bluuebunny/crossref_metadata_2025_split huggingface dataset:
Privacy preserving protocol for detecting genetic relatives using rare variants
Authors: Hormozdiari Farhad , Joo Jong Wha J , Wadia Akshay , Guan Feng , Ostrosky Rafail , Sahai Amit , Eskin Eleazar 
Published: June 2014

Abstract
Motivation: High-throughput sequencing technologies have impacted many areas of genetic research. One such area is the identification of relatives from genetic data. The standard approach for the identification of genetic relatives collects the genomic data of all individuals and stores it in a database. Then, each pair of individuals is compared to detect the set of genetic relatives, and the matched individuals are informed. The main drawback of this approach is the requirement of sharing your genetic data with a trusted third party to perform the relatedness test.
Results: In this work, we propose a secure protocol to detect the genetic relatives from sequencing data while not exposing any information about their genomes. We assume that individuals have access to their genome sequences but do not want to share their genomes with anyone else. Unlike previous approaches, our approach uses both common and rare variants which provide the ability to detect much more distant relationships securely. We use a simulated data generated from the 1000 genomes data and illustrate that we can easily detect up to fifth degree cousins which was not possible using the existing methods. We also show in the 1000 genomes data with cryptic relationships that our method can detect these individuals.
Availability: The software is freely available for download at http://genetics.cs.ucla.edu/crypto/.
Contact: fhormoz@cs.ucla.edu or eeskin@cs.ucla.edu
Supplementary information: Supplementary data are available at Bioinformatics online
LICRE: unsupervised feature correlation reduction for lipidomics
Authors: Wong Gerard , Chan Jeffrey , Kingwell Bronwyn A. , Leckie Christopher , Meikle Peter J. 
Published: June 2014

AbstractMotivation: Recent advances in high-throughput lipid profiling by liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) have made it possible to quantify hundreds of individual molecular lipid species (e.g. fatty acyls, glycerolipids, glycerophospholipids, sphingolipids) in a single experimental run for hundreds of samples. This enables the lipidome of large cohorts of subjects to be profiled to identify lipid biomarkers significantly associated with disease risk, progression and treatment response. Clinically, these lipid biomarkers can be used to construct classification models for the purpose of disease screening or diagnosis. However, the inclusion of a large number of highly correlated biomarkers within a model may reduce classification performance, unnecessarily inflate associated costs of a diagnosis or a screen and reduce the feasibility of clinical translation. An unsupervised feature reduction approach can reduce feature redundancy in lipidomic biomarkers by limiting the number of highly correlated lipids while retaining informative features to achieve good classification performance for various clinical outcomes. Good predictive models based on a reduced number of biomarkers are also more cost effective and feasible from a clinical translation perspective.Results: The application of LICRE to various lipidomic datasets in diabetes and cardiovascular disease demonstrated superior discrimination in terms of the area under the receiver operator characteristic curve while using fewer lipid markers when predicting various clinical outcomes.Availability and implementation: The MATLAB implementation of LICRE is available from https://sites.google.com/site/licrerepository/Contact: gerard.wong@bakeridi.edu.au or gerard.wong@unimelb.edu.auSupplementary information: Supplementary data are available at Bioinformatics online.
Cloud4Psi: cloud computing for 3D protein structure similarity searching
Authors: Mrozek Dariusz , Małysiak-Mrozek Bożena , Kłapciński Artur 
Published: June 2014

AbstractSummary: Popular methods for 3D protein structure similarity searching, especially those that generate high-quality alignments such as Combinatorial Extension (CE) and Flexible structure Alignment by Chaining Aligned fragment pairs allowing Twists (FATCAT) are still time consuming. As a consequence, performing similarity searching against large repositories of structural data requires increased computational resources that are not always available. Cloud computing provides huge amounts of computational power that can be provisioned on a pay-as-you-go basis. We have developed the cloud-based system that allows scaling of the similarity searching process vertically and horizontally. Cloud4Psi (Cloud for Protein Similarity) was tested in the Microsoft Azure cloud environment and provided good, almost linearly proportional acceleration when scaled out onto many computational units.Availability and implementation: Cloud4Psi is available as Software as a Service for testing purposes at: http://cloud4psi.cloudapp.net/ . For source code and software availability, please visit the Cloud4Psi project home page at http://zti.polsl.pl/dmrozek/science/cloud4psi.htm .Contact: dariusz.mrozek@polsl.pl
The Scramble conversion tool
Authors: Bonfield James K. 
Published: June 2014

