bluuebunny/crossref_metadata_2025 huggingface dataset:
Reproduction of French angelfish Pomacanthus paru (Teleostei: Pomacanthidae) and implications for management of the ornamental fish trade in Brazil
Authors: Feitosa Caroline Vieira , Marques Simone , de Araújo Maria Elisabeth , Ferreira Beatrice Padovani
Published: August 2015

Pomacanthus paru is one of the five most exported species in the Brazilian aquarium trade and is frequently caught by traps as bycatch. The present study is the first to describe the reproductive biology of this species in the South Atlantic. The population of P. paru was gonochoristic and presented size dimorphism in the larger classes, with males attaining larger sizes than females. Differences in sex ratios for size classes were recorded over the range 35–45-cm total length. At the spawning stage females were more abundant than males, suggesting that spawning females may be more vulnerable to trap fishing during this period. The size at maturity was 23.30-cm total length for females. Males and females of P. paru at the spawning and spent stages were observed nearly every month. The susceptibility of this species to trap fishing indicates that management of the aquarium trade through quotas of juvenile captures alone may be not effective. Thus, management measures should focus on controlling the amount harvested by monitoring current catch rates and should consider implementing trap-free areas in important spawning grounds.
A commentary on 'Long-term ecological trends of flow-dependent ecosystems in a major regulated river basin', by Matthew J. Colloff, Peter Caley, Neil Saintilan, Carmel A. Pollino and Neville D. Crossman
Authors: Kingsford Richard T. , Mac Nally Ralph , King Alison , Walker Keith F. , Bino Gilad , Thompson Ross , Wassens Skye , Humphries Paul
Published: August 2015

Colloff et al. in Marine and Freshwater Research (http:dx.doi.org/10.1071/MF14067) examined time-series data for flow-dependent vegetation, invertebrates, fish, frogs, reptiles and waterbirds in the Murray–Darling Basin, 1905–2013. They concluded that temporal patterns fluctuated, declining during droughts and recovering after floods. They suggested that major changes in land use in the late 19th century permanently modified these freshwater ecosystems, irretrievably degrading them before major water diversions. Restoring water to the environment might then be interpreted as not addressing biotic declines. We argue that their conclusions are inadequately supported, although data quality remains patchy and they neglected the influence of hydrology and the timing and extent of water resource development. We are critical of the lack of adequate model specification and the omission of statistical power analyses. We show that declines of native flow-dependent flora and fauna have continued through the 20th and early 21st centuries, in response to multiple factors, including long-term changes in flow regimes. We argue that flow-regime changes have been critical, but not in isolation. So, returning water to the environment is a prerequisite for sustained recovery but governments need to improve monitoring and analyses to adequately determine effectiveness of management of the rivers and wetlands of the Murray–Darling Basin.
Shape control and compartmentalization in active colloidal cells
Authors: Spellings Matthew , Engel Michael , Klotsa Daphne , Sabrina Syeda , Drews Aaron M. , Nguyen Nguyen H. P. , Bishop Kyle J. M. , Glotzer Sharon C.
Published: August 2015

Significance

Advances in simulation and synthesis of nanoparticles and colloids are leading to a new class of active colloidal systems where self-propelled and self-rotated particles convert energy to motion. Such systems hold promise for the possibility of colloidal machines––integrated systems of colloids able to carry out functions. An important step in this direction is appropriately confining colloids within cells whose shape can be controlled and within which activity can be compartmentalized. This paper uses theory and computer simulation to propose active colloidal cells and investigates their behavior. Our findings provide motivation and design rules for the fabrication of primitive colloidal machines.
A common glycan structure on immunoglobulin G for enhancement of effector functions
Authors: Lin Chin-Wei , Tsai Ming-Hung , Li Shiou-Ting , Tsai Tsung-I , Chu Kuo-Ching , Liu Ying-Chih , Lai Meng-Yu , Wu Chia-Yu , Tseng Yung-Chieh , Shivatare Sachin S. , Wang Chia-Hung , Chao Ping , Wang Shi-Yun , Shih Hao-Wei , Zeng Yi-Fang , You Tsai-Hong , Liao Jung-Yu , Tu Yu-Chen , Lin Yih-Shyan , Chuang Hong-Yang , Chen Chia-Lin , Tsai Charng-Sheng , Huang Chiu-Chen , Lin Nan-Horng , Ma Che , Wu Chung-Yi , Wong Chi-Huey
Published: August 2015

Significance

Antibodies are important therapeutic agents and have been used for the treatment of many diseases, including infectious and inflammatory diseases, and cancer. The therapeutic efficacy of an antibody is usually determined not only by the selectivity and affinity toward the target but also by the Fc-glycan structure interacting with the Fc receptors on immune cells. This study describes the preparation of various antibodies with different Fc-glycan structures as homogeneous glycoforms for the investigation of their effector activities. During this study, it was discovered that the biantennary N-glycan structure with two terminal alpha-2,6-linked sialic acids is a common and optimal structure that is able to enhance the activities of antibodies against cancer, influenza, and inflammatory diseases.
Enantioselective recognition of menthol by mouse odorant receptors
Authors: Takai Yoshiki , Touhara Kazushige
Published: August 2015

