bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative analysis of nonvolatile and volatile metabolites in Lichtheimia ramosa cultivated in different growth media
Authors: Chung Hyun , Lee NaKyeom , Seo Jeong-Ah , Kim Young-Suk 
Published: November 2016

Abstract
Lichtheimia ramosa is one of the predominant filamentous fungi in Korean traditional nuruk. The nonvolatile and volatile metabolites of L. ramosa cultivated in three growth media: complete medium (CM), potato dextrose broth (PDB), and sabouraud dextrose broth (SDB), were investigated and compared. Among nonvolatile metabolites, serine, lysine, and ornithine increased in CM and PDB cultivated with L. ramosa during the exponential phase. In addition, glucose level increased in CM whereas decreased in PDB and SDB. The major volatile metabolites in the extract samples were acetic acid, ethanol, 3-methyl-2-buten-1-ol, 2-phenylethanol, ethylacetate, 2-furaldehyde, 5-(hydroxymethyl)-2-furaldehyde, 2,3-dihydro-3,5,-dihydroxy-6-methyl-4H-pyran-4-one, and α-humulene. In particular, the levels of volatile metabolites related to makgeolli (e.g., acetic acid, ethanol, and ethyl acetate) were highest in extracts cultivated in CM. On the other hand, the level of 2-phenylethanol was relatively higher in PDB and SDB, possibly due to there being more phenylalanine present in the biomass sample in media.
Language choice for science education: policy and practice
Authors: Mifsud Jordan , Farrugia Josette 
Published: November 2016

ABSTRACTThe Maltese National Minimum Curriculum published in 1999 sought to strengthen bilingualism by reinforcing the practice of teaching and assessing some subjects in English and others in Maltese. It also pointed out that code‐switching should only be used in cases of severe pedagogical difficulties. As a new National Curriculum Framework was being prepared some educators suggested language as a possible barrier to student progress and argued that the traditional practice of teaching subjects such as science in English should be reconsidered. This study investigated language choices, function and code‐switching in science lessons. Classroom observations, interviews and focus groups showed that in state schools 12–13 year old students were being taught science predominantly in Maltese while reading, writing and formal assessment were in English. Students who were more exposed to English, irrespective of class stream, used this language more frequently than those who were less exposed to the language. The findings seem to suggest that teachers may be overcautious. While code‐switching may initially provide technical terms and serve as a bridge between the two languages, eventually it can give way to a more precise and formal use of English thus ensuring both learning of science and development of bilingualism.
Linearity of network proximity measures: implications for set-based queries and significance testing
Authors: Maxwell Sean , Chance Mark R , Koyutürk Mehmet 
Published: November 2016

Abstract

Motivation
In recent years, various network proximity measures have been proposed to facilitate the use of biomolecular interaction data in a broad range of applications. These applications include functional annotation, disease gene prioritization, comparative analysis of biological systems and prediction of new interactions. In such applications, a major task is the scoring or ranking of the nodes in the network in terms of their proximity to a given set of ‘seed’ nodes (e.g. a group of proteins that are identified to be associated with a disease, or are deferentially expressed in a certain condition). Many different network proximity measures are utilized for this purpose, and these measures are quite diverse in terms of the benefits they offer.

Results
We propose a unifying framework for characterizing network proximity measures for set-based queries. We observe that many existing measures are linear, in that the proximity of a node to a set of nodes can be represented as an aggregation of its proximity to the individual nodes in the set. Based on this observation, we propose methods for processing of set-based proximity queries that take advantage of sparse local proximity information. In addition, we provide an analytical framework for characterizing the distribution of proximity scores based on reference models that accurately capture the characteristics of the seed set (e.g. degree distribution and biological function). The resulting framework facilitates computation of exact figures for the statistical significance of network proximity scores, enabling assessment of the accuracy of Monte Carlo simulation based estimation methods.

