Large-Scale Refinement of Metal−Organic Framework Structures Using Density Functional Theory

Nazarian, Dalar,Camp, Jeffrey S.,Chung, Yongchul G.,Snurr, Randall Q.,Sholl, David S. American Chemical Society 2017 Chemistry of materials Vol.29 No.6

<P>Efforts to computationally characterize large numbers of nanoporous materials often rely on databases of experimentally resolved crystal structures. The accuracy of experimental crystal structures used in such calculations has a significant impact on the reliability of the results. In this work, we report structures optimized using periodic density functional theory (DFT) for more than 800 experimentally synthesized metal-organic frameworks (MOFs). Many MOFs changed significantly upon structural optimization, particularly materials that were crystallographically resolved in their solvated form. For each MOF, we simulated the adsorption of CH4 and CO2 using grand canonical Monte Carlo both before and after DFT optimization. The DFT optimization has a large impact on simulated gas adsorption in some cases. For example, CO2 loading at 1 bar changed by more than 25% in over 25% of the MOFs we considered.</P>

Health attributes of ethnic vegetables consumed in the Eastern Anatolia region of Turkey: Antioxidant and enzyme-inhibitory properties

Abdullah Dalar,Yusuf Uzun,Musa Turker,Muzaffer Mukemre,Izabela Konczak 한국식품연구원 2016 Journal of Ethnic Foods Vol.3 No.2

Background: Four ethnic vegetables from the Eastern Anatolia region of Turkey, Malva neglecta Wallr., Plantago lanceolata L., Cichorium intybus L. and Eryngium bornmuelleri Nab. are commonly used by the local population for food preparation. This study aimed at understanding their potential health attributes. Methods: Hydrophilic extracts obtained from roots, stems, leaves and flowers were evaluated for their antioxidant capacities [total phenolics (TP), ferric reducing antioxidant power (FRAP), and oxygen radical absorbance capacity (ORAC) assays] and suppression of two isolated key enzymes relevant to metabolic syndrome: a-glucosidase and pancreatic lipase. Phytochemical composition of extractswas investigated by high performance liquid chromatography (HPLC) and liquid chromatography mass spectrometry (LC-MS). Results: The evaluated extracts exhibited pronounced antioxidant capacities, comparable to those of common spices and herbs, and effectively suppressed the activities of isolated a-glucosidase and pancreatic lipase enzymes. These activities correlated well with total phenolics contents. Plantago lanceolata was an effective inhibitor of a-glucosidase and C. intybus of pancreatic lipase enzyme. High performance liquid chromatography mass spectrometry analyses revealed the dominance of luteolin glycosides in P. lanceolata. The same compound was present in C. intybus, where it was accompanied by significant amounts of cichoric, chlorogenic and caftaric acid. Malva neglecta and E. bornmuelleri contained the lowest levels of phenolic compounds and exhibited the lowest antioxidant and enzyme inhibitory activities. Conclusions: Among the investigated ethnic vegetables, P. lanceolata and C. intybus represent a valuable source of antioxidant phytochemicals of phenolic nature that modulated in vitro the activities of digestive enzymes. These ethnic food sources diversify diet and enhance health attributes of foods.

Characteristics of Active Tuberculosis Patients Requiring Intensive Care Monitoring and Factors Affecting Mortality

Filiz, Kosar A.,Levent, Dalar,Emel, Eryuksel,Pelin, Uysal,Turkay, Akbas,Aybuke, Kekecoglu The Korean Academy of Tuberculosis and Respiratory 2016 Tuberculosis and Respiratory Diseases Vol.79 No.3

Background: One to three percent of cases of acute tuberculosis (TB) require monitoring in the intensive care unit (ICU). The purpose of this study is to establish and determine the mortality rate and discuss the causes of high mortality in these cases, and to evaluate the clinical and laboratory findings of TB patients admitted to the pulmonary ICU. Methods: The data of patients admitted to the ICU of Yedikule Chest Diseases and Chest Surgery Education and Research Hospital due to active TB were retrospectively evaluated. Demographic characteristics, medical history, and clinical and laboratory findings were evaluated. Results: Thirty-five TB patients (27 males) with a median age of 47 years were included, of whom 20 died within 30 days (57%). The Acute Physiology and Chronic Health Evaluation II (APACHE II) and Sequential Organ Failure Assessment (SOFA) scores were significantly higher, and albumin and $PaO_2/FIO_2$ levels were significantly lower, and shock, multiple organ failure, the need for invasive mechanical ventilation and drug resistance were more common in the patients who died. The mortality risk was 7.58 times higher in the patients requiring invasive mechanical ventilation. The SOFA score alone was a significant risk factor affecting survival. Conclusion: The survival rate is low in cases of tuberculosis treated in an ICU. The predictors of mortality include the requirement of invasive mechanical ventilation and multiple organ failure. Another factor specific to TB patients is the presence of drug resistance, which should be taken seriously in countries where there is a high incidence of the disease. Finding new variables that can be established with new prospective studies may help to decrease the high mortality rate.

