bluuebunny/crossref_metadata_2025 huggingface dataset:
How can we demonstrate the public value of evidence-based policy making when government ministers declare that the people ‘have had enough of experts’?
Authors: Andrews Leighton
Published: October 2017

Recent political campaigns on both sides of the Atlantic have led some to argue that we live in the age of ‘post-factual’ or ‘post-truth’ politics, suggesting evidence has a limited role in debate and public policy. How can we demonstrate the public value of evidence-informed debate under those circumstances? Survey evidence on public attitudes to expertise offers some hope that the tone of much of this debate is unduly pessimistic. While policy-making always develops in an environment where evidence is contested, this paper will argue that understanding of the routines through which Ministers work and assimilate evidence is actually under-researched. Not only are Ministers open to evidence, but there is an institutional grounding for evidence-based policy in government. Meanwhile, the creation of devolved institutions has created new sites in the UK for evidence-based policy-making, despite the political tensions between UK and devolved governments. Drawing on academic and think tank insights, and experience as a Welsh Government Minister between 2007 and 2016, this paper argues for three key approaches for the academic community to adopt: understanding the temporal focus of ministers, building trust amongst ministers and those who advise them in the evidence-promoting capacity of the academic policy community, and shaping the wider authorising environment, including the media that contributes to the framing of key policy debates.
Solar geoengineering and the chemtrails conspiracy on social media
Authors: Tingley Dustin , Wagner Gernot
Published: October 2017

Discourse on social media of solar geoengineering has been rapidly increasing over the past decade, in line with increased attention by the scientific community and low but increasing awareness among the general public. The topic has also found increased attention online. But unlike scientific discourse, a majority of online discussion focuses on the so-called chemtrails conspiracy theory, the widely debunked idea that airplanes are spraying a toxic mix of chemicals through contrails, with supposed goals ranging from weather to mind control. This paper presents the results of a nationally representative 1000-subject poll part of the 36,000-subject 2016 Cooperative Congressional Election Study (CCES), and an analysis of the universe of social media mentions of geoengineering. The former shows ~ 10% of Americans declaring the chemtrails conspiracy as “completely” and a further ~ 20–30% as “somewhat” true, with no apparent difference by party affiliation or strength of partisanship. Conspiratorial views have accounted for ~ 60% of geoengineering discourse on social media over the past decade. Of that, Twitter has accounted for >90%, compared to ~ 75% of total geoengineering mentions. Further affinity analysis reveals a broad online community of conspiracy. Anonymity of social media appears to help its spread, so does the general ease of spreading unverified or outright false information. Online behavior has important real-world reverberations, with implications for climate science communication and policy.
Critical discourse analysis of war reporting in the international press: the case of the Gaza war of 2008–2009
Authors: Amer Mohammedwesam
Published: October 2017

This paper employs critical discourse analysis (CDA) to analyse the representation of political social actors in media coverage of the Gaza war of 2008–2009. The paper examines texts of systematically chosen news stories from four international newspapers: ‘The Guardian, The Times London, The New York Times and The Washington Post’. The findings show substantial similarities in representation patterns among the four newspapers. More specifically, the selected newspapers foreground Israeli agency in achieving a ceasefire, whereby Israeli actors are predominantly assigned activated roles. By contrast, the four newspapers foreground Palestinian agency in refusing ceasefire through assigning activated roles. The findings of this study suggest that news reports on the Gaza war of 2008–2009 are influenced by the political orientations of the newspapers and also their liberal and conservative ideological stances. Overall, the most represented actors are Israeli governmental officials, whereas Palestinian actors are Hamas members. This representation draws an overall image that the war is being directed against Hamas.
An experimental study of ultra-low power wireless sensor-based autonomous energy harvesting system
Authors: Ma Yuzhen , Ji Qing , Chen Song , Song Gangbing
Published: October 2017

Technological advances for low power consumption and flexible electronics have spurred research on energy harvesting. In this paper, an innovative methodology is proposed to power an ultra-low power wireless sensor node (milliwatt level) autonomously by using a piezoceramic patch which is bonded to a low-frequency vibrating beam. An LTC3588 based energy harvesting module was developed to transfer and collect the energy efficiently. Through a switching interface between the energy harvesting module and the wireless sensor, a 0.33F supercapacitor was charged for 12 h by the harvested vibrational energy to allow the wireless sensor node to join the network and transmit data packets. It was experimentally demonstrated that this applied switching interface could effectively provide on-off control to the power of the wireless sensor node. In order to allow this function, the supercapacitor worked alternatively in the charging mode and the discharging mode. When the supercapacitor stored enough harvested energy, the wireless sensor node initiated the effort to join the wireless network automatically and then sent data packets to the network manager which was connected to a monitoring computer. In addition, wireless sensors which were powered by the energy harvesting system could also send or receive data packets in the network. The developed piezoceramic based energy harvesting method has the potential to be used in structural health monitoring systems by harvesting the ambient mechanical energy.
Analysis of the threshold switching mechanism of a Te–SbO selector device for crosspoint nonvolatile memory applications
Authors: Kim Young Seok , Park Ji Woon , Lee Jong Ho , Choi In Ah , Heo Jaeyeong , Kim Hyeong Joon
Published: October 2017

