bluuebunny/crossref_metadata_2025_split huggingface dataset:
Daikenchuto (TU‐100) shapes gut microbiota architecture and increases the production of ginsenoside metabolite compound K
Authors: Hasebe Takumu , Ueno Nobuhiro , Musch Mark W. , Nadimpalli Anuradha , Kaneko Atsushi , Kaifuchi Noriko , Watanabe Junko , Yamamoto Masahiro , Kono Toru , Inaba Yuhei , Fujiya Mikihiro , Kohgo Yutaka , Chang Eugene B. 
Published: February 2016

AbstractMany pharmaceutical agents not only require microbial metabolism for increased bioavailability and bioactivity, but also have direct effects on gut microbial assemblage and function. We examined the possibility that these actions are not mutually exclusive and may be mutually reinforcing in ways that enhance long‐term of these agents. Daikenchuto, TU‐100, is a traditional Japanese medicine containing ginseng. Conversion of the ginsenoside Rb1 (Rb1) to bioactive compound K (CK) requires bacterial metabolism. Diet‐incorporated TU‐100 was administered to mice over a period of several weeks. T‐RFLP and 454 pyrosequencing were performed to analyze the time‐dependent effects on fecal microbial membership. Fecal microbial capacity to metabolize Rb1 to CK was measured by adding TU‐100 or ginseng to stool samples to assess the generation of bioactive metabolites. Levels of metabolized TU‐100 components in plasma and in stool samples were measured by LC‐MS/MS. Cecal and stool short‐chain fatty acids were measured by GC‐MS. Dietary administration of TU‐100 for 28 days altered the gut microbiota, increasing several bacteria genera including members of Clostridia and Lactococcus lactis. Progressive capacity of microbiota to convert Rb1 to CK was observed over the 28 days administration of dietary TU‐100. Concomitantly with these changes, increases in all SCFA were observed in cecal contents and in acetate and butyrate content of the stool. Chronic consumption of dietary TU‐100 promotes changes in gut microbiota enhancing metabolic capacity of TU‐100 and increased bioavailability. We believe these findings have broad implications in optimizing the efficacy of natural compounds that depend on microbial bioconversion in general.
Time‐bound key‐aggregate encryption for cloud storage
Authors: Lee Cheng‐Chi , Li Chun‐Ta , Chiu Shih‐Ting , Chen Shun‐Der 
Published: February 2016

AbstractHandling huge loads of data that are subject to change within every second, cloud storage services are facing the challenge of properly dealing with the problem of user legality management while making sure that the services are conveniently user‐friendly. Ideally, the concept of attribute‐based encryption should be applied, meaning that data should be able to be encrypted using some specific attributes before it is uploaded to cloud, so that fine access control is possible. However, in a traditional attribute‐based encryption scheme, the user typically needs to have different attribute‐based keys for the decryption of various pieces of data downloaded, which really is a lot of trouble. To solve this problem, the idea of key‐aggregate cryptosystem has been brought up. With key‐aggregate cryptosystem, the user gets to use one single aggregate key to decrypt data that match all the attributes specified by the user. In addition, in some cases of cloud data usage, we as users might not exactly want to share our cloud data with others 24 h a day and for as long as it gets. Therefore, in this paper, we shall propose a time‐bound key‐aggregate encryption scheme for cloud storage, together with the results of some comparisons as well as correctness and security analyses we have made to prove the superiority of our new scheme over related works. Not only will our new scheme take the burden of maintaining the attribute‐based keys off the user, but it will also provide satisfactory confidentiality and security for cloud data in a more efficient way. Copyright © 2016 John Wiley & Sons, Ltd.
Multilevel Probabilistic Morphological Analysis for Facilitating Modeling and Simulation of Notional Scenarios
Authors: Payan Alexia P. , Mavris Dimitri N. 
Published: February 2016

