bluuebunny/crossref_metadata_2025 huggingface dataset:
Pressure injury in Australian public hospitals: a cost-of-illness study
Authors: Nguyen Kim-Huong , Chaboyer Wendy , Whitty Jennifer A.
Published: March 2015

Objective Pressure injuries (PI) are largely preventable and can be viewed as an adverse outcome of a healthcare admission, yet they affect millions of people and consume billions of dollars in healthcare spending. The existing literature in Australia presents a patchy picture of the economic burden of PI on society and the health system. The aim of the present study was to provide a more comprehensive and updated picture of PI by state and severity using publicly available data. Methods A cost-of-illness analysis was conducted using a prevalence approach and a 1-year time horizon based on data from the existing literature extrapolated using simulation methods to estimate the costs by PI severity and state subgroups. Results The treatment cost across all states and severity in 2012–13 was estimated to be A$983 million per annum, representing approximately 1.9% of all public hospital expenditure or 0.6% of the public recurrent health expenditure. The opportunity cost was valued at an additional A$820 million per annum. These estimates were associated with a total number of 121 645 PI cases in 2012–13 and a total number of 524 661 bed days lost. Conclusions The costs estimated in the present study highlight the economic waste for the Australian health system associated with a largely avoidable injury. Wastage can also be reduced by preventing moderate injuries (Stage I and II) from developing into severe cases (Stage III and IV), because the severe cases, accounting for 12% of cases, mounted to 30% of the total cost.
Synthesis, Structural Characterisation, and Spectroscopic Properties of Copper(I) Complexes and their Applications to Dye-Sensitised Solar Cells
Authors: Huang Ting-Hong , Yan Jie , Liu Ye-Feng , Xie Yun-Tao , Jia Chen
Published: March 2015

Based on the ligand 1,4-bis(2-(diphenylphophino)benzylideneamino)benzene (pbb), two complexes, [Cu2(pbb)(2,2′-bipyridine)2](BF4)2 (1) and [Cu2(pbb)(phen)2](BF4)2 (2), have been prepared and characterised by IR, 1H NMR, 31P NMR, 19F NMR, and 11B NMR spectroscopy and X-ray crystal structure analysis. Structural analysis reveals that complexes 1 and 2 contain 1D infinite chains and 2D supramolecular networks constructed by C–H···π and π···π interactions, and an ordered-layer-lattice of BF4– is located between these 2D networks. The results show that C–H···π and π···π interactions play an important role in the formation of 2D supramolecular networks. The UV-vis absorption peaks of complexes 1 and 2 display intraligand charge transfer and metal to ligand charge transfer (MLCT) absorption. Complexes 1 and 2 display efficient luminescent emission assigned to MLCT excited states, and the maximum emissions of these complexes in acetonitrile solution are different from those of the solid-state samples. In addition, complexes 1 and 2 have been exploited as sensitisers in dye-sensitised solar cells, and efficiencies are also observed.
Publication outputs from a Primary and Community Health Research Unit, 2011–14
Authors: Friesen Emma L. , Comino Elizabeth J.
Published: March 2015

Publication of research is a goal of research capacity building initiatives. We reviewed the publications generated by practitioner researchers involved with the Primary and Community Health Research Unit (PCHRU), within the Division of Community Health in South Western Sydney Local Health District (SWSLHD), between 2011 and 2014. Publications were categorised using the Higher Education Research Data Collection Specifications. Published outputs included five refereed articles, one refereed full conference paper and 25 non-published conference presentations. A further 11 refereed articles in draft form were located. The majority of publications were considered ‘not published’ and not widely discoverable. Evidence for expected timeframes for project completion, including support for publication of research, is needed.
‘Drug users stick together’: HIV testing in peer-based drop-in centres among people who inject drugs in Thailand
Authors: Ti Lianping , Hayashi Kanna , Hattirat Sattara , Suwannawong Paisan , Kaplan Karyn , Kerr Thomas
Published: March 2015

Introduction
Although there is a well recognised need for novel approaches to HIV testing, particularly for marginalised populations at high risk for HIV infection, there remains a dearth of information on the acceptability of peer-based HIV testing among people who inject drugs (PWID). Methods: Between July 2011 and June 2012, 22 in-depth interviews were conducted with PWID participating in the Mitsampan Community Research Project in Bangkok, Thailand. Semi-structured interviews explored willingness to access rapid HIV testing delivered by a healthcare professional or a trained peer within peer-based drop-in centres. Audio-recorded interviews were transcribed verbatim and a thematic analysis was conducted. Results: All participants indicated interest in accessing rapid HIV testing by a healthcare professional at peer-based drop-in centres due to the advantage of receiving immediate results. Experiencing stigma and discrimination by healthcare workers and wanting to avoid administrative barriers in hospitals were also reported as reasons for why PWID preferred HIV testing in peer-based settings. Peer support and shared lived experiences were repeatedly mentioned as benefits of peer-based testing. However, some concerns regarding peer-delivered testing were expressed and included a fear of peers’ violating confidentiality and concerns regarding peers’ qualifications for conducting an HIV test. Conclusion: Many PWID in this study sample noted the value of a peer-based approach to receiving testing and indicated their willingness to access rapid HIV testing in peer-based drop-in centres. The findings from this study highlight the potential for novel peer-based methods to complement existing HIV services in an effort to improve access to testing among this population.
How many are there? The use and misuse of continental-scale wildlife abundance estimates
Authors: Hone Jim , Buckmaster Tony
Published: March 2015

