bluuebunny/crossref_metadata_2025 huggingface dataset:
Noncontact orientation of objects in three-dimensional space using magnetic levitation
Authors: Subramaniam Anand Bala , Yang Dian , Yu Hai-Dong , Nemiroski Alex , Tricard Simon , Ellerbee Audrey K. , Soh Siowling , Whitesides George M.
Published: August 2014

Significance

We describe several noncontact methods of orienting objects in three-dimensional (3D) space using Magnetic Levitation (MagLev), and report the discovery of a sharp geometry-dependent transition of the orientation of levitating objects. An analytical theory of the orientation of arbitrary objects in MagLev explains this transition. MagLev is capable of manipulating and orienting hard and soft objects, and objects of irregular shape. Because controlling the orientation of objects in space is a prerequisite for assembling complex structures from simpler components, this paper extends MagLev into 3D self-assembly, robotic assembly, and noncontact (stiction-free) orientation of hard and soft objects for applications in biomimetics, soft robotics, and stimulus-responsive materials, among others.
Hyperglycemia in rodent models of type 2 diabetes requires insulin-resistant alpha cells
Authors: Lee Young , Berglund Eric D. , Yu Xinxin , Wang May-Yun , Evans Matthew R. , Scherer Philipp E. , Holland William L. , Charron Maureen J. , Roth Michael G. , Unger Roger H.
Published: August 2014

Significance

Diet-induced type 2 diabetes (T2D) is becoming a worldwide epidemic. Patients with T2D fail to respond to insulin normally and have elevated blood glucose and insulin. In autoimmune diabetes, blood glucose is elevated due to uncontrolled glucagon, a hormone normally suppressed and opposed by insulin. To study the role of glucagon in T2D, rodent models of the disease were created lacking glucagon action. These animals failed to develop hyperglycemia unless glucagon action was restored or the animals were given the high concentrations of insulin typical of animals with T2D. This indicates that the unopposed glucagon action in T2D is necessary to support elevated blood glucose of diabetes. Suppressing glucagon or its action may benefit patients with T2D.
Three-dimensional cell body shape dictates the onset of traction force generation and growth of focal adhesions
Authors: Fouchard Jonathan , Bimbard Célian , Bufi Nathalie , Durand-Smet Pauline , Proag Amsha , Richert Alain , Cardoso Olivier , Asnacios Atef
Published: August 2014

Significance

Living cells interact with their environment through surface receptors. In particular, adhesion molecules form complexes that anchor cells to each other and to the extracellular matrix. These complexes ensure mechanical integrity of tissues and control cell function through specific biochemical signaling. This dual role is due to the ability of adhesion complexes to grow and change their composition and activity in response to mechanical forces. Here, we show how cell spreading, by modifying cell shape, controls the distribution of internal tension over adhesion complexes, inducing their growth above a well-defined spread area. Because such a threshold area was reported for many cell functions, our findings shed a new light on the possible mechanisms behind the geometric control of cell fate.
Commensal bacteria protect against food allergen sensitization
Authors: Stefka Andrew T. , Feehley Taylor , Tripathi Prabhanshu , Qiu Ju , McCoy Kathy , Mazmanian Sarkis K. , Tjota Melissa Y. , Seo Goo-Young , Cao Severine , Theriault Betty R. , Antonopoulos Dionysios A. , Zhou Liang , Chang Eugene B. , Fu Yang-Xin , Nagler Cathryn R.
Published: August 2014

Significance

The prevalence of food allergy is rising at an alarming rate; the US Centers for Disease Control and Prevention documented an 18% increase among children in the United States between 1997 and 2007. Twenty-first century environmental interventions are implicated by this dramatic generational increase. In this report we examine how alterations in the trillions of commensal bacteria that normally populate the gastrointestinal tract influence allergic responses to food. We identify a bacterial community that protects against sensitization and describe the mechanism by which these bacteria regulate epithelial permeability to food allergens. Our data support the development of novel adjunctive probiotic therapies to potentiate the induction of tolerance to dietary allergens.
Dynamic hydration shell restores Kauzmann's 1959 explanation of how the hydrophobic factor drives protein folding
Authors: Baldwin Robert L.
Published: August 2014

Significance

Kauzmann's proposal that the hydrophobicity of hydrocarbons in water is caused by their hydration shells is modified here by replacing his clathrate water shell with a dynamic shell formed by van der Waals attraction, as proposed by Jorgensen et al. The hydration energetics of alkanes are then shown to be proportional to n, the number of waters in the shell given by the simulations of Jorgensen et al. The Ben-Naim standard state, which is based on solute transfer between fixed positions in the gas and liquid phases, is used for the hydration energetics. Recent experimental evidence for hydration shells is reviewed.
Some People
Authors: Schick Laurie
Published: August 2014

