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1.
J Phys Chem B ; 128(13): 3282-3297, 2024 Apr 04.
Artigo em Inglês | MEDLINE | ID: mdl-38506668

RESUMO

New functionality is added to the LAMMPS molecular simulation package, which increases the versatility with which LAMMPS can interface with supporting software and manipulate information associated with bonded force fields. We introduce the "type label" framework that allows atom types and their higher-order interactions (bonds, angles, dihedrals, and impropers) to be represented in terms of the standard atom type strings of a bonded force field. Type labels increase the human readability of input files, enable bonded force fields to be supported by the OpenKIM repository, simplify the creation of reaction templates for the REACTER protocol, and increase compatibility with external visualization tools, such as VMD and OVITO. An introductory primer on the forms and use of bonded force fields is provided to motivate this new functionality and serve as an entry point for LAMMPS and OpenKIM users unfamiliar with bonded force fields. The type label framework has the potential to streamline modeling workflows that use LAMMPS by increasing the portability of software, files, and scripts for preprocessing, running, and postprocessing a molecular simulation.

2.
ACS Nano ; 15(12): 20253-20260, 2021 Dec 28.
Artigo em Inglês | MEDLINE | ID: mdl-34780160

RESUMO

Key properties of two-dimensional (2D) layered materials are highly strain tunable, arising from bond modulation and associated reconfiguration of the energy bands around the Fermi level. Approaches to locally controlling and patterning strain have included both active and passive elastic deformation via sustained loading and templating with nanostructures. Here, by float-capturing ultrathin flakes of single-crystal 2H-MoS2 on amorphous holey silicon nitride substrates, we find that highly symmetric, high-fidelity strain patterns are formed. The hexagonally arranged holes and surface topography combine to generate highly conformal flake-substrate coverage creating patterns that match optimal centroidal Voronoi tessellation in 2D Euclidean space. Using TEM imaging and diffraction, as well as AFM topographic mapping, we determine that the substrate-driven 3D geometry of the flakes over the holes consists of symmetric, out-of-plane bowl-like deformation of up to 35 nm, with in-plane, isotropic tensile strains of up to 1.8% (measured with both selected-area diffraction and AFM). Atomistic and image simulations accurately predict spontaneous formation of the strain patterns, with van der Waals forces and substrate topography as the input parameters. These results show that predictable patterns and 3D topography can be spontaneously induced in 2D materials captured on bare, holey substrates. The method also enables electron scattering studies of precisely aligned, substrate-free strained regions in transmission mode.

3.
Oncology ; 99(10): 665-672, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34515197

RESUMO

BACKGROUND: Due to few efficacious options in later lines of therapy in metastatic colorectal cancer (mCRC), there has been considerable interest in the possibility of retreatment with previously administered agents. This study investigated the efficacy and safety of irinotecan retreatment (IRI2) in patients with refractory mCRC. METHODS: We performed a retrospective analysis of patients with mCRC who were retreated with irinotecan-based regimens. The retreatment regimens with anti-epidermal growth factor receptor therapies were excluded. RESULTS: A total of 64 patients were included. Patients had a median age of 56 years and were offered mainly in the setting of third- or fourth-line therapy with IRI2. The disease control rate was 78.2% including an objective response of 23.5%. Median progression-free survival and overall survival were 5.5 and 19.3 months, respectively. The most frequent grade 3 or higher toxicities were nausea/vomiting (27.9%) and neutropenia (25%). CONCLUSION: IRI2 might be a reasonable option for heavily pretreated patients with mCRC who achieved disease control with prior irinotecan therapy.


Assuntos
Protocolos de Quimioterapia Combinada Antineoplásica/uso terapêutico , Neoplasias Colorretais/tratamento farmacológico , Adulto , Idoso , Protocolos de Quimioterapia Combinada Antineoplásica/efeitos adversos , Neoplasias Colorretais/patologia , Humanos , Irinotecano/administração & dosagem , Irinotecano/efeitos adversos , Pessoa de Meia-Idade , Metástase Neoplásica , Retratamento , Estudos Retrospectivos , Resultado do Tratamento
4.
PLoS One ; 15(8): e0237789, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32810188

RESUMO

Aquaporins are water-permeable membrane-channel proteins found in biological cell membranes that selectively exclude ions and large molecules and have high water permeability, which makes them promising candidates for water desalination systems. To effectively apply the properties of aquaporins in the desalination process, many studies have been conducted on aquaporin-lipid membrane systems using phospholipids, which are the main component of cell membranes. Many parametric studies have evaluated the permeability of such systems with various aquaporin types and lipid compositions. In this study, we performed molecular dynamics simulations for four cases with different protein-lipid molar ratios (1:50, 1:75, 1:100, and 1:150) between aquaporin Z and the phospholipids, and we propose a possibility of the existence of optimal protein-lipid molar ratio to maximize water permeability. Elucidating these simulation results from a structural viewpoint suggests that there is a relationship between the permeability and changes in the hydrophobic thickness of the lipid membrane adjacent to the aquaporin as a structural parameter. The results of this study can help optimize the design of an aquaporin-lipid membrane by considering its molar ratio at an early stage of development.