The olfactory system has a remarkable ability to detect and discriminate a vast variety of odorant molecules. In mammals, hundreds to thousands of odorant receptors (ORs) expressed in olfactory sensory neurons play an essential role in this discrimination. Odorants are recognized by ORs in a combinatorial fashion in which a single odorant activates a particular combination of receptors, leading to its perception as a particular aroma. It is well known that enantiomers emit different aromas in spite of exhibiting otherwise identical chemical properties. To elucidate the molecular basis for the difference, we recorded responses to l- and d-menthol in the mouse olfactory bulb and found that enantiomers elicited similar but overlapping and distinct receptor activation patterns. We then identified l-menthol-specific and d-menthol-biased receptors and performed detailed structure–activity relationship studies, revealing high stereoselectivity of the enantiospecific menthol receptor. The binding site on ORs appears to have evolved to distinguish subtle differences in very similar odorant structures.
Division of labor among oxidoreductases: TMX1 preferentially acts on transmembrane polypeptides
Authors: Pisoni Giorgia Brambilla , Ruddock Lloyd W. , Bulleid Neil , Molinari Maurizio
Published: August 2015

The endoplasmic reticulum (ER) is the site of maturation for secretory and membrane proteins in eukaryotic cells. The lumen of the mammalian ER contains >20 members of the protein disulfide isomerase (PDI) superfamily, which ensure formation of the correct set of intramolecular and intermolecular disulfide bonds as crucial, rate-limiting reactions of the protein folding process. Components of the PDI superfamily may also facilitate dislocation of misfolded polypeptides across the ER membrane for ER-associated degradation (ERAD). The reasons for the high redundancy of PDI family members and the substrate features required for preferential engagement of one or the other are poorly understood. Here we show that TMX1, one of the few transmembrane members of the family, forms functional complexes with the ER lectin calnexin and preferentially intervenes during maturation of cysteine-containing, membrane-associated proteins while ignoring the same cysteine-containing ectodomains if not anchored at the ER membrane. As such, TMX1 is the first example of a topology-specific client protein redox catalyst in living cells.
Lamins position the nuclear pores and centrosomes by modulating dynein
Authors: Guo Yuxuan , Zheng Yixian
Published: August 2015

Lamins, the type V nuclear intermediate filament proteins, are reported to function in both interphase and mitosis. For example, lamin deletion in various cell types can lead to an uneven distribution of the nuclear pore complexes (NPCs) in the interphase nuclear envelope, whereas deletion of B-type lamins results in spindle orientation defects in mitotic neural progenitor cells. How lamins regulate these functions is unknown. Using mouse cells deleted of different combinations or all lamins, we show that lamins are required to prevent the aggregation of NPCs in the nuclear envelope near centrosomes in late G2 and prophase. This asymmetric NPC distribution in the absence of lamins is caused by dynein forces acting on NPCs via the dynein adaptor BICD2. We further show that asymmetric NPC distribution upon lamin depletion disrupts the distribution of BICD2 and p150 dynactin on the nuclear envelope at prophase, which results in inefficient dynein-driven centrosome separation during prophase. Therefore lamins regulate microtubule-based motor forces in vivo to ensure proper NPC distribution in interphase and centrosome separation in the mitotic prophase.
Improving protein fold recognition with hybrid profiles combining sequence and structure evolution
Authors: Ghouzam Yassine , Postic Guillaume , de Brevern Alexandre G. , Gelly Jean-Christophe
Published: August 2015

Motivation: Template-based modeling, the most successful approach for predicting protein 3D structure, often requires detecting distant evolutionary relationships between the target sequence and proteins of known structure. Developed for this purpose, fold recognition methods use elaborate strategies to exploit evolutionary information, mainly by encoding amino acid sequence into profiles. Since protein structure is more conserved than sequence, the inclusion of structural information can improve the detection of remote homology.

Results: Here, we present ORION, a new fold recognition method based on the pairwise comparison of hybrid profiles that contain evolutionary information from both protein sequence and structure. Our method uses the 16-state structural alphabet Protein Blocks, which provides an accurate 1D description of protein structure local conformations. ORION systematically outperforms PSI-BLAST and HHsearch on several benchmarks, including target sequences from the modeling competitions CASP8, 9 and 10, and detects ∼10% more templates at fold and superfamily SCOP levels.

Availability: Software freely available for download at http://www.dsimb.inserm.fr/orion/.

Contact:  jean-christophe.gelly@univ-paris-diderot.fr

Supplementary information:  Supplementary data are available at Bioinformatics online.
TIPR: transcription initiation pattern recognition on a genome scale
Authors: Morton Taj , Wong Weng-Keen , Megraw Molly
Published: August 2015

Motivation: The computational identification of gene transcription start sites (TSSs) can provide insights into the regulation and function of genes without performing expensive experiments, particularly in organisms with incomplete annotations. High-resolution general-purpose TSS prediction remains a challenging problem, with little recent progress on the identification and differentiation of TSSs which are arranged in different spatial patterns along the chromosome.