ABSTRACTDespite advances in computational power, simulation‐based experiments of complex problems remain time‐consuming. Significant efforts are required to define an accurate representation of the problem and draw relevant conclusions about relationships between input parameters and output performance measures. To reduce the computational burden without sacrificing accuracy, it is customary to design a set of relevant scenarios. Doing so necessitates that the problem be decomposed into relevant parameters and that the consistency of these parameters be analyzed. To address this challenge, we propose a multilevel probabilistic morphological analysis. Traditionally, morphological analysis documents the decomposition of a system into its main components, and performs binary compatibility assessments to document relational data between component options. However, this approach leads to a rigid definition of the problem space and a static solution space that does not account for uncertain and dynamic behaviors associated with complex systems‐of‐systems. This research incorporates two important improvements. First, it explicitly incorporates a multilevel approach accommodating any successive decomposition steps that may be required when dealing with a complex system‐of‐systems problem. Second, this research introduces probabilistic cross‐consistency assessments instead of traditional binary assessments to account for uncertain future states of the world. This probabilistic scheme is used to describe degrees of likelihood that two elements may coexist in a given scenario. This way, more complex interactions may also be captured and more realistic scenarios may be defined. Finally, the proposed method is applied to a problem investigating the design of architectures of detection systems for the protection of homeland critical assets.
Implementing Systems Engineering in Civil Engineering Consulting Firm: An Evaluation
Authors: de Graaf Robin , Voordijk Hans , van den Heuvel Len 
Published: February 2016

ABSTRACTThis study explores the challenges that civil engineering consulting firms face in their projects when they apply Systems Engineering (SE). It is also explained were these firms should focus when improving the use of SE. To conduct this study, the methodology of Eisenhardt (Building theories from case study research, Acad Manage Rev 14 [1989], 532–550) for building theory from case study research is used. The extent, to which SE is applied, is assessed in six civil engineering projects, using a newly developed framework containing an extensive list of questions about how and why SE was applied. Based on this assessment, it is shown that there are three major reasons why SE was not applied to the full extent. First, SE procedures and responsibilities were not always clearly established and communicated to team members. Second, team members were in a learning process and did not yet possess all the SE knowledge and skills required. Finally, there was a lack of a demanding client to enforce the use of SE. This paper also presents recommendations for improving the application of SE in projects, related to methods, skills, and the client. Further research should focus on different (kinds of) companies within the civil engineering industry.
Integrated design of downwind land‐based wind turbines using analytic gradients
Authors: Ning Andrew , Petch Derek 
Published: February 2016

AbstractWind turbines are complex systems where component‐level changes can have significant system‐level effects. Effective wind turbine optimization generally requires an integrated analysis approach with a large number of design variables. Optimizing across large variable sets is orders of magnitude more efficient with gradient‐based methods as compared with gradient‐free method, particularly when using exact gradients. We have developed a wind turbine analysis set of over 100 components where 90% of the models provide numerically exact gradients through symbolic differentiation, automatic differentiation, and adjoint methods. This framework is applied to a specific design study focused on downwind land‐based wind turbines.Downwind machines are of potential interest for large wind turbines where the blades are often constrained by the stiffness required to prevent a tower strike. The mass of these rotor blades may be reduced by utilizing a downwind configuration where the constraints on tower strike are less restrictive. The large turbines of this study range in power rating from 5–7MW and in diameter from 105m to 175m. The changes in blade mass and power production have important effects on the rest of the system, and thus the nacelle and tower systems are also optimized. For high‐speed wind sites, downwind configurations do not appear advantageous. The decrease in blade mass (10%) is offset by increases in tower mass caused by the bending moment from the rotor‐nacelle‐assembly. For low‐wind speed sites, the decrease in blade mass is more significant (25–30%) and shows potential for modest decreases in overall cost of energy (around 1–2%). Copyright © 2016 John Wiley & Sons, Ltd.
Adaptive symbiotic organisms search (SOS) algorithm for structural design optimization
Authors: Tejani Ghanshyam G. , Savsani Vimal J. , Patel Vivek K. 
Published: February 2016

