bluuebunny/crossref_metadata_2025_split huggingface dataset:
A focus group consultation round exploring patient experiences of comfort during radiotherapy for head and neck cancer
Authors: Goldsworthy Simon D. , Tuke Kelly , Latour Jos M. 
Published: March 2016

AbstractPurposeThe aim of this study was to consult patients about their experiences of comfort while wearing a thermoplastic mask during head and neck radiotherapy before designing a study to develop a comfort scale for radiotherapy.MethodsA qualitative method using a focus group of patients receiving radiotherapy for head and neck cancer was deployed. Five patients were invited and agreed to participate. Semi-structured questions guided the focus group interview. Thematic analysis was used to identify themes.FindingsThree patients participated in the focus group. Three main themes were identified: Physical comfort, Mental perception, Passivity. Physical comfort derived from feelings of pressure, unpleasantness, and generally being uncomfortable. Mental perception derived from how the physical comfort was perceived and derived from feelings of shock, anxiety, indifference and sensory systems. Passivity arose from feelings such as the ‘doctor knows best’, ‘putting up with it’, and ‘being taken for a ride’.ConclusionThe insight of patient’s comfort and experiences are valuable for clinicians to provide patient-centred care. Findings of this study implicate further investigation of how the themes of patient comfort can be measured in radiotherapy to improve the patient experience.
Capturing the most wanted taxa through cross-sample correlations
Authors: Almeida Mathieu , Pop Mihai , Le Chatelier Emmanuelle , Prifti Edi , Pons Nicolas , Ghozlane Amine , Ehrlich S Dusko 
Published: March 2016

Abstract
The Human Microbiome Project (HMP) identified the 16S rRNA gene sequences of ‘most wanted’ taxa—prevalent in the healthy human microbiota but distant from previously known sequences. Since 2012, few of the corresponding genomes have been isolated and sequenced, and only through advanced isolation techniques. We demonstrate that the genomes of the most wanted taxa can be identified computationally through their correlation in abundance across multiple public metagenomic data sets. We link over 200 most wanted sequences with nearly complete genome sequences, including half of the taxa identified as high-priority targets by the HMP. The genomes we identify have strong similarity to genomes reconstructed through expensive isolation techniques, and provide a more complete functional characterization of these organisms than can be extrapolated from their 16S rRNA gene. We also provide insights into the function of organisms for which 16S rRNA gene signatures were recently reported to be associated with health and host genetic factors.
Commensurate antiferromagnetic excitations as a signature of the pseudogap in the tetragonal high-Tc cuprate HgBa2CuO4+δ
Authors: Chan M. K. , Dorow C. J. , Mangin-Thro L. , Tang Y. , Ge Y. , Veit M. J. , Yu G. , Zhao X. , Christianson A. D. , Park J. T. , Sidis Y. , Steffens P. , Abernathy D. L. , Bourges P. , Greven M. 
Published: March 2016

AbstractAntiferromagnetic correlations have been argued to be the cause of the d-wave superconductivity and the pseudogap phenomena exhibited by the cuprates. Although the antiferromagnetic response in the pseudogap state has been reported for a number of compounds, there exists no information for structurally simple HgBa2CuO4+δ. Here we report neutron-scattering results for HgBa2CuO4+δ (superconducting transition temperature Tc≈71 K, pseudogap temperature T*≈305 K) that demonstrate the absence of the two most prominent features of the magnetic excitation spectrum of the cuprates: the X-shaped ‘hourglass’ response and the resonance mode in the superconducting state. Instead, the response is Y-shaped, gapped and significantly enhanced below T*, and hence a prominent signature of the pseudogap state.
An Evaluation of Active Learning Causal Discovery Methods for Reverse-Engineering Local Causal Pathways of Gene Regulation
Authors: Ma Sisi , Kemmeren Patrick , Aliferis Constantin F. , Statnikov Alexander 
Published: March 2016