The threshold switching mechanism of Te–SbO thin films with a unique microstructure in which a Te nanocluster is present in the SbO matrix is analyzed. During the electro-forming process, amorphous Te filaments are formed in the Te nanocluster. However, unlike conventional Ovonic threshold switching (TS) selector devices, it has been demonstrated that the off-current flows along the filament. Numerical calculations show that the off-current is due to the trap present in the filament. We also observed changes in TS parameters through controls in the strength or volume of the filaments.
Quantum solvability of a general ordered position dependent mass system: Mathews-Lakshmanan oscillator
Authors: Karthiga S. , Chithiika Ruby V. , Senthilvelan M. , Lakshmanan M.
Published: October 2017

In position dependent mass (PDM) problems, the quantum dynamics of the associated systems have been understood well in the literature for particular orderings. However, no efforts seem to have been made to solve such PDM problems for general orderings to obtain a global picture. In this connection, we here consider the general ordered quantum Hamiltonian of an interesting position dependent mass problem, namely, the Mathews-Lakshmanan oscillator, and try to solve the quantum problem for all possible orderings including Hermitian and non-Hermitian ones. The other interesting point in our study is that for all possible orderings, although the Schrödinger equation of this Mathews-Lakshmanan oscillator is uniquely reduced to the associated Legendre differential equation, their eigenfunctions cannot be represented in terms of the associated Legendre polynomials with integral degree and order. Rather the eigenfunctions are represented in terms of associated Legendre polynomials with non-integral degree and order. We here explore such polynomials and represent the discrete and continuum states of the system. We also exploit the connection between associated Legendre polynomials with non-integral degree with other orthogonal polynomials such as Jacobi and Gegenbauer polynomials.
Person-centred care in a digital hospital: observations and perspectives from a specialist rehabilitation setting
Authors: Burridge Letitia , Foster Michele , Jones Rachel , Geraghty Timothy , Atresh Sridhar
Published: October 2017

Objective This study investigated use of electronic medical records (eMRs) in a spinal cord injury rehabilitation unit and the implications for person-centred care. Methods This exploratory mixed-methods study conducted 17.5 hours of observations of practitioner–patient encounters, 50 patient-experience surveys and 10 focus groups with 53 practitioners. Descriptive statistics and qualitative analysis were integrated into key themes. Results Practitioners in this specialised setting were reconciling the emergent challenges of eMR in practice with the advantages of improved accessibility and documentation legibility. eMR increased task complexity and information retrieval, particularly for nurses. Some documentation was an uneasy fit with the specialised setting, disrupting informal communications and aspects of person-centred care. Conclusions Technological change closely aligned with frontline practice brought expected and unexpected challenges that may resolve over time. Practitioners’ persistence and adaptability demonstrated their commitment to person-centred care in the digital environment. The impact of this less visible work of professional discretion seemed to vary, primarily by discipline-specific roles, with nurses experiencing the greatest pressure. What is known about this topic? Integrated electronic medical records (eMRs) bring benefits but challenge person-centred care. What does this paper add? These first insights regarding frontline implementation of eMR in spinal injury rehabilitation suggest nursing challenges when seeking to fit specialised work into the generic eMR. However, most patients reported receiving person-centred care. What are the implications for practitioners? Commitment to person-centred care appears to strengthen practitioners’ perseverance with the eMR implementation challenges.
An integrated risk-assessment framework for multiple threats to floodplain values in the Kakadu Region, Australia, under a changing climate
Authors: Bayliss P. , Finlayson C. M. , Innes J. , Norman-López A. , Bartolo R. , Harford A. , Pettit N. E. , Humphrey C. L. , van Dam R. , Dutra L. X. C. , Woodward E. , Ligtermoet E. , Steven A. , Chariton A. , Williams D. K.
Published: October 2017