AbstractMotivation: The reference CRAM file format implementation is in Java. We present ‘Scramble’: a new C implementation of SAM, BAM and CRAM file I/O.Results: The C implementation of for CRAM is 1.5–1.7× slower than BAM at decoding but 1.8–2.6× faster at encoding. We see file size savings of 34–55%.Availability and implementation: Source code is available at http://sourceforge.net/projects/staden/files/io_lib/ under the BSD software licence.Contact: jkb@sanger.ac.ukSupplementary information : Supplementary data are available at Bioinformatics online.
Multiple populations in globular clusters and the origin of the Oosterhoff period groups
Authors: Jang Sohee , Lee Young-Wook , Joo Seok-Joo , Na Chongsam 
Published: June 2014

Abstract
The presence of multiple populations is now well established in most globular clusters in the Milky Way. In light of this, here we propose a new model to explain the origin of the Sandage period-shift and the difference in mean period of type ab RR Lyrae variables between the two Oosterhoff groups. In our model, the instability strip in the metal-poor group II clusters, such as M15, is populated by second-generation stars (G2) with enhanced helium and CNO abundances, while the RR Lyraes in the relatively metal-rich group I clusters such as M3 are produced mostly by first-generation stars (G1) without these enhancements. This population shift within the instability strip with metallicity can create the observed period-shift between the two groups, as both helium and CNO abundances play a role in increasing the period of RR Lyraes. The presence of more metal-rich clusters having Oosterhoff-intermediate characteristics, such as NGC 1851, as well as of most metal-rich clusters having RR Lyraes with the longest periods (group III) can also be reproduced, as more helium-rich third and later generations of stars (G3) penetrate into the instability strip with a further increase in metallicity. Therefore, although there are systems in which the suggested population shift cannot be a viable explanation, for the most general cases our models predict that the RR Lyraes are produced mostly by G1, G2 and G3 for the Oosterhoff groups I, II and III, respectively.
Mitochondrial DNA variation and structure among North American populations ofMegaselia scalaris
Authors: Lesavoy Bret S. , McGaugh Suzanne E. , Noor Mohamed A. F. 
Published: June 2014

AbstractThe scuttle flyMegaselia scalarisis a pest species whose larvae consume living or dead plant or animal tissue, and parasitize humans. Although known to exist on most continents, often transported passively with humans, the connectivity between populations has not been investigated. We use mitochondrialcytochrome Bsequences to investigate structure among North American isolates of this species. Despite small sample sizes, we detected statistically significant structure among populations. This finding suggests that local measures may be effective in controlling this pest species.
Evaluation ofde novotranscriptome assemblies from RNA-Seq data
Authors: Li Bo , Fillmore Nathanael , Bai Yongsheng , Collins Mike , Thomson James A. , Stewart Ron , Dewey Colin N. 
Published: June 2014

AbstractDe novoRNA-Seq assembly facilitates the study of transcriptomes for species without sequenced genomes, but it is challenging to select the most accurate assembly in this context. To address this challenge, we developed a model-based score, RSEM-EVAL, for evaluating assemblies when the ground truth is unknown. Our experiments show that RSEM-EVAL correctly reflects assembly accuracy, as measured by REF-EVAL, a refined set of ground-truth-based scores that we also developed. With the guidance of RSEM-EVAL, we assembled the transcriptome of the regenerating axolotl limb; this assembly compares favorably to a previous assembly.
Value and store brand identification in food products
Authors: Rubio Natalia , Villaseñor Nieves , Oubiña Javier 
Published: June 2014

Purpose
– Store brands have become consolidated in the food market and are currently considered real brands. The purpose of this paper is to determine the factors that contribute to consumers’ identification with store brands, as well as the possible effect of consumers’ identification with store brands on their loyalty to the retail establishment.

Design/methodology/approach
– The paper achieves its goal by reviewing the academic literature on the topic and proposing and validating a theoretical model for consumer-store brand identification. The theoretical model is validated through an empirical study of the Spanish market for food products using data gathered from individuals responsible for shopping for their homes who claim to have purchased store brand food products at least once. Structural equations modeling is then used to estimate and perform a multigroup analysis for heavy and light buyers of store brands.

Findings
– The results obtained reveal, first, that consumers’ store brand identification mediates the relationship between their value consciousness and their loyalty to the retail establishment that manages a broad, competitive portfolio of store brands. Second, the study demonstrates the effect of other variables, such as perceived risk associated with the purchase of store brands, their perceived value and consumer satisfaction. Finally, the results show important differences between heavy and light buyers of store brands.

Research limitations/implications
– The main limitations of this research derive from the factors conditioning the information. Store brand value was analyzed on an aggregate level, for the Spanish food products market. Future research should include other store brands (e.g. premium store brands), control for store brands with different labels and expand the area of application to new product categories and new countries.

Practical implications
– The results obtained have interesting implications for food retailers. These implications concern the management of value store brands in the product portfolio to achieve loyalty to the retail establishment among value-conscious consumers (who constitute the main target of value store brands).

