Multi-omics analysis sandbox toolkit for swift derivations of clinically relevant genesets and biomarkers.

The utilization of multi-omics research has gained popularity in clinical investigations. However, effectively managing and merging extensive and diverse datasets presents a challenge due to its intricacy. This research introduces a Multi-Omics Analysis Sandbox Toolkit, an online platform designed to facilitate the exploration, integration, and visualization of datasets ranging from single-omics to multi-omics. This platform establishes connections between clinical data and omics information, allowing for versatile analysis and storage of both single and multi-omics data. Additionally, users can repeatedly utilize and exchange their findings within the platform. This toolkit offers diverse alternatives for data selection and gene set analysis. It also presents visualization outputs, potential candidates, and annotations. Furthermore, this platform empowers users to collaborate by sharing their datasets, analyses, and conclusions with others, thus enhancing its utility as a collaborative research tool. This Multi-Omics Analysis Sandbox Toolkit stands as a valuable asset in comprehensively grasping the influence of diverse factors in diseases and pinpointing potential biomarkers.

In-situ generation of reactive oxygen species using combination of electrochemical oxidation and metal sulfide.

In-situ chemical oxidation (ISCO) is commonly practiced to degrade organic pollutants in various fields. However, ISCO is deteriorated the oxidation efficiency due to the non-selective and self-decomposition of reagents. Therefore, in-situ generation of oxidants is being proposed to compensate for the demerits of conventional ISCO. In this study, the aim is to suggest a novel in-situ generation system using the combination of electrochemical oxidation (EO) and pyrite oxidation. It is hypothesized that EO system can generate the oxygen species, which can activate the pyrite surface to produce more oxidants. We evaluated three systems (1) EO system (2) pyrite oxidation system (3) combined system using sulfanilamide as a common antibiotic. The EO system degraded completely sulfanilamide and generated 150 µM of H2O2 and 8 mg/L of DO even at 10 mA. In other words, EO system can directly oxidize the sulfanilamide and produce oxygen species. The pyrite system produced 204 and 24 µM of hydroxyl radicals at pH 3 under oxic and anoxic conditions, respectively, and 118 and 20 µM at pH 7. Pyrite oxidation can generate more reactive species in the presence of oxygen. The combined system enhanced the oxidation-rate constant to 1.5 times (from 0.2561 to 0.3502 h-1). The additional supply of oxygen showed a higher oxidation rate to 1.5 and 1.3 times higher than single EO or pyrite oxidation, respectively. As a result, the co-presence of pyrite and oxygen shows a synergistic effect on the oxidation of the organic pollutant. Our results suggest that electrochemical generation of the oxygen species in the presence of pyrite is a promising technique to oxidize organic pollutants in groundwater.

Dual radicals-enhanced wet chemical oxidation of non-biodegradable chemicals.

Total organic carbon (TOC) has been suggested and utilized as an index of organic matter in aqueous phases. The overall performance of TOC is highly dependent on the method of oxidation of organic matter to carbon dioxide, such as high-temperature combustion (HTC) and wet chemical oxidation (WCO). HTC requires more energy and maintenance cost, it is a major barrier to the field application. In contrast, WCO is more suitable for the application of on-line monitoring systems due to requiring lower energy and easy maintenance. However, WCO shows lower oxidation than HTC, thus, oxidation performance should be improved for the application to the field. In this study, a dual radical system (DRS), including sulfate and hydroxyl radicals, was proposed to enhance oxidation ability. The DRS uses alkaline pH and persulfate to generate sulfate radicals, which have been used to activate hydroxyl radicals and oxidize organic matter. The oxidation mechanism for the DRS has been verified using model chemicals with different reaction rate constants. The applicability of the DRS has been confirmed using authentic wastewater with a high concentration of chloride. In this study, the DRS showed similar performance compared to the HTC within 10 % error range. The DRS shows similar oxidation performance with HTC even at a high concentration of chloride. DRS did not show interference by the presence of chloride up to 30,000 mg/L of chloride. Results of this study indicate that the DRS can enhance overall oxidation performance compared to the conventional WCO system.

