bluuebunny/crossref_metadata_2025 huggingface dataset:
Sizing methodology of a PV/wind hybrid system: Case study in cyprus
Authors: Al‐Ghussain Loiy , Taylan Onur
Published: October 2018

This study aims to suggest a method for sizing of a photovoltaic (PV)/wind hybrid system based on maximizing the annual renewable energy system (RES) fraction with levelized cost of electricity (LCOE) being equal to the grid tariff. The novelty of this article is the idea of maximizing the energy security, energy localization, and environmental benefits from the hybrid system and at the same time ensures the economic feasibility of the system where Middle East Technical University Northern Cyprus Campus (METU NCC) is the case study of this article. The resultant size of a hybrid system for METU NCC is one 2 MW wind turbine and 760 kW PV power plant with annual RES fraction of 52.96%, LCOE of 0.175 USD/kWh, and a payback period of 9.82 years. Such system will increase the localization of energy and cut the transmission losses and also will contribute in the energy security of the island by reducing the annual fuel consumption of the island by 9920 barrels which will also reduce the annual CO2 emissions by 3622 tons. © 2018 American Institute of Chemical Engineers Environ Prog, 38:e13052, 2019
Use of DPSIR Framework to Analyze Water Resources in Qatar and Overview of Reverse Osmosis as an Environment Friendly Technology
Authors: Ashfaq Mohammad Y. , Al‐Ghouti Mohammad A. , Qiblawey Hazim , Zouari Nabil , Rodrigues Debora F. , Hu Yandi
Published: October 2018

Qatar and other countries of Gulf Cooperation Council are among the most water scarce countries in the world and are being characterized as “high‐water risk” countries by Water Resource Institute. Therefore, it is important to implement sustainable water resource management that encompass economic, societal, and environmental aspects. In this review article, the Driver‐Pressure‐State‐Impact‐Response framework was used to analyze the water resource system in Qatar in terms of drivers, pressures, change in state, impacts, and responses. It was noted that both economic and population growth together with unsustainable water consumption are major driving forces that are pressurizing the Qatar's water resources (desalinated seawater and renewable groundwater). Currently, desalination plants using Multi‐Stage Flash (MSF) techniques are predominantly being used to meet the rising water demands. However, widespread use of MSF techniques poses several environmental and economic impacts. Therefore, in addition to other management and corrective measures, reverse osmosis (RO) technique has also been suggested to be utilized in desalination industry as a “response” to mitigate those impacts. Since, the performance of RO is mainly affected by biofouling and mineral scaling, the paper also highlights the recent materials (polymers and nano‐materials) used to tackle these problems. © 2018 American Institute of Chemical Engineers Environ Prog, 38:e13081, 2019
Landslides and increased debris‐flow activity: A systematic comparison of six catchments in Switzerland
Authors: Frank Florian , Huggel Christian , McArdell Brian W. , Vieli Andreas
Published: October 2018

An increase in debris‐flow frequency is expected in steep Alpine catchments after the occurrence of a large landslide, such as a rock avalanche. Herein we describe changes in debris‐flow activity following increases in sediment availability due to landslides, or accelerated rock‐glacier movement, for five catchments in the Swiss Alps, the Spreitgraben, Schipfenbach, Bondasca, Riascio, and Dorfbach catchments. Documentation on debris‐flow activity is available from both before and after the landslide that generated the new sediment deposits. Data from nearby meteorological stations were used to explore possible changes in rainfall activity, and how the intensity and duration of rainfall events may have changed. In all cases there was a considerable increase in debris‐flows frequency for one to eight years following the landslide. The annual number of days with debris‐flow activity following the landslide was similar to that observed for the Illgraben catchment, where many such landslides occur annually. No clear change in precipitation totals preceding debris flows was apparent for the Riascio catchment, suggesting that the increase in frequency of debris flows is related to the increase in the amount of sediment that can be readily mobilized. In the two cases where rainfall data were available on an hourly basis, no systematic changes in the intensity or duration of rainfall related to debris‐flow triggering were apparent, as shown by the close‐clustering of storms on the intensity‐duration plots. Following the sediment‐generating event, an initial and sudden increase of the sediment yield was observed, followed by a decrease over time towards pre‐disturbance values. The response of the catchments appears to be related to the amount of debris‐flow activity prior to the landslide: sediment yield from catchments with frequent debris flows prior to the landslide activity did not increase as dramatically as in catchments where debris‐flow activity was less common prior to the landslide. © 2018 John Wiley & Sons, Ltd.
NG2 expression in NG2 glia is regulated by binding of SoxE and bHLH transcription factors to a Cspg4 intronic enhancer
Authors: Gotoh Hitoshi , Wood William M. , Patel Kiran D. , Factor Daniel C. , Boshans Linda L. , Nomura Tadashi , Tesar Paul J. , Ono Katsuhiko , Nishiyama Akiko
Published: October 2018