Originality/value
– This paper analyzes consumer brand identification in an area that has not been studied to date: store brands. It contributes interesting and very useful findings for retailers who commercialize these brands in their establishments. The line of research on brand identification is quite new in academic research and has arisen due to the importance for companies of constructing close, lasting connections with the consumer.
Nutritional characteristics of mung bean foods
Authors: Kumar Dahiya Pradeep , Nout M.J.R. , A. van Boekel Martinus , Khetarpaul Neelam , Bala Grewal Raj , Linnemann Anita 
Published: June 2014

Purpose
– The purpose of this paper is to address malnourishment in developing countries by a food-based approach in which locally produced and consumed foods are improved by applying food processing techniques that benefit the amount and availability of desirable nutrients.

Design/methodology/approach
– To facilitate this approach, this paper reports on the composition and in vitro micronutrient accessibility of 14 traditional mung bean foods from India in relation to their preparation methods.

Findings
– Proximate composition, in vitro mineral accessibility, phytic acid and polyphenol contents varied among the range of products. Products requiring either fermentation or germination, had higher in vitro iron, zinc and calcium accessibility. Average in vitro iron, zinc and calcium accessibility of the mung bean products were 16, 9 and 418 mg kg−1 dry weight. Phytic acid and polyphenols averaged 2.1 and 1.8 g kg−1 dry weight, respectively, and were negatively correlated with in vitro mineral accessibility.

Practical implications
– Different mung bean products (100 g) cover 12.0-59.5, 5.2-45.6, 4.2-28.6 and 1.1-7.1 per cent of the recommended dietary allowance for protein, iron, zinc and calcium, respectively, for seven- to nine-year-old Indian children.

Originality/value
– This study demonstrated the wide range of traditional mung bean foods in India and presents options to tackle malnourishment by a food-based approach.
Food and culture: in search of a Singapore cuisine
Authors: Catherine Henderson Joan 
Published: June 2014

Purpose– The purpose of this paper is to illuminate aspects of the relationship between food and culture with particular emphasis on globalisation and its consequences, the ways in which food can represent people and places, and interest if food heritage. Issues are discussed within the context of Singapore.Design/methodology/approach– A case study methodology is employed using published information from assorted sources, both online and in conventional print form, supplemented by personal observation.Findings– A country's food culture is found to be influenced by globalising forces, yet these do not always overwhelm local distinctions and the international and domestic can co-exist and coalesce. Food is also shown to be a critical dimension of ethnic and national identity and to have a heritage worthy of protection. In addition, it is a tourist attraction which affords insights into destination culture. Defining a national cuisine, however, is complicated in multiracial societies and origins and ownership of so-called national dishes may be disputed.Practical implications– Enhanced knowledge about the wider role of food in established and emerging Asian economies and societies can improve understanding of its significance for residents and tourists, helping in formulating strategies to meet needs.Originality/value– New insights are offered into the meanings of food in relatively young countries of mixed races and how cuisines evolve and interact.
The implementation of an environmental management system in the not-for-profit sector
Authors: R.T. White Gareth , Lomax Matthew , Parry Glenn 
Published: June 2014

Purpose
– This paper aims to examine the implementation of the Eco-Management and Audit Scheme (EMAS) in a non-profit, small-to-medium sized-enterprise (SME) in the UK.

Design/methodology/approach
– A four-year participatory action research study is made upon knowledge transfer partnerships between the University of the West of England and the Royal Bath and West Society.

Findings
– Through the adoption of EMAS, the organisation was able to identify operational improvements as well as make significant efforts to improve its environmental performance, reducing its carbon footprint by 30 tCO2e per annum and gaining new business.

Research limitations/implications
– The study is made upon a single not-for-profit organisation in the UK.

Practical implications
– It presents the costs, benefits and challenges that the organisation faced. Techniques that were used to successfully manage the environmental management systems (EMS) development are also discussed. The investigation identifies deficiencies in the materials that are provided to support companies that are seeking EMAS certification. To improve the uptake of these EMS and assist companies in their successful pursuit of ISO 14001 and EMAS, this supporting documentation requires enhancement.