This paper integrates methods associated with language socialization and pragmatics to examine how participants in one middle school dance program use the indefinitely referential language of ‘some people’ as a robust resource for socializing embodied competencies related to dance, linguistic competencies related to the ability to use ‘some people’ in indexically and pragmatically complex ways, cognitive competencies related to error-correction and problem-solving, and social-moral competencies related to responsibility-taking. A key argument is that the referential vagueness inherent in ‘some’ as an indefinite determiner contributes fundamentally to the usefulness of ‘some people’ as a language socialization resource in this community of practice.
‘Father knows best’
Authors: Macaulay Marcia
Published: August 2014

This paper examines two realisations of the television talk show in North America: The Oprah Winfrey Show and Dr. Phil, looking specifically at how they function within the sub-genre of ‘therapeutic talk show’ in keeping with Livingstone and Lunt’s (1994) classification of talk shows. Talk shows are defined by Ilie (2001) as “semi-institutional discourse” having features of a given setting (TV studio), topic- and goal-oriented talk, high degree of topic control, as well as restrictions on time and turn-taking. Theorists examining this sub-genre of therapeutic talk show have argued that it provides a valuable means by which stories otherwise unrecognized have a forum, or that values of truth and honesty can be conveyed (Livingstone & Lunt 1994; Masciarotte 1991; Carbaugh 1988). However, theorists such as Abt and Seesholtz (1994) view therapeutic talk shows as potentially demeaning to guests who appear on them as well as a means by which suffering can be trivialized. Through an examination and analysis of requests for information, both direct and indirect, which are the principal features of all interviews, I look at how Oprah Winfrey and Dr. Phil problematize the narratives told by their guests. Both hosts rely heavily on one type of request, B-Event assertions functioning as indirect requests for information, to provoke specific response. My findings indicate that these talk shows do not in fact provide a forum for talk that would otherwise not be considered as suggested by Livingstone and Lunt (1994). Both Oprah Winfrey and Dr. Phil appropriate the stories provided by their guests; they also participate in their own overarching meta-narrative whereby as ‘heroes’ they solve their guests’ problems within a given time frame. Guests’ narrative responses share more with the speech act of confession than with free self-expression. The speech act of confession encouraged by these therapeutic talk shows serves in turn to reinforce conservatively-held values on the part of the at-home audience for whom such confession is also entertainment.
A New Approach to Researching the Etiology of Cannabis Use Disorder: Integrating Transmissible and Nontransmissible Risk within a Developmental Framework
Authors: Tarter Ralph , Kirisci Levent , Reynolds Maureen
Published: August 2014

Rapidly occurring changes in law enforcement and licensing of retail outlets to sell marijuana raises the prospect that the population of consumers will expand and accordingly the prevalence of cannabis use disorder (CUD) will increase. This report presents a novel approach to researching CUD etiology joining multivariate and ontogenetic perspectives. CUD is conceptualized as a developmental outcome consisting of transmissible (intergenerational) and nontransmissible components. Partitioning the liability for CUD into these 2 dimensions enables implementing interventions targeted at the particular source and severity of risk. In addition, results showing that infant temperament disturbances predict transmissible risk leading to CUD 2 decades later underscore the importance of implementing early prevention.
Two jacalin-related lectins from seeds of the African breadfruit (Treculia africana L.)
Authors: Shimokawa Michiko , Nsimba-Lubaki Shadrack Makuta , Hayashi Namiko , Minami Yuji , Yagi Fumio , Hiemori Keiko , Tateno Hiroaki , Hirabayashi Jun
Published: August 2014

Two jacalin-related lectins (JRLs) were purified by mannose-agarose and melibiose-agarose from seeds of Treculia africana. One is galactose-recognizing JRL (gJRL), named T. africana agglutinin-G (TAA-G), and another one is mannose-recognizing JRL (mJRL), TAA-M. The yields of the two lectins from the seed flour were approximately 7.0 mg/g for gJRL and 7.2 mg/g for mJRL. The primary structure of TAA-G was determined by protein sequencing of lysyl endopeptic peptides and chymotryptic peptides. The sequence identity of TAA-G to other gJRLs was around 70%. Two-residue insertion was found around the sugar-binding sites, compared with the sequences of other gJRLs. Crystallographic studies on other gJRLs have shown that the primary sugar-binding site of gJRLs can accommodate Gal, GalNAc, and GalNAc residue of T-antigen (Galβ1-3GalNAcα-). However, hemagglutination inhibition and glycan array showed that TAA-G did not recognize GalNAc itself and T-antigen. TAA-G preferred melibiose and core 3 O-glycan.
Two-dimensional segmentation for analyzing Hi-C data
Authors: Lévy-Leduc Celine , Delattre M. , Mary-Huard T. , Robin S.
Published: August 2014

Motivation: The spatial conformation of the chromosome has a deep influence on gene regulation and expression. Hi-C technology allows the evaluation of the spatial proximity between any pair of loci along the genome. It results in a data matrix where blocks corresponding to (self-)interacting regions appear. The delimitation of such blocks is critical to better understand the spatial organization of the chromatin. From a computational point of view, it results in a 2D segmentation problem.

