clinical data; however, it requires conversion of free text-based pathology reports into the CDM's format. There are few use cases of representing cancer data in CDM. OBJECTIVE: In this study, we aimed to construct a CDM database of colon cancer-related pathology with natural language processing (NLP) for a research platform that can utilize both clinical and omics data. The essential text entities from the pathology reports are extracted, standardized, and converted to the OMOP CDM format in order to utilize the pathology data in cancer research. METHODS: We extracted clinical text entities, mapped them to the standard concepts in the Observational Health Data Sciences and Informatics vocabularies, and built databases and defined relations for the CDM tables. Major clinical entities were extracted through NLP on pathology reports of surgical specimens, immunohistochemical studies, and molecular studies of colon cancer patients at a tertiary general hospital in South Korea. Items were extracted from each report using regular expressions in Python. Unstructured data, such as text that does not have a pattern, were handled with expert advice by adding regular expression rules. Our own dictionary was used for normalization and standardization to deal with biomarker and gene names and other ungrammatical expressions. The extracted clinical and genetic information was mapped to the Logical Observation Identifiers Names and Codes databases and the Systematized Nomenclature of Medicine (SNOMED) standard terminologies recommended by the OMOP CDM. The database-table relationships were newly defined through SNOMED standard terminology concepts. The standardized data were inserted into the CDM tables. For evaluation, 100 reports were randomly selected and independently annotated by a medical informatics expert and a nurse. RESULTS: We examined and standardized 1848 immunohistochemical study reports, 3890 molecular study reports, and 12,352 pathology reports of surgical specimens (from 2017 to 2018). The constructed and updated database contained the following extracted colorectal entities: (1) NOTE_NLP, (2) MEASUREMENT, (3) CONDITION_OCCURRENCE, (4) SPECIMEN, and (5) FACT_RELATIONSHIP of specimen with condition and measurement. CONCLUSIONS: This study aimed to prepare CDM data for a research platform to take advantage of all omics clinical and patient data at Seoul National University Bundang Hospital for colon cancer pathology. A more sophisticated preparation of the pathology data is needed for further research on cancer genomics, and various types of text narratives are the next target for additional research on the use of data in the CDM.

Clarification of glycosylphosphatidylinositol anchorage of OTOANCORIN and human OTOA variants associated with deafness.

Otoancorin (OTOA), encoded by OTOA, is required for the development of the tectorial membrane in the inner ear. Mutations in this gene cause nonsyndromic hearing loss (DFNB22). The molecular mechanisms underlying most DFNB22 remain poorly understood. Disruption of glycosylphosphatidylinositol (GPI) anchorage has been assumed to be the pathophysiology mandating experimental validation. From a Korean deaf family, we identified two trans OTOA variants (c.1320 + 5 G > C and p.Gln589ArgfsX55 [NM_144672.3]) . The pathogenic potential of c.1320 + 5 G > C was confirmed by a minigene splicing assay. To experimentally determine the GPI anchorage, wild-type (WT) and mutant OTOA harboring p.Gln589ArgfsX55 were expressed in HEK293T cells. The mutant OTOA with p.Gln589ArgfsX55 resulted in an uncontrolled release of OTOA into the medium in contrast with phosphatidylinositol-specific phospholipase C-induced controlled release of WT OTOA from the cell surface. Together, the results of this reverse translational study confirmed GPI-anchorage of OTOA and showed that downstream sequences from the 589th amino acid are critical for GPI-anchorage.

NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types.

In many next-generation sequencing (NGS) studies, multiple samples or data types are profiled for each individual. An important quality control (QC) step in these studies is to ensure that datasets from the same subject are properly paired. Given the heterogeneity of data types, file types and sequencing depths in a multi-dimensional study, a robust program that provides a standardized metric for genotype comparisons would be useful. Here, we describe NGSCheckMate, a user-friendly software package for verifying sample identities from FASTQ, BAM or VCF files. This tool uses a model-based method to compare allele read fractions at known single-nucleotide polymorphisms, considering depth-dependent behavior of similarity metrics for identical and unrelated samples. Our evaluation shows that NGSCheckMate is effective for a variety of data types, including exome sequencing, whole-genome sequencing, RNA-seq, ChIP-seq, targeted sequencing and single-cell whole-genome sequencing, with a minimal requirement for sequencing depth (>0.5X). An alignment-free module can be run directly on FASTQ files for a quick initial check. We recommend using this software as a QC step in NGS studies. AVAILABILITY: https://github.com/parklab/NGSCheckMate.

Influence of the Quantum Well Structure and Growth Temperature on a Five-Layer InGaMnAs Quantum Well with an InGaAs Buffer Layer.