AbstractReverse-engineering of causal pathways that implicate diseases and vital cellular functions is a fundamental problem in biomedicine. Discovery of the local causal pathway of a target variable (that consists of its direct causes and direct effects) is essential for effective intervention and can facilitate accurate diagnosis and prognosis. Recent research has provided several active learning methods that can leverage passively observed high-throughput data to draft causal pathways and then refine the inferred relations with a limited number of experiments. The current study provides a comprehensive evaluation of the performance of active learning methods for local causal pathway discovery in real biological data. Specifically, 54 active learning methods/variants from 3 families of algorithms were applied for local causal pathways reconstruction of gene regulation for 5 transcription factors inS. cerevisiae. Four aspects of the methods’ performance were assessed, including adjacency discovery quality, edge orientation accuracy, complete pathway discovery quality, and experimental cost. The results of this study show that some methods provide significant performance benefits over others and therefore should be routinely used for local causal pathway discovery tasks. This study also demonstrates the feasibility of local causal pathway reconstruction in real biological systems with significant quality and low experimental cost.
Self-Locking Optoelectronic Tweezers for Single-Cell and Microparticle Manipulation across a Large Area in High Conductivity Media
Authors: Yang Yajia , Mao Yufei , Shin Kyeong-Sik , Chui Chi On , Chiou Pei-Yu 
Published: March 2016

AbstractOptoelectronic tweezers (OET) has advanced within the past decade to become a promising tool for cell and microparticle manipulation. Its incompatibility with high conductivity media and limited throughput remain two major technical challenges. Here a novel manipulation concept and corresponding platform called Self-Locking Optoelectronic Tweezers (SLOT) are proposed and demonstrated to tackle these challenges concurrently. The SLOT platform comprises a periodic array of optically tunable phototransistor traps above which randomly dispersed single cells and microparticles are self-aligned to and retained without light illumination. Light beam illumination on a phototransistor turns off the trap and releases the trapped cell, which is then transported downstream via a background flow. The cell trapping and releasing functions in SLOT are decoupled, which is a unique feature that enables SLOT’s stepper-mode function to overcome the small field-of-view issue that all prior OET technologies encountered in manipulation with single-cell resolution across a large area. Massively parallel trapping of more than 100,000 microparticles has been demonstrated in high conductivity media. Even larger scale trapping and manipulation can be achieved by linearly scaling up the number of phototransistors and device area. Cells after manipulation on the SLOT platform maintain high cell viability and normal multi-day divisibility.
Microwave dielectric characterisation of 3D-printed BaTiO3/ABS polymer composites
Authors: Castles F. , Isakov D. , Lui A. , Lei Q. , Dancer C. E. J. , Wang Y. , Janurudin J. M. , Speller S. C. , Grovenor C. R. M. , Grant P. S. 
Published: March 2016

Abstract3D printing is used extensively in product prototyping and continues to emerge as a viable option for the direct manufacture of final parts. It is known that dielectric materials with relatively high real permittivity—which are required in important technology sectors such as electronics and communications—may be 3D printed using a variety of techniques. Among these, the fused deposition of polymer composites is particularly straightforward but the range of dielectric permittivities available through commercial feedstock materials is limited. Here we report on the fabrication of a series of composites composed of various loadings of BaTiO3microparticles in the polymer acrylonitrile butadiene styrene (ABS), which may be used with a commercial desktop 3D printer to produce printed parts containing user-defined regions with high permittivity. The microwave dielectric properties of printed parts with BaTiO3loadings up to 70 wt% were characterised using a 15 GHz split post dielectric resonator and had real relative permittivities in the range 2.6–8.7 and loss tangents in the range 0.005–0.027. Permittivities were reproducible over the entire process and matched those of bulk unprinted materials, to within ~1%, suggesting that the technique may be employed as a viable manufacturing process for dielectric composites.
MiR-630 Inhibits Endothelial-Mesenchymal Transition by Targeting Slug in Traumatic Heterotopic Ossification
Authors: Sun Yangbai , Cai Jiangyu , Yu Shiyang , Chen Shuai , Li Fengfeng , Fan Cunyi 
Published: March 2016