Availability and Implementation
Implementations of the methods in this paper are available at https://bioengine.case.edu/crosstalker which includes a robust visualization for results viewing.

Supplementary information
Supplementary data are available at Bioinformatics online.
Training alignment parameters for arbitrary sequencers with LAST-TRAIN
Authors: Hamada Michiaki , Ono Yukiteru , Asai Kiyoshi , Frith Martin C 
Published: November 2016

Abstract

Summary
LAST-TRAIN improves sequence alignment accuracy by inferring substitution and gap scores that fit the frequencies of substitutions, insertions, and deletions in a given dataset. We have applied it to mapping DNA reads from IonTorrent and PacBio RS, and we show that it reduces reference bias for Oxford Nanopore reads.

Availability and Implementation
the source code is freely available at http://last.cbrc.jp/

Supplementary information
Supplementary data are available at Bioinformatics online.
Exploring the predictive power of polygenic scores derived from genome-wide association studies: a study of 10 complex traits
Authors: So Hon-Cheong , Sham Pak C 
Published: November 2016

Abstract

Motivation
It is hoped that advances in our knowledge in disease genomics will contribute to personalized medicine such as individualized preventive strategies or early diagnoses of diseases. With the growth of genome-wide association studies (GWAS) in the past decade, how far have we reached this goal? In this study we explored the predictive ability of polygenic risk scores (PRSs) derived from GWAS for a range of complex disease and traits.

Results
We first proposed a new approach to evaluate predictive performances of PRS at arbitrary P-value thresholds. The method was based on corrected estimates of effect sizes, accounting for possible false positives and selection bias. This approach requires no distributional assumptions and only requires summary statistics as input. The validity of the approach was verified in simulations. We explored the predictive power of PRS for ten complex traits, including type 2 diabetes (DM), coronary artery disease (CAD), triglycerides, high- and low-density lipoprotein, total cholesterol, schizophrenia (SCZ), bipolar disorder (BD), major depressive disorder and anxiety disorders. We found that the predictive ability of PRS for CAD and DM were modest (best AUC = 0.608 and 0.607) while for lipid traits the prediction R-squared ranged from 16.1 to 29.8%. For psychiatric disorders, the predictive power for SCZ was estimated to be the highest (best AUC 0.820), followed by BD. Predictive performance of other psychiatric disorders ranged from 0.543 to 0.585. Psychiatric traits tend to have more gradual rise in AUC when significance thresholds increase and achieve the best predictive power at higher P-values than cardiometabolic traits.

Supplementary information
Supplementary data are available at Bioinformatics online.
Analysis of the mechanism of radiation-induced upregulation of mitochondrial abundance in mouse fibroblasts
Authors: Yamamori Tohru , Sasagawa Tomoya , Ichii Osamu , Hiyoshi Mie , Bo Tomoki , Yasui Hironobu , Kon Yasuhiro , Inanami Osamu 
Published: November 2016

AbstractMitochondria strongly contribute to the maintenance of cellular integrity through various mechanisms, including oxidative adenosine triphosphate production and calcium homeostasis regulation. Therefore, proper regulation of the abundance, distribution and activity of mitochondria is crucial for the maintenance of cellular homeostasis. Previous studies have shown that ionizing radiation (IR) alters mitochondrial functions, suggesting that mitochondria are likely to be an important target of IR. Though IR reportedly influences cellular mitochondrial abundance, the mechanism remains largely unknown. In this study, we examined how IR influences mitochondrial abundance in mouse fibroblasts. When mouse NIH/3T3 cells were exposed to X-rays, a time-dependent increase was observed in mitochondrial DNA (mtDNA) and mitochondrial mass, indicating radiation-induced upregulation of mitochondrial abundance. Meanwhile, not only did we not observe a significant change in autophagic activity after irradiation, but in addition, IR hardly influenced the expression of two mitochondrial proteins, cytochrome c oxidase subunit IV and cytochrome c, or the mRNA expression of Polg, a component of DNA polymerase γ. We also observed that the expression of transcription factors involved in mitochondrial biogenesis was only marginally affected by IR. These data imply that radiation-induced upregulation of mitochondrial abundance is an event independent of macroautophagy and mitochondrial biogenesis. Furthermore, we found evidence that IR induced long-term cell cycle arrest and cellular senescence, indicating that these events are involved in regulating mitochondrial abundance. Considering the growing significance of mitochondria in cellular radioresponses, we believe the present study provides novel insights into understanding the effects of IR on mitochondria.
Cosmological N-body simulations including radiation perturbations
Authors: Brandbyge Jacob , Rampf Cornelius , Tram Thomas , Leclercq Florent , Fidler Christian , Hannestad Steen 
Published: November 2016