The influence of quantum well structure and growth temperature on a synthesized multilayer system composed of a five-layer InMnGaAs quantum well with an InGaAs buffer layer grown on semi-insulating (100)-oriented substrates prepared by low temperature molecular beam epitaxy was studied. The magnetization measurements using a superconducting quantum interference device indicated the existence of ferromagnetism with a Curie temperature above room temperature in the five-layer InGaMnAs quantum well structure with an InGaAs buffer layer in a GaAs matrix. X-ray diffraction and secondary ion mass spectroscopy measurements confirmed the second phase formation of ferromagnetic GaMn clusters. The ferromagnetism that exists in the five-layer of the InMnGaAs quantum well with the InGaAs buffer layer results from a superposition of the ferromagnetism of the low temperature region from the substitutional Mn ions into Ga sites or interstitial Mn ions as well as the presence of manganese ions dopant clusters such as GaMn clusters.

Inferring new drug indications using the complementarity between clinical disease signatures and drug effects.

BACKGROUND: Drug repositioning is the process of finding new indications for existing drugs. Its importance has been dramatically increasing recently due to the enormous increase in new drug discovery cost. However, most of the previous molecular-centered drug repositioning work is not able to reflect the end-point physiological activities of drugs because of the inherent complexity of human physiological systems. METHODS: Here, we suggest a novel computational framework to make inferences for alternative indications of marketed drugs by using electronic clinical information which reflects the end-point physiological results of drug's effects on the biological activities of humans. In this work, we use the concept of complementarity between clinical disease signatures and clinical drug effects. With this framework, we establish disease-related clinical variable vectors (clinical disease signature vectors) and drug-related clinical variable vectors (clinical drug effect vectors) by applying two methodologies (i.e., statistical analysis and literature mining). Finally, we assign a repositioning possibility score to each disease-drug pair by the calculation of complementarity (anti-correlation) and association between clinical states ("up" or "down") of disease signatures and clinical effects ("up", "down" or "association") of drugs. A total of 717 clinical variables in the electronic clinical dataset (NHANES), are considered in this study. RESULTS: The statistical significance of our prediction results is supported through two benchmark datasets (Comparative Toxicogenomics Database and Clinical Trials). We discovered not only lots of known relationships between diseases and drugs, but also many hidden disease-drug relationships. For example, glutathione and edetic-acid may be investigated as candidate drugs for asthma treatment. We examined prediction results by using statistical experiments (enrichment verification, hyper-geometric and permutation test P<0.009 in Comparative Toxicogenomics Database and Clinical Trials) and presented evidences for those with already published literature. CONCLUSION: The results show that electronic clinical information is a feasible data resource and utilizing the complementarity (anti-correlated relationships) between clinical signatures of disease and clinical effects of drugs is a potentially predictive concept in drug repositioning research. It makes the proposed approach useful to identity novel relationships between diseases and drugs that have a high probability of being biologically valid.

Identification of genomic features in the classification of loss- and gain-of-function mutation.

BACKGROUND: Alterations of a genome can lead to changes in protein functions. Through these genetic mutations, a protein can lose its native function (loss-of-function, LoF), or it can confer a new function (gain-of-function, GoF). However, when a mutation occurs, it is difficult to determine whether it will result in a LoF or a GoF. Therefore, in this paper, we propose a study that analyzes the genomic features of LoF and GoF instances to find features that can be used to classify LoF and GoF mutations. METHODS: In order to collect experimentally verified LoF and GoF mutational information, we obtained 816 LoF mutations and 474 GoF mutations from a literature text-mining process. Next, with data-preprocessing steps, 258 LoF and 129 GoF mutations remained for a further analysis. We analyzed the properties of these LoF and GoF mutations. Among the properties, we selected features which show different tendencies between the two groups and implemented classifications using support vector machine, random forest, and linear logistic regression methods to confirm whether or not these features can identify LoF and GoF mutations. RESULTS: We analyzed the properties of the LoF and GoF mutations and identified six features which have discriminative power between LoF and GoF conditions: the reference allele, the substituted allele, mutation type, mutation impact, subcellular location, and protein domain. When using the six selected features with the random forest, support vector machine, and linear logistic regression classifiers, the result showed accuracy levels of 72.23%, 71.28%, and 70.19%, respectively. CONCLUSIONS: We analyzed LoF and GoF mutations and selected several properties which were different between the two classes. By implementing classifications with the selected features, it is demonstrated that the selected features have good discriminative power.

Observation of single electron transport via multiple quantum states of a silicon quantum dot at room temperature.

Single electron transport through multiple quantum levels is realized in a Si quantum-dot device at room-temperature conditions. The energy spacing of more than triple the omnipresent thermal energy is obtained from an extremely small ellipsoidal Si quantum dot, and high charge stability is attained through a construction of the gate-all-around structure. These properties may move us a step closer to practical applications of quantum devices at elevated temperatures. An in-depth analysis on the transport behavior and quantum structure is presented.

Vertical graphene-base hot-electron transistor.

We demonstrate vertical graphene-base hot-electron transistors (GB-HETs) with a variety of structures and material parameters. Our GB-HETs exhibit a current saturation with a high current on-off ratio (>10(5)), which results from both the vertical transport of hot electrons across the ultrathin graphene base and the filtering of hot electrons through a built-in energy barrier. The influences of the materials and their thicknesses used for the tunneling and filtering barriers on the common-base current gain α are studied. The optimization of the SiO2 thickness and using HfO2 as the filtering barrier significantly improves the common-base current gain α by more than 2 orders of magnitude. The results demonstrate that GB-HETs have a great potential for high-frequency, high-speed, and high-density integrated circuits.