Results: In this work, we present the Transcription Initiation Pattern Recognizer (TIPR), a sequence-based machine learning model that identifies TSSs with high accuracy and resolution for multiple spatial distribution patterns along the genome, including broadly distributed TSS patterns that have previously been difficult to characterize. TIPR predicts not only the locations of TSSs but also the expected spatial initiation pattern each TSS will form along the chromosome—a novel capability for TSS prediction algorithms. As spatial initiation patterns are associated with spatiotemporal expression patterns and gene function, this capability has the potential to improve gene annotations and our understanding of the regulation of transcription initiation. The high nucleotide resolution of this model locates TSSs within 10 nucleotides or less on average.

Availability and implementation: Model source code is made available online at http://megraw.cgrb.oregonstate.edu/software/TIPR/.

Contact:  megrawm@science.oregonstate.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements
Authors: De Witte Dieter , Van de Velde Jan , Decap Dries , Van Bel Michiel , Audenaert Pieter , Demeester Piet , Dhoedt Bart , Vandepoele Klaas , Fostier Jan
Published: August 2015

Motivation: The accurate discovery and annotation of regulatory elements remains a challenging problem. The growing number of sequenced genomes creates new opportunities for comparative approaches to motif discovery. Putative binding sites are then considered to be functional if they are conserved in orthologous promoter sequences of multiple related species. Existing methods for comparative motif discovery usually rely on pregenerated multiple sequence alignments, which are difficult to obtain for more diverged species such as plants. As a consequence, misaligned regulatory elements often remain undetected.

Results: We present a novel algorithm that supports both alignment-free and alignment-based motif discovery in the promoter sequences of related species. Putative motifs are exhaustively enumerated as words over the IUPAC alphabet and screened for conservation using the branch length score. Additionally, a confidence score is established in a genome-wide fashion. In order to take advantage of a cloud computing infrastructure, the MapReduce programming model is adopted. The method is applied to four monocotyledon plant species and it is shown that high-scoring motifs are significantly enriched for open chromatin regions in Oryza sativa and for transcription factor binding sites inferred through protein-binding microarrays in O.sativa and Zea mays. Furthermore, the method is shown to recover experimentally profiled ga2ox1-like KN1 binding sites in Z.mays.

Availability and implementation: BLSSpeller was written in Java. Source code and manual are available at http://bioinformatics.intec.ugent.be/blsspeller

Contact:  Klaas.Vandepoele@psb.vib-ugent.be or jan.fostier@intec.ugent.be

Supplementary information:  Supplementary data are available at Bioinformatics online.
Regulatory B10 cell development and function
Authors: Lykken Jacquelyn M. , Candando Kathleen M. , Tedder Thomas F.
Published: August 2015

B cells are known to instigate and promulgate immune responses by producing antibodies and presenting antigens to T cells. However, a rare but potent B-cell subset in both humans and mice is capable of inhibiting immune responses through the production of the anti-inflammatory cytokine IL-10. Regulatory B cells do not express any unique combination of surface markers but instead represent a small population of B cells that have acquired the unique ability to produce IL-10. This numerically rare B-cell subset is therefore functionally referred to as ‘B10 cells’ to reflect both their molecular program and the fact that their anti-inflammatory effects in models of autoimmunity, infection and cancer are solely attributable to IL-10 production. As with most B cells, B10 cell development and function appear to be predominantly, if not exclusively, driven by antigen-receptor signals. Once generated, B10 cells respond to both innate and adaptive immune signals, with a requirement for antigen-specific local interactions with T cells to induce IL-10 production and to provide optimal immune suppression in mouse models of autoimmune disease. B10 cells therefore provide an antigen-specific mechanism for delivering IL-10 locally to sites of immune activation and inflammation. The ability of B10 cells to regulate innate and adaptive immune responses makes them an ideal therapeutic target for the treatment of many immune-related disorders.
Active learning: a step towards automating medical concept extraction
Authors: Kholghi Mahnoosh , Sitbon Laurianne , Zuccon Guido , Nguyen Anthony
Published: August 2015

Objective This paper presents an automatic, active learning-based system for the extraction of medical concepts from clinical free-text reports. Specifically, (1) the contribution of active learning in reducing the annotation effort and (2) the robustness of incremental active learning framework across different selection criteria and data sets are determined.

Materials and methods The comparative performance of an active learning framework and a fully supervised approach were investigated to study how active learning reduces the annotation effort while achieving the same effectiveness as a supervised approach. Conditional random fields as the supervised method, and least confidence and information density as 2 selection criteria for active learning framework were used. The effect of incremental learning vs standard learning on the robustness of the models within the active learning framework with different selection criteria was also investigated. The following 2 clinical data sets were used for evaluation: the Informatics for Integrating Biology and the Bedside/Veteran Affairs (i2b2/VA) 2010 natural language processing challenge and the Shared Annotated Resources/Conference and Labs of the Evaluation Forum (ShARe/CLEF) 2013 eHealth Evaluation Lab.