Results: We focus on the detection of cis-interacting regions, which appear to be prominent in observed data. We define a block-wise segmentation model for the detection of such regions. We prove that the maximization of the likelihood with respect to the block boundaries can be rephrased in terms of a 1D segmentation problem, for which the standard dynamic programming applies. The performance of the proposed methods is assessed by a simulation study on both synthetic and resampled data. A comparative study on public data shows good concordance with biologically confirmed regions.

Availability and implementation: The HiCseg R package is available from the Comprehensive R Archive Network and from the Web page of the corresponding author.

Contact:  celine.levy-leduc@agroparistech.fr
Causal network inference using biochemical kinetics
Authors: Oates Chris J. , Dondelinger Frank , Bayani Nora , Korkola James , Gray Joe W. , Mukherjee Sach
Published: August 2014

Motivation: Networks are widely used as structural summaries of biochemical systems. Statistical estimation of networks is usually based on linear or discrete models. However, the dynamics of biochemical systems are generally non-linear, suggesting that suitable non-linear formulations may offer gains with respect to causal network inference and aid in associated prediction problems.

Results: We present a general framework for network inference and dynamical prediction using time course data that is rooted in non-linear biochemical kinetics. This is achieved by considering a dynamical system based on a chemical reaction graph with associated kinetic parameters. Both the graph and kinetic parameters are treated as unknown; inference is carried out within a Bayesian framework. This allows prediction of dynamical behavior even when the underlying reaction graph itself is unknown or uncertain. Results, based on (i) data simulated from a mechanistic model of mitogen-activated protein kinase signaling and (ii) phosphoproteomic data from cancer cell lines, demonstrate that non-linear formulations can yield gains in causal network inference and permit dynamical prediction and uncertainty quantification in the challenging setting where the reaction graph is unknown.

Availability and implementation: MATLAB R2014a software is available to download from warwick.ac.uk/chrisoates.

Contact:  c.oates@warwick.ac.uk or sach@mrc-bsu.cam.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
TEMPI: probabilistic modeling time-evolving differential PPI networks with multiPle information
Authors: Kim Yongsoo , Jang Jin-Hyeok , Choi Seungjin , Hwang Daehee
Published: August 2014

Motivation: Time-evolving differential protein–protein interaction (PPI) networks are essential to understand serial activation of differentially regulated (up- or downregulated) cellular processes (DRPs) and their interplays over time. Despite developments in the network inference, current methods are still limited in identifying temporal transition of structures of PPI networks, DRPs associated with the structural transition and the interplays among the DRPs over time.

Results: Here, we present a probabilistic model for estimating Time-Evolving differential PPI networks with MultiPle Information (TEMPI). This model describes probabilistic relationships among network structures, time-course gene expression data and Gene Ontology biological processes (GOBPs). By maximizing the likelihood of the probabilistic model, TEMPI estimates jointly the time-evolving differential PPI networks (TDNs) describing temporal transition of PPI network structures together with serial activation of DRPs associated with transiting networks. This joint estimation enables us to interpret the TDNs in terms of temporal transition of the DRPs. To demonstrate the utility of TEMPI, we applied it to two time-course datasets. TEMPI identified the TDNs that correctly delineated temporal transition of DRPs and time-dependent associations between the DRPs. These TDNs provide hypotheses for mechanisms underlying serial activation of key DRPs and their temporal associations.

Availability and implementation: Source code and sample data files are available at http://sbm.postech.ac.kr/tempi/sources.zip.

Contact:  seungjin@postech.ac.kr or dhwang@dgist.ac.kr

Supplementary information:  Supplementary data are available at Bioinformatics online.
Stronger findings for metabolomics through Bayesian modeling of multiple peaks and compound correlations
Authors: Suvitaival Tommi , Rogers Simon , Kaski Samuel
Published: August 2014

Motivation: Data analysis for metabolomics suffers from uncertainty because of the noisy measurement technology and the small sample size of experiments. Noise and the small sample size lead to a high probability of false findings. Further, individual compounds have natural variation between samples, which in many cases renders them unreliable as biomarkers. However, the levels of similar compounds are typically highly correlated, which is a phenomenon that we model in this work.

Results: We propose a hierarchical Bayesian model for inferring differences between groups of samples more accurately in metabolomic studies, where the observed compounds are collinear. We discover that the method decreases the error of weak and non-existent covariate effects, and thereby reduces false-positive findings. To achieve this, the method makes use of the mass spectral peak data by clustering similar peaks into latent compounds, and by further clustering latent compounds into groups that respond in a coherent way to the experimental covariates. We demonstrate the method with three simulated studies and validate it with a metabolomic benchmark dataset.

Availability and implementation: An implementation in R is available at http://research.ics.aalto.fi/mi/software/peakANOVA/.

Contact:  samuel.kaski@aalto.fi.
Unveiling new biological relationships using shared hits of chemical screening assay pairs
Authors: Liu Xueping , Campillos Monica
Published: August 2014

Motivation: Although the integration and analysis of the activity of small molecules across multiple chemical screens is a common approach to determine the specificity and toxicity of hits, the suitability of these approaches to reveal novel biological information is less explored. Here, we test the hypothesis that assays sharing selective hits are biologically related.