Abstract
Cosmological N-body simulations are the standard tools to study the emergence of the observed large-scale structure of the Universe. Such simulations usually solve for the gravitational dynamics of matter within the Newtonian approximation, thus discarding general relativistic effects such as the coupling between matter and radiation (≡ photons and neutrinos). In this Letter, we investigate novel hybrid simulations that incorporate interactions between radiation and matter to the leading order in General Relativity, whilst evolving the matter dynamics in full non-linearity according to Newtonian theory. Our hybrid simulations come with a relativistic space–time and make it possible to investigate structure formation in a unified framework. In this work, we focus on simulations initialized at z = 99 and show that the extracted matter power spectrum receives up to 3 per cent corrections on very large scales through radiation. Our numerical findings compare favourably with linear analytical results from Fidler et al., from which we deduce that there cannot be any significant non-linear mode-coupling induced through linear radiation corrections.
Feasibility of Implementing a Hospital-Based “Opt-Out” Tobacco-Cessation Service
Authors: Nahhas Georges J , Wilson Dianne , Talbot Vince , Cartmell Kathleen B , Warren Graham W , Toll Benjamin A , Carpenter Matthew J , Cummings K Michael 
Published: November 2016

Abstract

Objective
To assess the feasibility and outcomes of implementing a hospital-based “opt-out” tobacco-cessation service.

Methods
In 2014, the Medical University of South Carolina adopted a policy that all hospitalized patients who self-report using tobacco be referred to tobacco-cessation service. This is a descriptive study of a real-world effort to implement guidelines for a hospital-based cessation service consistent with Joint Commission’s standards. Between February 2014 and May 2015, 42 061 adults were admitted to the Medical University of South Carolina Hospital. Eligible current cigarette smokers were referred to the tobacco-cessation service, which consisted of a bedside consult and phone follow-up 3, 14, and 30 days after hospital discharge using interactive-voice-response. The primary study outcomes evaluated the proportions of smokers reached by the bedside counselor and/or phone follow-up, smokers who opted out, and smokers who self-reported not smoking when last contacted by phone.

Results
Records identified 8423 smokers, of whom 69.4% (n = 5843) were referred into the service. One full-time bedside counselor was able to speak with 1918 (32.8%) patients, of whom 96 (5%) denied currently smoking and 287 (14.9%) refused counselling. Reach at follow-up was achieved for 703 (55%) smokers who received bedside counselling and 1613 (49%) who did not, yielding an overall follow-up reach rate of 60%. Of those reached by phone, 36.4% reported not smoking (51% vs. 27% for those who did and did not receive bedside counselling, respectively). Intent-to-treat abstinence rate was 13.5% according to the last known smoking status.

Conclusions
Findings from this study suggest that an inpatient smoking-cessation service with an “opt-out” approach can positively impact short-term cessation outcomes.