Septal Reduction Using Transvenous Intramyocardial Cerclage Radiofrequency Ablation: Preclinical Feasibility.

Debulking of left ventricular septal mass is typically accomplished using surgical myectomy, which is morbid, or using transcoronary alcohol septal ablation, which can result in geographic miss and occasional catastrophic nontarget coronary injury. The authors developed and tested operational parameters in vitro and vivo for a device to accomplish transvenous intraseptal radiofrequency ablation to reduce ventricular septal mass using a technique derived from mitral cerclage, which the authors call cerclage ablation. Cerclage ablation appeared feasible in vitro and safe and effective in vivo. Cerclage ablation is an attractive new approach to debulk the interventricular septum in obstructive hypertrophic cardiomyopathy. These data support clinical investigation.

Recovering cavity effects in corrugated organic light emitting diodes.

Cavity effects play an important role in determining the out-coupling efficiency of an OLED. By fabricating OLEDs on corrugated substrates, the waveguide and SPP modes can be extracted by diffraction. However, corrugation does not always lead to an enhancement in out-coupling efficiency due to the reduction of the electrode reflectance and hence the cavity effects. Based on the results of our rigorous couple-wave analysis (RCWA) simulation, we found that the cavity effects can be partially recovered using a low index Teflon layer inserted between the ITO anode and the substrate due to the enhancement of the reflectance of the corrugated electrodes. To verify the simulation results, we fabricated corrugated OLEDs having a low-index Teflon interlayer with an EQE of 36%, which is 29% higher than an optimized planar OLED. By experimentally measuring the OLED air mode dispersion, we confirm the cavity emission of a corrugated OLED is enhanced by the low index layer.

Realization of high-efficiency fluorescent organic light-emitting diodes with low driving voltage.

It is commonly accepted that a full bandgap voltage is required to achieving efficient electroluminescence (EL) in organic light-emitting diodes. In this work, we demonstrated organic molecules with a large singlet-triplet splitting can achieve efficient EL at voltages below the bandgap voltage. The EL originates from delayed fluorescence due to triplet fusion. Finally, in spite of a lower quantum efficiency, a blue fluorescent organic light-emitting diode having a power efficiency higher than some of the best thermally activated delayed fluorescent and phosphorescent blue organic light-emitting diodes is demonstrated. The current findings suggest that leveraging triplet fusion from purely organic molecules in organic light-emitting diode materials offers an alternative route to achieve stable and high efficiency blue organic light-emitting diodes.

Design and Construction of Vibrio cholerae Strains That Harbor Various CTX Prophage Arrays.

Toxigenic Vibrio cholerae strains arise upon infection and integration of the lysogenic cholera toxin phage, the CTX phage, into bacterial chromosomes. The V. cholerae serogroup O1 strains identified to date can be broadly categorized into three main groups: the classical biotype strains, which harbor CTX-cla; the prototype El Tor strains (Wave 1 strains), which harbor CTX-1; and the atypical El Tor strains, which harbor CTX-2 (Wave 2 strains) or CTX-3~6 (Wave 3 strains). The efficiencies of replication and transmission of CTX phages are similar, suggesting the possibility of existence of more diverse bacterial strains harboring various CTX phages and their arrays in nature. In this study, a set of V. cholerae strains was constructed by the chromosomal integration of CTX phages into strains that already harbored CTX phages or those that did not harbor any CTX phage or RS1 element. Strains containing repeats of the same kind of CTX phage, strains containing the same kind of CTX phage in each chromosome, strains containing alternative CTX phages in one chromosome, or containing different CTX phages in each chromosome have been constructed. Thus, strains with any CTX array can be designed and constructed. Moreover, the strains described in this study contained the toxT-139F allele, which enhances the expression of TcpA and cholera toxin. These characteristics are considered to be important for cholera vaccine development. Once their capacity to provoke immunity in human against V. cholerae infection is evaluated, some of the generated strains could be developed further to yield cholera vaccine strains.

