bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Amordad database engine for metagenomics
Authors: Behnam Ehsan , Smith Andrew D. 
Published: June 2014

Abstract
Motivation: Several technical challenges in metagenomic data analysis, including assembling metagenomic sequence data or identifying operational taxonomic units, are both significant and well known. These forms of analysis are increasingly cited as conceptually flawed, given the extreme variation within traditionally defined species and rampant horizontal gene transfer. Furthermore, computational requirements of such analysis have hindered content-based organization of metagenomic data at large scale.
Results: In this article, we introduce the Amordad database engine for alignment-free, content-based indexing of metagenomic datasets. Amordad places the metagenome comparison problem in a geometric context, and uses an indexing strategy that combines random hashing with a regular nearest neighbor graph. This framework allows refinement of the database over time by continual application of random hash functions, with the effect of each hash function encoded in the nearest neighbor graph. This eliminates the need to explicitly maintain the hash functions in order for query efficiency to benefit from the accumulated randomness. Results on real and simulated data show that Amordad can support logarithmic query time for identifying similar metagenomes even as the database size reaches into the millions.
Availability and implementation: Source code, licensed under the GNU general public license (version 3) is freely available for download from http://smithlabresearch.org/amordad
Contact: andrewds@usc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
The effective founder effect in a spatially expanding population
Authors: Peter Benjamin 
Published: June 2014

1AbstractThe gradual loss of diversity associated with range expansions is a well known pattern observed in many species, and can be explained with a serial founder model. We show that under a branching process approximation, this loss in diversity is due to the difference in offspring variance between individuals at and away from the expansion front, which allows us to measure the strength of the founder effect, dependant on an effective founder size. We demonstrate that the predictions from the branching process model fit very well with Wright-Fisher forward simulations and backwards simulations under a modified Kingman coalescent, and further show that estimates of the effective founder size are robust to possibly confounding factors such as migration between subpopulations. We apply our method to a data set ofArabidopsis thaliana, where we find that the founder effect is about three times stronger in the Americas than in Europe, which may be attributed to the more recent, faster expansion.
Efficient inference of population size histories and locus-specific mutation rates from large-sample genomic variation data
Authors: Bhaskar Anand , Wang Y.X. Rachel , Song Yun S. 
Published: June 2014

AbstractWith the recent increase in study sample sizes in human genetics, there has been growing interest in inferring historical population demography from genomic variation data. Here, we present an efficient inference method that can scale up to very large samples, with tens or hundreds of thousands of individuals. Specifically, by utilizing analytic results on the expected frequency spectrum under the coalescent and by leveraging the technique of automatic differentiation, which allows us to compute gradients exactly, we develop a very efficient algorithm to infer piecewise-exponential models of the historical effective population size from the distribution of sample allele frequencies. Our method is orders of magnitude faster than previous demographic inference methods based on the frequency spectrum. In addition to inferring demography, our method can also accurately estimate locus-specific mutation rates. We perform extensive validation of our method on simulated data and show that it can accurately infer multiple recent epochs of rapid exponential growth, a signal which is difficult to pick up with small sample sizes. Lastly, we apply our method to analyze data from recent sequencing studies, including a large-sample exome-sequencing dataset of tens of thousands of individuals assayed at a few hundred genic regions.SoftwareWe have implemented the algorithms described in this paper in an open-source software package called fastNeutrino, which stands forfast Ne(effective population size) and mutationrateinference using analyticoptimization. It will be publicly available athttps://sourceforge.net/projects/fastneutrino.
New Product Development in Malaysia: Does Organizational Background Really Matter?
Authors: Kowang Tan Owee , Rasli Amran , Sang Long Choi 
Published: July 2014

