bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protocol for Computational Enzymatic Reactivity Based on Geometry Optimisation
Authors: Cerqueira N. M. F. S. A. , Fernandes P. A. , Ramos M. J. 
Published: October 2017

AbstractEnzymes play a biologically essential role in performing and controlling an important share of the chemical processes occurring in life. However, despite their critical role in nature, attaining a clear understanding of the way an enzyme acts is still cumbersome. Computational enzymology is playing an increasingly important role in this field of research. It allows the elucidation of a complete and detailed mechanism of an enzymatic reaction, including the characterization of reaction intermediates and transition states from both structural and energetic points of view, which is something that no other single experiment can produce alone.In this review, we present a general computational strategy to study enzymatic mechanisms based on adiabatic mapping and free geometry optimization. These methods allow chemical reactions to be studied with high theoretical levels, and allow a more exhaustive exploration of the chemical reactional space than other available methods, albeit being limited to the extent that they explore the enzyme conformational space.Special attention is given to the choice of the theoretical levels, as well as describing the model systems that are currently used to study enzymatic reactions. With this, we aim to provide a good introduction for non‐specialised users in this field of research. We also provide a selection of hand‐picked examples from our own work that illustrate the power of computational enzymology to study catalytic mechanisms. Some of these studies constitute pioneering work in the field that were later validated by experimental means.
How Chi Sequence Modifies RecBCD Single‐Stranded DNA Translocase Activity
Authors: Cho Chia‐Chuan , Chung Cinya , Li Hung‐Wen 
Published: October 2017

AbstractE. coli RecBCD initiates homologous repair as well as degrades foreign DNA. Recognition of chi sequence (5′‐GCTGGTGG‐3′) switches RecBCD from a destructive, nucleolytic mode into a repair‐active one that promotes RecA‐mediated recombination. RecBCD includes a 3′‐to‐5′ single‐stranded DNA (ssDNA) translocase in RecB subunit, a 5′‐to‐3′ translocase in RecD, and a secondary translocase activity associated with RecBC. To understand how chi specifically affects each translocase activity, we directly visualized individual RecBCD translocating along DNA substrates containing a ssDNA gap of different polarities, with or without chi. Disappearance of RecBCD from the ssDNA signals the loss of the ssDNA translocase activity. For substrates containing a ssDNA gap that RecBCD encounters in the 3′‐to‐5′ polarity (3′‐to‐5′ ssDNA), wild‐type RecBCD disappears from the DNA substrates with similarly high percentage, either with chi or without. This suggests that (1) the 3′‐to‐5′ translocase in RecB is unaffected by chi and (2) it is low in processivity. With substrates containing a ssDNA gap that RecBCD encounters in the 5′‐to‐3′ polarity (5′‐to‐3′ ssDNA), we found that the leaving percentage increases significantly with chi, implying inactivation of the 5′‐to‐3′ translocase of RecD upon chi recognition. Surprisingly, the RecD defective mutant RecBCDK177Q showed only ≈50 % leaving on 5′‐to‐3′ ssDNA, directly revealing the presence of RecBC secondary translocase and its activity is unaffected by chi. Multiple ssDNA translocases within the RecBCD complex both before and after chi ensures processive unwinding of DNA substrates required for efficient recombination events.
Non‐oxidative Coupling of Methane to Ethylene Using Mo2C/[B]ZSM‐5
Authors: Sheng Huibo , Schreiner Edward P. , Zheng Weiqing , Lobo Raul F. 
Published: October 2017

AbstractMethane non‐oxidative coupling to ethylene was investigated on Mo2C/[B]ZSM‐5 catalyst at 923 K and atmospheric pressure. In contrast to Mo2C/[Al]ZSM‐5 catalysts for methane aromatization, this material exhibits very high ethylene selectivity (>90 %) and low aromatics (benzene and naphthalene) selectivity. The much weaker Brønsted acidity of [B]ZSM‐5 leads to a slow rate of ethylene oligomerization. The stability of the catalyst is greatly enhanced with 93 % of the initial reaction rate remaining after 18 h of time on stream. In‐situ UV/VIS spectra indicate that prior to carburization, mono/binuclear Mo oxides are initially well dispersed onto the zeolite support. Mo carbides clusters, formed during carburization with methane, appear similar to clusters formed in [Al]ZSM‐5, as indicated by the X‐ray Absorption Spectroscopy (XAS) data.
Fabrication of a Robust Tantalum Nitride Photoanode from a Flame‐Heating‐Derived Compact Oxide Film
Authors: Shao Chenyi , Han Jingfeng , Liu Guiji , Wang Zhiliang , Zhao Yongle , Zong Xu , Li Can 
Published: October 2017