NG2 is a type 1 integral membrane glycoprotein encoded by the Cspg4 gene. It is expressed on glial progenitor cells known as NG2 glial cells or oligodendrocyte precursor cells that exist widely throughout the developing and mature central nervous system and vascular mural cells but not on mature oligodendrocytes, astrocytes, microglia, neurons, or neural stem cells. Hence NG2 is widely used as a marker for NG2 glia in the rodent and human. The regulatory elements of the mouse Cspg4 gene and its flanking sequences have been used successfully to target reporter and Cre recombinase to NG2 glia in transgenic mice when used in a large 200 kb bacterial artificial chromosome cassette containing the 38 kb Cspg4 gene in the center. Despite the tightly regulated cell type‐ and stage‐specific expression of NG2 in the brain and spinal cord, the mechanisms that regulate its transcription have remained unknown. Here, we describe a 1.45 kb intronic enhancer of the mouse Cspg4 gene that directed transcription of EGFP reporter to NG2 glia but not to pericytes in vitro and in transgenic mice. The 1.45 kb enhancer contained binding sites for SoxE and basic helix–loop–helix transcription factors, and its enhancer activity was augmented cooperatively by these factors, whose respective binding elements were found in close proximity to each other. Mutations in these binding elements abrogated the enhancer activity when tested in the postnatal mouse brain.
Loss of perivascular aquaporin‐4 in idiopathic normal pressure hydrocephalus
Authors: Hasan‐Olive Md Mahdi , Enger Rune , Hansson Hans‐Arne , Nagelhus Erlend A. , Eide Per Kristian
Published: October 2018

Idiopathic normal pressure hydrocephalus (iNPH) is a subtype of dementia that may be successfully treated with cerebrospinal fluid (CSF) diversion. Recently, magnetic resonance imaging (MRI) using a MRI contrast agent as a CSF tracer revealed impaired clearance of the CSF tracer from various brain regions such as the entorhinal cortex of iNPH patients. Hampered clearance of waste solutes, for example, soluble amyloid‐β, may underlie neurodegeneration and dementia in iNPH. The goal of the present study was to explore whether iNPH is associated with altered subcellular distribution of aquaporin‐4 (AQP4) water channels, which is reported to facilitate CSF circulation and paravascular glymphatic drainage of metabolites from the brain parenchyma. Cortical brain biopsies of 30 iNPH patients and 12 reference individuals were subjected to AQP4 immunogold cytochemistry. Electron microscopy revealed significantly reduced density of AQP4 water channels in astrocytic endfoot membranes along cortical microvessels in patients with iNPH versus reference subjects. There was a significant positive correlation between density of AQP4 toward endothelial cells (perivascular) and toward parenchyma, but the reduced density of AQP4 toward parenchyma was not significant in iNPH. We conclude that perivascular AQP4 expression is attenuated in iNPH, potentially contributing to impaired glymphatic circulation, and waste clearance, and subsequent neurodegeneration. Hence, restoring normal perivascular AQP4 distribution may emerge as a novel treatment strategy for iNPH.
Pharmaceutical expenditure and gross domestic product: Evidence of simultaneous effects using a two‐step instrumental variables strategy
Authors: Shaikh Mujaheed , Gandjour Afschin
Published: October 2018

This paper estimates the income elasticity of government pharmaceutical spending and assesses the simultaneous effect of such spending on gross domestic product (GDP). Using a panel dataset for 136 countries from 1995 to 2006, we employ a two‐step instrumental variable procedure where we first estimate the effect of GDP on public pharmaceutical expenditure using tourist receipts as an instrument for GDP. In the second step, we construct an adjusted pharmaceutical expenditure series where the response of public pharmaceutical expenditure to GDP is partialled out and use this endogeneity adjusted series as an instrument for pharmaceutical expenditure. Our estimations show that GDP has a strong positive impact on pharmaceutical spending with elasticity in excess of unity in countries with low spending on pharmaceuticals and countries with large economic freedom. In the second step, we find that when the quantitatively large reverse effect of GDP is accounted for, public pharmaceutical spending has a negative effect on GDP per capita particularly in countries with limited economic freedom.
Memory decline in elderly with cerebral small vessel disease explained by temporal interactions between white matter hyperintensities and hippocampal atrophy
Authors: van Leijsen Esther M. C. , Tay Jonathan , van Uden Ingeborg W. M. , Kooijmans Eline C. M. , Bergkamp Mayra I. , van der Holst Helena M. , Ghafoorian Mohsen , Platel Bram , Norris David G. , Kessels Roy P. C. , Markus Hugh S. , Tuladhar Anil M. , de Leeuw Frank‐Erik
Published: October 2018