Abstract
The symbiotic organisms search (SOS) algorithm is an effective metaheuristic developed in 2014, which mimics the symbiotic relationship among the living beings, such as mutualism, commensalism, and parasitism, to survive in the ecosystem. In this study, three modified versions of the SOS algorithm are proposed by introducing adaptive benefit factors in the basic SOS algorithm to improve its efficiency. The basic SOS algorithm only considers benefit factors, whereas the proposed variants of the SOS algorithm, consider effective combinations of adaptive benefit factors and benefit factors to study their competence to lay down a good balance between exploration and exploitation of the search space. The proposed algorithms are tested to suit its applications to the engineering structures subjected to dynamic excitation, which may lead to undesirable vibrations. Structure optimization problems become more challenging if the shape and size variables are taken into account along with the frequency. To check the feasibility and effectiveness of the proposed algorithms, six different planar and space trusses are subjected to experimental analysis. The results obtained using the proposed methods are compared with those obtained using other optimization methods well established in the literature. The results reveal that the adaptive SOS algorithm is more reliable and efficient than the basic SOS algorithm and other state-of-the-art algorithms.
Highlights Correlation between organisms, optimization and engineering. Adaptive symbiotic organisms search (SOS) algorithm is proposed. Implementation on structural design problems. Effective over other methods.
Knockdown of TMEM14A expression by RNAi inhibits the proliferation and invasion of human ovarian cancer cells
Authors: Zhang Qingmei , Chen Xiufeng , Zhang Xuan , Zhan Jingfen , Chen Jie 
Published: February 2016

Transmembrane protein 14A (TMEM14A) is a member of TMEMs. Alterations in TMEMs expression have been identified in several types of cancer, but the expression and function of TMEM14A in ovarian cancer is still unclear. Here, analysis on the expression data of the Cancer Genome Atlas (TCGA) ovarian serous cystadenocarcinoma (OV) dataset demonstrated the overexpression of TMEM14A in ovarian cancer tissues compared with normal tissues, which was consistent with our real-time PCR analysis on ovarian cancer and normal tissues collected from 30 patients. In addition, TMEM14A knockdown in two ovarian cancer cell lines, A2780 and HO-8910, reduced cell proliferation, causes cell cycle arrest and suppressed cell invasion. Moreover, silencing of TMEM14A notably repressed G1/S cell cycle transition and cell invasion via down-regulating the expression of cell cycle related proteins (Cyclin D1, Cyclin E and PCNA) and metastasis-related proteins (MMP-2 and MMP-9), respectively. TMEM14A knockdown significantly reduced the phosphorylation status of Smad2 and Smad3, downstream effectors of TGF-β signalling. In summary, these results indicate that TMEM14A has a pro-tumorigenic effect in ovarian cancer cells, suggesting an important role of this protein in ovarian cancer oncogenesis and metastasis.
Ventilatory acclimatisation is beneficial for high‐intensity exercise at altitude in elite cyclists
Authors: Townsend Nathan E. , Gore Christopher J. , Ebert Tammie R. , Martin David T. , Hahn Allan G. , Chow Chin‐Moi 
Published: February 2016

AbstractAim: The aim of this study was to examine the relationship between ventilatory adaptation and performance during altitude training at 2700 m. Methods: Seven elite cyclists (age: 21.2 ± 1.1 yr, body mass: 69.9 ± 5.6 kg, height 176.3 ± 4.9 cm) participated in this study. A hypoxic ventilatory response (HVR) test and a submaximal exercise test were performed at sea level prior to the training camp and again after 15 d at altitude (ALT15). Ventilation (VE), end‐tidal carbon‐dioxide partial pressure (PETCO2) and oxyhaemoglobin saturation via pulse oximetry (SpO2) were measured at rest and during submaximal cycling at 250 W. A hill climb (HC) performance test was conducted at sea level and after 14 d at altitude (ALT14) using a road of similar length (5.5–6 km) and gradient (4.8–5.3%). Power output was measured using SRM cranks. Average HC power at ALT14 was normalised to sea level power (HC%). Multiple regression was used to identify significant predictors of performance at altitude. Results: At ALT15, there was a significant increase in resting VE (10.3 ± 1.9 vs. 12.2 ± 2.4 L·min−1) and HVR (0.34 ± 0.24 vs. 0.71 ± 0.49 L·min−1·%−1), while PETCO2 (38.4 ± 2.3 vs. 32.1 ± 3.3 mmHg) and SpO2 (97.9 ± 0.7 vs. 94.0 ± 1.7%) were reduced (P < .05). Multiple regression revealed ΔHVR and exercise VE at altitude as significant predictors of HC% (adjusted r2 = 0.913; P = 0.003). Conclusions: Ventilatory acclimatisation occurred during a 2 wk altitude training camp in elite cyclists and a higher HVR was associated with better performance at altitude, relative to sea level. These results suggest that ventilatory acclimatisation is beneficial for cycling performance at altitude.
Multilevel biological characterization of exomic variants at the protein level significantly improves the identification of their deleterious effects
Authors: Raimondi Daniele , Gazzo Andrea M. , Rooman Marianne , Lenaerts Tom , Vranken Wim F. 
Published: February 2016