Clinicopathologic features of early gastric carcinoma with lymphoid stroma and feasibility of endoscopic submucosal dissection.

BACKGROUND: Gastric carcinoma with lymphoid stroma (GCLS) is a rare disease known to have unique features and a favorable prognosis. This study aimed to determine the clinicopathologic features of early GCLS (EGCLS) and define the feasibility of endoscopic submucosal dissection (ESD) for EGCLS. METHODS: We performed a retrospective analysis of 70 EGCLS patients treated via ESD or surgery and 1626 patients who underwent surgical resection for early non-GCLS (ENGCLS) between January 2007 and December 2014 at Pusan National University Hospital, Busan, Republic of Korea. RESULTS: The mean age of EGCLS patients was 58 years (range 36-77 years); a male predominance (3.7:1) was observed, and 81.4% showed Epstein-Barr virus positivity. Compared with ENGCLS, EGCLS was macroscopically more elevated (34.3 vs. 18.0%, P = 0.003) and located more proximally (upper third: 37.1 vs. 9.7%, P < 0.001). Tumor size was smaller (2.1 ± 1.1 vs. 3.1 ± 2.0 cm, P < 0.001), but submucosal invasion was more frequent (77.1 vs. 44.4%, P < 0.001) and deeper in the EGCLS group. Among the 59 EGCLS patients who were treated surgically, only two (3.4%) showed lymph node metastasis (LNM). Despite submucosal invasion, EGCLS showed a lower LNM rate (4.0 vs. 19.4%, P = 0.007) than ENGCLS, even in patients with SM3 EGCLS (5.3 vs. 24.5%, P = 0.007). There were no recurrences in the available ten patients who underwent ESD alone during a mean follow-up of 37.2 months. CONCLUSIONS: In this study, we observed unique clinicopathologic features with a very low LNM rate in EGCLS. We consider ESD a potentially curative treatment strategy for EGCLS despite deep submucosal invasion, especially in patients with poor performance status and significant comorbidities.

[A Case of Giant Fibrovascular Polyp of the Esophagus, Treated Successfully by Endoscopic Resection].

Fibrovascular polyps are rare benign intraluminal tumors that usually arise from the cervical esophagus. These often present as very large sized pedunculated polyps and cause symptoms including dysphagia and respiratory distress. Generally, large polyps are surgically excised, while endoscopic resection is limited to smaller polyps. Herein, we present a giant fibrovascular polyp of the esophagus treated successfully by endoscopic resection.

Synthesis of Cu3Sn alloy nanocrystals through sequential reduction induced by gradual increase of the reaction temperature.

Cu3Sn alloy nanocrystals are synthesized by sequential reduction of Cu and Sn precursors through a gradual increase of the reaction temperature. By transmission electron microscopy (TEM), energy-dispersive X-ray spectroscopy (EDS), UV/Vis spectroscopy, and X-ray diffraction (XRD) analyses, the alloy formation mechanism of Cu3Sn nanocrystals has been studied. The incremental increase of the reaction temperature sequentially induces the reduction of Sn, the diffusion of Sn into the preformed Cu nanocrystals, resulting in the intermediate phase of Cu-Sn alloy nanocrystals, and then the formation of Cu3Sn alloy nanocrystals. We anticipate that the synthesis of Cu3Sn alloy nanocrystals encourages studies toward the synthesis of various alloy nanomaterials.

Simultaneous enhancement of upconversion and downshifting luminescence via plasmonic structure.

We describe a metal nanodisk-insulator-metal (MIM) structure that enhances lanthanide-based upconversion (UC) and downshifting (DS) simultaneously. The structure was fabricated using a nanotransfer printing method that facilitates large-area applications of nanostructures for optoelectronic devices. The proposed MIM structure is a promising way to harness the entire solar spectrum by converting both ultraviolet and near-infrared to visible light concurrently through resonant-mode excitation. The overall photoluminescence enhancements of the UC and DS were 174- and 29-fold, respectively.

