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On electrostatic interactions of adenosine triphosphate-insulin-degrading enzyme revealed by quantum mechanics/molecular mechanics and molecular dynamics

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Quantitative Biology 2024年第4期12卷 414-432页

作者： Sarawoot Somin don Kulasiri Sandhya Samarasinghe Centre for Advanced Computational Solutions(C‐fACS) Lincoln UniversityChristchurchNew Zealand Department of Molecular Biosciences Lincoln UniversityChristchurchNew Zealand

The insulin-degrading enzyme(IDE)plays a significant role in the degradation of the amyloid beta(Aβ),a peptide found in the brain regions of the patients with early Alzheimer’s *** triphosphate(ATP)allosterically regulates the Aβ-degrading activity of *** present study investigates the electrostatic interactions between ATP-IDE at the allosteric site of IDE,including thermostabilities/flexibilities of IDE residues,which have not yet been explored *** study applies the quantum mechanics/molecular mechanics(QM/MM)to the proposed computational model for exploring electrostatic interactions between ATP and *** dynamic(MD)simulations are performed at different temperatures for identifying flexible and thermostable residues of *** proposed computational model predicts QM/MM energy-minimised structures providing the IDE residues(Lys530 and Asp385)with high binding *** root mean square fluctuation values during the MD simulations at 300.00 K including heat-shock temperatures(321.15 K and 315.15 K)indicates that Lys530 and Asp385 are also the thermostable residues of IDE,whereas Ser576 and Lys858 have high flexibilities with compromised *** present study sheds light on the phenomenon of biological recognition and interactions at the ATP-binding domain,which may have important implications for pharmacological drug *** proposed computational model may facilitate the development of allosteric IDE activators/inhibitors,which mimic ATP interactions.

关键词： electrostatic interactions molecular dynamic simulation QM/MM calculation method thermostability/flexibility

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Designing an optimal stope layout for underground mining based on a heuristic algorithm

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International Journal of Mining Science and Technology 2015年第5期25卷 767-772页

作者： Sandanayake don Suneth Sameera Topal Erkan Asad Mohammad Waqar Ali Mining Engineering Western Australian School of MinesCurtin University

An optimal layout or three-dimensional spatial distribution of stopes guarantees the maximum profitability over life span of an underground mining ***,stope optimization is one of the key areas in underground mine planning ***,the computational complexity in developing an optimal stope layout has been a reason for limited availability of the algorithms offering solution to this *** article shares a new and efficient heuristic algorithm that considers a three-dimensional ore body model as an input,maximizes the economic value,and satisfies the physical mining and geotechnical constraints for generating an optimal stope *** implementation at a copper deposit demonstrates the applicability and robustness of the algorithm.A parallel processing based modification improving the performance of the original algorithm in terms of enormous computational time saving is also presented.

关键词： Stope optimization Underground mining Underground mine planning Heuristic algorithm

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An updated scoring system for prediction of survival after resection of colorectal liver metastases: addition of KRAS status as an important risk modifier

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Hepatobiliary Surgery and Nutrition 2020年第1期9卷 70-72页

作者： Evan Jost don Major Elijah Dixon Department of Hepatobiliary Surgery University of CalgaryCalgaryCanada

Colorectal liver metastases (CRLM) were traditionally associated with a very poor prognosis after resection, with some historical series reporting 5-year survival rates as low as 14% for completely resected multiple metastases (1). However, as modern chemotherapy and surgical techniques have evolved, there has been much progress made in improving survival for this unique group of patients, with 5-year survival approaching 55% with R0 resection (2). However, not all CRLM are the same, with very different biological behaviour and ultimately oncologic outcomes in different patients. There have been many attempts to create a scoring system defining factors which will predict this behaviour, with the system created by Fong et al. in 1999 being the most commonly employed (3). These scoring systems are important because they help the selection of patients who are likely to benefit from surgical treatment of their metastases. Patients who are unlikely to benefit from surgical resection may be better treated by alternative and potentially less morbid therapies, such as the various forms of ablation, or with systemic treatments. It is apparent that the accuracy of this prediction is essential to allow patients to benefit either by having appropriate surgical therapy or by avoiding potentially unnecessary surgical morbidity.

