bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time-variant clustering model for understanding cell fate decisions
Authors: Huang Wei , Cao Xiaoyi , Biase Fernando H. , Yu Pengfei , Zhong Sheng 
Published: October 2014

SignificanceClustering, in essence, was a tool for describing spatial characteristics in the objects of concern. However, from social to biological studies, researchers’ interests in temporal characteristics often rival their interests in spatial features. Previous efforts to incorporate time information into clustering primarily relied on coding the time information into similarity metrics, thus reducing the problem into the classical paradigm of spatial clustering. The limitation is that the clustering outcomes are often time invariant. Here, we initiate a class of statistical methods that simultaneously infer spatial and temporal groupings. Such methods explicitly model the time dependencies of clustering indices over time. Our method inferred three genes to be associated with the earliest cell fate decision, which was corroborated by experimental validations.
Effect of the replacement of aspartic acid/glutamic acid residues with asparagine/glutamine residues in RNase He1 from Hericium erinaceus on inhibition of human leukemia cell line proliferation
Authors: Kobayashi Hiroko , Motoyoshi Naomi , Itagaki Tadashi , Suzuki Mamoru , Inokuchi Norio 
Published: October 2014

Abstract
RNase He1 from Hericium erinaceus, a member of the RNase T1 family, has high identity with RNase Po1 from Pleurotus ostreatus with complete conservation of the catalytic sequence. However, the optimal pH for RNase He1 activity is lower than that of RNase Po1, and the enzyme shows little inhibition of human tumor cell proliferation. Hence, to investigate the potential antitumor activity of recombinant RNase He1 and to possibly enhance its optimum pH, we generated RNase He1 mutants by replacing 12 Asn/Gln residues with Asp/Glu residues; the amino acid sequence of RNase Po1 was taken as reference. These mutants were then expressed in Escherichia coli. Using site-directed mutagenesis, we successfully modified the optimal pH for enzyme activity and generated a recombinant RNase He1 that inhibited the proliferation of cells in the human leukemia cell line. These properties are extremely important in the production of anticancer biologics that are based on RNase activity.
Probiotics supplementation for athletes – Clinical and physiological effects
Authors: Pyne David B. , West Nicholas P. , Cox Amanda J. , Cripps Allan W. 
Published: October 2014

AbstractProbiotic supplementation has traditionally focused on gut health. However, in recent years, the clinical applications of probiotics have broadened to allergic, metabolic, inflammatory, gastrointestinal and respiratory conditions. Gastrointestinal health is important for regulating adaptation to exercise and physical activity. Symptoms such as nausea, bloating, cramping, pain, diarrhoea and bleeding occur in some athletes, particularly during prolonged exhaustive events. Several studies conducted since 2006 examining probiotic supplementation in athletes or highly active individuals indicate modest clinical benefits in terms of reduced frequency, severity and/or duration of respiratory and gastrointestinal illness. The likely mechanisms of action for probiotics include direct interaction with the gut microbiota, interaction with the mucosal immune system and immune signalling to a variety of organs and systems. Practical issues to consider include medical and dietary screening of athletes, sourcing of recommended probiotics and formulations, dose–response requirements for different probiotic strains, storage, handling and transport of supplements and timing of supplementation in relation to travel and competition.
Electrokinetic particle separation in a single-spiral microchannel
Authors: DuBose John , Zhu Junjie , Patel Saurin , Lu Xinyu , Tupper Nathaniel , Stonaker John M , Xuan Xiangchun 
Published: October 2014

AbstractThe efficient separation of discrete particle species is a topic of interest in numerous research fields for its practical application to problems encountered in both academia and industry. We have recently developed an electrokinetic technique that exploits the curvature-induced dielectrophoresis (C-iDEP) to continuously sort particles by inherent properties in asymmetric double-spiral microchannels. Herein we demonstrate that a single-spiral microchannel is also sufficient for a continuous-flow sheathless electrokinetic particle separation. This method relies on C-iDEP to focus particles to a tight stream and the wall-induced electric lift to manipulate the aligned particles to size-dependent equilibrium positions, both of which happen simultaneously inside the spiral. A theoretical model is developed to understand this size-based separation, which has been implemented for both a binary mixture and a ternary mixture of colloidal particles. The obtained analytical formulae predict with a close agreement both the experimentally measured particle center–wall distance and the necessary electric field for a complete particle focusing in the spiral.
FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data
Authors: Hoogstrate Youri , Jenster Guido , Martens-Uzunova Elena S. 
Published: October 2014