Originality/value
– There has been relatively little empirical research around the development and benefits of organisational EMS. Even less has focussed upon the specific constraints and opportunities that face non-profit organisations when implementing EMAS. This paper addresses this gap, identifying its costs and tangible benefits.
IFRS and convergence in China and the USA
Authors: Moser Randy 
Published: June 2014

Purpose– The purpose of this paper is to perform a brief examination of International Financial Reporting Standards (IFRS) and the progress towards IFRS convergence in the accounting environments of China and the USA, providing useful information on the current status and future of IFRS convergence in these countries.Design/methodology/approach– A range of IFRS-related literature from 1993 to 2013 was analyzed to provide the current status of IFRS and to determine the past, present and future of IFRS convergence in the country examinations.Findings– IFRS convergence and adoption has occurred on a global scale due to the call for a single set of standards. China's most significant obstacles include training accounting professionals and becoming more involved in the International Accounting Standards Board (IASB) standard setting process. The USA's most significant obstacle is completing the Securities and Exchange Commission roadmap milestones, which will progressively move the accounting industry towards IFRS convergence.Research limitations/implications– These findings have been limited to an overview of IFRS convergence and adoption within China and the USA. Additional research opportunities exist by examining how successful countries have been in protecting individual economic interests by working with the IASB in the standard setting process for the IFRS, as opposed to being passive in the process. One economic indicator that should be examined is foreign direct investment, which has major impacts on country development and can be influenced by financial standards such as IFRS.Practical implications– China and the USA both have milestones identified in this paper that will need to be reached before benefits may be reaped from the converging to IFRS.Originality/value– These findings show that IFRS standards are being implemented globally in many nations, providing a common set of reporting tools to businesses and investors. Through these standards, China and the USA are working to be even more competitive forces in financial markets.
Internal multiple attenuation by Kirchhoff extrapolation
Authors: Lipari Vincenzo , Fortini Carlo , Spadavecchia Emmanuel , Bienati Nicola 
Published: June 2014

ABSTRACTSurface‐related multiple elimination is the leading methodology for surface multiple removal. This data‐driven approach can be extended to interbed multiple prediction at the expense of a huge increase of the computational burden. This cost makes model‐driven methods still attractive, especially for the three dimensional case. In this paper we present a methodology that extends Kirchhoff wavefield extrapolation to interbed multiple prediction. In Kirchhoff wavefield extrapolation for surface multiple prediction a single round trip to an interpreted reflector is added to the recorded data. Here we show that interbed multiples generated between two interpreted reflectors can be predicted by applying the Kirchhoff wavefield extrapolation operator twice. In the first extrapolation step Kirchhoff wavefield extrapolation propagates the data backward in time to simulate a round trip to the shallower reflector. In the second extrapolation step Kirchhoff wavefield extrapolation propagates the data forward in time to simulate a round trip to the deeper reflector. In the Kirchhoff extrapolation kernel we use asymptotic Green's functions. The prediction of multiples via Kirchhoff wavefield extrapolation is possibly sped up by computing the required traveltimes via a shifted hyperbola approximation. The effectiveness of the method is demonstrated by results on both synthetic and field data sets.
Relationship between growth and standard metabolic rate: measurement artefacts and implications for habitat use and life‐history adaptation in salmonids
Authors: Rosenfeld Jordan , Van Leeuwen Travis , Richards Jeffrey , Allen David 
Published: June 2014

Summary

Mass‐specific standard metabolic rate (SMR, or maintenance metabolism) varies greatly among individuals. Metabolism is particularly sensitive to variation in food consumption and growth creating the potential for significant bias in measured SMR for animals that are growing (e.g. juveniles) or of uncertain nutritional status.

Consequently, interpreting individual variation in metabolism requires a sound understanding of the potentially confounding role of growth and the relative importance of fixed (genetic) vs. environmental drivers of SMR variation.

We review the role of growth in measured SMR variation in juvenile salmonids, with the goals of (i) understanding the contribution of growth (and food consumption) to SMR variation through ontogeny, (ii) understanding the relative contributions of tissue maintenance and biosynthesis (overhead costs of growth) to apparent SMR variation, and (iii) using intrinsic growth effects on SMR to model how alternate life‐history strategies may influence growth and measured SMR in juvenile salmonids.

SMR measures on juveniles, even when post‐absorptive, may be inflated by delayed growth‐associated overhead costs, unless juveniles are on a maintenance ration (i.e. not growing). Empirical measurements of apparent SMR in food restricted vs. satiated 2–5 g juvenile salmon demonstrate that estimates may be inflated by as much as 67% due to delayed overhead costs of growth, even when SMR measurements are taken 35 h post‐feeding.

These results indicate that a substantial component of variation in apparent SMR among juvenile salmonids may be associated with (i) environmentally driven variation in ration (where elevated SMR measurements are an artefact of delayed growth overhead costs), (ii) intrinsic (genetic) or plastic organ‐system trade‐offs related to increasing investment in metabolically expensive digestive tissue responsible for processing food and (iii) intrinsic (genetic) variation in maximum body size and growth among individuals or life‐history types. We suggest that selection for differences in adult body size among resident and anadromous forms leading to differences in juvenile growth trajectories may contribute to both SMR variation and habitat segregation in freshwater, where juveniles with higher growth are constrained to foraging in high velocity habitats to meet their greater consumption needs.