White matter hyperintensities (WMH) constitute the visible spectrum of cerebral small vessel disease (SVD) markers and are associated with cognitive decline, although they do not fully account for memory decline observed in individuals with SVD. We hypothesize that WMH might exert their effect on memory decline indirectly by affecting remote brain structures such as the hippocampus. We investigated the temporal interactions between WMH, hippocampal atrophy and memory decline in older adults with SVD. Five hundred and three participants of the RUNDMC study underwent neuroimaging and cognitive assessments up to 3 times over 8.7 years. We assessed WMH volumes semi‐automatically and calculated hippocampal volumes (HV) using FreeSurfer. We used linear mixed effects models and causal mediation analyses to assess both interaction and mediation effects of hippocampal atrophy in the associations between WMH and memory decline, separately for working memory (WM) and episodic memory (EM). Linear mixed effect models revealed that the interaction between WMH and hippocampal volumes explained memory decline (WM: β = .067; 95%CI[.024–0.111]; p < .01; EM: β = .061; 95%CI[.025–.098]; p < .01), with better model fit when the WMH*HV interaction term was added to the model, for both WM (likelihood ratio test, χ2[1] = 9.3, p < .01) and for EM (likelihood ratio test, χ2[1] = 10.7, p < .01). Mediation models showed that both baseline WMH volume (β = −.170; p = .001) and hippocampal atrophy (β = 0.126; p = .009) were independently related to EM decline, but the effect of baseline WMH on EM decline was not mediated by hippocampal atrophy (p value indirect effect: 0.572). Memory decline in elderly with SVD was best explained by the interaction of WMH and hippocampal volumes. The relationship between WMH and memory was not causally mediated by hippocampal atrophy, suggesting that memory decline during aging is a heterogeneous condition in which different pathologies contribute to the memory decline observed in elderly with SVD.
A proof‐of‐principle study of the effect of combined haloperidol and levodopa administration on working memory‐related brain activation in humans
Authors: van Ruitenbeek Peter , Hernaus Dennis , Mehta Mitul Ashok
Published: October 2018

Objective

Cognitive deficits including impaired working memory are a hallmark feature of schizophrenia. Dopamine D1 receptor modulated changes in prefrontal cortex function play a potentially important role in the pathology underlying such deficits. However, pharmacological interventions that selectively engage the D1 receptor are severely restricted for research in humans. The present study is a proof‐of‐principle for enhancing cognitive performance and associated brain activation via indirect D1 stimulation, operationalised by combining the nonselective dopamine agonist L‐dopa with the D2‐antagonist haloperidol.

Methods

Fourteen healthy volunteers received placebo or combined carbidopa (25 mg)/L‐dopa (100 mg) plus haloperidol (2 mg) orally on two separate occasions according to a within‐subjects crossover design. Drug‐induced differences in brain activity were assessed during an N‐back working memory task in a 3T magnetic resonance imaging environment.

Results

Drug treatment was associated with greater functional connectivity between the dorsolateral prefrontal cortex and areas within the salience network during all N‐back trials. Drug treatment was also associated with reduced activation, most prominently in the occipital/temporal brain areas during 2‐back performance.

Conclusions

This preliminary study provides initial evidence for combined L‐dopa/haloperidol modulation in cognition‐related brain areas and networks, which is relevant for the treatment of cognitive impairments in mental illness.
From Active Sites to Machines: A Challenge for Enzyme Chemists
Authors: Khosla Chaitan
Published: October 2018

As researchers who study enzyme chemistry embrace increasingly complex systems, especially biological machines, our attention is also shifting from steps involving covalent bond formation or cleavage to those that exclusively involve changes in non‐covalent bonding. Assembly line polyketide synthases are an example of this growing challenge. By now, the chemical reactions underpinning polyketide biosynthesis can be unequivocally mapped to well‐defined active sites and are, for the most part, readily explicable in the language of physical organic chemistry. Yet, all of these insights merely serve as a backdrop to the real problem of explaining how the catalytic functions of dozens of active sites are synchronized in order to allow these remarkable machines to turn over with remarkable specificity. Notwithstanding the fact that the time‐honored language of physical organic chemistry can teach us a lot, it is often insufficient to describe many of these events, and must therefore evolve.
Some Efforts Toward Understanding Structural Features of MOF/COF
Authors: Mayoral Alvaro , Ma Yanhang , Terasaki Osamu
Published: October 2018

The 2018 Wolf Prize for Chemistry was given to Prof. Omar M. Yaghi for his revolutional contribution to “reticular chemistry via MOFs and COFs”. The discovery of reticular chemistry has brought us a new paradigm that overall structure and chemical functionality can be designed through judicious choices of secondary building units and organic linkages, instead of the combination of individual atoms with mathematical supports in structure descriptions for designing the crystals by Prof Mike O'Keeffe. The crystallinity, large permanent porosity and functionalization of the pores in MOF and MOF‐like materials have been intensively discussed since their discovery based on two principal experimental approaches, single crystal or powder X‐ray diffraction (PXRD) and nitrogen gas adsorption isotherm measurements. The electron microscopy provides structural information at local fine structure and/or individual nanocrystals unlike X‐Ray diffraction which produces in essence as average over the entire powder sample or individual crystal. The following three case studies illustrate the current the edge of MOF and MOF‐like research: a woven COF‐105 and −112 and MOF MIL‐101; a new pairwise model to explain superlattice structure observed in gas adsorption experiments on IRMOF‐74; and a new STEM study on NbO as nbo net was proposed from mathematical periodic nets and tilings but named after its reported structure.
Of leaders and followers—An econometric analysis of equity analysts and stock market investors
Authors: Baule Rainer , Wilke Hannes
Published: October 2018

We measure the information content of publicly available analyst consensus forecasts for 1‐year‐forward earnings per share based on two well‐established price discovery measures drawn from the area of market microstructure research. Employing a 36‐year sample of large U.S. companies listed in the S&P 100 Index, we compute (a) Hasbrouck's information shares and (b) Gonzalo and Granger's common factor component shares to measure the relative contribution that market participants and financial analysts working on the sell side of the market have in the process of value discovery. We find that although these analysts are far from leading the market, they have a small but significant share in the process of value discovery, amounting to 4.6% (Hasbrouck) and 18.0% (Gonzalo and Granger), on average. This share is persistent over time but varies significantly in the cross section. We identify the level of analyst coverage and company age as drivers of this heterogeneity.
The international diversification benefits of U.S.‐traded equity products
Authors: O'Hagan‐Luff Martha , Berrill Jenny
Published: October 2018