Open prospective study of ziprasidone in patients with schizophrenia with depressive symptoms: a multicenter study.

AIMS: The goal of this study was to examine the efficacy and safety of ziprasidone to treat depressive symptoms in Korean patients with schizophrenia who showed stable symptoms. METHODS: In this 8-week, open-label, prospective, non-randomized, multicenter study, 34 patients with schizophrenia who showed a stable response to previous medications, maintained a stable dose, and who had depressive symptoms, were recruited. Ziprasidone was the only antipsychotic agent allowed for 8 weeks after a 2-7-week washout period. RESULTS: Steady decreases were observed on the Montgomery-Asberg Depression Rating Scale, the Calgary Depression Scale for Schizophrenia, the Positive and Negative Syndrome Scale, and the Clinical Global Impression-Severity Scale scores. The Montgomery-Asberg Depression Rating Scale score was 20.26 ± 4.77 at baseline and 12.21 ± 7.94 at the end-point (P < 0.01). The Calgary Depression Scale for Schizophrenia score was 9.76 ± 4.11 at baseline and 5.00 ± 3.94 at the end-point (P < 0.01). The Positive and Negative Syndrome Scale total score was 75.24 ± 22.63 at baseline and 66.53 ± 24.28 at the end-point (P < 0.01). The Clinical Global Impression-Severity Scale score was 3.44 ± 0.66 at baseline and 3.15 ± 0.86 at the end-point (P < 0.05). No significant differences were observed for total scores on the Simpson and Angus Rating Scale, the Barnes Akathisia Rating Scale, or the Abnormal Involuntary Movement Scale between the baseline and end-point. CONCLUSIONS: Ziprasidone was effective for improving depressive symptom scores and was well tolerated. Switching to ziprasidone is a good strategy in patients with schizophrenia who are experiencing depressive symptoms.

Monosomal and complex karyotypes as prognostic parameters in patients with International Prognostic Scoring System higher risk myelodysplastic syndrome treated with azacitidine.

BACKGROUND: Azacitidine (AZA) is standard care for patients with myelodysplastic syndrome (MDS) who have not had allogeneic stem cell transplantation. Chromosomal abnormalities (CA) including complex karyotype (CK) or monosomal karyotype (MK) are associated with clinical outcome in patients with MDS. METHODS: We investigated which prognostic factors including CAs would predict clinical outcomes in patients with International Prognostic Scoring System (IPSS) higher risk MDS treated with AZA, retrospectively. CK was defined as the presence of three or more numerical or structural CAs. MK was defined as the presence of two or more distinct autosomal monosomies or single autosomal monosomy with at least one additional structural CA. RESULTS: A total of 243 patients who treated with AZA, were enrolled. CK was present in 124 patients and MK was present in 90 patients. Bone marrow blasts ≥15% and CK were associated with poorer response (P=0.038, P=0.007) and overall survival (OS) (P<0.001, P<0.001) independently. Although MK in CK group was not associated with prognosis, non-MK status in non-CK group reflected favorable OS (P=0.005). The group including >3 CAs was associated with poorer OS (group including <3 CAs vs. only three CAs, P=0.001; group with >3 CAs vs. only three CAs, P=0.001). CONCLUSION: CK was an important prognostic parameter associated with worse outcome. MK may predict poor survival in only non-CK status. The higher number of CAs was associated with poorer survival.

Influence of NK cell count on the survival of patients with diffuse large B-cell lymphoma treated with R-CHOP.