AbstractHeterotopic ossification (HO) is the abnormal formation of mature bone in extraskeletal soft tissues that occurs as a result of inflammation caused by traumatic injury or associated with genetic mutation. Despite extensive research to identify the source of osteogenic progenitors, the cellular origins of HO are controversial and the underlying mechanisms, which are important for the early detection of HO, remain unclear. Here, we used in vitro and in vivo models of BMP4 and TGF-β2-induced HO to identify the cellular origin and the mechanisms mediating the formation of ectopic bone in traumatic HO. Our results suggest an endothelial origin of ectopic bone in early phase of traumatic HO and indicate that the inhibition of endothelial-mesenchymal transition by miR-630 targeting Slug plays a role in the formation of ectopic bone in HO. A matched case-control study showed that miR-630 is specifically downregulated during the early stages of HO and can be used to distinguish HO from other processes leading to bone formation. Our findings suggest a potential mechanism of post-traumatic ectopic bone formation and identify miR-630 as a potential early indicator of HO.
High‐speed quantum cascade laser at room temperature
Authors: Zhou Yu Hong , Zhai Shen Qiang , Liu Junqi , Liu Fengqi , Zhang Jinchuan , Zhuo Ning , Wang Lijun , Wang Zhanguo 
Published: March 2016

Room‐temperature, high‐speed quantum cascade lasers at 4.7 μm are presented. An output power of 115 mW and threshold current of 230 mA are obtained for the lasers working in continuous‐wave mode. Reliable single‐mode emission with a side‐mode suppression ratio more than 30 dB is observed. Using microwave rectification technology, a flat frequency response up to roughly 3 GHz for the laser operating at 10°C is demonstrated.
Proteome analysis of Pueraria mirifica tubers collected in different seasons
Authors: Jungsukcharoen Jutarmas , Chokchaichamnankit Daranee , Srisomsap Chantragan , Cherdshewasart Wichai , Sangvanich Polkit 
Published: March 2016

Abstract
Pueraria mirifica-derived tuberous powder has been long-term consumed in Thailand as female hormone-replacement traditional remedies. The protein profiles of tubers collected in different seasons were evaluated. Phenol extraction, 2D-PAGE, and mass spectrometry were employed for tuberous proteome analysis. Out of the 322 proteins detected, over 59% were functionally classified as being involved in metabolism. The rest proteins were involved in defense, protein synthesis, cell structure, transportation, stress, storage, and also unidentified function. The proteins were found to be differentially expressed with respect to harvest season. Importantly, chalcone isomerase, isoflavone synthase, cytochrome p450, UDP-glycosyltransferase, and isoflavone reductase, which are all involved in the biosynthesis pathway of bioactive isoflavonoids, were most abundantly expressed in the summer-collected tubers. This is the first report on the proteomic patterns in P. mirifica tubers in relevant with seasonal variation. The study enlights the understanding of variance isoflavonoid production in P. mirifica tubers.
Efficient privacy-preserving string search and an application in genomics
Authors: Shimizu Kana , Nuida Koji , Rätsch Gunnar 
Published: March 2016

Abstract
Motivation: Personal genomes carry inherent privacy risks and protecting privacy poses major social and technological challenges. We consider the case where a user searches for genetic information (e.g. an allele) on a server that stores a large genomic database and aims to receive allele-associated information. The user would like to keep the query and result private and the server the database.
Approach: We propose a novel approach that combines efficient string data structures such as the Burrows–Wheeler transform with cryptographic techniques based on additive homomorphic encryption. We assume that the sequence data is searchable in efficient iterative query operations over a large indexed dictionary, for instance, from large genome collections and employing the (positional) Burrows–Wheeler transform. We use a technique called oblivious transfer that is based on additive homomorphic encryption to conceal the sequence query and the genomic region of interest in positional queries.
Results: We designed and implemented an efficient algorithm for searching sequences of SNPs in large genome databases. During search, the user can only identify the longest match while the server does not learn which sequence of SNPs the user queried. In an experiment based on 2184 aligned haploid genomes from the 1000 Genomes Project, our algorithm was able to perform typical queries within ≈ 4.6 s and ≈ 10.8 s for client and server side, respectively, on laptop computers. The presented algorithm is at least one order of magnitude faster than an exhaustive baseline algorithm.
Availability and implementation: https://github.com/iskana/PBWT-sec and https://github.com/ratschlab/PBWT-sec.
Contacts: shimizu-kana@aist.go.jp or Gunnar.Ratsch@ratschlab.org
Supplementary information: Supplementary data are available at Bioinformatics online.
Genotyping Allelic and Copy Number Variation in the Immunoglobulin Heavy Chain Locus
Authors: Luo Shishi , Yu Jane A. , Song Yun S. 
Published: March 2016