The benefits of international diversification for equity investors have been highlighted for decades. Despite the reduction of many previous barriers to foreign investment, investors are found to persistently overweight domestic equities. This paper examines whether the benefits of international diversification are available via U.S.‐traded equity products over a 15‐year period between 1996 and 2011. The equity products investigated are multinational corporations (MNCs), American depository receipts (ADRs), single‐country exchange‐traded funds, iShares, and closed‐end country funds. Mean‐variance spanning tests and Sharpe ratio analysis reveal that portfolios of ADRs and MNCs offer the greatest international diversification benefits to U.S. investors in a domestic setting. Whereas the benefits of international diversification vary during periods of differing market conditions, the findings for ADRs and MNCs remain robust. We conclude that it is possible to reap the benefits of international diversification via U.S.‐traded equity products but that the benefits of different equity types vary significantly.
Cancer of the corpus uteri
Authors: Amant Frédéric , Mirza Mansoor Raza , Koskas Martin , Creutzberg Carien L.
Published: October 2018

Endometrial cancer is the most common gynecological malignancy in high‐income countries. Although the overall prognosis is relatively good, high‐grade endometrial cancers have a tendency to recur. Recurrence needs to be prevented since the prognosis for recurrent endometrial cancer is dismal. Treatment tailored to tumor biology is the optimal strategy to balance treatment efficacy against toxicity. Standard treatment consists of hysterectomy and bilateral salpingo‐oophorectomy. Lymphadenectomy (with ongoing studies of sentinel node biopsy) enables identification of lymph node positive patients who need adjuvant treatment, including radiotherapy and chemotherapy. Adjuvant radiotherapy is used for Stage I–II patients with high‐risk factors and Stage III lymph node negative patients. In advanced disease, a combination of surgery to no residual disease and chemotherapy results in the best outcome. Surgery for recurrent disease is only advocated in patients with a good performance status with a relatively long disease‐free interval.
Pathology of cancers of the female genital tract including molecular pathology
Authors: Prat Jaime , Mutch David G.
Published: October 2018

To better understand pathology reports, gynecologic oncologists must be familiar with the terminology used in gynecologic pathology. This chapter of the FIGO Cancer Report 2018 summarizes the clinical and pathological features of the most common cancers of the female genital tract, as well as their main molecular genetic alterations. In selected cases, an approach for processing surgical specimens is also included.
Role of imaging in the routine management of endometrial cancer
Authors: Lin Ming Yin , Dobrotwir Andrew , McNally Orla , Abu‐Rustum Nadeem R. , Narayan Kailash
Published: October 2018

Endometrial cancer is the most common gynecologic cancer in women today. It is surgically staged, and while surgery is the primary treatment modality, the identification of disease extent—in particular extrauterine spread—prior to surgery is important to optimize treatment decision making. Ultrasound and MRI are useful for evaluating the extent of local disease, while CT and PET are used for detecting lymph node or distant metastases. Diffusion‐weighted MRI has also been used for detecting small metastatic deposits in lymph nodes and omentum. Extrauterine soft tissue involvement can be detected by ultrasound, CT, MRI, and PET. Recently, intraoperative visualization techniques, such as sentinel lymph node mapping, are increasingly used to avoid extensive surgical staging without compromising treatment. Imaging is also used for planning adjuvant treatment and detection of postoperative residual disease in high‐risk patients, monitoring and detecting recurrent disease, and in post‐treatment surveillance of asymptomatic patients with high risk of relapse.
Psychosexual health in gynecologic cancer
Authors: Boa Rosalind , Grénman Seija
Published: October 2018

More people are living with the long‐term effects of cancer owing to improvements in cancer treatments and an aging population. Many people diagnosed with cancer report a negative impact on sexual identity, sexual functioning, and their sexual relationship. Gynecologic cancer survivors are often the most severely affected. These cancers involve cancers of the ovaries, uterus, cervix, vagina, and vulva. The impact of these cancers on sexual health results not only from the disease process itself, but may also be due to the necessary treatments required. These can have a profound impact on psychological, physiological, and social well‐being both in the short and long term, which may result in negative impact on the quality of life of the patient as well as her partner. Although most patients express that they would like to be more informed about sexual health and would like to have the opportunity to discuss these issues with their therapeutic team, sexual health is often not discussed with the patient.
Palliative care in women's cancer care: Global challenges and advances
Authors: Cain Joanna M. , Denny Lynette
Published: October 2018