Abstract
Motivation: There are now many predictors capable of identifying the likely phenotypic effects of single nucleotide variants (SNVs) or short in-frame Insertions or Deletions (INDELs) on the increasing amount of genome sequence data. Most of these predictors focus on SNVs and use a combination of features related to sequence conservation, biophysical, and/or structural properties to link the observed variant to either neutral or disease phenotype. Despite notable successes, the mapping between genetic variants and their phenotypic effects is riddled with levels of complexity that are not yet fully understood and that are often not taken into account in the predictions, despite their promise of significantly improving the prediction of deleterious mutants.
Results: We present DEOGEN, a novel variant effect predictor that can handle both missense SNVs and in-frame INDELs. By integrating information from different biological scales and mimicking the complex mixture of effects that lead from the variant to the phenotype, we obtain significant improvements in the variant-effect prediction results. Next to the typical variant-oriented features based on the evolutionary conservation of the mutated positions, we added a collection of protein-oriented features that are based on functional aspects of the gene affected. We cross-validated DEOGEN on 36 825 polymorphisms, 20 821 deleterious SNVs, and 1038 INDELs from SwissProt. The multilevel contextualization of each (variant, protein) pair in DEOGEN provides a 10% improvement of MCC with respect to current state-of-the-art tools.
Availability and implementation: The software and the data presented here is publicly available at http://ibsquare.be/deogen.
Contact: wvranken@vub.ac.be
Supplementary information: Supplementary data are available at Bioinformatics online.
A Randomized Control Trial: Supplementing Hearing Aid Use with Listening and Communication Enhancement (LACE) Auditory Training
Authors: Saunders Gabrielle H. , Smith Sherri L. , Chisolm Theresa H. , Frederick Melissa T. , McArdle Rachel A. , Wilson Richard H. 
Published: February 2016

Objective:
To examine the effectiveness of the Listening and Communication Enhancement (LACE) program as a supplement to standard-of-care hearing aid intervention in a Veteran population.

Design:
A multisite randomized controlled trial was conducted to compare outcomes following standard-of-care hearing aid intervention supplemented with (1) LACE training using the 10-session DVD format, (2) LACE training using the 20-session computer-based format, (3) placebo auditory training (AT) consisting of actively listening to 10 hr of digitized books on a computer, and (4) educational counseling—the control group. The study involved 3 VA sites and enrolled 279 veterans. Both new and experienced hearing aid users participated to determine if outcomes differed as a function of hearing aid user status. Data for five behavioral and two self-report measures were collected during three research visits: baseline, immediately following the intervention period, and at 6 months postintervention. The five behavioral measures were selected to determine whether the perceptual and cognitive skills targeted in LACE training generalized to untrained tasks that required similar underlying skills. The two self-report measures were completed to determine whether the training resulted in a lessening of activity limitations and participation restrictions. Outcomes were obtained from 263 participants immediately following the intervention period and from 243 participants 6 months postintervention. Analyses of covariance comparing performance on each outcome measure separately were conducted using intervention and hearing aid user status as between-subject factors, visit as a within-subject factor, and baseline performance as a covariate.

Results:
No statistically significant main effects or interactions were found for the use of LACE on any outcome measure.