关键词： metastases resection prediction

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Effects of Temperature on Photosynthetic Rates in Korean Fir (Abies koreana) between Healthy and Dieback Population

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Journal of Integrative Plant Biology 2008年第2期50卷 190-193页

作者： Su Young Woo Jong-Hwan Lim don Koo Lee Department of Environmental Horticulture University of Seoul Seoul 130-743 Republic of Korea Korea Forest Research Institute Seoul 130-712Republic of Korea Department of Forest Sciences College of Agriculture and Life SciencesSeoul National UniversitySeoul 151-921Republic of Korea

The present study was carried out on natural Korean fir forests （Abies koreana） growing in Mount Halla in Jeju Island, Korea （33° 13-36＇ N and 126° 12-57＇ E）. Mount Halla is the highest mountain （1 950 m a.s.h） in South Korea. On the Korean fir forests near the top of Mount Halla in Korea, we established permanent plots between dieback and healthy population. Each permanent plot includes both dieback and relatively healthy Korean fir individuals. Three sites in this study showed similar altitude, topographic position, aspects, slope, diameter at breast height, average height and ages. Net photosynthetic rates （PN） on different temperature regimes were evaluated to explain the forest dieback phenomenon on Korean fir populations. Light response curves were determined on three different temperature regimes： 15 ℃, 20℃ and 25℃. The irradiance response curve showed higher values in lower air temperatures. Generally, irradiance response curves of healthy Korean fir populations were higher than the dieback population at all sites.

关键词： Abies koreana global warming forest decline photosynthetic rates temperature.

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Estimating risk factors of urban malaria in Blantyre, Malawi: A spatial regression analysis

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Asian Pacific Journal of Tropical Biomedicine 2016年第5期6卷 376-381页

作者： Lawrence N.Kazembe don P.Mathanga Statistics Department University of Namibia Malaria Alert Centre College of MedicineUniversity of Malawi Department of Community Health College of MedicineUniversity of Malawi

Objective: To estimate risk factors of urban malaria in Blantyre, Malawi, with the goal of understanding the epidemiology and ecology of the disease, and informing malaria elimination policies for African urban cities that have markedly low prevalence of ***: We used a case-control study design, with cases being children under the age of five years diagnosed with malaria, and matched controls obtained at hospital and communities. The data were obtained from Ndirande health facility catchment area. We then fitted a multivariate spatial logistic model of malaria risk. Covariate and risk factors in the model included child-specific, household and environmental risk factor(nearness to garden, standing water, river and swamps). The spatial component was assumed to follow a Gaussian process and model fitted using Bayesian ***: Our findings showed that children who visited rural areas were 6 times more likely to have malaria than those who did not [odds ratio(OR) = 6.66, 95% confidence interval(CI): 4.79–9.61]. The risk of malaria increased with age of the child(OR = 1.01,95% CI: 1.003–1.020), but reduced with high socio-economic status compared to lower status(OR = 0.39, 95% CI: 0.25–0.54 for the highest level and OR = 0.67, 95% CI: 0.47–0.94 for the medium level). Although nearness to a garden, river and standing water showed increased risk, these effects were not significant. Furthermore, significant spatial clusters of risk emerged, which does suggest other factors do explain malaria risk variability apart from those established ***: As malaria in urban areas is highly fuelled by rural-urban migration,emphasis should be to optimize information, education and communication prevention strategies, particularly targeting children from lower socio-economic position.