Assuntos
Aquaporinas/metabolismo , Proteínas de Escherichia coli/metabolismo , Bicamadas Lipídicas/metabolismo , Fosfolipídeos/metabolismo , Purificação da Água/métodos , Água/metabolismo , Aquaporinas/química , Proteínas de Escherichia coli/química , Interações Hidrofóbicas e Hidrofílicas , Bicamadas Lipídicas/química , Modelos Químicos , Simulação de Dinâmica Molecular , Pressão Osmótica , Fosfolipídeos/química , Salinidade , Água/química
5.
Sci Rep ; 10(1): 7995, 2020 05 14.
Artigo em Inglês | MEDLINE | ID: mdl-32409710

RESUMO

We set out to determine the usability of serum neurofilament light chain (sNfL), serum glial fibrillary acidic protein (sGFAP), and retinal parameters by using optical coherence tomography (OCT) as reliable biomarkers of the progression of oxaliplatin-induced peripheral neuropathy (OIPN). Forty-three patients scheduled to undergo oxaliplatin-based chemotherapy at the National Cancer Center of Korea between June 2018 and October 2019 were prospectively assessed at baseline, 3 months, and 6 months of chemotherapy. Patients were assessed on clinical scales and underwent OCT, sNfL, and sGFAP level measurement at each follow-up visit. By applying the National Cancer Institute-Common Toxicity Criteria (NCI-CTC), OIPN was classified as grade 1 in 12 (28%) patients, grade 2 in 25 (58%), and grade 3 in 5 (12%) at 6 months of chemotherapy. sNfL levels increased during oxaliplatin administration, while serial sGFAP levels or retinal parameters did not change. Patients with grade-3 OIPN showed significantly higher mean sNfL levels than patients with grade 0-2 OIPN at 6 months of treatment. At 4-6 months after completion of chemotherapy, sNfL levels were significantly reduced compared to the levels at 6 months of chemotherapy. Monitoring of sNfL during chemotherapy can indicate ongoing neuroaxonal injury and the severity of OIPN.


Assuntos
Biomarcadores , Proteínas de Neurofilamentos/sangue , Oxaliplatina/efeitos adversos , Doenças do Sistema Nervoso Periférico/sangue , Doenças do Sistema Nervoso Periférico/etiologia , Adulto , Relação Dose-Resposta a Droga , Fenômenos Eletrofisiológicos , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Condução Nervosa/efeitos dos fármacos , Doenças do Sistema Nervoso Periférico/diagnóstico , Doenças do Sistema Nervoso Periférico/fisiopatologia , Índice de Gravidade de Doença
6.
Int J Colorectal Dis ; 35(7): 1273-1282, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32347342

RESUMO

PURPOSE: The high incidence of metachronous colorectal tumours in patients with hereditary non-polyposis colorectal cancer (HNPCC) encourages extended resection (ER); however, the optimal surgical approach remains unclear. We evaluated the incidences of metachronous colorectal neoplasms following curative colorectal cancer segmental resection (SR) vs ER in patients with HNPCC and investigated patients' oncologic outcomes according to surgical modality and mismatch repair status. METHODS: We retrospectively investigated medical records of patients with HNPCC (per the Amsterdam II criteria) treated for primary colon cancer at our institution between 2001 and 2017. All patients underwent intensive endoscopic surveillance. RESULTS: We included 87 patients (36 who underwent SR and 51 who underwent ER). The cumulative incidence of metachronous adenoma was higher in the SR group. One patient in the SR group (2.8%) and 3 in the ER group (5.9%) developed metachronous colon cancer; the difference was not significant (P = 0.693). Four patients in the SR group (11.1%) and 1 in the ER group (2.0%) developed distant recurrences; again, the difference was not significant (P = 0.155). Moreover, no significant differences were observed in the 5-year overall survival rates of patients in the SR and ER groups (88.2% vs 95.5%, P = 0.446); the same was true for 5-year disease-free survival rates (79.5% vs 91.0%, P = 0.147). CONCLUSION: The incidence of metachronous cancer was not significantly different between the ER and SR groups; however, that of cumulative metachronous adenoma was higher in the SR group. Hence, intensive surveillance colonoscopy may be sufficient for patients with HNPCC after non-extensive colon resection.