The number of individuals in a wildlife population is often estimated and the estimates used for wildlife management. The scientific basis of published continental-scale estimates of individuals in Australia of feral cats and feral pigs is reviewed and contrasted with estimation of red kangaroo abundance and the usage of the estimates. We reviewed all papers on feral cats, feral pigs and red kangaroos found in a Web of Science search and in Australian Wildlife Research and Wildlife Research, and related Australian and overseas scientific and ‘grey’ literature. The estimated number of feral cats in Australia has often been repeated without rigorous evaluation of the origin of the estimate. We propose an origin. The number of feral pigs in Australia was estimated and since then has sometimes been quoted correctly and sometimes misquoted. In contrast, red kangaroo numbers in Australia have been estimated by more rigorous methods and the relevant literature demonstrates active refining and reviewing of estimation procedures and management usage. We propose four criteria for acceptable use of wildlife abundance estimates in wildlife management. The criteria are: use of appropriate statistical or mathematical analysis; precision estimated; original source cited; and age (current or out-of-date) of an estimate evaluated. The criteria are then used here to assess the strength of evidence of the abundance estimates and each has at least one deficiency (being out-of-date). We do know feral cats, feral pigs and red kangaroos occur in Australia but we do not know currently how many feral cats or feral pigs are in Australia. Our knowledge of red kangaroo abundance is stronger at the state than the continental scale, and is also out-of-date at the continental scale. We recommend greater consideration be given to whether abundance estimates at the continental scale are needed and to their use, and not misuse, in wildlife management.
Estimating rodent losses to stored rice as a means to assess efficacy of rodent management
Authors: Belmain Steven R. , Htwe Nyo Me , Kamal Nazira Q. , Singleton Grant R.
Published: March 2015

Context
Post-harvest losses by rodents have traditionally been calculated by estimates of consumption determined in the laboratory. Methods for assessing storage losses by rodents under smallholder conditions will help farmers and policy makers understand the impact rodents may have on food security, nutrition and health. Stored product loss assessment methods could also be used to monitor the effects of rodent control in villages.

Aims
The present study examined a method to measure the amount of rice eaten by rodents in household granaries. The effects of trapping and better hygiene around granaries to reduce rodent populations were investigated using the post-harvest monitoring method to determine whether the program was successful in lowering rodent numbers sufficiently to reduce post-harvest losses.

Methods
Baskets with known quantities of rice were placed within household granaries and monitored periodically for moisture content, weight loss, faecal contamination and percentage of rodent-damaged grains. Using an empirical treatment–control study, rodent management was performed at the community level through daily trapping in two Bangladesh villages and in Myanmar at the granary storehouse level. Post-harvest losses were monitored in granaries in villages with rodent management and in similar granaries in villages where there was no management.

Key results
Estimates of household losses in the absence of rodent control were 2.5% in Bangladesh and 17% in Myanmar. These losses were reduced when rodent control was implemented, down to 0.5% in Bangladesh and 5% in Myanmar.

Conclusions
The impact of rodents on smallholder storage can be accurately assessed in the field under realistic conditions. Intensive daily trapping at the community level together with improved hygiene practices can successfully reduce rodent numbers, and this can significantly reduce stored grain losses and rodent contamination and damage levels.

Implications
In addition to the threat of rodent pests during crop production, rodents are a major threat to food security after harvest and have, as of yet, unquantified impacts on household nutrition and health through potential transmission of gastroenteric diseases and zoonoses to householders and domestic livestock. Trapping and environmental management are affordable and effective tools to reduce rodent impacts on stored grain within communities and are viable alternatives to rodenticides.
Glutathione and multidrug resistance protein transporter mediate a self-propelled disposal of bismuth in human cells
Authors: Hong Yifan , Lai Yau-Tsz , Chan Godfrey Chi-Fung , Sun Hongzhe
Published: March 2015

Significance

Bismuth compounds have long been used in clinic for the treatment of various diseases, in particular, for
Helicobacter pylori
infection. We reported the mechanism of uptake of bismuth compounds by mammalian cells and bacteria, and demonstrated a passive transport of the metallodrug. We showed that glutathione and multidrug resistance protein transporter mediate a self-propelled disposal of bismuth antiulcer drug. A model was derived to elucidate the uptake of the metallodrug, and which may readily be extended to other drugs or drug candidates. Our work uncovered the secret of low toxicity of bismuth in human and relatively high drug selectivity against “glutathione-poor” pathogens such as
H. pylori
.
Noninvasive in vivo imaging reveals differences between tectorial membrane and basilar membrane traveling waves in the mouse cochlea
Authors: Lee Hee Yoon , Raphael Patrick D. , Park Jesung , Ellerbee Audrey K. , Applegate Brian E. , Oghalai John S.
Published: March 2015