Implications
(1)The findings demonstrate the feasibility of implementing an automated large-scale opt-out tobacco-cessation service for hospitalized patients that is consistent with the Joint Commission recommended standards for treating tobacco dependence. (2) Receiving a bedside tobacco-cessation consult while hospitalized increased the use of stop smoking medications and abstinence from smoking after discharge from the hospital. (3) Even in those patients who did not receive a bedside consult, 5% accepted a referral to the South Carolina Tobacco Quitline to get help to stop smoking.
Immunological Patterns from Four Melioidosis Cases: Constant and Variable Protein Antigens
Authors: Yi Jinhee , Herring Kelsey , Sanchez Timothy C. , Iyer Srinivas , Stone Joshua K. , Lee Judy , Mayo Mark , Currie Bart J. , Tuanyok Apichai , Keim Paul 
Published: November 2016

AbstractBurkholderia pseudomallei is the causative agent of the melioidosis and is endemic to Southeast Asia and northern Australia. There is no available vaccine and accurate diagnosis is difficult, time-consuming and labor intensive. Early diagnosis is an important part of successful treatment and current serological tests are inadequate and based upon multiple antigens. Identifying specific immunogenic proteins which are highly seroreactive may yield potential diagnostic targets for detecting antibodies and antigens specific to melioidosis. We have used 2D gel electrophoresis and Western blotting analysis to analyze protein antigenicity of whole cell lysates extracted from four B. pseudomallei strains and the sera from the specific infected humans. We found a total of 135 immunogenic proteins, 62 of which we were able to identify to a specific gene by mass-spectrometry. Results from the Western blotting of each strain’s proteins and the corresponding patient serum reveal between 30 – 40% serum x strain specific immunogenic proteins. In most cases, these differences exist despite the fact that the genes encoding these proteins were present among all four B. pseudomallei strains. Eight particular proteins were immunogenic in all four strain x serum combinations and could represent novel diagnostic and vaccine subunit targets.
Simulations ofCYP51AfromAspergillus fumigatusin a model bilayer provide insights into triazole drug resistance
Authors: Nash Anthony , Rhodes Johanna 
Published: November 2016

1AbstractAzole antifungal drugs targetCYP51AinAspergillus fumigatusby binding with the active site of the protein, blocking ergosterol biosynthesis. Resistance to azole anti-fungal drugs is now common, with a leucine to histidine amino acid substitution at position 98 the most frequent, conferring resistance to itraconazole. In this study, we create a homology model ofCYP51Ausing a recently published crystal structure of the paralog proteinCYP51B. The derived structures, wild-type and L98H mutant, are positioned within a lipid membrane bilayer and subjected to molecular dynamics simulations in order improve the accuracy of both models. The structural analysis from our simulations suggests a decrease in active site surface from the formation of hydrogen bonds between the histidine substitution and neighbouring polar side chains, potentially preventing the binding of azole drugs. This study yields a biologically relevant structure and set dynamics of theA. fumigatusLanosterol 14 alpha-demethylase enzyme and provides further insight into azole antifungal drug resistance.
Floral Radiometry: A Biophysical Basis to Characterize Landscapes
Authors: Jaishanker R. , Sooraj N.P. , Somasekheran Pillai M. , Athira K. , Joseph Ammini , Krishna Aswathy , Indu I , SarojKumar V 
Published: November 2016

AbstractThis paper presents early results on studies of floral spectral reflectance of angiosperms and introduces floral radiometry as an emergent dimension of ecological research in India. Floral spectral reflectance of 121 angiosperm species was measured using hand-held spectroradiometer. The authors describe spectral reflectance of seven representative species within 350-800 nanometer region of the electromagnetic spectrum. Characteristic absorption and reflection of flowers, in ultraviolet and visible regions of the spectrum is reported. Near infrared reflectance was consistently high for all species studied. Flower color is unique to a species and importance of understanding flower color from pollinator’s perspective is highlighted.
Engineered tRNA suppression of a CFTR nonsense mutation
Authors: Lueck John D. , Infield Daniel T. , Mackey Adam L. , Pope R. Marshall , McCray Paul B. , Ahern Christopher A. 
Published: November 2016