The internationally important river–floodplains of the Kakadu Region in northern Australia are at risk from invasive species and future sea-level rise–saltwater inundation (SLR–SWI), requiring assessments of multiple cumulative risks over different time frames. An integrated risk-assessment framework was developed to assess threats from feral animals and aquatic weeds at three SLR-scenario time frames (present-day, 2070 and 2100) to natural (magpie goose habitats), cultural (indigenous hunting–fishing sites) and economic (tourism revenue less invasive species control costs) values. Probability density functions (pdfs) were fitted to spatial data to characterise values and threats, and combined with Monte Carlo simulation and sensitivity analyses to account for uncertainties. All risks were integrated in a Bayesian belief network to undertake ‘what if’ management-scenario analyses, and incorporated known ecological interactions and uncertainties. Coastal landscapes and socio-ecological systems in the region will be very different by 2100 as a result of SLR; freshwater ecosystems will transform to marine-dominated ecosystems and cannot be managed back to analogue conditions. In this context, future invasive-species risks will decrease, reflecting substantial loss of freshwater habitats previously at risk and a reduction in the extent of invasive species, highlighting the importance of freshwater refugia for the survival of iconic species.
Intercellular competition and the inevitability of multicellular aging
Authors: Nelson Paul , Masel Joanna
Published: October 2017

Significance

We lay out the first general model of the interplay between intercellular competition, aging, and cancer. Our model shows that aging is a fundamental feature of multicellular life. Current understanding of the evolution of aging holds that aging is due to the weakness of selection to remove alleles that increase mortality only late in life. Our model, while fully compatible with current theory, makes a stronger statement: Multicellular organisms would age even if selection were perfect. These results inform how we think about the evolution of aging and the role of intercellular competition in senescence and cancer.
Patterns of conserved gp120 epitope presentation on attached HIV-1 virions
Authors: Mengistu Meron , Tang Ai-hui , Foulke James S. , Blanpied Thomas A. , Gonzalez Mileidy W. , Spouge John L. , Gallo Robert C. , Lewis George K. , DeVico Anthony L.
Published: October 2017

Significance

A complete picture of HIV antigenicity during early replication is needed to elucidate the full range of options for controlling infection through humoral immunity. The HIV envelope protein, gp120, experiences key structural rearrangements during host cell attachment, leading to exposure of highly conserved epitopes on the virion surface. These epitopes enable Fc-mediated antiviral effector functions that may be relevant to HIV prevention. Here, we used 3D superresolution microscopy to show how gp120 epitopes are rapidly exposed distal to cell–virus interfaces, introducing the opportunity for unconstrained antibody binding. These previously unrecognized facets of HIV antigenicity further define relationships between retroviral infection and immunity and should facilitate the development of antibody-based approaches for HIV prevention.
Mechanism of RNA polymerase II stalling by DNA alkylation
Authors: Malvezzi Stefano , Farnung Lucas , Aloisi Claudia M. N. , Angelov Todor , Cramer Patrick , Sturla Shana J.
Published: October 2017

Significance

RNA polymerase II (Pol II) catalyzes the transcription of DNA to RNA in the nucleus. DNA alkylating cancer drugs can stall transcription; however, the basis for Pol II stalling when encountering a DNA template with minor-groove alkylation adducts has remained elusive due to its inherent chemical instability. We characterized the behavior of Pol II in transcription over minor-groove alkylation adducts and uncovered a previously unobserved mode of Pol II stalling wherein clashes between DNA adducts and the mobile trigger loop of RNA Pol II prevent translocation of the enzyme after nucleotide insertion. These results provide a molecular basis for how DNA damage in transcribed portions of the genome initiates DNA repair contributing to drug resistance.
O
2
availability impacts iron homeostasis in
Escherichia coli
Authors: Beauchene Nicole A. , Mettert Erin L. , Moore Laura J. , Keleş Sündüz , Willey Emily R. , Kiley Patricia J.
Published: October 2017

Significance

Our understanding of how cells regulate intracellular iron pools has been largely shaped by studying cells grown under aerobic conditions, in which the barrier to iron acquisition is dominated by O
2
-dependent insolubility. However, less is known about how bacteria meet their iron demands in the O
2
-limiting or anaerobic environments that are common to many ecosystems and reflective of the ancient atmosphere of early Earth. Because the transcription factor ferric-uptake regulator (Fur) plays a central role in controlling iron homeostasis in many bacterial species, we use Fur activity as a surrogate for understanding how anaerobiosis alters iron homeostasis. Our finding that levels of active Fur are increased during anaerobiosis emphasizes fundamental differences in bacterial iron requirements between aerobic and anaerobic growth conditions.
Pathogen-mediated selection in free-ranging elk populations infected by chronic wasting disease
Authors: Monello Ryan J. , Galloway Nathan L. , Powers Jenny G. , Madsen-Bouterse Sally A. , Edwards William H. , Wood Mary E. , O’Rourke Katherine I. , Wild Margaret A.
Published: October 2017