Significance

The membranes within the cochlea vibrate in response to sound. However, measuring these vibrations to study the sense of hearing has been a technological challenge because invasive techniques have been required. Herein, we describe a new technique capable of depth-resolved displacement measurements in 3D space with picometer sensitivity within the unopened mouse cochlea. We used this technique to make, to our knowledge, the first measurements of the tectorial membrane, the structure that overlies the sensory hair cell stereociliary bundles, within a healthy cochlea. We found that the tectorial membrane sustains traveling wave propagation differently than the more commonly measured basilar membrane. This finding provides a clearer understanding of the mechanical stimulus at the level of the inner hair cell responsible for non-linear sound encoding.
Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators
Authors: Yan Qinghong , Weyn-Vanhentenryck Sebastien M. , Wu Jie , Sloan Steven A. , Zhang Ye , Chen Kenian , Wu Jia Qian , Barres Ben A. , Zhang Chaolin
Published: March 2015

Significance

Alternative splicing (AS) plays an important role in the mammalian brain, but our atlas of AS events is incomplete. Here, we conducted comprehensive analysis of deep RNA-Seq data of mouse cortex to identify new AS events and evaluate their functionality. We expanded the number of annotated AS events more than 10-fold and demonstrated that, like many known events, thousands of newly discovered events are regulated, conserved, and likely functional. In particular, some can regulate gene expression levels through nonsense-mediated decay, a known mechanism for RNA binding protein autoregulation. Surprisingly, we discovered a number of chromatin regulators as novel targets of this mechanism, revealing a new regulatory link between epigenetics and AS that primarily emerged in the mammalian lineage.
Reproductive Complexity in a Long‐Lived Deepwater Fish, the Blackgill Rockfish
Authors: Lefebvre Lyndsey S. , Field John C.
Published: March 2015

Fish populations are regulated by complex biological processes and ecosystem interactions. To inform stock assessments and management models, a clear understanding of a species’ reproductive biology is necessary, particularly in long‐lived species, for which estimates of sustainable yield are sensitive to such parameters. Deviations from traditional views of iteroparity in marine fishes (e.g., prolonged adolescent periods and skipped spawning) complicate estimates of maturity and, in turn, spawning output. The Blackgill Rockfish Sebastes melanostomus, an important component of California's commercial rockfish fishery, is a slow‐growing deepwater species whose population is currently thought to be increasing after being fished to below conservation target levels. The objectives of this study were to describe the annual reproductive cycle, update maturity estimates, and detect unusual patterns of ovarian development by using both macroscopic and histological methods. Females were collected between 2010 and 2013 at locations off central and southern California. The annual reproductive cycle was protracted: vitellogenesis was initiated 7 months prior to the first appearance of fertilized eggs, and parturition occurred in December–May. A prolonged adolescent period, potentially lasting up to 12 years, was characterized by the presence of previtellogenic secondary‐growth oocytes year‐round and abortive maturation events. The cold temperatures and low oxygen levels characteristic of the species’ habitat are hypothesized to be the main drivers behind this slow development. Macroscopic staging was found to be sufficient for maturity estimates when samples were temporally restricted. Estimates of length and age at 50% maturity were 33.6 cm and 25.7 years based on histological staging. Estimates of regional maturity based on commercial samples collected between 2001 and 2009 showed a trend of decreasing size at maturity with decreasing latitude. This study highlights the importance of histological examination in accurately assessing ovarian development and consequent baseline maturity information for managed fish populations.

Received June 17, 2014; accepted December 16, 2014
Does Catch‐and‐Release Angling Alter the Behavior and Fate of Adult Atlantic Salmon During Upriver Migration?
Authors: Lennox Robert J. , Uglem Ingebrigt , Cooke Steven J. , Næsje Tor F. , Whoriskey Frederick G. , Havn Torgeir B. , Ulvan Eva M. , Solem Øyvind , Thorstad Eva B.
Published: March 2015

To reproduce, Atlantic Salmon Salmo salar return to freshwater rivers and migrate upriver to spawning areas. This migration is the basis for recreational fisheries, which for conservation reasons are increasingly characterized by catch‐and‐release angling. The effectiveness of catch and release for Atlantic Salmon conservation is contingent on the ability of individuals to recover from angling, resume migration, and reach spawning grounds at appropriate times. We monitored 27 caught and released Atlantic Salmon in River Gaula in 2013, a prominent and relatively pristine Norwegian river, by affixing external radio transmitters to them. Those fish were compared with a control group of 33 individuals caught and radio‐tagged at sea in bag nets before river entry. Whereas none of the control fish died during the study period, there were three mortalities among the caught‐and‐released fish (11%; significant difference). All mortalities were qualitatively associated with poor angler care, emphasizing the responsibility of anglers in practicing effective catch and release of Atlantic Salmon. Both control and caught and released Atlantic Salmon spent similar time resting below and in transiting a large natural barrier to migration, an 80‐m gorge. The angled and released Atlantic Salmon were distributed in similar locations throughout the river during the spawning season compared with control fish, but those caught and released later in the season appeared to migrate shorter total distances than control fish. Among the caught and released Atlantic Salmon, 17% were recaptured by anglers, which was similar to the rate of recapture of the control fish (21%). Ultimately, individual and population fitness was not likely to be significantly compromised as a result of catch and release because individuals were recorded in spawning areas at appropriate times. Catch and release can therefore be considered a tenable strategy for balancing the costs and benefits associated with the recreational fishery.