Assuntos
Neoplasias Colorretais Hereditárias sem Polipose , Neoplasias Colorretais , Segunda Neoplasia Primária , Neoplasias Colorretais Hereditárias sem Polipose/cirurgia , Humanos , Recidiva Local de Neoplasia , Segunda Neoplasia Primária/epidemiologia , Estudos Retrospectivos
7.
Sci Rep ; 9(1): 5779, 2019 04 08.
Artigo em Inglês | MEDLINE | ID: mdl-30962494

RESUMO

Zeolitic imidazolate framework-302 (ZIF-302)-embedded cellulose acetate (CA) membranes for osmotic driven membrane process (ODMPs) were fabricated using the phase inversion method. We investigated the effects of different fractions of ZIF-302 in the CA membrane to understand their influence on ODMPs performance. Osmotic water transport was evaluated using different draw solution concentrations to investigate the effects of ZIF-302 contents on the performance parameters. CA/ZIF-302 membranes showed fouling resistance to sodium alginate by a decreased water flux decline and increased recovery ratio in the pressure retarded osmosis (PRO) mode. Results show that the hydrothermally stable ZIF-302-embedded CA/ZIF-302 composite membrane is expected to be durable in water and alginate-fouling conditions.

8.
Korean J Intern Med ; 34(5): 1107-1115, 2019 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-29914230

RESUMO

BACKGROUND/AIMS: We investigated the efficacy and toxicity of a weekly schedule of docetaxel and cisplatin as a first-line treatment in patients with recurrent or metastatic head and neck squamous cell carcinoma (R/M HNSCC). METHODS: In this study, 18 patients with previously diagnosed R/M HNSCC were treated with combination chemotherapy of weekly docetaxel 35 mg/m2 (day 1 and 8) and cisplatin 70 mg/m2 (day 1) as first-line chemotherapy, repeated every 3 weeks. RESULTS: Partial response and stable disease were observed in six patients (33.3%; 95% confidence interval [CI], 11.1% to 55.6%) and six patients (33.3%; 95% CI, 11.1% to 55.6%), respectively. The median overall survival and progression-free survival were 11.26 months (95% CI, 8.87 to 15.83) and 5.68 months (95% CI, 4.80 to 6.51), respectively. The major toxicity was grade 1/2 anemia (50%). Grade 3/4 neutropenia was observed in one patient (5.6%). Among the non-hematologic toxicities, grade 1/2 hepatotoxicity was most common (22.2%), and grade 3/4 infection was observed in one patient (5.6%). There was no treatment-related mortality. CONCLUSION: For patients with R/M HNSCC, a cisplatin and weekly docetaxel regimen showed high efficacy with tolerable toxicity as a first-line treatment.


Assuntos
Protocolos de Quimioterapia Combinada Antineoplásica/uso terapêutico , Cisplatino/administração & dosagem , Docetaxel/administração & dosagem , Neoplasias de Cabeça e Pescoço/tratamento farmacológico , Carcinoma de Células Escamosas de Cabeça e Pescoço/tratamento farmacológico , Adulto , Idoso , Protocolos de Quimioterapia Combinada Antineoplásica/efeitos adversos , Cisplatino/efeitos adversos , Progressão da Doença , Docetaxel/efeitos adversos , Esquema de Medicação , Feminino , Neoplasias de Cabeça e Pescoço/mortalidade , Neoplasias de Cabeça e Pescoço/patologia , Humanos , Masculino , Pessoa de Meia-Idade , Recidiva Local de Neoplasia , Intervalo Livre de Progressão , Estudos Retrospectivos , Carcinoma de Células Escamosas de Cabeça e Pescoço/mortalidade , Carcinoma de Células Escamosas de Cabeça e Pescoço/secundário , Fatores de Tempo
9.
Neoplasia ; 21(1): 146-155, 2019 01.
Artigo em Inglês | MEDLINE | ID: mdl-30562637