关键词： Urban malaria Travel history Spatial regression Geo-additive models Blantyre Malawi

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Hg and As Minerals in Fluid Inclusions from the Williams Mine, Hemlo, and Their Genetic Implications

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Chinese Journal Of Geochemistry 2002年第1期21卷 1-18页

作者：卢焕章 JAYANTA.GUHA don.C.HARRIS Sciences de la Terre Universite du Quebec a Chicoutimi Chicoutimi Quebec Canada G7H 2B 1 Geological Survey of Canada 601 Booth Street Ottawa Ont. Canada K1A 0E8

The Hemlo mineralization is enigmatic compared to general Archean lode gold deposits based on the fact that it is characterized by an exotic mineralogy containing elements such as As, Hg, Sb, Ba, V and Mo. The genetic concepts range from syngenetic to epigenetic types of mineralization. This reconnaissance study was designed to examine the relationship of Hg-As minerals with respect to fluid inclusions in the Williams mine (formerly known as the Page Williams mine) covering the A and C ore zones.

关键词：流体包裹体含汞矿物含砷矿物矿化作用金矿床

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Magnitude and rupture duration from high frequency teleseismic P wave with projected landweber deconvolution

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Science China Earth Sciences 2013年第1期56卷 13-21页

作者： ZHENG Yong NI SiDao CHEN Yong TAN Ying don HELMBERGER State Key Laboratory of Geodesy and Earth's Dynamics Institute of Geodesy and Geophysics Chinese Academy of Sciences Institute of Geophysics Chinese Earthquake Administration Seismological Laboratory California Institute of Technology

Earthquake magnitude and rupture duration are among the most important parameters characterizing an earthquake for the purpose of early tsunami warning. While they can be routinely determined from broadband P waveforms with iterative inver- sion procedures, the inversion procedures may fail when the rupture either lasts longer than the interval between P and later ar- rivals or requires too much time or human intervention. Little contaminated by later arrivals, high frequency P waves are useful for modeling earthquake source processes, though the envelope waveform is affected by strong scattering in lithosphere. With high frequency envelopes from aftershocks as Empirical Green＇s Function （EGF）, the coda effects can be removed and more accurate relative source time function （RSTF） of the main shock can be obtained. Assuming that RSTFs cannot be negative, we use the projected Landweber deconvolution method （PLD） to obtain high frequency RSTFs because PLD method has the ad- vantage of non-negativity, causality, and compactness （finite duration）. We are able to determine rupture durations of four large earthquakes： the 2004 Sumatra-Andaman earthquake, the 2005 Nias event, the 2006 Java event, and the 2011 Tokuko earthquake. The rupture durations of the Sumatra-Andaman, Nias, and Tohuko events are found to be around 550, 1 i0, and 120 s respectively, consistent with previous studies. The rupture duration of the Java event is about 130 s, supporting that the Java event is a tsunami earthquake. The magnitudes of these earthquakes are found to depend on both the amplitude and the duration of the deconvolved waveforms, and can be approximated by integrating these waveforms.

关键词： high frequency deconvolution rupture duration magnitude

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Driver Fatigue Detection System Based on Colored and Infrared Eye Features Fusion

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Computers, Materials & Continua 2020年第6期63卷 1563-1574页

作者： Yuyang Sun Peizhou Yan Zhengzheng Li Jiancheng Zou don Hong School of Mathematical Sciences Capital Normal UniversityBeijing100048China School of Electrical and Control Engineering North China University of TechnologyBeijing100144China School of Sciences North China University of TechnologyBeijing100144China Department of Mathematical Sciences Middle Tennessee State UniversityMurfreesboroTN 37132USA

Real-time detection of driver fatigue status is of great significance for road traffic *** this paper,a proposed novel driver fatigue detection method is able to detect the driver’s fatigue status around the *** driver’s face images were captured by a camera with a colored lens and an infrared lens mounted above the *** landmarks of the driver’s face were labeled and the eye-area was *** calculating the aspect ratios of the eyes,the duration of eye closure,frequency of blinks and PERCLOS of both colored and infrared,fatigue can be *** on the change of light intensity detected by a photosensitive device,the weight matrix of the colored features and the infrared features was adjusted adaptively to reduce the impact of lighting on fatigue *** samples of the driver’s face were recorded in the test *** training the classification model,the results showed that our method has high accuracy on driver fatigue detection in both daytime and nighttime.