AbstractPhotoelectrochemical (PEC) water splitting provides an attractive way of converting solar energy into hydrogen energy. To make this approach practical, it is crucial to develop strategies that can be used to fabricate efficient photoelectrodes in a scalable manner. Herein, we report a rapid flame heating method to prepare a Ta2O5 precursor film for a Ta3N5 photoanode. By varying the parameters of flame heating, rational control over the physicochemical nature of the Ta2O5 precursor film can be realized. With the following nitridation treatment, the compact precursor film can be transformed into a tight‐knit Ta3N5‐based nitride film which strongly stuck to the underlying conductive Ta substrate. As a result of the close interfacial connections and reasonable conductivity achieved through the manipulation of the duration of flame heating, an enhanced charge‐separation efficiency was obtained for the as‐prepared Ta3N5 photoanode. Furthermore, with the help of a ferrihydrite layer, the photocurrent density for PEC water oxidation on the optimum Ta3N5 photoanode reached circa 3.53 mA cm−2 at 1.23 V vs. RHE, which is among the best values reported for planar Ta3N5‐based photoanodes. This report highlights the advantages of flame heating over traditional heating methods for preparing precursor films for further processing or functionalization.
Testbed@TWISC: A network security experiment platform
Authors: Tsai Pang‐Wei , Yang Chu‐Sing 
Published: October 2017

SummaryAs the internet continues to grow in width and depth, its very architecture brings many challenges in network research. One significant issue is cybersecurity. Owing to the characteristics of network connectivity, malicious actions may cause losses during information exchanges in communication. Therefore, studying suspicious behaviors and covering potential exploits are necessary to protect networked computers. To determine possible threats, researchers need an experimental environment that enables them to explore and practice. A network emulation testbed provides such a platform to fulfill these purposes. This paper introduces Testbed@TWISC, a large‐scale network emulation testbed on Taiwan's research and education network that supported open research and cybersecurity education for almost 10 years. The paper reviews this testbed's origination, development, and operation experiences. Several findings and open issues of the testbed are also discussed. Readers who plan to build network security testbeds may find useful information in this paper for a case study.
Detection possibilities of pore structures
Authors: Anders Nicole 
Published: October 2017

AbstractAutoclaved aerated concrete, hereafter referred to as AAC, is characterized as a building material by its very good thermal insulation. This is achieved by a very high porosity of the microstructure. The size of the pores ranges from millimetres to nanometres and depends on the position as well as on the origin of the pore. These can be differentiated into propellant pores, web pores and intercrystalline or interparticle pores. Because of the broad pore size range, it has not been fully explained until now, which pore sizes significantly affect the building material qualities and to what extent. The overall pore size distribution of AAC can only be detected by a combination of different microstructure analysis methods.For this purpose, nitrogen sorption analysis, mercury intrusion and 3D micro computer tomography were used as an effective combination. Three samples were tested, which show different mineralogical phase compositions because of the differentiation of the formulation. On the basis of these samples and the pore size distribution, which is usually used for the description of the frost and resistance to de‐icing salt of concrete, initial insights into the influence of the respective pore size on the building material properties of AAC could be gained.
Extension of the conditions for application of the simplified calculation methods according to DIN EN 1996‐3/NA for the design of unreinforced masonry walls
Authors: Mazur René , Purkert Benjamin 
Published: October 2017