RESUMO

Aberrant promoter methylation plays a vital role in colorectal carcinogenesis. However, its role in treatment responses is unclear, especially for metastatic disease. Here, we investigated the association between promoter methylation and treatment outcomes of irinotecan-based chemotherapy in 102 patients with metastatic colorectal cancer. Promoter methylation was examined by methylation-specific polymerase chain reaction for three loci (CHFR, WRN, and SULF2) associated with chemotherapy response and five CpG island methylator phenotype (CIMP)-specific markers (CACNA1G, IGF2, NEUROG1, RUNX3, and SOCS1). Association between CHFR methylation and in vitro sensitivity to irinotecan was also evaluated. Promoter methylation of CHFR, WRN, and SULF2 was identified in 16 (15.7%), 24 (23.5%), and 33 (32.4%) patients, respectively. CIMP status was positive in 22 (21.6%) patients. CHFR methylation was associated with a significantly longer time to progression (TTP) (median: 8.77 vs. 4.43 months, P = .019), with trends favoring higher overall survival (OS) (median: 22.83 vs. 20.17 months, P = .300) and response rates (31.3% vs. 17.4%, P = .300). For patients with unmethylated CHFR, TTP (median: 5.60 vs. 3.53, P = .020) and OS (median: 20.57 vs. 9.23, P = .006) were significantly different according to CIMP status. Colorectal cancer cell lines with CHFR methylation demonstrated increased sensitivity to irinotecan. Both CHFR overexpression and combination with 5-aza-2'-deoxycytidine reversed irinotecan sensitivity in CHFR-methylated cell lines, whereas CHFR knockdown in unmethylated cells restored sensitivity to irinotecan. These data suggest that CHFR methylation may be associated with favorable treatment outcomes of irinotecan-based chemotherapy in patients with metastatic colorectal cancer.


Assuntos
Protocolos de Quimioterapia Combinada Antineoplásica/uso terapêutico , Proteínas de Ciclo Celular/genética , Neoplasias Colorretais/tratamento farmacológico , Neoplasias Colorretais/genética , Metilação de DNA , Proteínas de Neoplasias/genética , Proteínas de Ligação a Poli-ADP-Ribose/genética , Regiões Promotoras Genéticas , Ubiquitina-Proteína Ligases/genética , Adulto , Idoso , Idoso de 80 Anos ou mais , Protocolos de Quimioterapia Combinada Antineoplásica/efeitos adversos , Biomarcadores Tumorais , Proteínas de Transporte , Linhagem Celular Tumoral , Neoplasias Colorretais/mortalidade , Neoplasias Colorretais/patologia , Feminino , Humanos , Irinotecano/administração & dosagem , Estimativa de Kaplan-Meier , Masculino , Pessoa de Meia-Idade , Gradação de Tumores , Metástase Neoplásica , Estadiamento de Neoplasias , Resultado do Tratamento
10.
J Diabetes Complications ; 32(7): 630-634, 2018 07.
Artigo em Inglês | MEDLINE | ID: mdl-29753600

RESUMO

AIMS: The aim of this study was to evaluate ethnic- and sex-specific associations between DM and hearing impairment. METHODS: For this cross-sectional study using National Health and Nutrition Examination Survey in the U.S. and Korea, the total number of eligible participants included was 7081 in the U.S. and 15,704 in Korea. Hearing impairment was defined as a pure tone threshold level ≥ 25 dB. Multivariate logistic regression analysis was conducted, adjusting for age, sex, race/ethnicity, socioeconomic status, body mass index, noise exposure, smoking, hypertension, and dyslipidemia. RESULTS: The association between DM and hearing impairment was found to be sex-specific. The multivariate adjusted ORs of high-frequency impairment were 0.843 (95% CI, 0.524-1.356) in American men, and 1.073 (95% CI, 0.835-1.379) in Korean men, while the ORs in women from U.S. and Korea were 1.911 (95% CI, 1.244-2.935) and 1.421 (95% CI, 1.103-1.830), respectively. A subgroup analysis of each race/ethnicity among the U.S. adults showed similar results. In contrast to high-frequency impairment, there was no significant association between low-frequency impairment and DM in both men and women. CONCLUSION: Our results suggest that DM is associated with hearing impairment in only women, irrespective of race/ethnicity groups.