AbstractThe study of genomic regions that contain gene copies and structural variation is a major challenge in modern genomics. Unlike variation involving single nucleotide changes, data on the variation of copy number is difficult to collect and few tools exist for analyzing the variation between individuals. The immunoglobulin heavy variable (IGHV) locus, which plays an integral role in the adaptive immune response, is an example of a genomic region that is known to vary in gene copy number. Lack of standard methods to genotype this region prevents it from being included in association studies and is holding back the growing field of antibody repertoire analysis. Here, we establish a convention of representing the locus in terms of a reference panel of operationally distinguishable segments defined by hierarchical clustering. Using this reference set, we develop a pipeline that identifies copy number and allelic variation in the IGHV locus from whole-genome sequencing reads. Tests on simulated reads demonstrate that our approach is feasible and accurate for detecting the presence and absence of gene segments using reads as short as 70 bp. With reads 100 bp and longer, coverage depth can also be used to determine copy number. When applied to a family of European ancestry, our method finds new copy number variants and confirms existing variants. This study paves the way for analyzing population-level patterns of variation in the IGHV locus in larger diverse datasets and for quantitatively handling regions of copy number variation in other structurally varying and complex loci.
Simple and easy-operated method for filtering eco-friendly corrosion inhibitors
Authors: Yang Na , Liao Qin , Li Qing , Zhang Peng , Li Longqin 
Published: March 2016

Purpose
– The purpose of this paper was to find a simple and easy-operated method for filtering eco-friendly corrosion inhibitors.

Design/methodology/approach
– The molecular structures and atomic electronegativities of the four kinds of natural reagents, iota-Carrageenan, sodium alginate, sodium dodecanesulphonate (SDS) and sodium dodecylbenzene sulfonate were calculated by Gaussian and Natural Bond Orbital, and the corrosion inhibition rates were forecasted by the calculated results. Then, the realistic corrosion inhibition efficiency were confirmed by electrochemical impedance spectroscopy and potentiodynamic polarization tests in 3.5 Wt.% sodium chloride corrosive solutions. At the same time, the function of pefloxacin mesylate (PM) was explored in this paper polarization tests in 3.5 Wt.% sodium chloride corrosive solutions.

Findings
– Results showed that the order calculated by the chemical software was correct, and the corrosion inhibition of SDS was the best. Optimum addition of PM not only can reduce microbial corrosion but also can improve the corrosion inhibition by spatial cooperation.

Practical implications
– This method can be used to filter eco-friendly corrosion inhibitors quickly. PM can be also used to improve the corrosion inhibition rate of corrosion inhibitors.

Originality/value
– The present method to filter corrosion inhibitors was time-consuming, which needed lots of experiments to verify the corrosion inhibitive efficiency. The calculated method was simpler than others, which need complicated calculation process.
The concept of Datenherrschaft of patient information from a Lockean perspective
Authors: Koskinen Jani Simo Sakari , Kainu Ville Matti Antero , Kimppa Kai Kristian 
Published: March 2016

Purpose
– The purpose of this paper is to analyse the current status of ownership of patient information from a Lockean perspective and then present Datenherrschaft (German for “mastery over information”) as a new model for patient ownership of patient information.

Design/methodology/approach
– This paper is theoretical in approach. It is based on arguments derived from Locke’s Two Treatises of Government. Legal examples of the current situation are derived from Finnish, UK and Swedish legislation.

Findings
– Current legislation concerning patient information is not clearly formulated and so recognising a new right on the part of the patient, Datenherrschaft, would be an ethically justifiable way of remedying the issue.

Research limitations/implications
– The legal analysis was limited to Finland, the UK and Sweden, and so other legislation should be looked at in future research. Datenherrschaft is used as an example of an ethically justified way of regulating patient information ownership and should be analysed further.