Significance

Chronic wasting disease (CWD) is a fatal neurodegenerative disease that can cause declines in deer and elk populations. Theoretical work suggests elk will adapt to the disease by favoring a naturally occurring but underrepresented prion protein variant (leucine allele) that enables individuals to live and reproduce for several years after infection with CWD. Using genetic and disease samples from different populations, we found that elk herds infected with CWD for 30–50 y exhibited leucine allele frequencies that were twice as great as those in unexposed populations. Our results are consistent with the hypothesis that genetic selection has occurred due to CWD, but it remains unknown if this will allow elk to mitigate the negative population impacts of CWD.
Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation
Authors: Bazin Jérémie , Baerenfaller Katja , Gosai Sager J. , Gregory Brian D. , Crespi Martin , Bailey-Serres Julia
Published: October 2017

Significance

Noncoding RNAs are an underexplored reservoir of regulatory molecules in eukaryotes. We analyzed the environmental response of roots to phosphorus (Pi) nutrition to understand how a change in availability of an essential element is managed. Pi availability influenced translational regulation mediated by small upstream ORFs on protein-coding mRNAs. Discovery, classification, and evaluation of long noncoding RNAs (lncRNAs) associated with translating ribosomes uncovered diverse new examples of translational regulation. These included Pi-regulated small peptide synthesis, ribosome-coupled phased small interfering RNA production, and the translational regulation of natural antisense RNAs and other regulatory RNAs. This study demonstrates that translational control contributes to the stability and activity of regulatory RNAs, providing an avenue for manipulation of traits.
DNA–RNA interactions are critical for chromosome condensation in
Escherichia coli
Authors: Qian Zhong , Zhurkin Victor B. , Adhya Sankar
Published: October 2017

Significance

This study focuses on the molecular mechanisms of a noncoding RNA-mediated chromosome organization in
Escherichia coli
. We show for the first time that noncoding RNA, naRNA4, a critical element at least in part of chromosome structural organization (DNA condensation), may form DNA–RNA complexes in an uncommon way. Surprisingly, we found that HU protein catalyzes the DNA–RNA interactions without being part of the “final” complexes. There are several important examples of noncoding RNA playing critical roles in eukaryotic chromatin functioning, e.g., heterochromatin assembly, gene silencing, and X-inactivation, although nothing is known about the nature of DNA–RNA interaction(s) in these processes. Our findings will be of great interest in the chromatin field, providing mechanistic insights into the large-scale organization of DNA.
Protocadherin
cis
-dimer architecture and recognition unit diversity
Authors: Goodman Kerry M. , Rubinstein Rotem , Dan Hanbin , Bahna Fabiana , Mannepalli Seetha , Ahlsén Göran , Aye Thu Chan , Sampogna Rosemary V. , Maniatis Tom , Honig Barry , Shapiro Lawrence
Published: October 2017

Significance

Pcdhs are cell surface homophilic recognition proteins expressed stochastically to assign individual identities to each neuron. These individual identities ensure repulsion between neurites from the same cell and ensure that neurites from different cells do not repel. However, it is difficult to understand how only ∼60 Pcdh isoforms can provide sufficient diversity for the billions of neurons in vertebrate nervous systems. Here, we report the crystal structure of a Pcdh
cis
-dimer through which individual Pcdh isoforms associate to form diverse bivalent recognition units. The structure reveals asymmetry in the
cis
-dimer interaction and suggests restrictions on isoform combinations compatible with
cis
-dimerization. These findings provide a framework to understand Pcdh
cis
-dimerization and the compositions of functional repertoires of Pcdh recognition units.
MPSR1 is a cytoplasmic PQC E3 ligase for eliminating emergent misfolded proteins in
Arabidopsis thaliana
Authors: Kim Jong Hum , Cho Seok Keun , Oh Tae Rin , Ryu Moon Young , Yang Seong Wook , Kim Woo Taek
Published: October 2017