Assuntos
Complicações do Diabetes/epidemiologia , Diabetes Mellitus/epidemiologia , Perda Auditiva/epidemiologia , Adulto , Estudos Transversais , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Inquéritos Nutricionais , Prevalência , República da Coreia/epidemiologia , Fatores de Risco , Classe Social , Estados Unidos/epidemiologia
11.
PLoS One ; 13(4): e0194730, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29641535

RESUMO

AZD9291 (osimertinib) is approved for standard care in patients with EGFR T790M-positive non-small cell lung cancer (NSCLC) after prior EGFR TKI progression. Furthermore, AZD9291 is now being evaluated as a first-line treatment for NSCLC patients with activation EGFR mutations. Based on previous experiments, resistance to AZD9291 as a first-line treatment may also emerge. Thus, identification and understanding of resistance mechanisms to AZD9291 as a first-line treatment can help direct development of future therapies. AZD9291-resistant cells (PC9/AZDR) were established using EGFR inhibitor-naïve PC9 cells. Resistance mechanisms were analyzed using next-generation sequencing (NGS) and a proteome profiler array. Resistance to AZD9291 developed through aberrant activation of ERK signaling by an EGFR-independent mechanism. The combination of a MEK inhibitor with AZD9291 restored the sensitivity of PC9/AZDR cells in vitro and in vivo. PC9/AZDR cells also showed increased MET expression and an HRAS G13R mutation. In addition, maspin expression was higher after AZD9291 treatment in PC9/AZDR cells. Sustained ERK activation confers resistance to AZD9291 as a first-line therapy. Thus, co-targeting EGFR and MEK may be an effective strategy to overcome resistance to AZD9291.


Assuntos
Acrilamidas/farmacologia , Compostos de Anilina/farmacologia , Carcinoma Pulmonar de Células não Pequenas/tratamento farmacológico , Resistencia a Medicamentos Antineoplásicos , MAP Quinases Reguladas por Sinal Extracelular/metabolismo , Regulação Neoplásica da Expressão Gênica , Neoplasias Pulmonares/tratamento farmacológico , Animais , Antineoplásicos/farmacologia , Peso Corporal , Carcinoma Pulmonar de Células não Pequenas/metabolismo , Linhagem Celular Tumoral , Proliferação de Células , Sobrevivência Celular , Receptores ErbB/genética , Feminino , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Neoplasias Pulmonares/metabolismo , Camundongos , Camundongos Endogâmicos BALB C , Mutação , Transplante de Neoplasias , Proteoma , Transdução de Sinais
12.
Lung Cancer ; 119: 36-41, 2018 05.
Artigo em Inglês | MEDLINE | ID: mdl-29656750

RESUMO

INTRODUCTION: Afatinib, an irreversible ErbB family blocker, approved for first-line treatment of epidermal growth factor receptor (EGFR) mutated advanced non-small cell lung cancer (NSCLC). This study investigated experience of afatinib within a compassionate use program (CUP). METHODS: The afatinib CUP was an open-label, multicenter, single-arm program in Korea. We enrolled patients with stage IV NSCLC and who had received at least one line of previous cytotoxic chemotherapy and previous EGFR TKI treatment with either an EGFR mutation or documented clinical benefit. The starting dose of afatinib was 50 mg once daily. RESULTS: From August 2011 to September 2014, 332 patients received at least one dose of afatinib. Most patients were registered in the CUP for fourth- or fifth-line treatment with afatinib. Adverse events (AEs) occurred in 98.1% of patients, including 29.8% with serious AEs. The most common AEs (all grades) were diarrhea (90.1%) and skin rash (62.0%). Dose reductions occurred in 60.5% of patients and discontinuations due to AEs were reported in 11.1% of patients. The response rate and median time to treatment failure (TTF) were 27.4% and 3.3 months (CI 95%, 2.8-3.8 months), respectively, in this highly pretreated population. In subgroup analysis, ECOG PS 0 or 1 and immediate pretreatment with pemetrexed monotherapy or a platinum doublet were associated with a longer TTF for afatinib. CONCLUSIONS: No additional or unexpected safety concerns were observed, and afatinib demonstrated moderate antitumor activity in advanced NSCLC patients with acquired resistance to gefitinib or erlotinib in a real-world setting.


Assuntos
Afatinib/uso terapêutico , Protocolos de Quimioterapia Combinada Antineoplásica/uso terapêutico , Carcinoma Pulmonar de Células não Pequenas/tratamento farmacológico , Neoplasias Pulmonares/tratamento farmacológico , Adulto , Idoso , Idoso de 80 Anos ou mais , Carcinoma Pulmonar de Células não Pequenas/patologia , Ensaios de Uso Compassivo , Resistencia a Medicamentos Antineoplásicos , Receptores ErbB/antagonistas & inibidores , Cloridrato de Erlotinib/uso terapêutico , Feminino , Gefitinibe/uso terapêutico , Humanos , Neoplasias Pulmonares/patologia , Masculino , Pessoa de Meia-Idade , Estadiamento de Neoplasias , República da Coreia , Resultado do Tratamento , Adulto Jovem
13.
Oncology ; 95(1): 20-30, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29694959