Received September 26, 2014; accepted December 16, 2014
hiHMM: Bayesian non-parametric joint inference of chromatin state maps
Authors: Sohn Kyung-Ah , Ho Joshua W. K. , Djordjevic Djordje , Jeong Hyun-hwan , Park Peter J. , Kim Ju Han
Published: March 2015

Motivation: Genome-wide mapping of chromatin states is essential for defining regulatory elements and inferring their activities in eukaryotic genomes. A number of hidden Markov model (HMM)-based methods have been developed to infer chromatin state maps from genome-wide histone modification data for an individual genome. To perform a principled comparison of evolutionarily distant epigenomes, we must consider species-specific biases such as differences in genome size, strength of signal enrichment and co-occurrence patterns of histone modifications.

Results: Here, we present a new Bayesian non-parametric method called hierarchically linked infinite HMM (hiHMM) to jointly infer chromatin state maps in multiple genomes (different species, cell types and developmental stages) using genome-wide histone modification data. This flexible framework provides a new way to learn a consistent definition of chromatin states across multiple genomes, thus facilitating a direct comparison among them. We demonstrate the utility of this method using synthetic data as well as multiple modENCODE ChIP-seq datasets.

Conclusion: The hierarchical and Bayesian non-parametric formulation in our approach is an important extension to the current set of methodologies for comparative chromatin landscape analysis.

Availability and implementation: Source codes are available at https://github.com/kasohn/hiHMM. Chromatin data are available at http://encode-x.med.harvard.edu/data_sets/chromatin/.

Contact:  peter_park@harvard.edu or juhan@snu.ac.kr

Supplementary information:  Supplementary data are available at Bioinformatics online.
IVA: accurate de novo assembly of RNA virus genomes
Authors: Hunt Martin , Gall Astrid , Ong Swee Hoe , Brener Jacqui , Ferns Bridget , Goulder Philip , Nastouli Eleni , Keane Jacqueline A. , Kellam Paul , Otto Thomas D.
Published: March 2015

Motivation: An accurate genome assembly from short read sequencing data is critical for downstream analysis, for example allowing investigation of variants within a sequenced population. However, assembling sequencing data from virus samples, especially RNA viruses, into a genome sequence is challenging due to the combination of viral population diversity and extremely uneven read depth caused by amplification bias in the inevitable reverse transcription and polymerase chain reaction amplification process of current methods.

Results: We developed a new de novo assembler called IVA (Iterative Virus Assembler) designed specifically for read pairs sequenced at highly variable depth from RNA virus samples. We tested IVA on datasets from 140 sequenced samples from human immunodeficiency virus-1 or influenza-virus-infected people and demonstrated that IVA outperforms all other virus de novo assemblers.

Availability and implementation: The software runs under Linux, has the GPLv3 licence and is freely available from http://sanger-pathogens.github.io/iva

Contact:  iva@sanger.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Mammalian genome evolution is governed by multiple pacemakers
Authors: Duchêne Sebastián , Ho Simon Y. W.
Published: March 2015

Genomic evolution is shaped by a dynamic combination of mutation, selection and genetic drift. These processes lead to evolutionary rate variation across loci and among lineages. In turn, interactions between these two forms of rate variation can produce residual effects, whereby the pattern of among-lineage rate heterogeneity varies across loci. The nature of rate variation is encapsulated in the pacemaker models of genome evolution, which differ in the degree of importance assigned to residual effects: none (Universal Pacemaker), some (Multiple Pacemaker) or total (Degenerate Multiple Pacemaker). Here we use a phylogenetic method to partition the rate variation across loci, allowing comparison of these pacemaker models. Our analysis of 431 genes from 29 mammalian taxa reveals that rate variation across these genes can be explained by 13 pacemakers, consistent with the Multiple Pacemaker model. We find no evidence that these pacemakers correspond to gene function. Our results have important consequences for understanding the factors driving genomic evolution and for molecular-clock analyses.

Availability and implementation: ClockstaR-G is freely available for download from github (https://github.com/sebastianduchene/clockstarg).

Contact:  simon.ho@sydney.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
GeLL: a generalized likelihood library for phylogenetic models
Authors: Money Daniel , Whelan Simon
Published: March 2015

Summary: Phylogenetic models are an important tool in molecular evolution allowing us to study the pattern and rate of sequence change. The recent influx of new sequence data in the biosciences means that to address evolutionary questions, we need a means for rapid and easy model development and implementation. Here we present GeLL, a Java library that lets users use text to quickly and efficiently define novel forms of discrete data and create new substitution models that describe how those data change on a phylogeny. GeLL allows users to define general substitution models and data structures in a way that is not possible in other existing libraries, including mixture models and non-reversible models. Classes are provided for calculating likelihoods, optimizing model parameters and branch lengths, ancestral reconstruction and sequence simulation.

Availability and implementation:  http://phylo.bio.ku.edu/GeLL under a GPL v3 license.