Originality/value
– Patient information ownership is an issue that is not unambiguously solved in many countries, nor has it, in our view, been ethically justified. The potential solution presented in this paper is clear and has strong ethical justifications.
Making it clear and relevant: patients and carers add value to studies through research document reviews
Authors: Staley Kristina , Ashcroft Joanne , Doughty Lisa , Szmukler George 
Published: March 2016

Purpose
– The National Institute of Health Research MHRN established the Feasibility and Support to Timely recruitment for Research (FAST-R) service in 2011, to provide rapid patient and carer feedback on research documents, prior to ethical review. The aims were to improve the feasibility of studies, to speed up regulatory processes and enhance study set up and completion. The purpose of this paper is to explore whether and how the FAST-R service benefits the review process.

Design/methodology/approach
– An independent evaluator analysed the comments made by FAST-R members on 85 studies over the past 3.5 years. The evaluation team reflected on the nature of these comments and the implications for future practice.

Findings
– The FAST-R members’ comments fell into seven categories relating to: the quality of the information, the informed consent process, care and protection of participants, practical arrangements for participants, data protection and confidentiality, recruitment and research design. Based on the evaluation team’s experience of research document review, some of these comments were similar to those made by ethics committees. In other cases, the FAST-R Panel provided a different kind of input by identifying concerns specific to service users and carers.

Practical implications
– Patient/carer involvement in reviewing research documents brings added benefits to existing processes because their views are informed by their knowledge and experience. They are able to question assumptions and highlight concerns that people lacking their perspective might otherwise miss. These findings suggest that patient/carer involvement should form an integral part of ethical review, and that the FAST-R model might be usefully applied to other areas of health and social care research.

Originality/value
– This original work adds value to the practice of patient and public involvement in research.
Genome Sequence of a
Mycoplasma meleagridis
Field Strain
Authors: Rocha Ticiana S. , Bertolotti Luigi , Catania Salvatore , Pourquier Philippe , Rosati Sergio 
Published: March 2016

ABSTRACT

Mycoplasma meleagridis
is a major cause of disease and economic loss in turkeys. Here, we report the genome sequence of an
M. meleagridis
field strain, which enlarges the knowledge about this bacterium and helps the identification of possible coding sequences for drug resistance genes and specific antigens.
Complete Genome Sequence of
Pseudomonas syringae
pv. lapsa Strain ATCC 10859, Isolated from Infected Wheat
Authors: Kong Jun , Jiang Hongshan , Li Baiyun , Zhao Wenjun , Li Zhihong , Zhu Shuifang 
Published: March 2016

ABSTRACT

Pseudomonas syringae
pv. lapsa is a pathovar of
Pseudomonas syringae
that can infect wheat. The complete genome of
P. syringae
pv. lapsa strain ATCC 10859 contains a 5,918,899-bp circular chromosome with 4,973 coding sequences, 16 rRNAs, 69 tRNAs, and an average GC content of 59.13%. The analysis of this genome revealed several gene clusters that are related to pathogenesis and virulence.
Draft Genome Sequence of a Strictly Anaerobic Dichloromethane-Degrading Bacterium
Authors: Kleindienst Sara , Higgins Steven A. , Tsementzi Despina , Konstantinidis Konstantinos T. , Mack E. Erin , Löffler Frank E. 
Published: March 2016

ABSTRACTAn anaerobic, dichloromethane-degrading bacterium affiliated with novelPeptococcaceaewas maintained in a microbial consortium. The organism originated from pristine freshwater sediment collected from Rio Mameyes in Luquillo, Puerto Rico, in October 2009 (latitude 18°21′43.9″, longitude −65°46′8.4″). The draft genome sequence is 2.1 Mb and has a G+C content of 43.5%.
Complete Genome Sequence of Bovine Polyomavirus Type 1 from Aborted Cattle, Isolated in Belgium in 2014
Authors: Van Borm Steven , Rosseel Toon , Behaeghel Isabelle , Saulmont Marc , Delooz Laurent , Petitjean Thierry , Mathijs Elisabeth , Vandenbussche Frank 
Published: March 2016

ABSTRACT
The complete and fully annotated genome sequence of a bovine polyomavirus type 1 (BPyV/BEL/1/2014) from aborted cattle was assembled from a metagenomics data set. The 4,697-bp circular dsDNA genome contains 6 protein-coding genes. Bovine polyomavirus is unlikely to be causally related to the abortion cases.