Women's cancer rates are increasing in low‐ and middle‐income countries, with presentations that are often far advanced requiring intense symptom management, thus advancing the urgent need to address palliative care. Most resource settings have some options available to assist women with advanced gynecologic cancer, and a combination of leveraging these and expanding on emerging models for palliative care could lessen suffering and improve care for women with gynecologic cancers globally. Providing palliative care for women with cancer is constrained by resources (human and physical), lack of equipment, lack of access, and policy absence or barriers. There is important work to be done in advocating for appropriate infrastructure development and legislation to assure that these options are available to women and their families. Access to adequate opioid and other pain relief options for cancer‐related pain is a particular concern given that availability, cost, and legislative prohibitions create barriers that cause suffering for patients and grief for their families who are unable to address their suffering. All of these require ongoing advocacy for continual advances to improve access and infrastructure for palliative care.
Effect of Irrigation Depth Reduction, Planting Date and Cropping Pattern on Water Productivity in West Lake Urmia, Iran
Authors: Alizadeh Dizaj Amin , Noory Hamideh , Ebrahimian Hamed
Published: October 2018

Lake Urmia in Iran has faced extreme water loss in recent years due to overuse and mismanagement of water resources, particularly in agriculture. In this study, three strategies including irrigation depth reduction, changing planting dates and crop rotation in crop patterns of Urmia city were assessed for improvement of water productivity to mitigate the crisis of Lake Urmia. For this purpose, the AquaCrop simulation model was applied. The effects of the three strategies were investigated with four indicators: (i) total water productivity (TWP); (ii) economic water productivity (EWP); (iii) farmers' benefit (FB); (iv) dry yield (DY). The results showed that a 60% reduction of current irrigation depth for winter wheat, winter barley, forage maize and tomato and a 40% reduction for sunflower substantially increased TWP and EWP without considerable reduction in DY and FB. Early planting dates for autumn planting crops (wheat and barley) and delaying planting dates for spring planting crops led to a decreased irrigation requirement and increased benefit from rainfall. For the autumn planting pattern, selecting winter barley reduced water consumption by 2170 m3 ha−1 compared to winter wheat, and for the spring planting pattern, selecting forage maize decreased water consumption by 2080 and 3150 m3 ha−1 compared to sunflower and tomato, respectively. © 2018 John Wiley & Sons, Ltd.
Developing a comparative framework of ICT4D initiatives in the global South: A critical realist approach
Authors: Hussain Faheem , Brown Suzana
Published: October 2018

The paper aims to develop a comparative framework for ICT4D initiatives in the global South by adopting a critical realist philosophical approach. For that purpose, the research utilizes field data and observations from two information and communication technology (ICT)–driven community health care services in Rwanda and Bangladesh. The data collected were analyzed through a critical realist–based framework, and the two mechanisms that played key roles in these ICT projects were identified as follows: trust in social structures and good governance. This study suggests that both mechanisms play a greater role in Bangladesh than in Rwanda. The identified mechanisms further highlight the challenges Rwanda needs to overcome in order to achieve comparable success. Based on the analysis of those two cases, we suggest that our critical realist–based philosophical and methodological approach adds unique value to ICT4D research, and such an approach allows us to gather valuable insights on these comparable ICT4D projects. Consequently, we are able to provide the stakeholders in these projects with better insights into why the community health care services evolved the way they did and the mechanisms that determined this outcome.
Type of endothelial cells affects HepaRG cell acetaminophen metabolism in both 2D and 3D porous scaffold cultures
Authors: German Carrie L. , Madihally Sundararajan V.
Published: October 2018

Recent advances in developing in vitro tissue models show that function of hepatocytes is altered in when cultured in 3D configuration and co‐culturing with various non‐parenchymal cells. However, tissue source for such non‐parenchymal cells on viability and metabolic products of hepatocytes have not been explored. In this study, we evaluated the effect of 2D and 3D cultures either with HepaRG cells alone or in combination with liver sinusoidal endothelial cells (LSECs) and human umbilical vein ECs (HUVECs). For 3D cultures, we used chitosan‐gelatin porous structures formed by freeze‐drying. We cultured cells for 8 days before challenging with 1 mm acetaminophen (APAP) and assessed APAP, APAP‐sulfate and APAP‐glucuronide for 24 hours at 6‐hour time intervals using high‐performance liquid chromatography. We used multiple methods (phase contrast, confocal and scanning electron microscopy and histology via hematoxylin and eosin staining) to ensure cell distribution. We also measured total protein content and albumin secretion and viability. HUVEC 3D co‐cultures showed the lowest HepaRG cell viability, while both 2D and 3D LSEC co‐cultures had highest HepaRG cell viability. In addition, 3D cultures had significantly higher EC viability relative to 2D cultures. Further, HUVEC co‐cultures showed reduced total protein content and albumin expression as early as day 4. However, urea production on a total protein content basis did not change. In addition, LSEC 3D co‐cultures had the highest APAP conversion with reduced APAP‐sulfate and APAP‐glucuronide formation. CYP3A4 was higher in co‐culture with HUVEC for 2D and 3D cultures. In conclusion, HepaRG cells with EC co‐cultures demonstrated sensitivity to the EC line used.
Implementing dimer metadynamics using gromacs
Authors: Nava M.
Published: October 2018

We develop a Gromacs implementation of dimer metadynamics (DM) (JCTC 13, 425 [2017]) for enhanced sampling through artificial delocalization effects. This implementation is based entirely on a Plumed collective variable developed for this purpose, the fine tuning of Gromacs input parameters, modified forcefields and custom nonbonded interactions. We demonstrate this implementation on alanine dipeptide in vacuum and in water, and on the 12‐residue alanine polypeptide in water and compare the results with a standard multiple‐replica technique such as parallel tempering. In all the considered cases, this comparison is consistent and the results with DM are smoother and require shorter simulations, thus proving the consistency and effectiveness of this Gromacs implementation. © 2018 Wiley Periodicals, Inc.
A new protein nucleic‐acid coarse‐grained force field based on the UNRES and NARES‐2P force fields
Authors: Sieradzan Adam K. , Giełdoń Artur , Yin Yanping , He Yi , Scheraga Harold A. , Liwo Adam
Published: October 2018