Contact:  daniel.money@dal.ca

Supplementary information:  Supplementary data are available at Bioinformatics online.
L-GRAAL: Lagrangian graphlet-based network aligner
Authors: Malod-Dognin Noël , Pržulj Nataša
Published: March 2015

Motivation: Discovering and understanding patterns in networks of protein–protein interactions (PPIs) is a central problem in systems biology. Alignments between these networks aid functional understanding as they uncover important information, such as evolutionary conserved pathways, protein complexes and functional orthologs. A few methods have been proposed for global PPI network alignments, but because of NP-completeness of underlying sub-graph isomorphism problem, producing topologically and biologically accurate alignments remains a challenge.

Results: We introduce a novel global network alignment tool, Lagrangian GRAphlet-based ALigner (L-GRAAL), which directly optimizes both the protein and the interaction functional conservations, using a novel alignment search heuristic based on integer programming and Lagrangian relaxation. We compare L-GRAAL with the state-of-the-art network aligners on the largest available PPI networks from BioGRID and observe that L-GRAAL uncovers the largest common sub-graphs between the networks, as measured by edge-correctness and symmetric sub-structures scores, which allow transferring more functional information across networks. We assess the biological quality of the protein mappings using the semantic similarity of their Gene Ontology annotations and observe that L-GRAAL best uncovers functionally conserved proteins. Furthermore, we introduce for the first time a measure of the semantic similarity of the mapped interactions and show that L-GRAAL also uncovers best functionally conserved interactions. In addition, we illustrate on the PPI networks of baker's yeast and human the ability of L-GRAAL to predict new PPIs. Finally, L-GRAAL's results are the first to show that topological information is more important than sequence information for uncovering functionally conserved interactions.

Availability and implementation: L-GRAAL is coded in C++. Software is available at: http://bio-nets.doc.ic.ac.uk/L-GRAAL/.

Contact:  n.malod-dognin@imperial.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Mining viral proteins for antimicrobial and cell-penetrating drug delivery peptides
Authors: Freire João Miguel , Almeida Dias Susana , Flores Luís , Veiga Ana Salomé , Castanho Miguel A.R.B.
Published: March 2015

Motivation: The need for more effective and safer pharmaceuticals is a persistent quest. Microbial adaptations create the need to permanently develop new antimicrobials (AMPs), for instance. Similarly, intracellular delivery of drugs is still a challenge and translocation of membranes for drug delivery is an area of intense research. Peptides can be used both as AMP drug leads and drug carrier systems for intracellular delivery. Multifunctional proteins are abundant in viruses but, surprisingly, have never been thoroughly screened for bioactive peptide sequences.

Results: Using the AMPA and CellPPD online tools, we have evaluated the propensity of viral proteins to comprise AMP or cell-penetrating peptides (CPPs). Capsid proteins from both enveloped and non-enveloped viruses, and membrane and envelope proteins from enveloped viruses, in a total of 272 proteins from 133 viruses, were screened to detect the presence of potential AMP and CPP sequences. A pool of 2444 and 426 CPP and AMP sequences, respectively, were discovered. The capsids of flaviviruses are the best sources of these peptides reaching more than 80% of CPP sequence coverage per protein. Selected sequences were tested experimentally and validated the results. Overall, this study reveals that viruses form a natural multivalent biotechnological platform still underexplored in drug discovery and the heterogeneous abundance of CPP/AMP sequences among viral families opens new avenues in viral biology research.

Contacts:  aveiga@medicina.ulisboa.pt or macastanho@medicina.ulisboa.pt

Supplementary information:  supplementary data are available at Bioinformatics online.
Medical student awareness of and interest in clinical informatics
Authors: Banerjee Rahul , George Paul , Priebe Cedric , Alper Eric
Published: March 2015

Objective We aimed to investigate medical students’ attitudes about Clinical Informatics (CI) training and careers.

Materials and Methods We distributed a web-based survey to students at four US allopathic medical schools.

Results Five hundred and fifty-seven medical students responded. Interest in CI training opportunities (medical school electives, residency electives, or academic fellowships) surpassed respondents’ prior awareness of these opportunities. Thirty percent of student respondents expressed at least some interest in a CI-related career, but they were no more aware of training opportunities than their peers who did not express such an interest.

Discussion Almost one third of medical students who responded to our survey expressed an interest in a CI-related career, but they were generally unaware of CI training and mentoring opportunities available to them. Early outreach to such medical students, through elective classes, professional society incentives, or expert partnerships, may positively influence the size and skill set of the future CI workforce.

Conclusion We should work as a field to increase the quantity, quality, and publicity of CI learning opportunities for interested medical students.
Technology-mediated interventions for enhancing medication adherence
Authors: Mistry Niraj , Keepanasseril Arun , Wilczynski Nancy L. , Nieuwlaat Robby , Ravall Manthan , Haynes R. Brian ,   the Patient Adherence Review Team
Published: March 2015

Background Despite effective therapies for many conditions, patients find it difficult to adhere to prescribed treatments. Technology-mediated interventions (TMIs) are increasingly being used with the hope of improving adherence.

Objective To assess the effects of TMI, intended to enhance patient adherence to prescribed medications, on both medication adherence and clinical outcomes.