New Product Development (NPD) is vital in assisting Research and Development (R&D) based organizations to adapt to the changes in markets and technology for competitive advantage. Ensuring the success of new products and optimization of new product performance is critical and essential for Research and Development based organizations. Hence, this study is carried out to explore does organizational background in term of company’s ownership (i.e. local or multinational companies) and operational scales (i.e. number of Research and Development staffs) affect NPD performance of Research and Development companies in Malaysia. In line with this, 8 New Product Development performance attributes were identified from literature review. These attributes were subsequently formulated into a survey questionnaire and responded by 186 respondents. Thereafter, the effect of organizational ownership and operational scale toward NPD performance are examined separately via Independent Sample t-test and Analysis of Variance (ANOVA). Finding from the study revealed that the level of NPD performance in multinational R&D companies is higher than local R&D companies. Findings from this research also implied that NPD performance can be further improved by increasing number of R&D staffs.
Nehari-Type Ground State Positive Solutions for Superlinear Asymptotically Periodic Schrödinger Equations
Authors: Lin Xiaoyan , Tang X. H. 
Published: June 2014

We deal with the existence of Nehari-type ground state positive solutions for the nonlinear Schrödinger equation-Δu+Vxu=fx, u, x ∈ RN, u ∈ H1 RN. Under a weaker Nehari condition, we establish some existence criteria to guarantee that the above problem has Nehari-type ground state solutions by using a more direct method in two cases: the periodic case and the asymptotically periodic case.
South Korean Cinema’s Postwar Pain: Gender and National Division in Korean War Films from the 1950s to the 2000s
Authors: Martin Daniel 
Published: June 2014

Abstract
For South Korean filmmakers and cinemagoers, the Korean War (1950–53)—and the broader issue of the North/South divide—has been one of the most enduring and appealing subjects. Contemporary films on this topic articulate the tragic dimensions of the national division and suggest that war itself is the true enemy, emphasizing that the conflict still has a meaningful impact on people’s lives. Bombastic blockbusters such as Taegukgi: The Brotherhood of War (T’aekǔkki hwinallimyŏ, 2004) serve as a “prosthetic memory” of the event for younger audiences, while more contemplative and artistic films like Welcome to Dongmakgol (Welk’ŏm t’u Tongmakkol, 2005) present a starkly anti-American ideology, blaming US intervention for shattering any chance at true peace between a divided Korea. Yet, while films about the Korean War have proliferated for sixty years, filmmakers seem even more haunted by the post-Armistice atmosphere of military tension. Both during and after the period when the South Korean government enforced strict censorship and was stridently anticommunist, filmmakers have frequently turned to the figure of the female North Korean spy to represent both the danger and the tragedy of division. This article, therefore, traces the historical development and ideological subtext of Korean War films, and, to a greater extent, the postwar espionage thrillers, focusing, in particular, on the role of gender and filmmaking at two important moments: the immediate postwar period and the revival of South Korean cinema at the turn of the century.
Democratic Transition and Intraparty Politics: The Distribution of Key Party Positions in Democratizing South Korea
Authors: Choi Joon Nak , Kang Myung-koo , Shin Gi-Wook 
Published: June 2014

Abstract
This article examines the changing pattern of key party position assignments in three leader-centric political parties during the democratization of South Korea. We examine the interplay of three key variables: (1) party members’ relationship to the party leader, (2) leaders’ relationships to the party’s core faction, and (3) political seniority, as factors that determine who receives key party positions. More specifically, we focus on the way seniority interacts with factionalism and patrimonialism to affect the assignment of key positions. Our analysis highlights the substantial variation between our focal parties depending on the configuration of these three variables. In contrast with a conventional view that has focused on uniformity in South Korean intraparty politics, we find that a seniority-based institution has emerged for the assignment of key party positions. Our study contributes to an understanding of the interplay of personalistic behaviors and informal rules in intraparty politics and how this interplay contributes to the institutionalization of informal but important institutions governing intraparty politics during democratic consolidation.
Ethical statement in medical research manuscripts: A Necessary step for quality control
Authors: Sathian Brijesh , Banerjee Indrajit , Sreedharan Jayadevan , Roy B , Yadav RJ 
Published: June 2014