Results The annotation effort saved by active learning to achieve the same effectiveness as supervised learning is up to 77%, 57%, and 46% of the total number of sequences, tokens, and concepts, respectively. Compared with the random sampling baseline, the saving is at least doubled.

Conclusion Incremental active learning is a promising approach for building effective and robust medical concept extraction models while significantly reducing the burden of manual annotation.
K2 and MAXI observations of Sco X-1 – evidence for disc precession?
Authors: Hakala Pasi , Ramsay Gavin , Barclay Thomas , Charles Phil
Published: August 2015

Sco X-1 is the archetypal low-mass X-ray binary and the brightest persistent extrasolar X-ray source in the sky. It was included in the K2 Campaign 2 field and was observed continuously for 71 d with 1 min time resolution. In this Letter, we report these results and underline the potential of K2 for similar observations of other accreting compact binaries. We reconfirm that Sco X-1 shows a bimodal distribution of optical ‘high’ and ‘low’ states and rapid transitions between them on time-scales less than 3 h (or 0.15 orbits). We also find evidence that this behaviour has a typical systemic time-scale of 4.8 d, which we interpret as a possible disc precession period in the system. Finally, we confirm the complex optical versus X-ray correlation/anticorrelation behaviour for ‘high’ and ‘low’ optical states, respectively.
High speed BLASTN: an accelerated MegaBLAST search
tool
Authors: Chen Ying , Ye Weicai , Zhang Yongdong , Xu Yuesheng
Published: August 2015

Sequence alignment is a long standing problem in bioinformatics. The Basic Local Alignment Search Tool (BLAST) is one of the most popular and fundamental alignment tools. The explosive growth of biological sequences calls for speedup of sequence alignment tools such as BLAST. To this end, we develop high speed BLASTN (HS-BLASTN), a parallel and fast nucleotide database search tool that accelerates MegaBLAST—the default module of NCBI-BLASTN. HS-BLASTN builds a new lookup table using the FMD-index of the database and employs an accurate and effective seeding method to find short stretches of identities (called seeds) between the query and the database. HS-BLASTN produces the same alignment results as MegaBLAST and its computational speed is much faster than MegaBLAST. Specifically, our experiments conducted on a 12-core server show that HS-BLASTN can be 22 times faster than MegaBLAST and exhibits better parallel performance than MegaBLAST. HS-BLASTN is written in C++ and the related source code is available at https://github.com/chenying2016/queries under the GPLv3 license.
Diagnostic Accuracy of Respiratory Distress Observation Scales as Surrogates of Dyspnea Self-report in Intensive Care Unit Patients
Authors: Persichini Romain , Gay Frédérick , Schmidt Matthieu , Mayaux Julien , Demoule Alexandre , Morélot-Panzini Capucine , Similowski Thomas
Published: August 2015

AbstractAbstract

In 220 intensive care unit patients able to communicate, an observational scale containing five nonverbal signs was derived and validated respective to dyspnea self-report. This should help better understand and manage mechanically ventilated patients in the future.

Supplemental Digital Content is available in the text.

Background:

Dyspnea, like pain, can cause major suffering in intensive care unit (ICU) patients. Its evaluation relies on self-report; hence, the risk of being overlooked when verbal communication is impaired. Observation scales incorporating respiratory and behavioral signs (respiratory distress observation scales [RDOS]) can provide surrogates of dyspnea self-report in similar clinical contexts (palliative care).

Methods:

The authors prospectively studied (single center, 16-bed ICU, large university hospital) 220 communicating ICU patients (derivation cohort, 120 patients; separate validation cohort, 100 patients). Dyspnea was assessed by dyspnea visual analog scale (D-VAS) and RDOS calculated from its eight components (heart rate, respiratory rate, nonpurposeful movements, neck muscle use during inspiration, abdominal paradox, end-expiratory grunting, nasal flaring, and facial expression of fear). An iterative principal component analysis and partial least square regression process aimed at identifying an optimized D-VAS correlate (intensive care RDOS [IC-RDOS]).

Results:

In the derivation cohort, RDOS significantly correlated with D-VAS (r = 0.43; 95% CI, 0.29 to 0.58). A five-item IC-RDOS (heart rate, neck muscle use during inspiration, abdominal paradox, facial expression of fear, and supplemental oxygen) significantly better correlated with D-VAS (r = 0.61; 95% CI, 0.50 to 0.72). The median area under the receiver operating curve of IC-RDOS to predict D-VAS was 0.83 (interquartile range, 0.81 to 0.84). An IC-RDOS of 2.4 predicted D-VAS of 4 or greater with equal sensitivity and specificity (72%); an IC-RDOS of 6.3 predicted D-VAS of 4 or greater with 100% specificity. Similar results were found in the validation cohort.