Methods A secondary in-depth analysis was conducted of the subset of studies that utilized technology in at least one component of the intervention from an updated Cochrane review on all interventions for enhancing medication adherence. We included studies that clearly described an information and communication technology or medical device as the sole or major component of the adherence intervention.

Results Thirty-eight studies were eligible for in-depth review. Only seven had a low risk of bias for study design features, primary adherence, and clinical outcomes. Eighteen studies used a TMI for education and/or counseling, 11 studies used a TMI for self-monitoring and/or feedback, and nine studies used electronic reminders. Studies used a variety of TMIs, with telephone the most common technology in use. Studies targeted a wide distribution of diseases and used a variety of adherence and clinical outcome measures. A minority targeted children and adolescents. Fourteen studies reported significant effects in both adherence and clinical outcome measures.

Conclusions This review provides evidence for the inconsistent effectiveness of TMI for medication adherence and clinical outcomes. These results must be interpreted with caution due to a lack of high-quality studies.
Development of data representation standards by the human proteome organization proteomics standards initiative
Authors: Deutsch Eric W , Albar Juan Pablo , Binz Pierre-Alain , Eisenacher Martin , Jones Andrew R , Mayer Gerhard , Omenn Gilbert S , Orchard Sandra , Vizcaíno Juan Antonio , Hermjakob Henning
Published: March 2015

Objective To describe the goals of the Proteomics Standards Initiative (PSI) of the Human Proteome Organization, the methods that the PSI has employed to create data standards, the resulting output of the PSI, lessons learned from the PSI’s evolution, and future directions and synergies for the group.

Materials and Methods The PSI has 5 categories of deliverables that have guided the group. These are minimum information guidelines, data formats, controlled vocabularies, resources and software tools, and dissemination activities. These deliverables are produced via the leadership and working group organization of the initiative, driven by frequent workshops and ongoing communication within the working groups. Official standards are subjected to a rigorous document process that includes several levels of peer review prior to release.

Results We have produced and published minimum information guidelines describing what information should be provided when making data public, either via public repositories or other means. The PSI has produced a series of standard formats covering mass spectrometer input, mass spectrometer output, results of informatics analysis (both qualitative and quantitative analyses), reports of molecular interaction data, and gel electrophoresis analyses. We have produced controlled vocabularies that ensure that concepts are uniformly annotated in the formats and engaged in extensive software development and dissemination efforts so that the standards can efficiently be used by the community.

Conclusion In its first dozen years of operation, the PSI has produced many standards that have accelerated the field of proteomics by facilitating data exchange and deposition to data repositories. We look to the future to continue developing standards for new proteomics technologies and workflows and mechanisms for integration with other omics data types. Our products facilitate the translation of genomics and proteomics findings to clinical and biological phenotypes. The PSI website can be accessed at http://www.psidev.info.
Constraining the distribution of dark matter in dwarf spheroidal galaxies with stellar tidal streams
Authors: Errani Raphaël , Peñarrubia Jorge , Tormen Giuseppe
Published: March 2015

We use high-resolution N-body simulations to follow the formation and evolution of tidal streams associated with dwarf spheroidal galaxies (dSphs). The dSph models are embedded in dark matter (DM) haloes with either a centrally divergent ‘cusp’, or a homogeneous-density ‘core’. In agreement with previous studies, we find that as tides strip the galaxy the evolution of the half-light radius and the averaged velocity dispersion follows well-defined tracks that are mainly controlled by the amount of mass lost. Crucially, the evolutionary tracks behave differently depending on the shape of the DM profile: at a fixed remnant mass, dSphs embedded in cored haloes have larger sizes and higher velocity dispersions than their cuspy counterparts. The divergent evolution is particularly pronounced in galaxies whose stellar component is strongly segregated within their DM halo and becomes more disparate as the remnant mass decreases. Our analysis indicates that the DM profile plays an important role in defining the internal dynamics of tidal streams. We find that stellar streams associated with cored DM models have velocity dispersions that lie systematically above their cuspy counterparts. These results suggest that modelling the dynamics of streams with known dSph progenitors may reveal the distribution of DM on the smallest galactic scales.
Spatially resolved kinematic observations of the planetary nebulae Hen 3-1333 and Hen 2-113
Authors: Danehkar A. , Parker Q. A.
Published: March 2015

We have performed integral field spectroscopy of the planetary nebulae Hen 3-1333 (PNG332.9−09.9) and Hen 2-113 (PNG321.0+03.9), which are unusual in exhibiting dual-dust chemistry and multipolar lobes but also ionized by late-type [WC 10] central stars. The spatially resolved velocity distributions of the Hα emission line were used to determine their primary orientations. The integrated Hα emission profiles indicate that Hen 3-1333 and Hen 2-113 expand with velocities of ∼32 and 23 km s−1, respectively. The Hubble Space Telescope observations suggest that these planetary nebulae have two pairs of tenuous lobes extending upwardly from their bright compact cores. From three-dimensional geometric models, the primary lobes of Hen 3-1333 and Hen 2-113 were found to have inclination angles of about −30° and 40° relative to the line of sight, and position angles of −15° and 65° measured east of north in the equatorial coordinate system, respectively.
(Contrastive) Topic
Authors: Büring Daniel
Published: March 2015