AbstractTen percent of human diseases are caused by ‘nonsense’ mutations that lead to premature truncation of the protein reading frame. Small molecules that promote read-through of such PTC have significant clinical promise but current iterations suffer from lowin vivoefficacy and the nonselective amino acid incorporation. Alternatively, while gene-modifying approaches, such as CRISPR/Cas9, represent a long-term solution, such treatments may be far from reaching the clinical setting. Building on previous work by our group and others, we describe a tRNA engineering approach that enables the conversion of an in frame nonsense stop mutation to the naturally occurring amino acid, thus rescuing the full-length wild type protein. Data is presented demonstrating the functionality of the approach with the rescue of CFTR W1282X, a human mutation that causes cystic fibrosis (CF). The stringency of the approach is confirmed by mass spectrometry in a model protein indicating the encoding of only tryptophan at the TGA suppression site. The data describe the first use of an edited tRNA to repair a CF causative mutation and serve a proof of principle for the eventual use of codon-edited tRNA for the therapeutic rescue of PTC disease codons.
Life-cycle information management using open-standard BIM
Authors: Hoeber Hans , Alsem Daan 
Published: November 2016

Purpose
The purpose of this paper is to present a way of working with open-standard building information modeling (BIM), object type libraries, systems engineering and an Information Delivery Manual for the management of information over the life-cycle of infrastructure assets. The concept is presented as a source of inspiration, proof of concept and to underpin the value of different parts of the concept leading to an integrated approach to life-cycle information management.

Design/methodology/approach
The paper presents a concept for a way of working. A proof of concept is provided in the form of a case study in which this concept is operational. It shows that this way of working using open-standard BIM can be applied to manage information in the life-cycle. It does not provide, nor suggest to provide, empirical evidence for specific benefits in terms of efficiency.

Findings
The paper shows that open-standard BIM can be applied for information management in the life-cycle of (construction) assets. The specific approach that is applied in practice in a Dutch Infrastructure Project is explained including a case project.

Research limitations/implications
The example of Traverse Dieren attests to a implementation of the approach in practice. From this case it can be concluded that the suggested approach is feasible in the initiation and design phase and applicable during realization. Based on the example as described in this paper it cannot be concluded to what extent the known information management problems in the life-cycle are solved. Therefore a detailed evaluation on the information exchange would be required which is beyond the scope of this paper.

Practical implications
This paper shows how different (theoretical) concepts are successfully combined and implemented in practice to attain the defined BIM goals.

Originality/value
This paper shows a practical case implementation of open-standard BIM (using COINS). It provides a way of working that combines BIM, systems engineering, libraries and contractual arrangements for the management of information over the life-cycle of infrastructure assets.
Fog computing architectures for healthcare
Authors: Prieto González Lisardo , Jaedicke Corvin , Schubert Johannes , Stantchev Vladimir 
Published: November 2016

Purpose
The purpose of this study is to analyze how embedding of self-powered wireless sensors into cloud computing further enables such a system to become a sustainable part of work environment.

Design/methodology/approach
This is exemplified by an application scenario in healthcare that was developed in the context of the OpSIT project in Germany. A clearly outlined three-layer architecture, in the sense of Internet of Things, is presented. It provides the basis for integrating a broad range of sensors into smart healthcare infrastructure. More specifically, by making use of short-range communication sensors (sensing layer), gateways which implement data transmission and low-level computation (fog layer) and cloud computing for processing the data (application layer).

Findings
A technical in-depth analysis of the first two layers of the infrastructure is given to prove reliability and to determine the communication quality and availability in real-world scenarios. Furthermore, two example use-cases that directly apply to a healthcare environment are examined, concluding with the feasibility of the presented approach.

Practical implications
Finally, the next research steps, oriented towards the semantic tagging and classification of data received from sensors, and the usage of advanced artificial intelligence-based algorithms on this information to produce useful knowledge, are described together with the derived social benefits.

Originality/value
The work presents an innovative, extensible and scalable system, proven to be useful in healthcare environments.