Motivation: Recent discoveries show that most types of small non-coding RNAs (sncRNAs) such as miRNAs, snoRNAs and tRNAs get further processed into putatively active smaller RNA species. Their roles, genetic profiles and underlying processing mechanisms are only partially understood. To find their quantities and characteristics, a proper annotation is essential. Here, we present FlaiMapper, a method that extracts and annotates the locations of sncRNA-derived RNAs (sncdRNAs). These sncdRNAs are often detected in sequencing data and observed as fragments of their precursor sncRNA. Using small RNA-seq read alignments, FlaiMapper is able to annotate fragments primarily by peak detection on the start and end position densities followed by filtering and a reconstruction process.
Results: To assess performance of FlaiMapper, we used independent publicly available small RNA-seq data. We were able to detect fragments representing putative sncdRNAs from nearly all types of sncRNA, including 97.8% of the annotated miRNAs in miRBase that have supporting reads. Comparison of FlaiMapper-predicted boundaries of miRNAs with miRBase entries demonstrated that 89% of the start and 54% of the end positions are identical. Additional benchmarking showed that FlaiMapper is superior in performance compared with existing software. Further analysis indicated a variety of characteristics in the fragments, including sequence motifs and relations with RNA interacting factors. These characteristics set a good basis for further research on sncdRNAs.
Availability and implementation: The platform independent GPL licensed Python 2.7 code is available at: https://github.com/yhoogstrate/flaimapper. Corresponding Linux-specific scripts and annotations can be found in the same repository.
Contact: e.martens@erasmusmc.nl
Supplementary information: Supplementary Data are available at Bioinformatics online.
Context similarity scoring improves protein sequence alignments in the midnight zone
Authors: Meier Armin , Söding Johannes 
Published: October 2014

Motivation: High-quality protein sequence alignments are essential for a number of downstream applications such as template-based protein structure prediction. In addition to the similarity score between sequence profile columns, many current profile–profile alignment tools use extra terms that compare 1D-structural properties such as secondary structure and solvent accessibility, which are predicted from short profile windows around each sequence position. Such scores add non-redundant information by evaluating the conservation of local patterns of hydrophobicity and other amino acid properties and thus exploiting correlations between profile columns.Results: Here, instead of predicting and comparing known 1D properties, we follow an agnostic approach. We learn in an unsupervised fashion a set of maximally conserved patterns represented by 13-residue sequence profiles, without the need to know the cause of the conservation of these patterns. We use a maximum likelihood approach to train a set of 32 such profiles that can best represent patterns conserved within pairs of remotely homologs, structurally aligned training profiles. We include the new context score into our Hmm-Hmm alignment tool hhsearch and improve especially the quality of difficult alignments significantly.Conclusion: The context similarity score improves the quality of homology models and other methods that depend on accurate pairwise alignments.Contact: soeding@mpibpc.mpg.deSupplementary information: Supplementary Data are available at Bioinformatics online.
Waggawagga: comparative visualization of coiled-coil predictions and detection of stable single α-helices (SAH domains)
Authors: Simm Dominic , Hatje Klas , Kollmar Martin 
Published: October 2014

Summary: Waggawagga is a web-based tool for the comparative visualization of coiled-coil predictions and the detection of stable single α-helices (SAH domains). Overview schemes show the predicted coiled-coil regions found in the query sequence and provide sliders, which can be used to select segments for detailed helical wheel and helical net views. A window-based score has been developed to predict SAH domains. Export to several bitmap and vector graphics formats is supported.
Availability and implementation: http://waggawagga.motorprotein.de
Contact: mako@nmr.mpibpc.mpg.de
MACOED: a multi-objective ant colony optimization algorithm for SNP epistasis detection in genome-wide association studies
Authors: Jing Peng-Jie , Shen Hong-Bin 
Published: October 2014

Motivation: The existing methods for genetic-interaction detection in genome-wide association studies are designed from different paradigms, and their performances vary considerably for different disease models. One important reason for this variability is that their construction is based on a single-correlation model between SNPs and disease. Due to potential model preference and disease complexity, a single-objective method will therefore not work well in general, resulting in low power and a high false-positive rate.
Method: In this work, we present a multi-objective heuristic optimization methodology named MACOED for detecting genetic interactions. In MACOED, we combine both logistical regression and Bayesian network methods, which are from opposing schools of statistics. The combination of these two evaluation objectives proved to be complementary, resulting in higher power with a lower false-positive rate than observed for optimizing either objective independently. To solve the space and time complexity for high-dimension problems, a memory-based multi-objective ant colony optimization algorithm is designed in MACOED that is able to retain non-dominated solutions found in past iterations.
Results: We compared MACOED with other recent algorithms using both simulated and real datasets. The experimental results demonstrate that our method outperforms others in both detection power and computational feasibility for large datasets.
Availability and implementation: Codes and datasets are available at: www.csbio.sjtu.edu.cn/bioinf/MACOED/.
Contact: hbshen@sjtu.edu.cn
Supplementary information: Supplementary Data are available at Bioinformatics online.
A theoretical justification for single molecule peptide sequencing
Authors: Swaminathan Jagannath , Boulgakov Alexander A. , Marcotte Edward M. 
Published: October 2014