This chapter discusses the semantics and pragmatics of contrastive topics vis-à-vis focus. A semi-formal characterization of its main properties is given, using the techniques of alternative semantics and questions under discussion. This treatment is compared to various analyses proposed in the literature for contrastive topics and arguably related constructions, such as the English rise–fall–rise contour. Finally a brief discussion of non-contrastive topics is provided.
The Sounds of Indigenous Ancestors
Authors: Wilde Guillermo
Published: March 2015

This article examines how music, corporality, and memory were intertwined in the Jesuit missions of South America during the colonial period. More specifically, it considers how European music was imposed upon indigenous peoples whereas traditional indigenous musical traditions were censured as part of a larger project of political and cultural domination that was not completely unilateral. It argues that the Jesuits used censure and the mechanisms of adaptation in various regions of South America to disconnect musical expression and corporality that had characterized preexisting native rituals involving music, or, more broadly, sound, together with dance and movement. The chapter concludes by assessing the significance and persistence of indigenous music within the context of the Jesuit missions.
Formation of young massive clusters from turbulent molecular clouds
Authors: Fujii Michiko S.
Published: March 2015

Young massive clusters are as young as open clusters but more massive and compact compared with typical open clusters. The formation process of young massive clusters is still unclear, and it is an open question whether the formation process is the same for typical open clusters or not. We perform a series of N-body simulations starting from initial conditions constructed from the results of hydrodynamical simulations of turbulent molecular clouds. In our simulations, both open clusters and young massive clusters form when we assume a density-dependent star-formation efficiency. We find that a local star-formation efficiency higher than 50% is necessary for the formation of young massive clusters, but open clusters form from less dense regions with a local star formation efficiency of < 50%. We confirm that the young massive clusters formed in our simulations have mass, size, and density profile similar to those of observed young massive clusters such as NGC 3603 and Trumpler 14. We also find that these simulated clusters evolve via hierarchical mergers of sub-clusters within a few mega years, as is suggested by recent simulations and observations. Although we do not assume initial mass segregation, we observe that the simulated massive clusters show a shallower slope of the mass function (Γ ∼ −1) in the cluster center compared to that of the entire cluster (Γ ∼ −1.3). These values are consistent with those of some young massive clusters in the Milky Way such as Westerlund 1 and Arches.
The Aggregate Effect of School Choice: Evidence from a Two-Stage Experiment in India *
Authors: Muralidharan Karthik , Sundararaman Venkatesh
Published: March 2015

We present experimental evidence on the impact of a school choice program in the Indian state of Andhra Pradesh that provided students with a voucher to finance attending a private school of their choice. The study design featured a unique two-stage lottery-based allocation of vouchers that created both student-level and market-level experiments, which allows us to study the individual and the aggregate effects of school choice (including spillovers). After two and four years of the program, we find no difference between test scores of lottery winners and losers on Telugu (native language), math, English, and science/social studies, suggesting that the large cross-sectional differences in test scores across public and private schools mostly reflect omitted variables. However, private schools also teach Hindi, which is not taught by the public schools, and lottery winners have much higher test scores in Hindi. Furthermore, the mean cost per student in the private schools in our sample was less than a third of the cost in public schools. Thus, private schools in this setting deliver slightly better test score gains than their public counterparts (better on Hindi and same in other subjects), and do so at a substantially lower cost per student. Finally, we find no evidence of spillovers on public school students who do not apply for the voucher, or on private school students, suggesting that the positive effects on voucher winners did not come at the expense of other students.
Reported maternal tendencies predict the reward value of infant facial cuteness, but not cuteness detection
Authors: Hahn Amanda C. , DeBruine Lisa M. , Jones Benedict C.
Published: March 2015

The factors that contribute to individual differences in the reward value of cute infant facial characteristics are poorly understood. Here we show that the effect of cuteness on a behavioural measure of the reward value of infant faces is greater among women reporting strong maternal tendencies. By contrast, maternal tendencies did not predict women's subjective ratings of the cuteness of these infant faces. These results show, for the first time, that the reward value of infant facial cuteness is greater among women who report being more interested in interacting with infants, implicating maternal tendencies in individual differences in the reward value of infant cuteness. Moreover, our results indicate that the relationship between maternal tendencies and the reward value of infant facial cuteness is not due to individual differences in women's ability to detect infant cuteness. This latter result suggests that individual differences in the reward value of infant cuteness are not simply a by-product of low-cost, functionless biases in the visual system.
Locomotion control of hybrid cockroach robots
Authors: Sanchez Carlos J. , Chiu Chen-Wei , Zhou Yan , González Jorge M. , Vinson S. Bradleigh , Liang Hong
Published: March 2015