Results: We annotated the biological activities (i.e. biological processes or molecular activities) measured in assays and constructed chemical hit profiles with sets of compounds differing on their selectivity level for 1640 assays of ChemBank repository. We compared the similarity of chemical hit profiles of pairs of assays with their biological relationships and observed that assay pairs sharing non-promiscuous chemical hits tend to be biologically related. A detailed analysis of a network containing assay pairs with the highest hit similarity confirmed biological meaningful relationships. Furthermore, the biological roles of predicted molecular targets of the shared hits reinforced the biological associations between assay pairs.

Contact:  monica.campillos@helmholtz-muenchen.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Microarray R-based analysis of complex lysate experiments with MIRACLE
Authors: List Markus , Block Ines , Pedersen Marlene Lemvig , Christiansen Helle , Schmidt Steffen , Thomassen Mads , Tan Qihua , Baumbach Jan , Mollenhauer Jan
Published: August 2014

Motivation: Reverse-phase protein arrays (RPPAs) allow sensitive quantification of relative protein abundance in thousands of samples in parallel. Typical challenges involved in this technology are antibody selection, sample preparation and optimization of staining conditions. The issue of combining effective sample management and data analysis, however, has been widely neglected.

Results: This motivated us to develop MIRACLE, a comprehensive and user-friendly web application bridging the gap between spotting and array analysis by conveniently keeping track of sample information. Data processing includes correction of staining bias, estimation of protein concentration from response curves, normalization for total protein amount per sample and statistical evaluation. Established analysis methods have been integrated with MIRACLE, offering experimental scientists an end-to-end solution for sample management and for carrying out data analysis. In addition, experienced users have the possibility to export data to R for more complex analyses. MIRACLE thus has the potential to further spread utilization of RPPAs as an emerging technology for high-throughput protein analysis.

Availability: Project URL: http://www.nanocan.org/miracle/

Contact: mlist@health.sdu.dk

Supplementary information:  Supplementary data are available at Bioinformatics online.
cnvOffSeq: detecting intergenic copy number variation using off-target exome sequencing data
Authors: Bellos Evangelos , Coin Lachlan J. M.
Published: August 2014

Motivation: Exome sequencing technologies have transformed the field of Mendelian genetics and allowed for efficient detection of genomic variants in protein-coding regions. The target enrichment process that is intrinsic to exome sequencing is inherently imperfect, generating large amounts of unintended off-target sequence. Off-target data are characterized by very low and highly heterogeneous coverage and are usually discarded by exome analysis pipelines. We posit that off-target read depth is a rich, but overlooked, source of information that could be mined to detect intergenic copy number variation (CNV). We propose cnvOffseq, a novel normalization framework for off-target read depth that is based on local adaptive singular value decomposition (SVD). This method is designed to address the heterogeneity of the underlying data and allows for accurate and precise CNV detection and genotyping in off-target regions.

Results: cnvOffSeq was benchmarked on whole-exome sequencing samples from the 1000 Genomes Project. In a set of 104 gold standard intergenic deletions, our method achieved a sensitivity of 57.5% and a specificity of 99.2%, while maintaining a low FDR of 5%. For gold standard deletions longer than 5 kb, cnvOffSeq achieves a sensitivity of 90.4% without increasing the FDR. cnvOffSeq outperforms both whole-genome and whole-exome CNV detection methods considerably and is shown to offer a substantial improvement over naïve local SVD.

Availability and Implementation: cnvOffSeq is available at http://sourceforge.net/p/cnvoffseq/

Contact:  evangelos.bellos09@imperial.ac.uk or l.coin@imb.uq.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
Entropy-driven partitioning of the hierarchical protein space
Authors: Rappoport Nadav , Stern Amos , Linial Nathan , Linial Michal
Published: August 2014

Motivation: Modern protein sequencing techniques have led to the determination of >50 million protein sequences. ProtoNet is a clustering system that provides a continuous hierarchical agglomerative clustering tree for all proteins. While ProtoNet performs unsupervised classification of all included proteins, finding an optimal level of granularity for the purpose of focusing on protein functional groups remain elusive. Here, we ask whether knowledge-based annotations on protein families can support the automatic unsupervised methods for identifying high-quality protein families. We present a method that yields within the ProtoNet hierarchy an optimal partition of clusters, relative to manual annotation schemes. The method’s principle is to minimize the entropy-derived distance between annotation-based partitions and all available hierarchical partitions. We describe the best front (BF) partition of 2 478 328 proteins from UniRef50. Of 4 929 553 ProtoNet tree clusters, BF based on Pfam annotations contain 26 891 clusters. The high quality of the partition is validated by the close correspondence with the set of clusters that best describe thousands of keywords of Pfam. The BF is shown to be superior to naïve cut in the ProtoNet tree that yields a similar number of clusters. Finally, we used parameters intrinsic to the clustering process to enrich a priori the BF’s clusters. We present the entropy-based method’s benefit in overcoming the unavoidable limitations of nested clusters in ProtoNet. We suggest that this automatic information-based cluster selection can be useful for other large-scale annotation schemes, as well as for systematically testing and comparing putative families derived from alternative clustering methods.