AbstractDedicated to University Prof. Dr.‐Ing. Carl‐Alexander Graubner for his 60th birthdayThe simplified calculation methods for unreinforced masonry structures given in DIN EN 1996‐3/NA are an easily applicable design standard for an efficient and fast verification of the resistance of mainly vertically loaded masonry walls. However, the design rules are not based on mechanical models. Instead, they are empirical approaches for a simplified estimation of the load bearing capacity. For this reason, the range of application of DIN EN 1996‐3/NA is limited by several conditions to ensure a sufficient safety of this design procedure.With regard to extending the conditions for application, extensive comparative calculations were carried out. Thereby, considering clearly defined boundary conditions, the load bearing capacity according to DIN EN 1996‐3/NA was compared to that according to DIN EN 1996‐1‐1/NA. It was the aim of this comparison to identify load bearing reserves of the simplified calculation methods to point out potential for an extension regarding the maximum permissible clear wall height and the slab span. As a result, it can be stated, that an increase of the maximum wall height up to 6.0 m and the maximum slab span of 7.0 m is possible in certain cases.
Useful aspects of diagnosis of imprint cytology in intraoperative consultation of ovarian tumors: comparison between imprint cytology and frozen sections
Authors: Azami Shiho , Aoki Yuuji , Iino Mizuki , Sakaguchi Asumi , Ogura Kanako , Ogishima Daiki , Matsumoto Toshiharu 
Published: October 2017

BackgroundIn the intraoperative consultation of ovarian tumors, the histological diagnosis of frozen sections (FS) of large tumors is frequently difficult because of the limited number of tumor samples. The application of imprint cytology (IC), in which samples are obtained from wide areas of the tumors, is useful for intraoperative consultation. However, the useful aspects of IC have not been clearly defined. The present study is a detailed comparison of IC and FS that clearly defines the useful aspects of IC.MethodsFifty‐five cases of ovarian tumors that were examined using both IC and FS were evaluated. The histological diagnoses consisted of benign (16), borderline (6), and malignancy (33). All of the malignant tumors consisted of various types of carcinoma.ResultsBenignity and malignancy were accurately diagnosed by both IC and FS. In the borderline group, the diagnostic accuracy of IC was very low (1/6: 16.6%) compared with FS (4/6: 66.6%). The diagnostic accuracy including benign, borderline, and malignant groups was 90.9% (50/55) for IC and 96.3% (53/55) for FS. Concerning the diagnosis of the types of carcinoma, the overall diagnostic accuracy of IC (25/31: 80.6%) was greater than that of FS (21/31: 67.7%), especially for the diagnosis of clear cell carcinoma (IC, 100%; FS, 80%) and mixed carcinoma (IC, 66.6%; FS, 16.6%).ConclusionThe useful aspects of IC in the intraoperative consultation are the diagnosis of benignity or malignancy and the accuracy of diagnosing clear cell carcinoma and mixed carcinoma.
Weight suppression and bulimic syndrome maintenance: Preliminary findings for the mediating role of leptin
Authors: Keel Pamela K. , Bodell Lindsay P. , Haedt‐Matt Alissa A. , Williams Diana L. , Appelbaum Jonathan 
Published: October 2017

AbstractObjectiveLongitudinal studies support a prospective relationship between weight suppression (WS) and bulimic syndrome (BN‐S) maintenance. Although biobehavioral mechanisms have been proposed to explain this link, such mechanisms have yet to be identified. Given that weight loss would reduce leptin levels which may influence eating, this study examined whether reduced leptin levels mediate the link between greater WS and longer illness duration.MethodWomen (N = 53), ages 18–45 years, were recruited from the community if they met criteria for a BN‐S, including either DSM‐5 bulimia nervosa (BN; n = 33) or purging disorder (PD: n = 20), and fell within a healthy weight range (18.5–26.5 kg/m2). Participants completed clinical assessments and provided blood samples to measure circulating leptin.ResultsSignificant associations were found among greater WS, lower leptin concentrations, and longer duration of illness. Mediation analyses using bootstrapping procedures indicated all paths were significant and that leptin mediated the link between WS and illness duration. An alternative model in which longer illness duration contributed to leptin, via greater WS, was not supported.DiscussionLongitudinal research is needed to support temporal associations and explore behavioral mechanisms linking leptin to illness trajectory.
Geoarchaeological study of abandoned Roman urban and suburban contexts from central Adriatic Italy
Authors: Vermeulen Frank , Pincé Possum , Weekers Lara , De Dapper Morgan 
Published: October 2017