Natural systems retain significant advantages over engineered systems in many aspects, including size and versatility. In this research, we develop a hybrid robotic system using American (
Periplaneta americana
) and discoid (
Blaberus discoidalis
) cockroaches that uses the natural locomotion and robustness of the insect. A tethered control system was firstly characterized using American cockroaches, wherein implanted electrodes were used to apply an electrical stimulus to the prothoracic ganglia. Using this approach, larger discoid cockroaches were engineered into a remotely controlled hybrid robotic system. Locomotion control was achieved through electrical stimulation of the prothoracic ganglia, via a remotely operated backpack system and implanted electrodes. The backpack consisted of a microcontroller with integrated transceiver protocol, and a rechargeable battery. The hybrid discoid roach was able to walk, and turn in response to an electrical stimulus to its nervous system with high repeatability of 60%.
Helicobacter himalayensis sp. nov. isolated from gastric mucosa of Marmota himalayana
Authors: Hu Shoukui , Jin Dong , Lu Shan , Liu Sha , Zhang Ji , Wang Yiting , Bai Xiangning , Xiong Yanwen , Huang Ying , Xu Huaqing , Wang Yi , Du Xiaoli , Ye Changyun , Hänninen Marja-Liisa , Xu Jianguo
Published: March 2015

A Gram-stain-negative, microaerophilic strain, 80(YS1)T, with a spiral-shaped morphology and 1–2 sheathed flagella at each end of the cells was isolated from the gastric mucosa of Marmota himalayana, the animal reservoir of

Yersinia pestis

in China, on the Qinghai-Tibet Plateau. The strain grew at 30, 35 and 42 °C, but not at 25 °C. Growth was in the form of a thinly spreading film on brain heart infusion agar containing 8 % sheep blood under microaerobic conditions. The strain did not hydrolyse urea or hippurate, and did not grow on media containing 1 % glycine. It reduced nitrate to nitrite, and was catalase- and alkaline-phosphatase-positive, susceptible to nalidixic acid and resistant to cefalotin. It was positive for genus-specific PCR for the genus

Helicobacter

, but could not be classified to any recognized species according biochemical tests results. Therefore, a phylogenetic study based on 16S rRNA, 23S rRNA, 60 kDa heat-shock protein (hsp60) and gyrase subunit B (gyrB) genes was conducted. The 16S rRNA gene sequence (1468 bp) analysis showed that strain 80(YS1)T was most closely related to

Helicobacter marmotae

(96.7 % similarity). The 23S rRNA gene sequence (2879 bp) analysis showed that the strain was most closely related to

Helicobacter canis

(96 % similarity). The complete gyrB gene sequence (2325 bp) analysis showed that it was related phylogenetically to

Helicobacter cinaedi

(79.4 % similarity) and

H. marmotae

(79.1 % similarity). Analysis of the partial sequence of the hsp60 gene of strain 80(YS1)T showed closest similarity to the sequences of

Helicobacter equorum

(82 %) and

H. cinaedi

(81 %), respectively. However, there was no hsp60 sequence of

H. marmotae

available for analysis. The data of morphological, biochemical and phylogenetic characteristics all supported that this strain represents a novel species. The name Helicobacter himalayensis sp. nov. is proposed for this novel species with the type strain 80(YS1)T ( = CGMCC 1.12864T = DSM 28742T)
Caloranaerobacter ferrireducens sp. nov., an anaerobic, thermophilic, iron (III)-reducing bacterium isolated from deep-sea hydrothermal sulfide deposits
Authors: Zeng Xiang , Zhang Zhao , Li Xi , Jebbar Mohamed , Alain Karine , Shao Zongze
Published: March 2015

A thermophilic, anaerobic, iron-reducing bacterium (strain DY22619T) was isolated from a sulfide sample collected from an East Pacific Ocean hydrothermal field at a depth of 2901 m. Cells were Gram-stain-negative, motile rods (2–10 µm in length, 0.5 µm in width) with multiple peritrichous flagella. The strain grew at 40–70 °C inclusive (optimum 60 °C), at pH 4.5–8.5 inclusive (optimum pH 7.0) and with sea salts concentrations of 1–10 % (w/v) (optimum 3 % sea salts) and NaCl concentrations of 1.5–5.0 % (w/v) (optimum 2.5 % NaCl). Under optimal growth conditions, the generation time was around 55 min. The isolate was an obligate chemoorganoheterotroph, utilizing complex organic compounds, amino acids, carbohydrates and organic acids including peptone, tryptone, beef extract, yeast extract, alanine, glutamate, methionine, threonine, fructose, mannose, galactose, glucose, palatinose, rhamnose, turanose, gentiobiose, xylose, sorbose, pyruvate, tartaric acid, α-ketobutyric acid, α-ketovaleric acid, galacturonic acid and glucosaminic acid. Strain DY22619T was strictly anaerobic and facultatively dependent on various forms of Fe(III) as an electron acceptor: insoluble forms and soluble forms. It did not reduce sulfite, sulfate, thiosulfate or nitrate. The genomic DNA G+C content was 29.0 mol%. Phylogenetic 16S rRNA gene sequence analyses revealed that the closest relative of strain DY22619T was

Caloranaerobacter azorensis

MV1087T, sharing 97.41 % 16S rRNA gene sequence similarity. On the basis of physiological distinctness and phylogenetic distance, the isolate is considered to represent a novel species of the genus

Caloranaerobacter

, for which the name Caloranaerobacter
http://dx.doi.org/10.1601/nm.4081
ferrireducens sp. nov. is proposed. The type strain is DY22619T ( = JCM 19467T = DSM 27799T = MCCC1A06455T).