Significance

The essential roles of cytoplasmic E3 ligases in the protein quality control (PQC) pathways have been increasingly highlighted in yeast and animal studies. However, in plants, only CHIP E3 ligase has been characterized, while the knowledge of cytoplasmic PQC E3 ligases remains rudimentary. Misfolded Protein Sensing RING E3 ligase 1 (MPSR1), a self-regulatory sensor system that functions only in the occurrence of misfolded proteins, is an identified cytoplasmic PQC E3 ligase in plants that directly recognizes emergent misfolded proteins independently of chaperones. In addition, MPSR1 sustains the integrity and activity of the 26S proteasome under proteotoxic stress. Given that MPSR1 RING E3 ligase is well conserved in eukaryotes, this study sheds light on a PQC pathway that is present particularly in plants and beyond.
Genome diversity of tuber-bearing
Solanum
uncovers complex evolutionary history and targets of domestication in the cultivated potato
Authors: Hardigan Michael A. , Laimbeer F. Parker E. , Newton Linsey , Crisovan Emily , Hamilton John P. , Vaillancourt Brieanne , Wiegert-Rininger Krystle , Wood Joshua C. , Douches David S. , Farré Eva M. , Veilleux Richard E. , Buell C. Robin
Published: October 2017

Significance

Worldwide, potato is the third most important crop grown for direct human consumption, but breeders have struggled to produce new varieties that outperform those released over a century ago, as evidenced by the most widely grown North American cultivar (Russet Burbank) released in 1876. Despite its importance, potato genetic diversity at the whole-genome level remains largely unexplored. Analysis of cultivated potato and its wild relatives using modern genomics approaches can provide insight into the genomic diversity of extant germplasm, reveal historic introgressions and hybridization events, and identify genes targeted during domestication that control variance for agricultural traits, all critical information to address food security in 21st century agriculture.
Characterization of extracellular vesicles derived from cardiac cells in an in vitro model of preconditioning
Authors: Borosch Sebastian , Dahmen Eva , Beckers Christian , Stoppe Christian , Buhl Eva Miriam , Denecke Bernd , Goetzenich Andreas , Kraemer Sandra
Published: October 2017

Preconditioning is a promising technique to protect the heart from ischaemia‐reperfusion injury. In this context, the crosstalk between different cardiac cell types and especially the exchange of cardioprotective mediators has come into the focus of current research. Recently, extracellular vesicles (EVs), nano‐sized structures, emerged as possible communication mediators. They are taken up by recipient cells and can alter gene expression or activate intracellular signal cascades. It has been shown that all cardiac cell types are able to secrete EVs, but so far the influence of an in vitro preconditioning stimulus on EV concentration and composition has not been investigated. Therefore, we stimulated primary cardiac myocytes and fibroblasts from neonatal rats, as well as H9c2 cells, with two known in vitro preconditioning stimuli: hypoxia or isoflurane. EVs were isolated from cell culture supernatants 48 h after stimulation by differential centrifugation and size exclusion chromatography. They were characterized by transmission electron microscopy, tunable resistive pulse sensing, miRNA array and Western blot analysis. The detected EVs had the typical cup‐shaped morphology and a size of about 150 nm. No significant differences in EV concentration were observed between the different groups. The protein and miRNA load was affected by in vitro preconditioning with isoflurane or hypoxia. EV markers like Alix, CD63, flotillin‐1 and especially heat shock protein 70 were significantly up‐regulated by the treatments. Several miRNAs like miR‐92b‐3p, miR‐761 and miR‐101a‐5p were also significantly affected. A migration assay confirmed the physiological benefit of these EVs. Taken together, our findings show that a model of in vitro preconditioning of cardiac cells does not influence EV concentration but strongly regulates the EV cargo and affects migration. This might indicate a role for EV‐mediated communication in isoflurane‐ and hypoxia‐induced in vitro preconditioning.
On-site comparison of Quantum Hall Effect resistance standards of the CMI and the BIPM: ongoing key comparison BIPM.EM-K12
Authors: Gournay Pierre , Rolland Benjamin , Kučera Jan , Vojáčková Lucie
Published: October 2017

An on-site comparison of the quantum Hall effect (QHE) resistance standards of the Czech Metrology Institute (CMI) and of the Bureau International des Poids et Mesures (BIPM) was made in April 2017. Measurements of a 100 Ω standard in terms of the conventional value of the von Klitzing constant, R
K-90, agreed to 6 parts in 1010 with a relative combined standard uncertainty u
c = 25 × 10−10. Measurements of 10000 Ω/100 Ω and 100 Ω/1 Ω ratios agreed to 11 parts in 1010 with u
c = 22 × 10−10 and to 33 parts in 1010 with u
c = 32 × 10−10, respectively. The influence of the current reversal time has been systematically investigated in order to take into account possible errors due to the Peltier effect, which may be particularly large in 1 Ω standards.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCEM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Supplementary comparison of 500 microgram, 200 microgram, 100 microgram and 50 microgram weights—EURAMET.M.M-S9
Authors: Davidson Stuart , Valcu Adriana , Medina Nieves , Zuda Jaroslav , Snopko Laurenc , Kolozinska Irena
Published: October 2017

A comparison of sub-milligram mass standards was undertaken within EURAMET between NPL (as the pilot laboratory), INM (Romania), CEM (Spain), CMI (Czech Republic), SMU (Slovakia) and NSC IM (Ukraine). The weights circulated had nominal values of 500 micrograms, 200 micrograms (2 weights), 100 micrograms and 50 micrograms.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.