Conclusions:

Combinations of observable signs correlate with dyspnea in communicating ICU patients. Future studies in noncommunicating patients will be needed to determine the responsiveness to therapeutic interventions and clinical usefulness.
The variation trends of SFRP2 methylation of tissue, feces, and blood detection in colorectal cancer development
Authors: Sui Chengguang , Ma Jianzhong , Chen Qun , Yang Yang
Published: August 2015

The susceptibility of secreted frizzled-related protein 2 (SFRP2) methylation in colorectal cancer (CRC) has been studied previously. The aim of this study was to determine the risk sizes and variation trends of SFRP2 methylation in CRC development in Chinese populations. Subgroup meta-analysis and the least-squares curve-fitting method were carried out to analyze the risk of SFRP2 methylation in tissue, feces, and blood detection from 2221 samples, including a total of 1103 cases of CRC, 459 cases of adenoma, 257 cases of polyps, and 402 controls. The data showed that odds ratios (95% confidence intervals) between CRC and controls for tissue, feces, and blood detection were 334.01 (104.42–1068.39), 63.76 (20.62–197.63), and 133.75 (18.32–976.32), respectively. There were also significant differences between tissue and feces or blood as well as between feces and blood methylation frequency. These results showed that the risk size in tissue was much greater than that in feces and that in blood. The results pointed out that three curves in tissue, feces, and blood detection described the variation trends of methylation incidence from the control to polyp, to adenoma and to CRC, and that the variation trend of the risk size of SFRP2 methylation was synchronized with the histological evolution process of CRC. The variation trend of the risk size of SFRP2 methylation incidence is consistent with the histological evolution process of CRC. The susceptibility to SFRP2 methylation is an important biomarker in the study of early diagnosis of CRC and high-risk patients.
Two sides of the safety coin?
Authors: Schiffinger Michael , Latzke Markus , Steyrer Johannes
Published: August 2015

Background:

Safety climate (SC) and more recently patient engagement (PE) have been identified as potential determinants of patient safety, but conceptual and empirical studies combining both are lacking.

Purposes:

On the basis of extant theories and concepts in safety research, this study investigates the effect of PE in conjunction with SC on perceived error occurrence (pEO) in hospitals, controlling for various staff-, patient-, and hospital-related variables as well as the amount of stress and (lack of) organizational support experienced by staff. Besides the main effects of PE and SC on error occurrence, their interaction is examined, too.

Methodology/Approach:

In 66 hospital units, 4,345 patients assessed the degree of PE, and 811 staff assessed SC and pEO. PE was measured with a new instrument, capturing its core elements according to a recent literature review: Information Provision (both active and passive) and Activation and Collaboration. SC and pEO were measured with validated German-language questionnaires. Besides standard regression and correlational analyses, partial least squares analysis was employed to model the main and interaction effects of PE and SC on pEO, also controlling for stress and (lack of) support perceived by staff, various staff and patient attributes, and potential single-source bias.

Findings:

Both PE and SC are associated with lower pEO, to a similar extent. The joint effect of these predictors suggests a substitution rather than mutually reinforcing interaction. Accounting for control variables and/or potential single-source bias slightly attenuates some effects without altering the results.

Practice Implications:

Ignoring PE potentially amounts to forgoing a potential source of additional safety. On the other hand, despite the abovementioned substitution effect and conjectures of SC being inert, PE should not be considered as a replacement for SC.
Mammalian development does not recapitulate suspected key transformations in the evolution of the mammalian middle ear
Authors: Ramírez-Chaves Héctor E. , Wroe Stephen W. , Selwood Lynne , Hinds Lyn A. , Leigh Chris , Koyabu Daisuke , Kardjilov Nikolay , Weisbecker Vera
Published: August 2015

The tympanic ring, malleus and incus of the mammalian middle ear derive from the ancestral primary jaw joint of land vertebrates. In Mesozoic mammals, evolutionary detachment of the mammalian middle ear from the lower jaw occurred when Meckel’s cartilage - the last connection between the middle ear bones and the dentary – disappeared. This disappearance is famously recapitulated in early mammalian development. By extension, it was suggested that other developmental processes also recapitulate specific evolutionary processes that led to mammalian middle ear detachment in Mesozoic mammals. Specifically, developmental posterior/medial displacement and negative allometry of the growing ear ossicles relative to the lower jaw are thought to reflect evolutionary triggers of mammalian middle ear detachment. However, these hypotheses rest on scant developmental data, and have not been tested in a quantitative framework. Here we show, based on μCT scans of developmental series of several marsupials and monotremes, that negative allometry of mammalian middle ear bones relative to the skull occurs only after mammalian middle ear detachment, ruling it out as a developmental detachment trigger. There is also no positional change of ectotympanic or malleus relative to the dentary. The mammalian middle ear bones are differently positioned in two monotreme species, a recent change which is not developmentally recapitulated. Together, our results challenge the developmental prerequisites of previously proposed evolutionary detachment processes, arguing specifically against causal links between mammalian middle ear detachment and brain expansion. Our data are more consistent with a biomechanical detachment trigger relating to the onset of dentary function, but more biomechanical work and palaeontological data are required to test this notion.
How to develop objective-driven comprehensive science outreach initiatives aiming at multiple audiences
Authors: Patel Sanjai , Prokop Andreas
Published: August 2015