BACKGROUND: Although adding rituximab to the chemotherapy regimen of cyclophosphamide, vincristine, doxorubicin, and prednisone (R-CHOP) has improved clinical outcomes of patients with diffuse large B-cell lymphoma (DLBCL), several recent studies have shown that the effect of rituximab is dominantly in the non-germinal center (non-GC) subtype compared to the germinal center (GC) subtype. Natural killer (NK) cell count, a surrogate marker of immune status, is associated with clinical outcomes in DLBCL patients in the rituximab era. We investigated whether the impact of NK cells on clinical outcomes differed according to the immunophenotype of DLBCL. METHODS: This study analyzed 72 DLBCL patients treated with R-CHOP between January 2010 and January 2014. RESULTS: Low NK cell counts (<100/µL) were associated with poor progression-free survival (PFS) and overall survival (OS) compared to high NK cell counts. In multivariate analysis, low NK cell count was an independent prognostic factor for PFS and OS. However, survival did not significantly differ between the GC and non-GC subtypes. We examined the clinical influence of NK cells according to the immunophenotype and found that low NK cell counts were significantly associated with poor PFS and OS in non-GC cases, but not in GC cases. CONCLUSION: Low NK cell counts at diagnosis are associated with poor clinical outcomes in DLBCL patients treated with R-CHOP therapy. However, the impact is significant only in non-GC subtype DLBCL, not in the GC subtype.

Incidentally detected inoperable malignant pheochromocytoma with hepatic metastasis treated by transcatheter arterial chemoembolization.

Malignant pheochromocytoma (PCC) is a rare condition. Although the liver is the second most frequent site of metastasis in malignant PCC, no definite treatments have been established. Herein, we report a case of liver metastasis of PCC that was successfully treated by transcatheter arterial chemoembolization (TACE). A 69-year-old man was admitted to the Department of Gastroenterology for evaluation of an incidental hepatic mass in August 2013. He had undergone right adrenalectomy in May 2005 and PCC had been confirmed on the basis of histopathological findings. Liver biopsy was performed, and metastatic PCC was diagnosed. The lesion appeared inoperable because of invasion of the portal vein and metastases in the lymph nodes along the hepatoduodenal ligament. Thus, TACE was performed instead. After TACE, symptoms including dizziness and cold sweating improved, and the patient's serum catecholamine levels decreased. On the basis of this case, we believe that TACE may be a useful treatment for liver metastasis in malignant PCC.

Primary squamous cell carcinoma of the stomach: A case report.

Pure squamous cell carcinoma (SCC) of the stomach is rare and resembles SCC arising elsewhere in the body. The pathogenesis of SCC remains unclear and controversial. At present, <100 cases of primary SCC of the stomach have been reported. The current study presents a case of SCC of the stomach in a 61-year-old male. Total gastrectomy was performed and a 7.0×6.7×4.5-cm tumor with a superiorly located ulcer was identified in the cardia. Upon histological examination, a moderately-differentiated SCC was observed. Tumor cells extended to the serosa, and the perigastric regional lymph node was also involved. No evidence of human papillomavirus (HPV) or Epstein-Barr virus (EBV) infection was identified using a DNA microarray and in situ hybridization, respectively. A post-operative computed tomography scan four months after the gastrectomy revealed tumor recurrence and dissemination of the tumor to the jejunum and pancreas. The patient succumbed to the disease six months later despite the administration of low-dose adjuvant 5-fluorouracil/cisplatin chemotherapy.

FDG PET/CT in the detection of pancreatic metastasis in a patient with follicular thyroid carcinoma and negative I-131 whole body scan findings.

We identified a rare follicular thyroid carcinoma (FTC) metastasis to the pancreas in a patient of FTC. A 65-year-old woman presented at our hospital for evaluation of a pancreatic mass. She had a history of FTC. After total thyroidectomy, I-131 whole body scan showed increased I-131 uptake in the thyroid bed, but there was no evidence of distant metastasis. However, F-18 FDG PET/CT showed a mass with FDG uptake in the pancreatic head. Follow-up PET/CT showed FDG uptake in the pancreatic head and thyroid bed. Pylorus preserving pancreaticoduodenectomy was performed. Histopathological examination supported the diagnosis of metastatic FTC to pancreas.

A self-reducible and alcohol-soluble copper-based metal-organic decomposition ink for printed electronics.