ABSTRACTThe proteomes of cells, tissues, and organisms reflect active cellular processes and change continuously in response to intracellular and extracellular cues. Deep, quantitative profiling of the proteome, especially if combined with mRNA and metabolite measurements, should provide an unprecedented view of cell state, better revealing functions and interactions of cell components. Molecular diagnostics and biomarker should benefit particularly from the accurate quantification of proteomes, since complex diseases like cancer change protein abundances and modifications. Currently, shotgun mass spectrometry is the primary technology for high-throughput protein identification and quantification; while powerful, it lacks high sensitivity and coverage. We draw parallels with next-generation DNA sequencing and propose a strategy, termed fluorosequencing, for sequencing peptides in a complex protein sample at the level of single molecules. In the proposed approach, millions of individual fluorescently labeled peptides are visualized in parallel, monitoring changing patterns of fluorescence intensity as N-terminal amino acids are sequentially removed, and using the resulting fluorescence signatures (fluorosequences) to uniquely identify individual peptides. We introduce a theoretical foundation for fluorosequencing, and by using Monte Carlo computer simulations, we explore its feasibility, anticipate the most likely experimental errors, quantify their potential impact, and discuss the broad potential utility offered by a high-throughput peptide sequencing technology.AUTHOR SUMMARYThe development of next-generation DNA and RNA sequencing methods has transformed biology, with current platforms generating >1 billion sequencing reads per run. Unfortunately, no method of similar scale and throughput exists to identify and quantify specific proteins in complex mixtures, representing a critical bottleneck in many biochemical and molecular diagnostic assays. What is urgently needed is a massively parallel method, akin to next-gen DNA sequencing, for identifying and quantifying peptides or proteins in a sample. In principle, single-molecule peptide sequencing could achieve this goal, allowing billions of distinct peptides to be sequenced in parallel and thereby identifying proteins composing the sample and digitally quantifying them by direct counting of peptides. Here, we discuss theoretical considerations of single molecule peptide sequencing, suggest one possible experimental strategy, and, using computer simulations, characterize the potential utility and unusual properties of this future proteomics technology.
Planning for relocation in recovery after the Great East Japan Earthquake
Authors: Maly Elizabeth , Ishikawa Eiko 
Published: October 2014

Purpose
– This paper aims to consider the current situation of relocation in Japan after the 2011 Great East Japan Earthquake (GEJE) in the context of past examples and post-disaster housing relocation projects in other countries.

Design/methodology/approach
– Information about international cases of post-disaster housing relocation was gathered though desk and literature review, supplemented by field visits to the sites for direct observation and interviews with people involved in the relocation projects.

Findings
– To be successful, residential relocation must consider livelihood, especially in regards to location. Involvement of the residents in the planning and decision making process creates housing relocation projects that better meet residents’ needs. Japan faces some unique challenges, yet shares commonalities with other countries, for example, in tsunami-stricken fishing areas. Housing relocation in Tohoku must strive to be accountable to the needs of the residents and the specific contexts of their communities.

Originality/value
– There is still a limited amount of literature in English that considers the issues of relocation in recovery after the GEJE in an international context, especially comprehensive comparisons with multiple countries. Although this paper does not deal with each international case in great detail, the comparison provides a good overview of the key issues for residents in post-disaster relocation, and suggests how lessons from international cases could be applied to the challenges that Japan currently faces in relocation planning in the Tohoku region.
Eliciting experts’ knowledge in emergency response organizations
Authors: Okechukwu Okoli Justin , Weller Gordon , Watt John 
Published: October 2014

Purpose
– Experienced fire ground commanders are known to make decisions in time-pressured and dynamic environments. The purpose of this paper is to report some of the tacit knowledge and skills expert firefighters use in performing complex fire ground tasks.

Design/methodology/approach
– This study utilized a structured knowledge elicitation tool, known as the critical decision method (CDM), to elicit expert knowledge. Totally, 17 experienced firefighters were interviewed in-depth using a semi-structured CDM interview protocol. The CDM protocol was analysed using the emergent themes analysis approach.