Conclusions:
Findings from this randomized controlled trial show that LACE training does not result in improved outcomes over standard-of-care hearing aid intervention alone. Potential benefits of AT may be different than those assessed by the performance and self-report measures utilized here. Individual differences not assessed in this study should be examined to evaluate whether AT with LACE has any benefits for particular individuals. Clinically, these findings suggest that audiologists may want to temper the expectations of their patients who embark on LACE training.
Nicorandil Infusion during Off-Pump Coronary Artery Bypass Grafting Reduces Incidence of Intra-aortic Balloon Pump Insertion
Authors: Saha Kamales Kumar , Kumar Ajay , Deval Mandar Manohar , Saha Kakalee K. , Jacob Rinu V. , Jagdale Lukash , Kaul Shibban K. 
Published: February 2016

Objective Off-pump coronary artery bypass grafting in patients with left ventricular dysfunction has proven to be advantageous. However, it carries risk of emergency conversion to cardiopulmonary bypass. We have successfully used an intra-aortic balloon pump to prevent such conversion. The objective of the present study was to evaluate if intravenous nicorandil infusion reduces the incidence of intraoperative intra-aortic balloon pump insertion. Methods Consecutive cases of isolated off-pump coronary artery bypass surgery performed by a single surgeon were studied. Patients were divided into two groups. The first group did not receive nicorandil, and the second group received intraoperative nicorandil infusion (started in the operating room after central line insertion). Results A total of 375 patients were included in the study. Four patients in the non-nicorandil group and the patients in nicorandil group were on preoperative intra-aortic balloon pump and hence excluded from the study. After routine use of nicorandil infusion, incidence of intra-aortic balloon pump insertion during off-pump coronary artery bypass surgery decreased from 12.4% (21/169) to 2.9% (6/206). Conclusions Nicorandil infusion significantly (P = 0.007) reduced the incidence of intra-aortic balloon pump insertion in our series. In patients with left ventricular dysfunction (ejection fraction ≤ 30%), this difference (P = 0.008) assumes a special significance as off-pump bypass surgery is considered high risk in this subset. Nicorandil is an inexpensive drug, and the reduction in cost of surgery by avoiding intra-aortic balloon pump insertion is an added advantage. The use of nicorandil infusion during off-pump coronary artery bypass may result in favorable patient outcomes by reducing invasive intra-aortic balloon pump insertion during off-pump coronary artery bypass grafting.
Trends in the Treatment of Metastatic Colon and Rectal Cancer in Elderly Patients
Authors: Bradley Cathy J. , Yabroff K. Robin , Warren Joan L. , Zeruto Christopher , Chawla Neetu , Lamont Elizabeth B. 
Published: February 2016

Background:
Little is known about the use and costs of antineoplastic regimens for elderly patients with metastatic colorectal cancer (mCRC). We report population-based trends over a 10-year period in the treatment, survival, and costs in mCRC patients, stratified by ages 65–74 and 75+.

Methods:
We used Surveillance, Epidemiology, and End Results–Medicare data for persons diagnosed with metastatic colon (N=16117) or rectal cancer (N=4008) between 2000 and 2009. We estimated the adjusted percent of patients who received antineoplastic agents, by type, number, and their costs 12 months following diagnosis. We report the percent of patients who received 3 or more of commonly prescribed agents and estimate survival for the 24-month period following diagnosis by age and treatment.

Results:
The percentage that received 3 or more agents increased from 3% to 73% in colon patients aged 65–74 and from 2% to 53% in patients 75+. Similar increases were observed in rectal patients. Average 1-year costs per patient in 2009 were $106,461 and $102,680 for colon and rectal cancers, respectively, reflecting an increase of 32% and 20%, for patients who received antineoplastic agents. Median survival increased by about 6 and 10 months, respectively, for colon and rectal patients aged 65–74 who received antineoplastic agents, but an improvement of only 1 month of median survival was observed for patients 75+.

Conclusions:
Expensive multiple agent regimens are increasingly used in older mCRC patients. For patients aged 64–75 years, these treatments may be associated with several months of additional life, but patients aged 75+ may incur considerable expense without any survival benefit.