Availability and implementation: A catalog of BF clusters for thousands of Pfam keywords is provided at http://protonet.cs.huji.ac.il/bestFront/

Contact: michall@cc.huji.ac.il
The circumgalactic medium of high-redshift galaxies
Authors: Pallottini A. , Gallerani S. , Ferrara A.
Published: August 2014

We study the properties of the circumgalactic medium (CGM) of high-z galaxies in the metal enrichment simulations presented in Pallottini et al. At z = 4, we find that the simulated CGM gas density profiles are self-similar, once scaled with the virial radius of the parent dark matter halo. We also find a simple analytical expression relating the neutral hydrogen equivalent width (EWH i) of CGM absorbers as a function of the line-of-sight impact parameter (b). We test our predictions against mock spectra extracted from the simulations and show that the model reproduces the EWH i(b) profile extracted from the synthetic spectra analysis. When compared with available data, our CGM model nicely predicts the observed EWH i(b) in z ≲ 2 galaxies, and supports the idea that the CGM profile does not evolve with redshift.
Sustaining observations of the unsteady ocean circulation
Authors: Frajka-Williams E.
Published: August 2014

Sustained observations of ocean properties reveal a global warming trend and rising sea levels. These changes have been documented by traditional ship-based measurements of ocean properties, whereas more recent Argo profiling floats and satellite records permit estimates of ocean changes on a near real-time basis. Through these and newer methods of observing the oceans, scientists are moving from quantifying the ‘state of the ocean’ to monitoring its variability, and distinguishing the physical processes bringing signals of change. In this paper, I give a brief overview of the UK contributions to the physical oceanographic observations, and the role they have played in the wider global observing systems. While temperature and salinity are the primary measurements of physical oceanography, new transbasin mooring arrays also resolve changes in ocean circulation on daily timescales. Emerging technologies permit routine observations at higher-than-ever spatial resolutions. Following this, I then give a personal perspective on the future of sustained observations. New measurement techniques promise exciting discoveries concerning the role of smaller scales and boundary processes in setting the large-scale ocean circulation and the ocean's role in climate. The challenges now facing the scientific community include sustaining critical observations in the case of funding system changes or shifts in government priorities. These long records will enable a determination of the role and response of the ocean to climate change.
Sustaining observations in the polar oceans
Authors: Abrahamsen E. P.
Published: August 2014

Polar oceans present a unique set of challenges to sustained observations. Sea ice cover restricts navigation for ships and autonomous measurement platforms alike, and icebergs present a hazard to instruments deployed in the upper ocean and in shelf seas. However, the important role of the poles in the global ocean circulation provides ample justification for sustained observations in these regions, both to monitor the rapid changes taking place, and to better understand climate processes in these traditionally poorly sampled areas. In the past, the vast majority of polar measurements took place in the summer. In recent years, novel techniques such as miniature CTD (conductivity–temperature–depth) tags carried by seals have provided an explosion in year-round measurements in areas largely inaccessible to ships, and, as ice avoidance is added to autonomous profiling floats and gliders, these promise to provide further enhancements to observing systems. In addition, remote sensing provides vital information about changes taking place in sea ice cover at both poles. To make these observations sustainable into the future, improved international coordination and collaboration is necessary to gain optimum utilization of observing networks.
Diffraction-limited storage-ring vacuum technology
Authors: Al-Dmour Eshraq , Ahlback Jonny , Einfeld Dieter , Tavares Pedro Fernandes , Grabski Marek
Published: August 2014

Some of the characteristics of recent ultralow-emittance storage-ring designs and possibly future diffraction-limited storage rings are a compact lattice combined with small magnet apertures. Such requirements present a challenge for the design and performance of the vacuum system. The vacuum system should provide the required vacuum pressure for machine operation and be able to handle the heat load from synchrotron radiation. Small magnet apertures result in the conductance of the chamber being low, and lumped pumps are ineffective. One way to provide the required vacuum level is by distributed pumping, which can be realised by the use of a non-evaporable getter (NEG) coating of the chamber walls. It may not be possible to use crotch absorbers to absorb the heat from the synchrotron radiation because an antechamber is difficult to realise with such a compact lattice. To solve this, the chamber walls can work as distributed absorbers if they are made of a material with good thermal conductivity, and distributed cooling is used at the location where the synchrotron radiation hits the wall. The vacuum system of the 3 GeV storage ring of MAX IV is used as an example of possible solutions for vacuum technologies for diffraction-limited storage rings.
The MAX IV storage ring project
Authors: Tavares Pedro F. , Leemann Simon C. , Sjöström Magnus , Andersson Åke
Published: August 2014