The final report has been peer-reviewed and approved for publication by the CCM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
Stress Intensity Factors of Slanted Cracks in Bi-Material Plates
Authors: Ismail Al Emran , Kamarudin Kamarul Azhar , Nor Nik Hisyamudin Muhd
Published: October 2017

In this study, the stress intensity factors (SIF) of slanted cracks in bi-material plates subjected to mode I loading is numerically solved. Based on the literature survey, tremendous amount of research works are available studying the normal cracks in both similar and dissimilar plates. However, lack of SIF behavior for slanted cracks especially when it is embedded in bi-material plates. The slanted cracks are then modelled numerically using ANSYS finite element program. Two plates of different in mechanical properties are firmly bonded obliquely and then slanted edge cracks are introduced at the lower inclined edge. Isoparametric singular element is used to model the crack tip and the SIF is determined which is based on the domain integral method. Three mechanical mismatched and four slanted angles are used to model the cracks. According to the present results, the effects of mechanical mismatch on the SIF for normal cracks are not significant. However, it is played an important role when slanted angles are introduced. It is suggested that higher SIF can be obtained when the cracks are inclined comparing with the normal cracks. Consequently, accelerating the crack growth at the interface between two distinct materials.
A Delayed Yule Process
Authors: Dascaliuc Radu , Michalowski Nicholas , Thomann Enrique , Waymire Edward
Published: October 2017

In now classic work, David Kendall (1966) recognized that the Yule process and Poisson process could be related by a (random) time change. Furthermore, he showed that the Yule population size rescaled by its mean has an almost sure exponentially distributed limit as

t
→
∞

t\to \infty

. In this note we introduce a class of coupled delayed continuous time Yule processes parameterized by

0
>
α
≤
1

0 > \alpha \le 1

and find a representation of the Poisson process as a delayed Yule process at delay rate

α
=

1

/

2

\alpha = {1/2}

. Moreover we extend Kendall’s limit theorem to include a larger class of positive martingales derived from functionals that gauge the population genealogy. Specifically, the latter is exploited to uniquely characterize the moment generating functions of distributions of the limit martingales, generalizing Kendall’s mean one exponential limit. A connection with fixed points of the Holley-Liggett smoothing transformation also emerges in this context, about which much is known from general theory in terms of moments, tail decay, and so on.
Fifty years of mentoring and advising
Authors: Lodish Harvey F.
Published: October 2017

Advancement of science depends on thoughtfully mentoring a rare group of scientists that are highly educated, creative, and motivated—and that come from every country in the world. On the basis of my own experiences, I suggest ways to recruit top young scientists of both genders, support their development into leading researchers, and advise them about careers inside and outside of academia. Creating a family-friendly environment within the laboratory and the institution is crucial to these efforts.
Mosdepth: quick coverage calculation for genomes and exomes
Authors: Pedersen Brent S , Quinlan Aaron R
Published: October 2017

Mosdepth is a new command-line tool for rapidly calculating genome-wide sequencing coverage. It measures depth from BAM or CRAM files at either each nucleotide position in a genome or for sets of genomic regions. Genomic regions may be specified as either a BED file to evaluate coverage across capture regions, or as a fixed-size window as required for copy-number calling. Mosdepth uses a simple algorithm that is computationally efficient and enables it to quickly produce coverage summaries. We demonstrate that mosdepth is faster than existing tools and provides flexibility in the types of coverage profiles produced.

Availability and implementation

mosdepth is available from https://github.com/brentp/mosdepth under the MIT license.

Supplementary information

Supplementary data are available at Bioinformatics online.
BEAM web server: a tool for structural RNA motif discovery
Authors: Pietrosanto Marco , Adinolfi Marta , Casula Riccardo , Ausiello Gabriele , Ferrè Fabrizio , Helmer-Citterich Manuela
Published: October 2017

Motivation

RNA structural motif finding is a relevant problem that becomes computationally hard when working on high-throughput data (e.g. eCLIP, PAR-CLIP), often represented by thousands of RNA molecules. Currently, the BEAM server is the only web tool capable to handle tens of thousands of RNA in input with a motif discovery procedure that is only limited by the current secondary structure prediction accuracies.