Recently there are several budding medical journals which are coming from developing countries and also there is a large number of publishers. It will foster medical research from these countries. Authors will improve the skill of medical writing because of these journals senior, experienced international/ national editorial and review board. Also this team is responsible for the quality of the journal. Journals primary aim should not be making money and get other benefit to the people who are dealing with it. Journals should produce evidence based new information to the medical science which will benefit to the new generation physicians, scientists and readers. There is a tremendous increase in the medical research articles in the recent years because most of the institutions, universities and funding agencies consider the publication history of the scientists for their promotion and incentive. It results with good practice and bad practice of research. There are several scientists and teaching faculty members who publish the articles without proper data or they plagiarise other scientist work. It can be stopped only by the national medical research authorities like Indian Council of Medical Research [India], Nepal Health Research Council [Nepal], etc. for each country level and the Institutional Research and Ethics Committee in the institutional level. DOI: http://dx.doi.org/10.3126/nje.v4i3.10661Nepal Journal of Epidemiology 2014; 4(3):348-50
ZargisCardioscan™ Aided Heart Murmurs Recognition has high negative predictive values when correlated and validated with Echocardiography: A Potential Dawn for Valvular Heart Disease Prevalence Studies in Rural India
Authors: Aggarwal P , Kumar R , Kandpal SD , Gupta D , Rai T 
Published: June 2014

Background The purpose of this open-label study was to correlate the auscultation findings of ZargisCardioscan™ with the echocardiographic findings in our patient population who were referred for echocardiography so as to investigate and ensure the validity of this technology before instituting its applicability in community health events among rural Indian population. Materials and Methods This was a double blinded prospective correlation study in outpatients presenting for echocardiography. Methods: One hundred patients, who had presented for echocardiography at Cardiology Center of an academic university hospital in rural India, were enrolled in this double blinded prospective correlation study. Principal investigator who is a community medicine physician performed the auscultation of patients’ hearts in sitting position. Subsequently, the ZargisCardioscan™ software was used to analyze the heart sounds auscultated by the 3M™ Littmann® Model 3200 stethoscope. Thereafter, the scheduled echocardiography for which the patient had presented to hospital was performed by co-investigator cardiologist who was blinded to the results obtained by the ZargisCardioscan™.Finally, all these data were statistically analyzed by blinded investigator for the presence of correlation between the two modalities. Results The most important finding was the high 90s negative predictive values when the stethoscope-software combination was used for auscultation and analysis of heart murmurs. Additionally, presence of isolated systolic murmurs had higher incidence of appreciable significant valvular lesions and presence of isolated diastolic murmurs primarily had underlying minimal-mild regurgitant valvular lesion, if any. The Bland-Altman Plot confirmed good correlation between stethoscope-echocardiography findings. Conclusion Stethoscope-software combination, 3M™ Littmann® Model 3200 and ZargisCardioscan™, accurately predicts the absence of valvular heart disease on echocardiography.DOI: http://dx.doi.org/10.3126/nje.v4i3.10665 Nepal Journal of Epidemiology 2014; 4(3): 363-369
The Prognostic Role of the Neutrophil-to-Lymphocyte Ratio in Oropharyngeal Carcinoma Treated with Chemoradiotherapy
Authors: Young Caroline A. , Murray Louise J. , Karakaya Ebru , Thygesen Helene H. , Sen Mehmet , Prestwich Robin J. D. 
Published: June 2014

Background The aim of the study is to investigate the prognostic role of pre-treatment of markers of the systemic inflammatory response (neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), and albumin) in patients with oropharyngeal carcinoma treated with chemoradiotherapy. Methods A total of 251 patients with oropharyngeal squamous cell cancer treated with chemoradiotherapy between 2004 and 2010 were retrospectively identified. NLR, PLR, and albumin were recorded from baseline blood parameters. NLR threshold of >5 and PLR thresholds of ≤150, >150 and ≤300, and >300 were used for analysis. Results Median follow-up was 46 months (range 9–98). The 3 year overall survival, local control, regional control, and distant control were 70%, 85%, 87%, and 87%, respectively. On multivariate analysis, locoregional control was associated with T stage (HR 3.3 (95% CI 1.5–6.9), P = 0.002) and NLR (HR 2.1 (95% CI 1.1–3.9), P = 0.023). Overall survival was associated with T stage (HR 2.47 (95% CI 1.45–4.2), P = 0.001) and grade (HR 0.61 (95% CI 0.38–0.99), P = 0.048). PLR and albumin were not significantly associated with disease outcomes or survival. Conclusions The NLR is an independent prognostic factor for locoregional control in oropharyngeal cancer treated with chemoradiotherapy.
SPITFIRE within the MPI Earth system model: Model development and evaluation
Authors: Lasslop Gitta , Thonicke Kirsten , Kloster Silvia 
Published: July 2014