Based on the coarse‐grained UNRES and NARES‐2P models of proteins and nucleic acids, respectively, developed in our laboratory, in this work we have developed a coarse‐grained model of systems containing proteins and nucleic acids. The UNRES and NARES‐2P effective energy functions have been applied to the protein and nucleic‐acid components of a system, respectively, while protein–nucleic‐acid interactions have been described by the respective coarse‐grained potentials developed in our recent work (Yin et al., J. Chem Theory Comput. 2015, 11, 1792). The Debye–Hückel screening has been applied to the electrostatic‐interaction energy between the phosphate groups and charged amino‐acid side chains. The model has been integrated into the UNRES package for coarse‐grained molecular dynamics simulations of proteins and the implementation has been tested for energy conservation in microcanonical molecular dynamics runs and for temperature conservation in canonical molecular dynamics runs. Two case studies were performed: (i) the dynamics of the Ku protein heterodimer bound to DNA, for which it was found that the Ku70/Ku80 protein complex plays an active role in DNA repairing and (ii) conformational changes of the multiple antibiotic resistance (MarA) protein occurring during DNA binding, for which the functionally important motions occurring during this process were identified. © 2018 Wiley Periodicals, Inc.
Modulating stability of functionalized fullerene cations [R‐C60]+with the nature of R‐group
Authors: Li Jingbai , Tadakamalla Divya , Rogachev Andrey Yu.
Published: October 2018

In this study, the first comprehensive theoretical investigation of the stability of functionalized fullerene‐based cations [R‐C60]+and its relationship with the nature of the attached R‐group was performed. C60‐Fullerene core was functionalized with an alkyl group of different length (R = (CH2)nCH3, wheren= 0–9). This set was further complemented by bulky isopropyl andtert‐butyl and conjugated phenyl groups. A detailed study of the relative stability of target cationic species was accompanied by in‐depth investigation of their electronic structure and aromaticity using a large set of descriptors of different nature. The stability of target species was considered with respect to two alternative and competing mechanisms of bond breaking, namely, heterolytic ([R‐C60]+→ R++ C60) and homolytic ([R‐C60]+→ R•+ C60+•) ones. The transformation of strained sp2‐carbon atom in unperturbed C60‐fullerene to nonconstrained tetrahedral sp3‐type in functionalized derivatives was found to be the driving force for the formation of its functionalized cations. In spite of the fact that all systems under consideration were found to be corresponding to local minima on corresponding potential energy surfaces, the functionalization of C60‐core with the smallest and simplest methyl group resulted in most stable compound, as evaluated by bonding energy between R+and fullerene fragment (in the light of both mechanisms). Subsequent elongation of the alkyl chain or introducing bulky groups led to notable decrease of the bonding energy and, as consequence, of the stability within the framework of heterolytic bond cleavage, whereas homolytic pathway assumes opposite—slight increase of stability along with lengthening of the R‐group. The orbital interaction (ΔEorb) was identified as the main driving force for these trends. In general, the homolytic path was found to be dominating for small‐length R‐groups such as those withn= 0 and 1. Atn= 2, heterolytic and homolytic pathways are equally probable (the difference in corresponding bonding energies is about 1 kcal/mol). However, when the alkyl chain becomes longer (n= 3–9), the cationic bond cleavage appears as the most energetically favorable. © 2018 Wiley Periodicals, Inc.
Ab initio molecular dynamics study of prebiotic production processes of organic compounds at meteorite impacts on ocean
Authors: Shimamura Kohei , Shimojo Fuyuki , Nakano Aiichiro , Tanaka Shigenori
Published: October 2018

Recent experiments concerning prebiotic materials syntheses suggest that the iron‐bearing meteorite impacts on ocean during Late Heavy Bombardment provided abundant organic compounds associated with biomolecules such as amino acids and nucleobases. However, the molecular mechanism of a series of chemical reactions to produce such compounds is not well understood. In this study, we simulate the shock compression state of a meteorite impact for a model system composed of CO2, H2O, and metallic iron slab by ab initio molecular dynamics combined with multiscale shock technique, and clarify possible elementary reaction processes up to production of organic compounds. The reactions included not only pathways similar to the Fischer–Tropsch process known as an important hydrocarbon synthesis in many planetary processes but also those resulting in production of a carboxylic acid. It is also found that bicarbonate ions formed from CO2 and H2O participated in some forms in most of these observed elementary reaction processes. These findings would deepen the understanding of the full range of chemical reactions that could occur in the meteorite impact events. © 2018 Wiley Periodicals, Inc.
Thermodynamic integration network approach to ion transport through protein channels: Perspectives and limits
Authors: Na Sehee , Steinbrecher Thomas , Koslowski Thorsten
Published: October 2018