Results

The recently developed method BEAM (BEAr Motifs finder) can analyze tens of thousands of RNA molecules and identify RNA secondary structure motifs associated to a measure of their statistical significance. BEAM is extremely fast thanks to the BEAR encoding that transforms each RNA secondary structure in a string of characters. BEAM also exploits the evolutionary knowledge contained in a substitution matrix of secondary structure elements, extracted from the RFAM database of families of homologous RNAs. The BEAM web server has been designed to streamline data pre-processing by automatically handling folding and encoding of RNA sequences, giving users a choice for the preferred folding program. The server provides an intuitive and informative results page with the list of secondary structure motifs identified, the logo of each motif, its significance, graphic representation and information about its position in the RNA molecules sharing it.

Availability and implementation

The web server is freely available at http://beam.uniroma2.it/ and it is implemented in NodeJS and Python with all major browsers supported.

Supplementary information

Supplementary data are available at Bioinformatics online.
2017 HIV Medicine Association of Infectious Diseases Society of America Clinical Practice Guideline for the Management of Chronic Pain in Patients Living With Human Immunodeficiency Virus
Authors: Bruce R Douglas , Merlin Jessica , Lum Paula J , Ahmed Ebtesam , Alexander Carla , Corbett Amanda H , Foley Kathleen , Leonard Kate , Treisman Glenn Jordan , Selwyn Peter
Published: October 2017

Pain has always been an important part of human immunodeficiency virus (HIV) disease and its experience for patients. In this guideline, we review the types of chronic pain commonly seen among persons living with HIV (PLWH) and review the limited evidence base for treatment of chronic noncancer pain in this population. We also review the management of chronic pain in special populations of PLWH, including persons with substance use and mental health disorders. Finally, a general review of possible pharmacokinetic interactions is included to assist the HIV clinician in the treatment of chronic pain in this population.

It is important to realize that guidelines cannot always account for individual variation among patients. They are not intended to supplant physician judgment with respect to particular patients or special clinical situations. The Infectious Diseases Society of American considers adherence to these guidelines to be voluntary, with the ultimate determination regarding their application to be made by the physician in the light of each patient’s individual circumstances.
Interviewers’ Ratings of Respondents’ Health: Predictors and Association With Mortality
Authors: Garbarski Dana , Schaeffer Nora Cate , Dykema Jennifer
Published: October 2017

Objectives

Recent research indicates that survey interviewers’ ratings of respondents’ health (IRH) may provide supplementary health information about respondents in surveys of older adults. Although IRH is a potentially promising measure of health to include in surveys, our understanding of the factors contributing to IRH remains incomplete.

Methods

We use data from the 2011 face-to-face wave of the Wisconsin Longitudinal Study, a longitudinal study of older adults from the Wisconsin high school class of 1957 and their selected siblings. We first examine whether a range of factors predict IRH: respondents’ characteristics that interviewers learn about and observe as respondents answer survey questions, interviewers’ evaluations of some of what they observe, and interviewers’ characteristics. We then examine the role of IRH, respondents’ self-rated health (SRH), and associated factors in predicting mortality over a 3-year follow-up.

Results

As in prior studies, we find that IRH is associated with respondents’ characteristics. In addition, this study is the first to document how IRH is associated with both interviewers’ evaluations of respondents and interviewers’ characteristics. Furthermore, we find that the association between IRH and the strong criterion of mortality remains after controlling for respondents’ characteristics and interviewers’ evaluations of respondents.

Discussion

We propose that researchers incorporate IRH in surveys of older adults as a cost-effective, easily implemented, and supplementary measure of health.
Aging and Disability Among Hispanics in the United States: Current Knowledge and Future Directions
Authors: Garcia Marc A , Downer Brian , Crowe Michael , Markides Kyriakos S
Published: October 2017

Background and Objectives

Hispanics are the most rapidly aging minority population in the United States. Our objective is to provide a summary of current knowledge regarding disability among Hispanics, and to propose an agenda for future research.

Research Design and Methods

A literature review was conducted to identify major areas of research. A life course perspective and the Hispanic Paradox were used as frameworks for the literature review and for identifying future areas of research.

Results

Four research areas were identified: (1) Ethnic disparities in disability; (2) Heterogeneity of the U.S. older Hispanic population; (3) Risk factors for disability; and (4) Disabled life expectancy. Older Hispanics are more likely than non-Hispanic whites to be disabled or to become disabled. Disability varied by country of origin, nativity, age of migration, and duration in the United States. Important risk factors for disability included chronic health conditions, depression, and cognitive impairment. Protective factors included positive affect and physical activity. Older Hispanics have longer life expectancy than non-Hispanic whites but spend a greater proportion of old age disabled. Future research should continue to monitor trends in disability as younger generations of Hispanics reach old age. Attention needs to be given to regional variation within the United States for disability prevalence, early-life risk factors, and factors that may contribute to variation in disabled life expectancy. There is also an urgent need for interventions that can effectively prevent or delay the onset of disability in older Hispanics.