关键词： Driver fatigue detection feature fusion colored and infrared eye features

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Acute infectious osteomyelitis in children: new treatment strategies for an old enemy

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World Journal of Pediatrics 2020年第5期16卷 446-455页

作者： Sabrina Congedi Chiara Minotti Carlo Giaquinto Liviana Da Dalt Daniele don Department of Women's and Children's Health University of PaduaPaduaItaly Division of Paediatric Infectious Diseases Department of Women's and Children's HealthUniversity of PaduaPaduaItaly Paediatric Emergency Department Department of Women's and Children's HealthUniversity of PaduaPaduaItaly

Background Acute osteomyelitis still represents a significant clinical challenge,with an increasing incidence in paediatric population.A careful assessment and a rapid diagnosis with proper timing and choice of empirical antimicrobial therapy are necessary to avoid *** initial treatment should consist of empirical antibiotic therapy,to cover the major responsible pathogens in each age *** sources We made a literature search with PubMed and Cochrane database from 2000 to 2019 in English,French,and Spanish languages using the key words"osteomyelitis,children,clinical,diagnosis,and treatment".Results The child's clinical features,age,and the microbiological profile of the geographic area should be evaluated for diagnosis and in the choice of antibiotic *** data suggest the administration of intravenous antibiotics for a short period,with subsequent oral therapy,according to the improvement of clinical status and inflammatory *** children older than 3 months,the shift to oral medications is already possible after a short course of intravenous therapy,until *** timing for the shift from cefazolin to cephalexin or cefuroxime,intravenous clindamycin to oral clindamycin,and intravenous ceftriaxone+oxacillin to oral equivalents will be decided according to the improvement of clinical status and inflammatory *** also present the approach to osteomyelitis due to difficult pathogens,such as Methicillin-resistant Staphylococcus aureus(MRSA)and Panton-Valentine leukocidin(PVL)-positive *** *** In this review,we present the current approach to the clinical diagnosis and management of osteomyelitis in childhood,with an update on recent recommendations,as a useful instrument to understand the rationale of antibiotic therapy.

关键词： Acute osteomyelitis Children Diagnosis Treatment

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Isolation of intact bacteria from blood by selective cell lysis in a microfluidic porous silica monolith

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Microsystems & Nanoengineering 2019年第1期5卷 418-428页

作者： Jung Y.Han Michael Wiederoder don L.DeVoe Department of Mechanical Engineering University of MarylandCollege ParkMD 20742USA Department of Chemical and Biomolecular Engineering University of MarylandCollege ParkMD 20742USA Fischell Department of Bioengineering University of MarylandCollege ParkMD 20742USA

Rapid and efficient isolation of bacteria from complex biological matrices is necessary for effective pathogen identification in emerging single-cell ***,we demonstrate the isolation of intact and viable bacteria from whole blood through the selective lysis of blood cells during flow through a porous silica *** mechanical hemolysis is achieved while providing passage of intact and viable bacteria through the monoliths,allowing size-based isolation of bacteria to be performed following selective lysis.A process for synthesizing large quantities of discrete capillary-bound monolith elements and millimeter-scale monolith bricks is described,together with the seamless integration of individual monoliths into microfluidic *** impact of monolith morphology,geometry,and flow conditions on cell lysis is explored,and flow regimes are identified wherein robust selective blood cell lysis and intact bacteria passage are achieved for multiple gram-negative and gram-positive *** technique is shown to enable rapid sample preparation and bacteria analysis by single-cell Raman *** selective lysis technique presents a unique sample preparation step supporting rapid and culture-free analysis of bacteria for the point of care.

关键词： silica porous quantities

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