We report a novel method for the synthesis of a self-reducible (thermally reducible without a reducing atmosphere) and alcohol-soluble copper-based metal-organic decomposition (MOD) ink for printed electronics. Alcohol-solvent-based conductive inks are necessary for commercial printing processes such as reverse offset printing. We selected copper(II) formate as a precursor and alkanolamine (2-amino-2-methyl-1-propanol) as a ligand to make an alcohol-solvent-based conductive ink and to assist in the reduction reaction of copper(II) formate. In addition, a co-complexing agent (octylamine) and a sintering helper (hexanoic acid) were introduced to improve the metallic copper film. The specific resistivity of copper-based MOD ink (Cuf-AMP-OH ink) after heat treatment at 350 °C is 9.46 µΩ·cm, which is 5.5 times higher than the specific resistivity of bulk copper. A simple stamping transfer was conducted to demonstrate the potential of our ink for commercial printing processes.

Expression and significance of the TLR4/MyD88 signaling pathway in ovarian epithelial cancers.

BACKGROUND: Toll-like receptors (TLR) are a family of pattern recognition receptors that constitutes a major part of the innate immune system. The TLR4/(Myeloid differentiation factor 88 (MyD88) signaling pathway has been shown to have oncogenic effects. METHODS: To demonstrate the role of TLR4/MyD88 signaling in ovarian epithelial cancers (OECs), we examined the expression of TLR4, MyD88 and nuclear factor- κB (NF-κB) in OECs. The expression of TLR4, MyD88, and NF-κB was detected by immunohistochemistry, and the relationships between these and clinicopathologic features in 123 cases of OECs were also analyzed. RESULTS: The expression of TLR4, MyD88, and NF-κB in OECs was observed in 46.3% (57/123), 36.6% (45/123) and 65% (80/123) of OEC cases, respectively. The TLR4, MyD88, and NF-κB expressions were associated with the histologic type of OECs, particularly with the clear cell type of OEC. There was no significant correlation between TLR4 or NF-κB expression and histologic grade, tumor size, mitotic count, FIGO (International Federation of Gynecology and Obstetrics) stage, disease recurrence. However, there was a significant correlation between MyD88 expression and FIGO stage, disease recurrence as well as histologic type. In univariate analysis, the expression of TLR4 and MyD88, and the coexpression of TLR4/MyD88 and TLR4/MyD88/NF-κB had a significant impact on the survival of patients with OECs. Only MyD88 expression had an independent prognostic significance in multivariate analysis. CONCLUSIONS: Our findings suggest that the TLR4/MyD88 signaling pathway is associated with the survival of patients with OECs, and that MyD88 is an independent prognostic predictor in patients with OECs. The TLR4/MyD88 signaling pathway may be a mechanism responsible for poor prognosis in patients with clear cell type of OEC.

Prognostic Relevance of the Expression of CA IX, GLUT-1, and VEGF in Ovarian Epithelial Cancers.

BACKGROUND: Tumor hypoxia is associated with malignant progression and treatment resistance. Hypoxia-related factors, such as carbonic anhydrase IX (CA IX), glucose transporter-1 (GLUT-1), and vascular endothelial growth factor (VEGF) permit tumor cell adaptation to hypoxia. We attempted to elucidate the correlation of these markers with variable clinicopathological factors and overall prognosis. METHODS: Immunohistochemistry for CA IX, GLUT-1, and VEGF was performed on formalin-fixed, paraffin-embedded tissues from 125 cases of ovarian epithelial cancer (OEC). RESULTS: CA IX expression was significantly associated with an endometrioid and mucinous histology, nuclear grade, tumor necrosis, and mitosis. GLUT-1 expression was associated with tumor necrosis and mitosis. VEGF expression was correlated only with disease recurrence. Expression of each marker was not significant in terms of overall survival in OECs; however, there was a significant correlation between poor overall survival rate and high coexpression of these markers. CONCLUSIONS: The present study suggests that it is questionable whether CA IX, GLUT-1, or VEGF can be used alone as independent prognostic factors in OECs. Using at least two markers helps to predict patient outcomes in total OECs. Moreover, the inhibition of two target gene combinations might prove to be a novel anticancer therapy.