We present a molecular dynamics simulation study of alkali metal cation transport through the double‐helical and the head‐to‐head conformers of the gramicidin ion channel. Our approach is based on a thermodynamic integration network, which consists of a sequence of transport reactions, absolute free energies of solvation and cycles of alchemical transmutations of the ions. In this manner, we can reliably estimate free energies and their statistical errors via a least‐squares method without imposing external forces on the system. Within the double helical channel, we find a free energy surface typical for hopping transport between isoenergetic sites of ion localization, separated by comparatively large activation barriers. For fast transport through the head‐to‐head conformation, the thermodynamic network scheme starts to break down. © 2018 Wiley Periodicals, Inc.
Impact of finite‐temperature and condensed‐phase effects on theoretical X‐ray absorption spectra of transition metal complexes
Authors: Müller Patrick , Karhan Kristof , Krack Matthias , Gerstmann Uwe , Schmidt Wolf Gero , Bauer Matthias , Kühne Thomas D.
Published: October 2018

The impact of condensed‐phase and finite‐temperature effects on the theoretical X‐ray absorption spectra of transition metal complexes is assessed. The former are included in terms of the all‐electron Gaussian and augmented plane‐wave approach, whereas the latter are taken into account by extensive ensemble averaging along second‐generation Car–Parrinello ab initio molecular dynamics trajectories. We find that employing the periodic boundary conditions and including finite‐temperature effects systematically improves the agreement between our simulated X‐ray absorption spectra and experimental measurements. © 2018 Wiley Periodicals, Inc.
Implication of ultrasound contrast‐enhancement of carotid plaques in prevalence of acute coronary syndrome and occurrence of cardiovascular outcomes
Authors: Choi Sang‐Woong , Kim Hyungseop , Kim In‐Cheol , Lee Cheol‐Hyun , Hwang Jongmin , Park Hyoung‐Seob , Cho Yun‐Kyeong , Yoon Hyuck‐Jun , Nam Chang‐Wook , Han Seongwook , Hur Seung‐Ho
Published: October 2018

Purpose

Ultrasonographic contrast enhancement of carotid plaque (CECP) has been used to detect neovascularization of vasa vasorum and plaque. However, it is uncertain whether CECP can provide risk stratification of coronary artery disease (CAD). This study aimed to evaluate the relationship between CECP and manifestations of acute coronary syndrome (ACS) in established CAD patients and to explore the prognostic implication of CECP for cardiovascular (CV) clinical outcomes.

Methods

A medical record review revealed that contrast‐enhanced ultrasonography was performed to evaluate carotid atherosclerosis in 209 coronary artery‐stented and 105 non‐stented patients. The rate of ACS manifestations was compared depending on contrast uptake patterns: grade 0, absent; grade 1, dot; and grade 2, diffuse pattern. CV primary outcomes were assessed during a mean 7.6 months of follow‐up.

Results

Male sex, smoking, history of old myocardial infarction, intensive medications, and a favorable lipid profile were common in the stented versus non‐stented group. Patients with grade 2 CECP had a higher rate of ACS, greater plaque thickness, and class I‐II of Gray‐Weale plaque echogenicity. During follow‐up, 10 coronary revascularizations (nine ACSs), six strokes, and four heart failures occurred. Grade 2 CECP was more closely related with CV primary outcomes and showed a tendency toward more acute CV outcomes.

Conclusion

ACS manifestations were proportionate to CECP grade. Diffuse CECP uptake could be a risk factor for acute CV outcomes.
Retrospectively seroprevalence study on anti‐HEV‐IgG antibody in patients with chronic hepatitis or liver cirrhosis in a Chinese teaching hospital
Authors: Yang Hongying , Wu Jianguo , Yuan Yuan , Huang Wenxiang , Jia Bei
Published: October 2018

Background and Objective

To investigate the serum anti‐hepatitis E virus (HEV) antibody positive rate in patients with different types of chronic hepatitis (CH) or cirrhosis.

Methods

A total of 1751 hospitalized patients were chart reviewed, who were diagnosed with mono‐CH or cirrhosis between 2011 and 2016.

Results

The total anti‐HEV‐IgG positive rate was 1.33% (13/981) in CH patients, which was significantly lower than that (6.49%; 50/770) in cirrhosis patients (odds ratio [OR], 4.78 [2.51‐9.10]; P = 0.00). The comparison of positive rate of anti‐HEV‐IgG between the same etiology CH and cirrhosis groups was as follows: chronic hepatitis B 1.27% (10/790) versus hepatitis B virus (HBV)‐related cirrhosis 4.21% (22/522) (OR, 3.04 [1.36‐6.77]; P = 0.00); chronic alcoholic hepatitis 1.41% (1/71) versus alcoholic cirrhosis 9.40% (11/117) (OR, 8.00 [1.00‐64.25]; P = 0.03); chronic autoimmune hepatitis 1.69% (1/59) versus autoimmune cirrhosis 13.33% (12/90) (OR, 13.11 [1.49‐115.27]; P = 0.01); the differences above were statistically significant. And chronic hepatitis C 3.23% (1/31) versus hepatitis C virus‐related cirrhosis 10.81% (4/37) (OR, 4.40 [0.45‐43.53]; P > 0.05); chronic NASH 0.00% (0/30) versus NASH‐related cirrhosis 25.00% (1/4) (P > 0.05), the differences were not statistically significant. Anti‐HEV‐IgG positive rates were also compared among different types of CH groups and no significant difference was found. Likewise, anti‐HEV‐IgG positive rate was compared among different types of cirrhosis groups, showing that the positive rates of both alcoholic cirrhosis (9.40%) and autoimmune cirrhosis (13.33%) were significantly higher than that of HBV‐related cirrhosis (4.21%) (P < 0.05).