AbstractQuantification of the role of fire within the Earth system requires an adequate representation of fire as a climate‐controlled process within an Earth system model. To be able to address questions on the interaction between fire and the Earth system, we implemented the mechanistic fire model SPITFIRE, in JSBACH, the land surface model of the MPI Earth system model. Here, we document the model implementation as well as model modifications. We evaluate our model results by comparing the simulation to the GFED version 3 satellite‐based data set. In addition, we assess the sensitivity of the model to the meteorological forcing and to the spatial variability of a number of fire relevant model parameters. A first comparison of model results with burned area observations showed a strong correlation of the residuals with wind speed. Further analysis revealed that the response of the fire spread to wind speed was too strong for the application on global scale. Therefore, we developed an improved parametrization to account for this effect. The evaluation of the improved model shows that the model is able to capture the global gradients and the seasonality of burned area. Some areas of model‐data mismatch can be explained by differences in vegetation cover compared to observations. We achieve benchmarking scores comparable to other state‐of‐the‐art fire models. The global total burned area is sensitive to the meteorological forcing. Adjustment of parameters leads to similar model results for both forcing data sets with respect to spatial and seasonal patterns.
Fabrication of Poly(methyl methacrylate) Nanofibers and Polyethylene Nonwoven with Sandwich Structures for Thermal Insulator Application
Authors: Valipour Peiman , Babaahmadi Vahid , Nasouri Komeil 
Published: July 2014

ABSTRACTThe effects of variation in average nanofibers diameter and surface density of nanofibers web on thermal conductivity of poly(methyl methacrylate) (PMMA) nanofibers web are investigated in this paper. With an increase in the concentration of PMMA in the solution from 18 to 26 w/v%, the mean diameter of nanofibers increased from 73 ± 16 to 968 ± 97 nm. The results demonstrate that the use of thinner PMMA nanofibers results in a lower limit of thermal conductivity and better thermal insulation performance that means lower radiative conductivity. It can be related to a higher specific surface of thinner PMMA nanofibers that means more surface area for radiative scatter and absorption lead to lower conductivity. With increasing surface density of PMMA nanofibers web, the thermal conductivity was reduced and water vapor transmission rate and thermal insulation ability were improved. Higher porosity percentage and smaller pore sizes in the web with higher surface density could result in lower thermal conductivity.
The nasoseptal flap for reconstruction of the medial and inferior orbit
Authors: Chhabra Nipun , Healy David Y. , Freitag Suzanne K. , Bleier Benjamin S. 
Published: July 2014

BackgroundEndoscopic endonasal orbital surgery may result in large orbital defects that mandate reconstruction to minimize the risk of diplopia and enophthalmos. The purpose of this study is to determine whether the nasoseptal flap can provide adequate coverage of maximal orbital defects.MethodsThis was an anatomic cadaveric study. Morphometric measurements were completed in 5 cadaveric orbits to determine the dimensions of an orbital defect comprising the entire lamina papyracea and the orbital floor. The dimensions of a planned nasoseptal flap were then calculated and an appropriately sized flap was harvested to verify complete coverage of the defect.ResultsThe mean ± standard deviation (SD) medial orbital defect was a depth of 47.3 mm ± 2.52, height of 13.67 mm ± 2.73, and width of 13.33 mm ± 1.03 for the orbital floor. The mean flap dimensions were a width of 55 ± 6.16 mm, height of 48 ± 4.47 mm, and depth of 70 ± 3.54 mm. In all cases, the harvested flap adequately covered the orbital defect. These dimensions correlated with flap incisions subtending the mucocutaneous junction anteriorly, the inferior meatus laterally, the attachment of the middle turbinate superiorly, and the choanal arch posteriorly.ConclusionEndoscopic orbital approaches may result in large orbital defects with significant orbital fat herniation and extraocular muscle exposure. Immediate vascularized flap reconstruction of the orbit may help to limit the attendant morbidity including diplopia and enophthalmos. This study is the first to demonstrate the feasibility of the nasoseptal flap for the reconstruction of maximal orbital defects.
Bimetallic NiCo Functional Graphene: An Efficient Catalyst for Hydrogen‐Storage Properties of MgH2
Authors: Wang Ying , Liu Guang , An Cuihua , Li Li , Qiu Fangyuan , Wang Yijing , Jiao Lifang , Yuan Huatang 
Published: July 2014