Characteristics of Active Tuberculosis Patients Requiring Intensive Care Monitoring and Factors Affecting Mortality

( Kosar A. Filiz ),( Dalar Levent ),( Eryuksel Emel ),( Uysal Pelin ),( Akbas Turkay ),( Kekecoglu Aybuke ) 대한결핵 및 호흡기학회 2016 Tuberculosis and Respiratory Diseases Vol.79 No.3

Background: One to three percent of cases of acute tuberculosis (TB) require monitoring in the intensive care unit (ICU). The purpose of this study is to establish and determine the mortality rate and discuss the causes of high mortality in these cases, and to evaluate the clinical and laboratory findings of TB patients admitted to the pulmonary ICU. Methods: The data of patients admitted to the ICU of Yedikule Chest Diseases and Chest Surgery Education and Research Hospital due to active TB were retrospectively evaluated. Demographic characteristics, medical history, and clinical and laboratory findings were evaluated. Results: Thirty-five TB patients (27 males) with a median age of 47 years were included, of whom 20 died within 30 days (57%). The Acute Physiology and Chronic Health Evaluation II (APACHE II) and Sequential Organ Failure Assessment (SOFA) scores were significantly higher, and albumin and PaO2/FIO2 levels were significantly lower, and shock, multiple organ failure, the need for invasive mechanical ventilation and drug resistance were more common in the patients who died. The mortality risk was 7.58 times higher in the patients requiring invasive mechanical ventilation. The SOFA score alone was a significant risk factor affecting survival. Conclusion: The survival rate is low in cases of tuberculosis treated in an ICU. The predictors of mortality include the requirement of invasive mechanical ventilation and multiple organ failure. Another factor specific to TB patients is the presence of drug resistance, which should be taken seriously in countries where there is a high incidence of the disease. Finding new variables that can be established with new prospective studies may help to decrease the high mortality rate.

Predictive and Prognostic Significance of p27, Akt, PTEN and PI3K Expression in HER2-Positive Metastatic Breast Cancer

Okutur, Kerem,Bassulu, Nuray,Dalar, Levent,Aydin, Kubra,Bozkurt, Mustafa,Pilanci, Kezban Nur,Dogusoy, Gulen Bulbul,Tecimer, Coskun,Mandel, Nil Molinas,Demir, Gokhan Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.7

Background: The phosphatidylinositol 3'-kinase/Akt (PI3K/Akt) pathway is a key regulator for HER2-overexpressing breast cancer, but data about whether activation of PI3K/Akt is associated with poor prognosis and resistance to trastuzumab therapy is controversial. In this study we investigated predictive and prognostic significance of expression of p27, Akt, PTEN and PI3K, which are components of the PI3K/Akt signaling pathway, in HER2-positive metastatic breast cancer (MBC), retrospectively. Materials and Methods: Fifty-four HER2-positive MBC patients who had received first-line trastuzumab-based therapy were recruited for the study group. All of the patient's breast tissue samples were examined for p27 and Akt expression. In addition, twenty-five patients with sufficient amount of tumor tissue were also examined for PTEN and PI3K expression. p27, Akt, PTEN and PI3K were evaluated by immunohistochemistry and their relationship with patient demographic features, tumor characteristics, response to trastuzumab-based treatment and survival outcomes were analyzed. Results: p27, Akt, PTEN and PI3K were positive in 25.9%, 70.4%, 24% and 96% of the cases, respectively. Nomne were significantly associated with response to trastuzumab and time to progression (TTP). A trend toward statistical significance for longer overall survival (OS) was found for PTEN-positive patients (p=0.058); there was no significant relationship between the other immunohistochemical variables and OS. When we analyzed groups regarding co-expression, the PTEN-negative/Akt-negative group had a significantly lower objective response rate (ORR) (20% vs 80%, p=0.023) and the PTEN-negative/p27-negative and PTEN-negative/Akt-negative groups had significantly lower median OS compared to other patients (26.4 months vs 76.1 months, p=0.005 and 25.6 months vs 52.0 months, p=0.007, respectively). Conclusions: p27, Akt, PTEN and PI3K expression is not statistically significantly associated with ORR, TTP and OS, individually. However, the combined evaluation of p27, Akt and PTEN could be helpful to predict the response to trastuzumab-based therapy and prognosis in HER2-positive MBC.