Conclusion

We observed that the cirrhosis patients had a significantly higher anti‐HEV‐IgG positive rate comparing with the CH patients, especially in those with HBV‐related, alcohol‐related, and autoimmune‐related cirrhosis (after adjusted for age). Additionally, it seems that the conditions of alcoholic cirrhosis and autoimmune cirrhosis are more susceptible to HEV infection due to the significantly higher positive anti‐HEV‐IgG rate in these patients.
Diamond nanoparticles coating for in‐tube solid‐phase microextraction to detect polycyclic aromatic hydrocarbons
Authors: Ji Xiangping , Feng Juanjuan , Wang Xiuqin , Tian Yu , Li Chunying , Luo Chuannan , Sun Min
Published: October 2018

Diamond nanoparticles were coated onto stainless steel wires as a extraction material, then it was filled into a poly(ether ether ketone) tube for in‐tube solid‐phase microextraction. Coupled with high‐performance liquid chromatography, the extraction tube was evaluated with different types of analytes including polycyclic aromatic hydrocarbons, estrogens and plasticizers. As the coating, diamond nanoparticles exhibited greater extraction capacity for hydrophobic analytes. Several polycyclic aromatic hydrocarbons were used as model analytes, four main extraction and desorption factors were optimized, including sampling volume, sampling rate, methanol content in sample and desorption time. A sensitive analysis method was established with wide linear range (0.016–20 μg/L), good correlation coefficients (0.9991–0.9997), low limits of detection (0.005–0.020 μg/L), low limits of quantitation (0.016–0.070 μg/L) and high enrichment factors (305‐2396). Relative standard deviations for intra‐ and interday were less than 2.4% (n = 3) and 8.4% (n = 3), respectively. Durability and chemical stability were satisfactory with relative standard deviations less than 7.9% (n = 3). Finally, the method has been successfully applied to the detection of polycyclic aromatic hydrocarbons in real samples.
Application of Greenberg's conjecture in the capitulation problem
Authors: Mouhib Ali
Published: October 2018

Let r be a positive integer. Assume Greenberg's conjecture for some totally real number fields, we show that there exists an infinite family of imaginary cyclic number fields F over the field of rational number field , with an elementary 2‐class group of rank equal to r that capitulates in an unramified quadratic extension over F. Also, we give necessary and sufficient conditions for the Galois group of the unramified maximal 2‐extension over F to be abelian.
Air filled substrate integrated waveguide cavity backed slot antenna
Authors: Adhikary Moitreya , Mukherjee Soumava , Biswas Animesh , Akhtar Mohammad Jaleel
Published: October 2018

In this letter, an air filled substrate integrated waveguide (SIW) based cavity backed slot antenna design is proposed to achieve high radiation efficiency and gain by reducing the dielectric loss component by removing the dielectric inside the cavity. An effective miniaturization is also achieved by introducing a specialized slot backed by the cavity.
Study of ferrite material characterization using transmission line model
Authors: Maleki Mostafa , Mohseni Armaki Seyyed Hossein , Hamidi Emad
Published: October 2018

In this paper, wave interaction with a ferrite material in a rectangular waveguide system is analyzed by using the transmission line (TL) model at Ku band. Using the presented model, the equivalent transverse admittance of the system is extracted. According to the corresponding relationship between the transverse admittance and the scattering parameters (S11, S21) of the system, the saturation magnetization and permittivity of a ferrite material (4πMs and
ɛ
r) are extracted. In comparison to other works, the proposed method has made the implementation very easy and has eliminated the problems associated with phase measurement and calibration. The presented model is simulated on the several types of ferrites and experimentally is tested on an SL‐470 ferrite sample. Comparison of the results shows that the extracted parameters are close to the manufacturing values with %5 error.
High‐density WGM probes generated by a ChG ring resonator for high‐density 3D imaging and applications
Authors: Youplao Phichai , Pornsuwancharoen Nithiroth , Suwanarat Suksan , Chaiwong Khomyuth , Jalil Muhammad Arif , Amiri Iraj. S. , Ali Jalil , Singh Ghanshyam , Yupapin Preecha , Grattan Kenneth T.V.
Published: October 2018

In this paper, the ultra‐wideband source for light fidelity (LiFi) and high‐density 3D imaging applications is proposed. The system consists of an add‐drop multiplexer. The center ring is formed by the Chalcogenide glass (ChG), which is coupled with two GaAsInP/P side rings. The nonlinear effect within the side rings (phase modulators) is induced in the central ring. The superposition of light signals from side rings generates wider wavelength band, which makes the original input. The output is the set of squeezed light pulses known as whispering gallery mode (WGM) which is generated at the center of the system. Three different input sources are investigated, where the simulated results are comparatively plotted and discussed. The results show that the wavelength of 1.30 μm is the best input source. The output wavelengths band is ranged from 0.7‐3.1 μm, which is suitable for LiFi source and high‐density 3D imaging applications.