Science outreach has become increasingly important for researchers and needs to be of ever improving quality, although the time available aside our science, teaching and administration activities is steadily decreasing. To square this circle, effective strategies are required. Here we argue that this can be achieved by setting simple but ambitious overarching objectives for comprehensive outreach initiatives which target multiple audiences, supported by cumulative build-up of shared high-quality resources, as well as the exchange and collaboration amongst scientists with a common outreach aim. To exemplify this strategy, we explain the low-budget, yet high-quality outreach initiative of the Manchester Fly Facility which aims to promote public awareness of the importance of the model organismDrosophilafor biomedical research. (1) This initiative targets the general public at science fairs, through public videos, or through extracurricular activities in schools as well as the development of curriculum-relevant sample lessons for teachers - all supported by a dedicated website. (2) The initiative targets university students: by adapting the public outreach resources for their teaching, and through newly developed advanced training strategies that amalgamate the outreach objectives. (3) It targets fellow scientists through blogs, conference presentations and a second website that provides a one-stop-shop for resources, arguments and strategies. As will be explained, this multi-pronged approach is time-saving in the long run and it is powerful because it reaches a wide range of audiences, helps to gain momentum, to build resource, and to gradually improve quality through cross-fertilisation between different activities, and through exchange within the science community. This helps to build communities, and high-quality outreach will have further important added value: arguments that impress the public, tend to be most effective also with reviewers and grant panel members, and often help to readjust aspects of your own scientific work.
More efficacious drugs lead to harder selective sweeps in the evolution of drug resistance in HIV-1
Authors: Feder Alison F , Rhee Soo-Yon , Shafer Robert W , Petrov Dmitri A , Pennings Pleuni S
Published: August 2015

In the early days of HIV treatment, drug resistance occurred rapidly and predictably in all patients, but under modern treatments, resistance arises slowly, if at all. The probability of resistance should be controlled by the rate of generation of resistant mutations. If many adaptive mutations arise simultaneously, then adaptation proceeds by soft selective sweeps in which multiple adaptive mutations spread concomitantly, but if adaptive mutations occur rarely in the population, then a single adaptive mutation should spread alone in a hard selective sweep. Here we use 6,717 HIV-1 consensus sequences from patients treated with first-line therapies between 1989 and 2013 to confirm that the transition from fast to slow evolution of drug resistance was indeed accompanied with the expected transition from soft to hard selective sweeps. This suggests more generally that evolution proceeds via hard sweeps if resistance is unlikely and via soft sweeps if it is likely.
A digital approach to protein identification and quantity estimation using tandem nanopores, peptidases, and database search
Authors: Sampath G.
Published: August 2015

A digital approach to protein identification and quantity estimation using electrical measurements and database search is proposed. It is based on an electrolytic cell with two (three) nanopores and one (two) peptidase(s) covalently attached to thetransside of a pore. An unknown protein is digested by a reagent or peptidase into peptides ending in a known amino acid; the peptides enter the cell, pass through the first pore, and are fragmented by a high-specificity endopeptidase. The second enzyme, if present, is an exopeptidase that cleaves the fragments into single residues after the second pore. Level transitions in an ionic blockade or transverse current pulse due to residues in a fragment or individual pulses due to single residues are counted. This yields the positions of the endopeptidase’s target in the peptide, and, together with the peptide’s terminal residue, a partial sequence. Search through the Uniprot database for such sequences identifies over 90% of the proteins in the human proteome. The percentage can be increased by repeating the procedure with other reagents and cells specific to other residues, close to 100% may be possible. Sample purification to homogeneity is not required as the method applies to an arbitrary mixture of proteins; the quantity of a protein in the sample is estimated from the number of identifying peptides sensed over a long run. A Fokker-Planck model gives minimum enzyme turnover intervals required for ordered sensing of peptide fragments. With thick (80-100 nm) pores, required pulse resolution times are within the capability of CMOS detectors. The method can be implemented with existing technology; several related issues are discussed.
Genome variation and meiotic recombination inPlasmodium falciparum: insights from deep sequencing of genetic crosses
Authors: Miles Alistair , Iqbal Zamin , Vauterin Paul , Pearson Richard , Campino Susana , Theron Michel , Gould Kelda , Mead Daniel , Drury Eleanor , O’Brien John , Ruano Rubio Valentin , MacInnis Bronwyn , Mwangi Jonathan , Samarakoon Upeka , Ranford-Cartwright Lisa , Ferdig Michael , Hayton Karen , Su Xinzhuan , Wellems Thomas , Rayner Julian , McVean Gil , Kwiatkowski Dominic
Published: August 2015