The MAX IV facility, currently under construction in Lund, Sweden, features two electron storage rings operated at 3 GeV and 1.5 GeV and optimized for the hard X-ray and soft X-ray/VUV spectral ranges, respectively. A 3 GeV linear accelerator serves as a full-energy injector into both rings as well as a driver for a short-pulse facility, in which undulators produce X-ray pulses as short as 100 fs. The 3 GeV ring employs a multibend achromat (MBA) lattice to achieve, in a relatively short circumference of 528 m, a bare lattice emittance of 0.33 nm rad, which reduces to 0.2 nm rad as insertion devices are added. The engineering implementation of the MBA lattice raises several technological problems. The large number of strong magnets per achromat calls for a compact design featuring small-gap combined-function magnets grouped into cells and sharing a common iron yoke. The small apertures lead to a low-conductance vacuum chamber design that relies on the chamber itself as a distributed copper absorber for the heat deposited by synchrotron radiation, while non-evaporable getter (NEG) coating provides for reduced photodesorption yields and distributed pumping. Finally, a low main frequency (100 MHz) is chosen for the RF system yielding long bunches, which are further elongated by passively operated third-harmonic Landau cavities, thus alleviating collective effects, both coherent (e.g.resistive wall instabilities) and incoherent (intrabeam scattering). In this paper, we focus on the MAX IV 3 GeV ring and present the lattice design as well as the engineering solutions to the challenges inherent to such a design. As the first realisation of a light source based on the MBA concept, the MAX IV 3 GeV ring offers an opportunity for validation of concepts that are likely to be essential ingredients of future diffraction-limited light sources.
The Sirius project
Authors: Liu Lin , Milas Natalia , Mukai Afonso H. C. , Resende Ximenes R. , de Sá Fernando H.
Published: August 2014

The lattice design and beam dynamics optimization for Sirius, a new low-emittance synchrotron light source presently under construction at the Brazilian Synchrotron Light Laboratory (LNLS) in Campinas, Brazil, is presented. The electron storage ring is based on a five-bend achromat (5BA) design achieving a bare lattice emittance of 0.28 nm rad for a 3 GeV beam. The circumference of 518 m contains 20 achromatic straight sections of alternating 7 m and 6 m in length. An innovative approach is adopted to enhance the performance of the storage ring dipoles by combining low-field (0.58 T) magnets for the main beam deflection with a very short 2 T permanent-magnet superbend sandwiched in the center dipole. This superbend creates 12 keV critical photon energy dipole sources with modest total energy loss from dipoles. In addition it also creates a longitudinal dipole field gradient that reduces the emittance by about 10%. The optimized dynamic aperture allows for top-up operation with off-axis injection and the optimized energy acceptance allows for a total beam lifetime of around 11 h at nominal current with a third-harmonic cavity.
High-pressure X-ray science on the ultimate storage ring
Authors: McMahon Malcolm I.
Published: August 2014

The advent of the ESRF, APS and SPring-8 third-generation synchrotron sources in the mid-1990s heralded a golden age of high-pressure X-ray science. The high-energy monochromatic micro-focused X-ray beams from these storage rings, combined with the new high-pressure diffraction and spectroscopy techniques developed in the late 1980s, meant that researchers were immediately able to make detailed structural studies at pressures comparable with those at the centre of the Earth, studies that were simply not possible only five years previously. And new techniques, such as X-ray inelastic scattering and X-ray nuclear scattering, became possible at high pressure for the first time, providing wholly-new insight into the behaviour of materials at high densities. The arrival of new diffraction-limited storage rings, with their much greater brightness, and ability to achieve focal-spot diameters for high-energy X-ray beams of below 1 µm, offers the possibility of a new generation of high-pressure science, both extending the scope of what is already possible, and also opening ways to wholly-new areas of investigation.
Spectromicroscopy and coherent diffraction imaging: focus on energy materials applications
Authors: Hitchcock Adam P. , Toney Michael F.
Published: August 2014

Current and future capabilities of X-ray spectromicroscopy are discussed based on coherence-limited imaging methods which will benefit from the dramatic increase in brightness expected from a diffraction-limited storage ring (DLSR). The methods discussed include advanced coherent diffraction techniques and nanoprobe-based real-space imaging using Fresnel zone plates or other diffractive optics whose performance is affected by the degree of coherence. The capabilities of current systems, improvements which can be expected, and some of the important scientific themes which will be impacted are described, with focus on energy materials applications. Potential performance improvements of these techniques based on anticipated DLSR performance are estimated. Several examples of energy sciences research problems which are out of reach of current instrumentation, but which might be solved with the enhanced DLSR performance, are discussed.
Coherent imaging at the diffraction limit
Authors: Thibault Pierre , Guizar-Sicairos Manuel , Menzel Andreas
Published: August 2014