RESUMO

OBJECTIVE: Multimodal treatments that include preoperative platinum-based chemotherapy are fundamental to the treatment of advanced non-small cell lung cancer (NSCLC). This study aimed to investigate the predictive value of DNA repair protein expression in surgically resected NSCLCs in terms of prognosis and responses to platinum-containing chemotherapy. METHODS: This retrospective study included 136 patients with NSCLC who were treated with preoperative platinum-based chemotherapy, followed by curative lung resection. ATM, RAD51, LKB1, H2AX, and SIRT1 expression levels were analyzed in resected tumor specimens via immunostaining and were used to classify patients and compare survival and responses to chemotherapy. RESULTS: SIRT1 expression correlated significantly with improved responses to platinum-based chemotherapy (odds ratio, 2.28; p = 0.024), progression-free survival (hazard ratio [HR], 0.74; p = 0.036), overall survival (HR, 0.63; p = 0.006), and tumor-bearing survival (HR, 0.62; p = 0.014). After adjusting for clinical variables, the HR of SIRT1 expression remained significant for overall survival (HR, 0.59; p = 0.039) but not for progression-free survival (HR, 0.74; p = 0.183). No prognostic stratification was observed for the other 4 markers. CONCLUSION: Patients with SIRT1-expressing NSCLC had superior responses to chemotherapy and longer survival durations than those with SIRT1-negative cancer.


Assuntos
Protocolos de Quimioterapia Combinada Antineoplásica/uso terapêutico , Biomarcadores Tumorais/genética , Carboplatina/uso terapêutico , Carcinoma Pulmonar de Células não Pequenas/tratamento farmacológico , Cisplatino/uso terapêutico , Neoplasias Pulmonares/tratamento farmacológico , Sirtuína 1/biossíntese , Sirtuína 1/genética , Quinases Proteína-Quinases Ativadas por AMP , Adulto , Idoso , Idoso de 80 Anos ou mais , Proteínas Mutadas de Ataxia Telangiectasia/biossíntese , Proteínas Mutadas de Ataxia Telangiectasia/genética , Carboplatina/efeitos adversos , Carcinoma Pulmonar de Células não Pequenas/mortalidade , Cisplatino/efeitos adversos , Terapia Combinada/métodos , Dano ao DNA/efeitos dos fármacos , Dano ao DNA/genética , Reparo do DNA/genética , Intervalo Livre de Doença , Feminino , Histonas/biossíntese , Histonas/genética , Humanos , Estimativa de Kaplan-Meier , Neoplasias Pulmonares/mortalidade , Masculino , Pessoa de Meia-Idade , Proteínas Serina-Treonina Quinases/biossíntese , Proteínas Serina-Treonina Quinases/genética , Rad51 Recombinase/biossíntese , Rad51 Recombinase/genética , Estudos Retrospectivos , Resultado do Tratamento
14.
Adv Mater ; 30(14): e1705944, 2018 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-29484720

RESUMO

Water purification by membranes is widely investigated to address concerns related to the scarcity of clean water. Achieving high flux and rejection simultaneously is a difficult challenge using such membranes because these properties are mutually exclusive in common artificial membranes. Nature has developed a method for this task involving water-channel membrane proteins known as aquaporins. Here, the design and fabrication of graphene oxide (GO)-based membranes with a surface-tethered peptide motif designed to mimic the water-selective filter of natural aquaporins is reported. The short RF8 (RFRFRFRF, where R and F represent arginine and phenylalanine, respectively) octapeptide is a concentrated form of the core component of the Ar/R (aromatic/arginine) water-selective filter in aquaporin. The resulting GO-RF8 shows superior flux and high rejection similar to natural aquaporins. Molecular dynamics simulation reveal the unique configuration of RF8 peptides and the transport of water in GO-RF8 membranes, supporting that RF8 effectively emulates the core function of aquaporins.