The malaria parasitePlasmodium falciparumhas a great capacity for evolutionary adaptation to evade host immunity and develop drug resistance. Current understanding of parasite evolution is impeded by the fact that a large fraction of the genome is either highly repetitive or highly variable, and thus difficult to analyse using short read technologies. Here we describe a resource of deep sequencing data on parents and progeny from genetic crosses, which has enabled us to perform the first genome-wide, integrated analysis of SNP, INDEL and complex polymorphisms, using Mendelian error rates as an indicator of genotypic accuracy. These data reveal that INDELs are exceptionally abundant, being more common than SNPs and thus the dominant mode of polymorphism within the core genome. We use the high density of SNP and INDEL markers to analyse patterns of meiotic recombination, confirming a high rate of crossover events, and providing the first estimates for the rate of non-crossover events and the length of conversion tracts. We observe several instances of recombination that modify copy number variants associated with drug resistance, demonstrating a mechanism whereby fitness costs associated with resistance mutations could be compensated and greater phenotypic plasticity could be acquired. We describe a novel web application that allows these data to be explored in detail.
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Authors: Ewing Brent , Green Phil
Published: August 2015

Elimination of the data processing bottleneck in high-throughput sequencing will require both improved accuracy of data processing software and reliable measures of that accuracy. We have developed and implemented in our base-calling program phred the ability to estimate a probability of error for each base-call, as a function of certain parameters computed from the trace data. These error probabilities are shown here to be valid (correspond to actual error rates) and to have high power to discriminate correct base-calls from incorrect ones, for read data collected under several different chemistries and electrophoretic conditions. They play a critical role in our assembly program phrap and our finishing programconsed.
The neglected part in historic districts: case studies on the non-heritage buildings in two historic blocks in Wuxi City, China
Authors: Wang Fang , Xue Xiaoning , Wang Yingying
Published: August 2015

Purpose

– Maintaining a city’s identity and locality is an urgent problem in urban construction. Historical districts are very important parts of a city. However, non-heritage buildings, which make a significant contribution to the character and appearance of historical areas, are facing arbitrary demolition. They are more often ignored compared with buildings on the protection list. The paper aims to discuss these issues.

Design/methodology/approach

– This paper chooses two historic blocks in Wuxi, in which 256 non-heritage buildings were examined, the SPSS method and the AHP method are used to find renewal modes for the buildings that had not finished updates, and the two blocks are then used as practical cases to validate the matching results.

Findings

– In conclusion, on the one hand, according to different building categories, different renewal modes are found. On the other hand, this study finds differences in the renewal modes of different historic districts.

Originality/value

– The study shows a renewal method for non-heritage buildings, which require attention due to their dangerous situation, as these buildings in historical districts also contribute to a city’s uniqueness and locality. These results should be helpful in the planning and practices for urban historical districts.
Corporate environmental sustainability disclosures and environmental risk
Authors: Dobler Michael , Lajili Kaouthar , Zéghal Daniel
Published: August 2015

Purpose

– This paper aims to propose and apply a novel risk-based approach to explore whether socio-political theories explain the level of corporate environmental disclosures given inconclusive evidence on the relation between environmental disclosure and environmental performance.

Design/methodology/approach

– Based on content analysis of corporate risk reporting, the paper develops measures of environmental risk to proxy for a firm’s exposure to public pressure in regard to environmental concerns that should be positively associated with the level of corporate environmental disclosures according to socio-political theories. Multiple regressions are used to test the predictions of socio-political theories for US Standards and Poor’s 500 constituents from polluting sectors.

Findings

– The level of environmental disclosures is found to be positively associated with a firm’s environmental risk while unrelated to its environmental performance. The findings suggest that firms tend to provide higher levels of environmental disclosures in response to greater exposure to public pressure as depicted by broad environmental indicators. The results are robust to alternative measures of environmental disclosures, environmental risk and environmental performance, alternative specifications of the economic model and additional sensitivity checks.

Research limitations/implications

– This study is limited to US firms in polluting sectors. The risk-based approach proposed may not be appropriate to cover sectors where corporate risk reporting is less likely to address environmental risk, but it could potentially be adopted in other countries with advanced risk reporting regulation or practice.

Practical implications

– Findings are important to understand a firm’s incentives to disclose environmental information. Cross-sectional differences found in environmental disclosures, risk and performance, highlight the importance of considering industry affiliation when analyzing environmental data.

Originality/value

– This paper is the first to use firm-level environmental risk variables to explain the level of corporate environmental disclosures. The risk-based approach taken suggests opportunities for research at the multi-country level and in countries where corporate environmental performance data are not publicly available.
Retail store environment and customer experience: a paradigm
Authors: Sachdeva Ishita , Goel Suhsma
Published: August 2015

Purpose

– The current context of retail is extremely challenging. Retail environments are pushing consumers to appreciate hedonic aspects of consumption. Retailers are finding new ways to offer customers something unique or special in order to encourage traffic to physical stores. People like to touch, feel, smell, taste, inspect, test and try on. It is a holistic approach that involves both emotional and rational triggers (Meyer, 2006, p. 1). The paper aims to discuss these issues.