X-ray ptychography, a scanning coherent diffractive imaging technique, holds promise for imaging with dose-limited resolution and sensitivity. If the foreseen increase of coherent flux by orders of magnitude can be matched by additional technological and analytical advances, ptychography may approach imaging speeds familiar from full-field methods while retaining its inherently quantitative nature and metrological versatility. Beyond promises of high throughput, spectroscopic applications in three dimensions become feasible, as do measurements of sample dynamics through time-resolved imaging or careful characterization of decoherence effects.
X-ray nanoprobes and diffraction-limited storage rings: opportunities and challenges of fluorescence tomography of biological specimens
Authors: de Jonge Martin D. , Ryan Christopher G. , Jacobsen Chris J.
Published: August 2014

X-ray nanoprobes require coherent illumination to achieve optic-limited resolution, and so will benefit directly from diffraction-limited storage rings. Here, the example of high-resolution X-ray fluorescence tomography is focused on as one of the most voracious demanders of coherent photons, since the detected signal is only a small fraction of the incident flux. Alternative schemes are considered for beam delivery, sample scanning and detectors. One must consider as well the steps before and after the X-ray experiment: sample preparation and examination conditions, and analysis complexity due to minimum dose requirements and self-absorption. By understanding the requirements and opportunities for nanoscale fluorescence tomography, one gains insight into the R&D challenges in optics and instrumentation needed to fully exploit the source advances that diffraction-limited storage rings offer.
X-ray photon correlation spectroscopy
Authors: Shpyrko Oleg G.
Published: August 2014

In recent years, X-ray photon correlation spectroscopy (XPCS) has emerged as one of the key probes of slow nanoscale fluctuations, applicable to a wide range of condensed matter and materials systems. This article briefly reviews the basic principles of XPCS as well as some of its recent applications, and discusses some novel approaches to XPCS analysis. It concludes with a discussion of the future impact of diffraction-limited storage rings on new types of XPCS experiments, pushing the temporal resolution to nanosecond and possibly even picosecond time scales.
A case study exploring FM components for elderly in care and attention homes using post occupancy evaluation
Authors: Leung Mei-yung , Yu Jingyu , Dongyu Chen , Yuan Ting
Published: August 2014

Purpose

– The paper aims to investigate the key components of facilities management (FM) in care and attention (C & A) homes from the end users’ perspective based on a post-occupancy evaluation method. Hong Kong is a rapidly ageing society. Elderly population may reach 24.3 per cent in the next 20 years, causing an increase in the demand for care services. Therefore, it is necessary to provide sufficient and satisfactory residential C & A homes with appropriate facilities for our elderly.

Design/methodology/approach

– To collect subjective data from end users, a questionnaire survey was conducted in 119 respondents consisting of both elderly residents and staff of the C & A homes. To further understand the actual situations, site measurements were also used to collect the objective data from the representative homes.

Findings

– The results indicate that three aspects of key FM components, namely, architect, building services and supporting, all have significant relationships with the overall satisfaction. The site measurements further revealed the actual environment of the seven C & A homes, especially the contrasts between homes with highest scores (Homes E and F) and lowest scores (B and D).

Practical implications

– To provide a clear picture to the government and construction professionals, a number of practical recommendations were proposed, such as sufficient space with single or couple bedrooms, sufficient corridor width for two people in wheelchairs and white or pink as the colour scheme in architectural aspect; sufficient lighting, central air conditioning system and adequate quantities of natural fresh air in the building service aspect; and frequently updated menus, door lock and CCTV system for supporting facilities.

Originality/value

– This paper applied site measurement on the representative homes to cross-check the quantitative results. The findings of this study can assist architects and facilities managers in C & A homes to improve FM services during the design and operational stages for improving the satisfaction levels of elderly residents.
The evolution of public services from co-production to co-creation and beyond
Authors: Virtanen Petri , Stenvall Jari
Published: August 2014

Purpose

– Based on the concept of “intelligent public organisation” as a new theoretical trajectory for New Public Management (NPM) theory, this paper brings together the recent critical discussion on NPM as it relates to public services and service science while specifically pinpointing the nature of public sector intelligence, evaluation, as well as management and leadership of public services. The paper aims to discuss these issues.

Design/methodology/approach

– The paper highlights the ongoing discussion on service-dominant logic and reflects the major innovations in service research, innovation studies, organisational learning, development methods, and evaluation from the public services’ perspective.

Findings

– It is argued that contemporary public management theories and practices – and theories reflecting the role of public services – should make more use of that body of literature focusing on substantive service-dominant theories found in marketing and business studies. The paper concludes that the academic discourse on NPM and New Public Governance (NPG) has been rich in content, but to date rather biased from a public services perspective.

Practical implications

– It is argued that public services are arenas for interaction, co-operation, and co-creation, orchestrated by the networks of organisations providing these services. The essence of “service user” has also changed in recent decades. This development has practical implications for developing leadership practices in public services.

Originality/value

– Doctrines of NPM and NPG have been missing an appreciation of the comprehensive role played by public services and the role of evaluation of public services has also been largely ignored. In this light and in regards to public services in particular, the new wave of public policy evaluation paradigms could usefully be integrated with NPG.
Perceptions of clinical leadership amongst West Midlands registrars
Authors: Mendis Dulani , Paton Calum
Published: August 2014

Purpose

– Previously published studies about trainee perceptions of clinical leadership, although small in number, have not assessed the opinions of senior registrars nor established their awareness of the relevant leadership frameworks. The paper aims to discuss these issues.