15.
Comput Biol Chem ; 72: 53-61, 2018 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-29414097

RESUMO

In recent years, Zika virus (ZIKV) caused a new pandemic due to its rapid spread and close relationship with microcephaly. As a result, ZIKV has become an obvious global health concern. Information about the fundamental viral features or the biological process of infection remains limited, despite considerable efforts. Meanwhile, the icosahedral shell structure of the mature ZIKV was recently revealed by cryo-electron microscopy. This structural information enabled us to simulate ZIKV. In this study, we analyzed the dynamic properties of ZIKV through simulation from the mechanical viewpoint. We performed normal mode analysis (NMA) for a dimeric structure of ZIKV consisting of the envelope proteins and the membrane proteins as a unit structure. By analyzing low-frequency normal modes, we captured intrinsic vibrational motions and defined basic vibrational properties of the unit structure. Moreover, we also simulated the entire shell structure of ZIKV at the reduced computational cost, similar to the case of the unit structure, by utilizing its icosahedral symmetry. From the NMA results, we can not only comprehend the putative dynamic fluctuations of ZIKV but also verify previous inference such that highly mobile glycosylation sites would play an important role in ZIKV. Consequently, this theoretical study is expected to give us an insight on the underlying biological functions and infection mechanism of ZIKV.


Assuntos
Proteínas da Matriz Viral/química , Zika virus/química , Glicosilação , Modelos Químicos , Simulação de Dinâmica Molecular , Vibração
16.
Nanotechnology ; 29(11): 115702, 2018 Mar 16.
Artigo em Inglês | MEDLINE | ID: mdl-29332844

RESUMO

Carbon nanotubes (CNTs) have been considered a prominent nano-channel in cell membranes because of their prominent ion-conductance and ion-selectivity, offering agents for a biomimetic channel platform. Using a coarse-grained molecular dynamics simulation, we clarify a construction mechanism of vertical CNT nano-channels in a lipid membrane for a long period, which has been difficult to observe in previous CNT-lipid interaction simulations. The result shows that both the lipid coating density and length of CNT affect the suitable fabrication condition for a vertical and stable CNT channel. Also, simulation elucidated that a lipid coating on the surface of the CNT prevents the CNT from burrowing into the lipid membrane and the vertical channel is stabilized by the repulsion force between the lipids in the coating and membrane. Our study provides an essential understanding of how CNTs can form stable and vertical channels in the membrane, which is important for designing new types of artificial channels as biosensors for bio-fluidic studies.

17.
Korean J Intern Med ; 33(3): 585-594, 2018 05.
Artigo em Inglês | MEDLINE | ID: mdl-28190327

RESUMO

BACKGROUND/AIMS: The purpose of the present study was to assess the prevalence of and factors associated with anxiety and depression in Korean patients with advanced gastrointestinal cancer. METHODS: One hundred and twenty consecutive patients with newly diagnosed, advanced gastrointestinal cancer who were scheduled to receive palliative chemotherapy between July 2012 and June 2014 were enrolled in this observational prospective study. Anxiety and depression were assessed using the Hospital Anxiety and Depression Scale (HADS) and Patient Health Questionnaire-9 (PHQ-9). RESULTS: Thirty-seven patients (30.8%) had anxiety or depression with clinical significance according to HADS or PHQ-9. Multivariate analysis identified lower performance status (odds ratio [OR], 4.19; 95% confidence interval [CI], 1.22 to 14.35; p = 0.023), gastric cancer (OR, 5.39; 95% CI, 0.37 to 78.23; p = 0.018), and knowledge of advanced cancer (OR, 15.07; 95% CI, 1.80 to 125.90; p = 0.012) as significantly associated with anxiety or depression. Twenty-one patients with anxiety or depression visited the psycho-oncologic clinic. In these patients, PHQ-9 score (p = 0.008), global health status (p = 0.023), fatigue (p = 0.047), and appetite loss (p = 0.006) improved from baseline to 3 months after study enrollment. CONCLUSIONS: Approximately 30% of Korean patients with advanced gastrointestinal cancer had anxiety or depression. The prevalence of anxiety or depression was higher in patients with poor performance status, gastric cancer, or knowledge of advanced cancer. Psychiatric interventions may be effective in reducing depression and improving quality of life in cancer patients with anxiety or depression.