High-Performance Memristive Synapse Composed of Ferroelectric ZnVO-Based Schottky Junction.

In pursuit of realizing neuromorphic computing devices, we demonstrated the high-performance synaptic functions on the top-to-bottom Au/ZnVO/Pt two-terminal ferroelectric Schottky junction (FSJ) device architecture. The active layer of ZnVO exhibited the ferroelectric characteristics because of the broken lattice-translational symmetry, arising from the incorporation of smaller V5+ ions into smaller Zn2+ host lattice sites. The fabricated FSJ devices displayed an asymmetric hysteresis behavior attributed to the ferroelectric polarization-dependent Schottky field-emission rate difference in between positive and negative bias voltage regions. Additionally, it was observed that the magnitude of the on-state current could be systematically controlled by changing either the amplitude or the width of the applied voltage pulses. Owing to these voltage pulse-tunable multi-state memory characteristics, the device revealed diverse synaptic functions such as short-term memory, dynamic range-tunable long-term memory, and versatile rules in spike time-dependent synaptic plasticity. For the pattern-recognition simulation, furthermore, more than 95% accuracy was recorded when using the optimized experimental device parameters. These findings suggest the ZnVO-based FSJ device holds significant promise for application in next-generation brain-inspired neuromorphic computing systems.

Late-Onset Slowly Progressing Cone/Macular Dystrophy in Patients With the Biallelic Hypomorphic Variant p.Arg1933Ter in RP1.

Purpose: Homozygous hypomorphic variants of the RP1 gene, including c.5797C>T, p.Arg1933Ter, have traditionally been considered non-pathogenic. This study aimed to elucidate the clinical manifestations of late-onset, slowly progressive cone/macular dystrophy in patients homozygous for p.Arg1933Ter in the RP1 gene. Methods: Five patients with biallelic p.Arg1933Ter in RP1 were retrospectively recruited, and their clinical profiles were analyzed. Copy number variation analysis and Alu insertion assessment of genes associated with inherited retinal diseases were conducted. The results of comprehensive ophthalmological examinations, multimodal imaging, and full-field electroretinogram tests were analyzed. Results: No specific sequencing errors or structural variations associated with the clinical phenotypes were identified. Alu element insertion in RP1 was not detected. The mean ± SD age at the first visit was 62.2 ± 9.8 years, with symptoms typically starting between 45 and 50 years of age. Two patients exhibited a mild form of cone/macular dystrophy, characterized by a relatively preserved fundus appearance and blurring of the ellipsoid zone on optical coherence tomography. Three patients had late-onset cone/macular dystrophy with significant atrophy. Conclusions: To our knowledge, this study is the first to report that a homozygous hypomorphic variant of RP1, previously considered non-pathogenic, leads to cone/macular dystrophy. Translational Relevance: The study introduces novel possibilities suggesting that the homozygous hypomorphic variant of RP1 may be linked to variant pathogenicity.

Genomic Landscape of Pulmonary Sarcomatoid Carcinoma.

PURPOSE: Pulmonary sarcomatoid carcinoma (PSC) is a rare aggressive subtype of non-small cell lung cancer (NSCLC) with limited therapeutic strategies. We attempted to elucidate the evolutionary trajectories of PSC using multiregional and longitudinal tumor samples. MATERIALS AND METHODS: A total of 31 patients were enrolled in this study and 11 longitudinal samples were available from them. Using whole exome sequencing data, we analyzed the mutational signatures in both carcinomatous and sarcomatous areas in primary tumors of the 31 patients and longitudinal samples obtained from 11 patients. Furthermore, digital droplet polymerase chain reaction (ddPCR), and programmed death-ligand 1 (PD-L1) immunohistochemistry using the Ventana SP263 assay were performed. RESULTS: TP53 was identified as the most frequently altered gene in the primary (74%) and metastatic (73%) samples. MET exon 14 skipping mutations, confirmed by ddPCR, and TP53 mutations were mutually exclusive; whereas, MET exon 14 skipping mutations frequently co-occurred with MDM2 amplification. Metastatic tumors showed dissimilar genetic profiles from either primary component. During metastasis, the signatures of APOBEC decreased in metastatic lesions compared with that in primary lesions. PSC showed higher MET and KEAP1 mutations and stronger PD-L1 protein expression compared with that recorded in other NSCLCs. CONCLUSION: Decreased APOBEC signatures and subclonal diversity were detected during malignant progression in PSC. Frequent MET mutations and strong PD-L1 expression distinguished PSC from other NSCLCs. The aggressiveness and therapeutic difficulties of PSC were possibly attributable to profound intratumoral and intertumoral genetic diversity. Next-generation sequencing could suggest the appropriate treatment strategy for PSC.