Design/methodology/approach

– Survey questions and interview questions were designed and a comparison of the relevant literature was performed. An online survey was sent via e-mail to a potential of 2,126 registrar trainees within the deanery and a series of semi-structured interviews (analysed via a content analysis) were conducted amongst voluntary subjects.

Findings

– The response rate for the questionnaire was 247/2,126 (11.6 per cent). Respondents recognised the importance of leadership (90.4 per cent), professionalism (99.6 per cent) and promoted team-working (89.8 per cent). In total, 94.3 per cent of respondents have had ideas for improvement in their workplace; however, only 27.9 per cent have had their ideas for change implemented. Of the 85.5 per cent of trainees who are not aware of the leadership frameworks, 89.1 per cent performed leadership activities either daily or sometimes. The priorities of registrars did appear to differ between the junior and senior grades.

Originality/value

– Registrar trainees have a desire to engage and a perceived ability to contribute to service improvement; however, a lack of encouragement, awareness and limited training opportunities serve to hamper the development of clinical leadership potential. This study presents itself as a pilot and will hopefully prompt a larger deanery study to gain a thorough assessment of all trainee perceptions, in order to improve the training programme and ultimately create a generation of consultants equipped to engage in clinical leadership throughout their lifelong career in the National Health Service.
Library instruction for first-year students
Authors: Dhawan Amrita , j Chen Ching-Jung
Published: August 2014

Purpose

– This paper aims to discuss the background, design and implementation of the new library instruction. When a new core curriculum for first-year students was adopted at the City College of New York in the fall of 2008, the City College Library took this opportunity to establish a new approach to teach library research to freshmen. Two library workshops were embedded into a six-credit combined content and writing course.

Design/methodology/approach

– This paper documents the process by which the City College Library successfully transitioned to the new system and also reflects on the theory and practice of teaching information literacy in an academic setting.

Findings

– Library workshops embedded within the new core curriculum have clear advantages over previous library instruction. By designing and implementing library workshops to blend with the new course, the Library has become a partner in an innovative first-year program.

Practical implications

– This study will provide useful information on the teaching and assessment of embedded library instruction and stimulate further thought on the role of information instruction in furthering the mission of undergraduate education.

Originality/value

– This paper presents opportunities to expand library instruction to the first-year seminar, the most commonly implemented curricular intervention designed for freshman students. By taking part in this important project, the Library becomes an integral participant in the initiative for retention and success for undergraduate education.
Student reflections on multimodal course content delivery
Authors: A. Jackson Shaun
Published: August 2014

Purpose

– The purpose of this paper is to illustrate a for-credit information literacy course redesign that used a flexible multimodal framework to address individual student learning preferences, personal differences and abilities as well as teaching preferences.

Design/methodology/approach

– Students taking the course were surveyed as to their preferences for content delivery. A qualitative analysis of student reflections was conducted to determine the efficacy of maintaining multiple course formats and to solicit feedback for course improvements.

Findings

– Results show that students were definitive in their preferences for how they access course materials and that enough students used each format to justify maintaining both. Findings also showed students’ appreciation for being given options.

Research limitations/implications

– Content delivery modes are changing rapidly. Future studies should explore the efficacy of other modes of delivery.

Practical implications

– As technology and students’ familiarity with course delivery modes change, how we deliver content to students will also change. The key to reaching students in an effective manner is flexibility.

Originality/value

– Exploring why and how students choose to learn provides valuable feedback into how we should or should not deliver course content. Learning what works, and providing multiple options, will increase the likelihood of success for a diverse student body.
Limits to robustness and reproducibility in the demarcation of operational taxonomic units
Authors: Schmidt Thomas S. B. , Matias Rodrigues João F. , von Mering Christian
Published: August 2014

The demarcation of operational taxonomic units (OTUs) from complex sequence data sets is a key step in contemporary studies of microbial ecology. However, as biologically motivated ‘optimal’ OTU‐binning algorithms remain elusive, many conceptually distinct approaches continue to be used. Using a global data set of 887 870 bacterial 16S rRNA gene sequences, we objectively quantified biases introduced by several widely employed sequence clustering algorithms. We found that OTU‐binning methods often provided surprisingly non‐equivalent partitions of identical data sets, notably when clustering to the same nominal similarity thresholds; and we quantified the resulting impact on ecological data description for a well‐defined human skin microbiome data set. We observed that some methods were very robust to varying clustering thresholds, while others were found to be highly susceptible even to slight threshold variations. Moreover, we comprehensively quantified the impact of the choice of 16S rRNA gene subregion, as well as of data set scope and context on algorithm performance. Our findings may contribute to an enhanced comparability of results across sequence‐processing pipelines, and we arrive at recommendations towards higher levels of standardization in established workflows.