Findings
– Findings from the CDM protocol reveal both the salient cues sought, which the authors termed critical cue inventory (CCI), and the goals pursued by the fire ground commanders at each decision point. The CCI is categorized into five classes based on the type of information each cue generates to the incident commanders.

Practical implications
– Since the CDM is a useful tool for identifying training needs, this study discussed the practical implications for transferring experts’ knowledge to novice firefighters.

Originality/value
– Although many authors recognize that experts perform exceptionally well in their domains of practice, the difficulty still lies in getting a structured method for unmasking experts’ tacit knowledge. This paper is therefore relevant as it presents useful findings following a naturalistic knowledge elicitation study that was conducted across different fire stations in the UK and Nigeria.
Educating the chartered surveyor: looking back to look forward
Authors: de Silva Carrie 
Published: October 2014

Purpose
– The purpose of this paper is to consider perennial issues in the education of chartered surveyors and to use the debates and experiences of the past to inform the present and future, particularly the question of the balance between academic and practical training.

Design/methodology/approach
– Primary and secondary sources were used to establish a history of the growth of the profession and the development of formal education and assessment from the 19th century and to consider current issues with reference to wider theories of education.

Findings
– The profession grew from vocational roots and did not enjoy the centuries of status of, say, the law. The 19th century saw an increasing technicalisation and professionalisation of surveying, with developments in various strands of the discipline, from the rural land agents to construction and public housing specialists. The muted reception from the universities in recognising the discipline is instructive. Looking at the relationship between classroom education and apprenticeship and what is needed in the preliminary education and assessment of surveyors holds contemporary lessons as increasing university fees has prompted renewed review of the most economical ways of training, while maintaining rigour.

Originality/value
– There have been histories of surveying and of the Royal Institution of Chartered Surveyors, but this paper relates the past to the present. Its value is in highlighting the tension between the practical and academic, allowing current debates to benefit from earlier discussions and longitudinal experience of different models of education. This paves the way for a wider consideration of experiential learning theory to be applied to a fundamental review of surveying education.
Compulsory mediation: civil justice, human rights and proportionality
Authors: Sidoli del Ceno Julian 
Published: October 2014

Purpose– This purpose of this paper is to critically examine jurisprudentially the current judicial and academic scepticism that exists in some quarters with regard to compulsory mediation primarily from the context of England and Wales. In doing so, it seeks to respond to well-articulated and established concerns with regard to any compulsion in mediation as outlined by Hazel Genn among others as well as some senior members of the judiciary.Design/methodology/approach– This paper seeks to critically examine jurisprudentially the current judicial and academic scepticism that exists in some quarters with regard to compulsory mediation primarily from the context of England and Wales. In doing so, it seeks to respond to well-articulated and established concerns with regard to any compulsion in mediation as outlined by Hazel Genn among others as well as some senior members of the judiciary.Findings– This paper argues that the worries concerning compulsory mediation are unnecessary as they are based on a narrow reading of Article 6 rights, one not shared by many European lawyers, in particular the view taken by them with regards to proportionality. It further argues that compulsory mediation can be an appropriate, proportionate method of dispute resolution in some cases recognising that mediation is not a barper seto subsequent litigation.Originality/value– Mediation is an important topic in contemporary law. The theoretical and jurisprudential aspects of mediation have as yet been underdeveloped. This paper is a contribution to this developing debate.
What's in a WordTM? When one electronic document format standard is not enough
Authors: Magee Liam , A. Thom James 
Published: October 2014

Purpose– The purpose of this paper is to examine the history of the standardisation of two largely overlapping electronic document formats between 2005 and 2008, and its implications for future IT standards development.Design/methodology/approach– The document format controversy is researched as an exemplary case study of the institutional rivalries, perspectives and strategic interests at play in standardisation processes. The study adopts a methodological lens of discursive institutionalism in order to explain how actors assume and perform a variety of roles during the controversy. It consults a range of documentary sources, including media commentary, corporate press releases and blog posts, financial reports and technical specifications.Findings– The study shows that: first, intentions to increase competition in the office software market through the standardisation of document formats led to a standards “arms race”; second, this further entrenched the position of a single market actor; and third, the resulting public debate nevertheless has reinvigorated the push for genuinely open standards.Social implications– Information technology standards are often touted as mechanisms for increasing the competitiveness of a market, thereby benefitting consumers and the greater public. In the presence of dominant institutional actors, efforts to standardise can, perversely, undermine this benefit. Increased public scrutiny through online media offers a potential remedy.Originality/value– This research presents a novel account of the controversy over the document format standardisation process, understood through the lens of discursive institutionalism. It also shows the increasing and potentially putative role of online media in the development of IT standards generally.