AbstractOver the past 15 years the Potenza Valley Survey project investigated Iron Age to Medieval settlement dynamics in the Central Adriatic Potenza Valley. Part of this research focuses on the Roman abandoned towns of Potentia and Trea by performing an integrated geoarchaeological study of their townscape. This largely noninvasive research consists of remote sensing analysis, geophysical surveys (magnetometry, electrical resistivity, and ground‐penetrating radar), and geomorphological fieldwork such as microtopographic measurements and hand augering. The chosen techniques depend on the nature of each town and are integrated with more traditionally achieved research data. This paper presents the main interdisciplinary results of work on these two Roman towns and highlights the importance of obtaining complementary data and performing hand augering as a stratigraphic control of the remote sensing and geophysical results. Insights into the character and layout of the cities, the structural influence on the surrounding area, and the human‐environment interactions and dynamics through time of both Roman cities could be achieved. Moreover, the results offer guidelines for conservation strategies of these abandoned towns and their suburbium, which are necessary to protect them from present‐day threats such as agriculture and tourism. In this way the paper offers an insight in the tremendous potential of well‐integrated geoarchaeological investigations of partly or fully abandoned urban contexts in the Mediterranean area and beyond.
One‐pot reactions for the synthesis of 5‐sulfonyl quinolines via domino N‐acylation and remote C‐H sulfonylation
Authors: Du Yi , Wei Li , Liu Yunyun 
Published: October 2017

AbstractThe synthesis of N‐acylated 5‐sulfonyl 8‐aminoquinolines has been performed via the three‐component reactions of 8‐aminoquinolines, acyl chlorides and sodium sulfinates for the first time. This new synthetic approach is highly facile by employing cheap copper salt as promoter and enabling the product formation via domino N‐acylation and selective remote C‐5 sulfonylation.
Efficacy and safety of vinorelbine plus cisplatin chemotherapy for patients with recurrent and/or metastatic salivary gland cancer of the head and neck
Authors: Hong Min Hee , Kim Chang Gon , Koh Yoon Woo , Choi Eun Chang , Kim Jinna , Yoon Sun Och , Kim Hye Ryun , Cho Byoung Chul 
Published: October 2017

AbstractBackgroundThe purpose of this study was to investigate the efficacy and safety of vinorelbine plus cisplatin chemotherapy in patients with recurrent and/or metastatic salivary gland cancer of the head and neck.MethodsIn this single‐arm phase II study, patients with recurrent and/or metastatic salivary gland cancer were treated with i.v. vinorelbine (25 mg/m2) on days 1 and 8 plus cisplatin (80 mg/m2) on day 1 every 3 weeks for 4 or 6 cycles. The primary endpoint was the objective response rate. Progression‐free survival (PFS), overall survival (OS), and adverse events were also assessed.ResultsBetween September 2008 and November 2014, 40 patients with recurrent and/or metastatic salivary gland cancer received vinorelbine plus cisplatin chemotherapy. The objective response rate was 35.0%, including 1 complete response. Median PFS and OS rates were 6.3 months and 16.9 months, respectively. No treatment‐related deaths occurred.ConclusionAdministering vinorelbine plus cisplatin chemotherapy to patients with recurrent and/or metastatic salivary gland cancers is safe and effective.
Management of the lateral neck compartment in patients with sporadic medullary thyroid cancer
Authors: Pena Israel , Clayman Gary L. , Grubbs Elizabeth G. , Bergeron Jeffrey M. , Waguespack Steven G. , Cabanillas Maria E. , Dadu Ramona , Hu Mimi I. , Fellman Bryan M. , Li Yisheng , Gross Neil D. , Lai Stephen Y. , Sturgis Erich M. , Zafereo Mark E. 
Published: October 2017

AbstractBackgroundThe purpose of this retrospective analysis was to evaluate the benefits of an elective lateral neck dissection (ELND) in patients with medullary thyroid cancer (MTC) without radiographically apparent lateral neck metastases.MethodsPatients with sporadic MTC without radiographic evidence of lateral neck metastasis who underwent definitive surgery were divided into 2 groups based on surgical approach: no ELND (the observation group) and ipsilateral or bilateral ELND (the ELND group). Primary outcomes were biochemical cure, locoregional recurrence, distant metastasis, and overall survival (OS).ResultsSixty‐six patients met inclusion criteria: 44 patients (67%) in the observation group and 22 patients (33%) in the ELND group. Two of 44 patients (5%) in the observation group developed subsequent (ipsilateral) lateral neck disease. At last follow‐up, locoregional disease control rates among the observation and ELND groups were 98% and 100% (P > .999), respectively, whereas biochemical cure rates were 82% and 85% (P > .999), respectively, and 5‐year OSs were 84% and 100% (P = .156), respectively.ConclusionPatients with MTC without lateral neck metastasis have similar biochemical cure rates with observation or elective dissection of lateral neck compartments.
Local control in sinonasal malignant melanoma: Comparing conventional to hypofractionated radiotherapy
Authors: Lansu Jules , Klop Willem Martin , Heemsbergen Wilma , Navran Arash , Al‐Mamgani Abrahim , Langendijk Johannes A. , Kaanders Johannes H. , Terhaard Chris , Karakullukcu Baris , Hamming‐Vrieze Olga 
Published: October 2017