AbstractBimetallic NiCo functional graphene (NiCo/rGO) was synthesized by a facile one‐pot method. During the coreduction process, the as‐synthesized ultrafine NiCo nanoparticles (NPs), with a typical size of 4–6 nm, were uniformly anchored onto the surface of reduced graphene oxide (rGO). The NiCo bimetal‐supported graphene was found to be more efficient than their single metals. Synergetic catalysis of NiCo NPs and rGO was confirmed, which can significantly improve the hydrogen‐storage properties of MgH2. The apparent activation energy (Ea) of the MgH2NiCo/rGO sample decreases to 105 kJ mol−1, which is 40.7 % lower than that of pure MgH2. More importantly, the as‐prepared MgH2NiCo/rGO sample can absorb 5.5 and 6.1 wt % hydrogen within 100 and 350 s, respectively, at 300 °C under 0.9 MPa H2 pressure. Further cyclic kinetics investigation indicates that MgH2NiCo/rGO nanocomposites have excellent cycle stability.
Pyrrolysine‐Inspired Protein Cyclization
Authors: Lee Marianne M. , Fekner Tomasz , Lu Jia , Heater Bradley S. , Behrman Edward J. , Zhang Liwen , Hsu Pang‐Hung , Chan Michael K. 
Published: July 2014

AbstractThe pyrrolysine translational machinery has been extensively explored for the production of recombinant proteins containing a variety of “site‐specific” non‐canonical amino acids for both in vitro and in vivo biochemical studies. In this study, we report the first use of this technology for the production of branched cyclic proteins with a tadpole‐like topology. As a proof of concept, we fused the well‐studied RGD peptide to the C terminus of an mCherry reporter protein. Previous studies have shown that cyclization of the RGD peptide enhances its internalization into cells compared to its linear counterpart. The cellular uptake efficiencies of mCherry‐cyclo(RGD), mCherry‐linear(RGD), and wild‐type mCherry determined by flow cytometry follow the trends expected, thereby confirming the feasibility and potential utility of this cyclization approach.
Structural Insights into Enzymatic Degradation of Oxidized Polyvinyl Alcohol
Authors: Yang Yu , Ko Tzu‐Ping , Liu Long , Li Jianghua , Huang Chun‐Hsiang , Chan Hsiu‐Chien , Ren Feifei , Jia Dongxu , Wang Andrew H.‐J. , Guo Rey‐Ting , Chen Jian , Du Guocheng 
Published: July 2014

AbstractThe ever‐increasing production and use of polyvinyl alcohol (PVA) threaten our environment. Yet PVA can be assimilated by microbes in two steps: oxidation and cleavage. Here we report novel α/β‐hydrolase structures of oxidized PVA hydrolase (OPH) from two known PVA‐degrading organisms, Sphingopyxis sp. 113P3 and Pseudomonas sp. VM15C, including complexes with substrate analogues, acetylacetone and caprylate. The active site is covered by a lid‐like β‐ribbon. Unlike other esterase and amidase, OPH is unique in cleaving the CC bond of β‐diketone, although it has a catalytic triad similar to that of most α/β‐hydrolases. Analysis of the crystal structures suggests a double‐oxyanion‐hole mechanism, previously only found in thiolase cleaving β‐ketoacyl‐CoA. Three mutations in the lid region showed enhanced activity, with potential in industrial applications.