Design/methodology/approach

– The basic proposition is that a shopper’s behavior is influenced by the environment. The environment (store) influences a shopper’s emotions and mood, which in turn influence the shopper’s behavior (Ebster and Garaus, 2011, p. 108). Mehrabian found a significant amount of research to back Holbrook’s findings that “emotion is a key link in the shopping experience” determining that consumers’ reactions within stores are based on their emotional states, which are stimulated by store designs (Mehrabian, 1977).

Findings

– It is important to focus on engaging the customer both emotionally and behaviorally, which means that the communication on social media and physical retail stores should both excel in emotional appeal, and encourage various forms of interaction with the brand. Increasingly, success at retail is less about what the retailer has to sell and more about how they sell it. This is the new experiential paradigm shift in shopping. This will become even more critical in the future as success at retail will continue to shift toward how well retailers play to the emotions, psychology and feelings of the shopper (Danziger, 2006, p. 17). The need whether utilitarian or hedonic carries them to the store but emotions make them stay and shop.

Originality/value

– Both utilitarian and hedonic experiences – whether they are derived from consuming products or total experience, including products, people, places and the environment – contribute in differing degrees, to the overall experience of consumption.
Preparing strata titled communities for climate change: an empirical examination
Authors: Guilding Chris , Lamminmaki Dawne , Warnken Jan
Published: August 2015

Purpose

– The purpose of this paper is twofold: first, to advance a set of recommendations concerned with enhancing residential strata title (ST) communities’ preparation for property management in a world of climate change (CC) and second, to examine the Australian ST community’s perceptions of the recommendations advanced.

Design/methodology/approach

– The study comprised three empirical phases: three meetings with an 11 person industry reference group, conduct of 18 exploratory interviews and also an on-line questionnaire survey. The survey was designed to gauge the relative merit of sixteen recommendations developed during the study’s exploratory interview phase. The survey was completed by 450 individuals representing a broad cross-section of ST stakeholders.

Findings

– The study’s findings are extensive. Amongst them it is notable that the survey respondents ranked procedures taken prior and during a ST building’s construction as more important CC management opportunities than steps and procedures implemented post-building construction.

Research limitations/implications

– While considerable care was taken to approach the analysis of interview data in an objective manner, it should be acknowledged that, like any research based on qualitative data, a researcher’s background is bound to introduce some biases in the way that themes in the collected data are determined and interpreted.

Practical implications

– The range of practical implications arising from the study are very evident from the range of issues addressed in the 16 recommendations advanced by the study. These implications range widely from internal management suggestions such as identifying a CC champion in ST complexes, to insurance issues such as creating a low insurance or “uninsurable” ST building category.

Social implications

– The survey findings reveal the extent to which expressed opinions concerning how best to adapt ST buildings and communities for CC are affected by the stakeholder group that is expressing the opinion. This highlights the likelihood that any new ST policy making relating to CC is likely to become highly politicised due to conflicting lobbying interests represented by these distinct ST stakeholders.

Originality/value

– The study is believed to embody an exceedingly high level of originality. It is the first to: provide an examination of the vulnerability of ST complexes to CC, and advance recommendations concerned with changes that should be made to the building and management of ST complexes in order to address the CC challenge.
Involvement of sinoaortic afferents in renal sympathoinhibition and vasodilation induced by acute hypernatremia
Authors: Silva Elaine F , Sera Celisa TN , Mourão Aline A , Lopes Paulo R , Moreira Marina CS , Ferreira‐Neto Marcos L , Colombari Débora AS , Cravo Sérgio LD , Pedrino Gustavo R
Published: August 2015

Despite the abundance of evidence that supports the important role of aortic and carotid afferents to short‐term regulation of blood pressure and detection of variation in the arterial PO2, PCO2 and pH, relatively little is known regarding the role of these afferents during changes in the volume and composition of extracellular compartments. The present study sought to determine the involvement of these afferents in the renal vasodilation and sympathoinhibition induced by hypertonic saline (HS) infusion. Sinoaortic‐denervated and sham male Wistar rats were anaesthetised with intravenous (i.v.) urethane (1.2 g/kg body weight (bw)) prior to the measurement of the mean arterial pressure (MAP), renal vascular conductance (RVC) and renal sympathetic nerve activity (RSNA). In the sham group, the HS infusion (3 mol/L NaCl, 1.8 mL/kg bw, i.v.) induced transient hypertension (12 ± 4 mmHg from baseline, peak at 10 min; P < 0.05), an increase in RVC (127 ± 9% and 150 ± 13% from baseline, at 20 and 60 min respectively; P < 0.05) and a decrease in RSNA (−34 ± 10% and −29 ± 5% from baseline, at 10 and 60 min respectively; P < 0.05). In sinoaortic‐denervated rats, HS infusion promoted a sustained pressor response (30 ± 5 and 17 ± 6 mmHg of baseline values, at 10 and 30 min respectively; P < 0.05) and abolished the increase in RVC (85 ± 8% from baseline, at 10 min) and decrease in RSNA (−4 ± 3% from baseline, at 10 min). These results suggest that aortic and carotid afferents are involved in cardiovascular and renal sympathoinhibition responses induced by acute hypernatremia.