Assuntos
Ansiedade , Depressão , Neoplasias Gastrointestinais , Adulto , Idoso , Idoso de 80 Anos ou mais , Ansiedade/complicações , Depressão/complicações , Feminino , Neoplasias Gastrointestinais/complicações , Neoplasias Gastrointestinais/psicologia , Humanos , Masculino , Pessoa de Meia-Idade , Prevalência , Estudos Prospectivos , Qualidade de Vida , Inquéritos e Questionários
18.
PLoS One ; 12(10): e0185658, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-29020017

RESUMO

The biological function of proteins is closely related to its structural motion. For instance, structurally misfolded proteins do not function properly. Although we are able to experimentally obtain structural information on proteins, it is still challenging to capture their dynamics, such as transition processes. Therefore, we need a simulation method to predict the transition pathways of a protein in order to understand and study large functional deformations. Here, we present a new simulation method called normal mode-guided elastic network interpolation (NGENI) that performs normal modes analysis iteratively to predict transition pathways of proteins. To be more specific, NGENI obtains displacement vectors that determine intermediate structures by interpolating the distance between two end-point conformations, similar to a morphing method called elastic network interpolation. However, the displacement vector is regarded as a linear combination of the normal mode vectors of each intermediate structure, in order to enhance the physical sense of the proposed pathways. As a result, we can generate more reasonable transition pathways geometrically and thermodynamically. By using not only all normal modes, but also in part using only the lowest normal modes, NGENI can still generate reasonable pathways for large deformations in proteins. This study shows that global protein transitions are dominated by collective motion, which means that a few lowest normal modes play an important role in this process. NGENI has considerable merit in terms of computational cost because it is possible to generate transition pathways by partial degrees of freedom, while conventional methods are not capable of this.


Assuntos
Algoritmos , Proteínas/química , Simulação por Computador , Modelos Moleculares , Reprodutibilidade dos Testes
19.
J Mol Graph Model ; 78: 81-87, 2017 11.
Artigo em Inglês | MEDLINE | ID: mdl-29054097

RESUMO

At the base of a flagellar motor, its rotational direction and speed are regulated by the interaction between rotor and stator proteins. A switching event occurs when the cytoplasmic rotor protein, called C-ring, changes its conformation in response to binding of the CheY signal protein. The C-ring structure consists of FliG, FliM, and FliN proteins and its conformational changes in FliM and FliG including HelixMC play an important role in switching the motor direction. Therefore, clarifying their dynamic properties as well as conformational changes is a key to understanding the switching mechanism of the motor protein. In this study, to elucidate dynamic characteristics of the C-ring structure, both harmonic (intrinsic vibration) and anharmonic (transition pathway) analyses are conducted by using the symmetry-constrained elastic network model. As a result, the first three normal modes successfully capture the essence of transition pathway from wild type to CW-biased state. Their cumulative square overlap value reaches up to 0.842. Remarkably, it is also noted from the transition pathway that the cascade of interactions from the signal protein to FliM to FliG, highlighted by the major mode shapes from the first three normal modes, induces the reorientation (∼100° rotation of FliGC5) of FliG C-terminal that directly interacts with the stator protein. Presumably, the rotational direction of the motor protein is switched by this substantial change in the stator-rotor interaction.


Assuntos
Modelos Moleculares , Conformação Proteica , Thermotoga maritima/química , Proteínas de Bactérias/química , Cristalografia por Raios X , Escherichia coli/química , Proteínas de Escherichia coli , Proteínas Quimiotáticas Aceptoras de Metil/química , Ligação Proteica
20.
PLoS One ; 12(9): e0185127, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28949994

RESUMO

The metabolic outcomes of metabolically healthy obesity (MHO) remain controversial. The aim of the present study was to determine the effect of physical activity on the cardiovascular disease (CVD) outcomes of MHO. The study included participants who were followed for 10 years and recruited from the Korean Genome and Epidemiology Study (KoGES), a population-based cohort study. Participants with previously recorded CVDs or cancer, or who had received steroids or anticoagulants at baseline were excluded. A total of 8144 participants (3,942 men and 4,202 women) fulfilled inclusion criteria. In a multivariate Cox regression model adjusted for age and sex, MHO participants were not at elevated risk of CVD compared with their metabolically healthy non-obese (MHNO) counterparts (HR, 1.28; 95% CI, 0.96-1.71), although both the non-obese (HR, 1.50; 95% CI, 1.19-1.90) and obese (HR, 1.85; 95% CI, 1.48-2.30) participants with metabolic abnormalities were at elevated risk. However, in the subgroup analysis by physical activity, physically inactive MHO participants had a significantly higher HR for CVD events compared to active MHNO participants (HR, 1.54; 95% CI, 1.03-2.30), while active MHO participants were not at elevated risk (HR, 1.15; 95% CI, 0.70-1.89). Physically inactive MHO participants had significantly increased risk of CVD compared to physically active MHNO participants whereas physically active MHO participants did not.


Assuntos
Doenças Cardiovasculares/epidemiologia , Exercício Físico , Obesidade/epidemiologia , Adulto , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Fatores de Risco
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