AbstractBackgroundThe purpose of this study was to analyze the effect of fractionation schedule on local control in postoperative radiotherapy (RT) for sinonasal malignant melanoma.MethodsSixty‐three patients who were treated with surgery and postoperative RT in 4 accredited head and neck cancer centers in the Netherlands between 1998 and 2013 were retrospectively studied. Outcomes with conventional fractionation (2‐2.4 Gy per fraction; n = 27) were compared to hypofractionation (4‐6 Gy per fraction; n = 36). The primary endpoint was local control and the secondary endpoint was toxicity.ResultsComparable local control rates were found after 2 and 5 years (63% vs 64% and 47% vs 53%; P = .73 for, respectively, conventional fractionation vs hypofractionation). Local recurrences were predominantly present ipsilateral (92%) and within the irradiated volume (88%). Late toxicity grade ≥ 3 was observed in 2 of 63 patients, 1 patient in both groups.ConclusionRadiotherapy fractionation schedule did not influence the local control rate or the incidence of late toxicity in patients treated with surgery and RT for sinonasal malignant melanoma in this retrospective analysis. Due to this retrospective nature and the limited number of patients, strong recommendations cannot be made. Expected toxicity, patient convenience, and workload may be taken into account for the choice of fractionation schedule until conclusive evidence becomes available.
Memory encoding‐related anterior hippocampal potentials are modulated by deep brain stimulation of the entorhinal area
Authors: Hansen Niels , Chaieb Leila , Derner Marlene , Hampel Kevin G. , Elger Christian E. , Surges Rainer , Staresina Bernhard , Axmacher Nikolai , Fell Juergen 
Published: October 2017

AbstractBackgroundDeep brain stimulation (DBS) of the human entorhinal area using 50 Hz pulses has revealed conflicting results regarding memory performance. Moreover, its impact on memory‐related hippocampal potentials has not yet been investigated.MethodsWe recorded data from seven epilepsy patients implanted with depth electrodes in the entorhinal cortex, hippocampus, amygdala, and parahippocampal cortex. Entorhinal DBS (bipolar, biphasic 50 Hz pulses, on‐ and off‐cycles of 15 s) was applied with low amplitude (0.1 mA) to resemble physiologic conditions. During DBS on‐ and off‐periods, patients learned noun‐color associations that were later tested.ResultsDuring entorhinal DBS we observed more positive deflections of event‐related potentials (ranging from 700 to 950 ms) in the anterior hippocampus for the on‐ vs. off‐condition. We detected no effects in the amygdala, mid hippocampus and parahippocampal cortex. On the behavioral level, no differences in memory performance (item and source memory) were apparent in the on‐ vs. off‐condition, neither across all trials nor across patients.DiscussionOur findings indicate that entorhinal DBS with low amplitude has an impact on memory encoding‐related potentials within the anterior hippocampus, but not on memory performance per se.
The assessment of the United States quantitative easing policy: Evidence from global stock markets
Authors: Su Jung‐Bin , Hung Ken 
Published: October 2017

AbstractThis study assesses the performance of the quantitative easing policy implemented by the United States (US) on the stock markets with a framework of structure break. The empirical results show that the business cycle or the value of gross domestic production has a negative impact on the stock markets for most of the countries even if both gross domestic production and many stock prices are procyclical. Moreover, the purchases of US Treasury securities and mortgage‐backed securities respectively affect the stock markets synchronously and laggardly. Notably, they both have a positive impact on the stock markets during the study period. Finally, during the after structure break period, the volatility can be easily affected by bad news, and the investors have the lower profit or even the greater loss and bear the greater risk and variation of risk owing to the global financial crisis caused by the US. On the basis of the above findings, some policy implications are offered in this study.