Discussion and Implications

Considerable research has examined disability among older Hispanics, but continued research is needed. It is important that research findings be used to inform public policies that can address the burden of disability for older Hispanic populations.
On one-parametric formula relating the frequencies of twin-peak quasi-periodic oscillations
Authors: Török Gabriel , Goluchová Kateřina , Šrámková Eva , Horák Jiří , Bakala Pavel , Urbanec Martin
Published: October 2017

Twin-peak quasi-periodic oscillations (QPOs) are observed in several low-mass X-ray binary systems containing neutron stars. Timing the analysis of X-ray fluxes of more than dozen of such systems reveals remarkable correlations between the frequencies of two characteristic peaks present in the power density spectra. The individual correlations clearly differ, but they roughly follow a common individual pattern. High values of measured QPO frequencies and strong modulation of the X-ray flux both suggest that the observed correlations are connected to orbital motion in the innermost part of an accretion disc. Several attempts to model these correlations with simple geodesic orbital models or phenomenological relations have failed in the past. We find and explore a surprisingly simple analytic relation that reproduces individual correlations for a group of several sources through a single parameter. When an additional free parameter is considered within our relation, it well reproduces the data of a large group of 14 sources. The very existence and form of this simple relation support the hypothesis of the orbital origin of QPOs and provide the key for further development of QPO models. We discuss a possible physical interpretation of our relation’s parameters and their links to concrete QPO models.
Advances in Diagnostics of Downy Mildews: Lessons Learned from Other Oomycetes and Future Challenges
Authors: Crandall Sharifa G. , Rahman Alamgir , Quesada-Ocampo Lina M. , Martin Frank N. , Bilodeau Guillaume J. , Miles Timothy D.
Published: October 2017

Downy mildews are plant pathogens that damage crop quality and yield worldwide. Among the most severe and notorious crop epidemics of downy mildew occurred on grapes in the mid-1880s, which almost destroyed the wine industry in France. Since then, there have been multiple outbreaks on sorghum and millet in Africa, tobacco in Europe, and recent widespread epidemics on lettuce, basil, cucurbits, and spinach throughout North America. In the mid-1970s, loss of corn to downy mildew in the Philippines was estimated at US$23 million. Today, crops that are susceptible to downy mildews are worth at least $7.5 billion of the United States’ economy. Although downy mildews cause devastating economic losses in the United States and globally, this pathogen group remains understudied because they are difficult to culture and accurately identify. Early detection of downy mildews in the environment is critical to establish pathogen presence and identity, determine fungicide resistance, and understand how pathogen populations disperse. Knowing when and where pathogens emerge is also important for identifying critical control points to restrict movement and to contain populations. Reducing the spread of pathogens also decreases the likelihood of sexual recombination events and discourages the emergence of novel virulent strains. A major challenge in detecting downy mildews is that they are obligate pathogens and thus cannot be cultured in artificial media to identify and maintain specimens. However, advances in molecular detection techniques hold promise for rapid and in some cases, relatively inexpensive diagnosis. In this article, we discuss recent advances in diagnostic tools that can be used to detect downy mildews. First, we briefly describe downy mildew taxonomy and genetic loci used for detection. Next, we review issues encountered when identifying loci and compare various traditional and novel platforms for diagnostics. We discuss diagnosis of downy mildew traits and issues to consider when detecting this group of organisms in different environments. We conclude with challenges and future directions for successful downy mildew detection.
Virulence Differences in Blumeria graminis f. sp. tritici from the Central and Eastern United States
Authors: Cowger Christina , Mehra Lucky , Arellano Consuelo , Meyers Emily , Murphy J. Paul
Published: October 2017

Wheat powdery mildew is a disease of global importance that occurs across a wide geographic area in the United States. A virulence survey of Blumeria graminis f. sp. tritici, the causal agent, was conducted by sampling 36 wheat fields in 15 U.S. states in the years 2013 and 2014. Using a hierarchical sampling protocol, isolates were derived from three separated plants at each of five separated sites within each field in order to assess the spatial distribution of pathotypes. In total, 1,017 isolates from those fields were tested individually on single-gene differential cultivars containing a total of 21 powdery mildew resistance (Pm) genes. Several recently introgressed mildew resistance genes from wild wheat relatives (Pm37, Pm53, MlAG12, NCAG13, and MlUM15) exhibited complete or nearly complete resistance to all local B. graminis f. sp. tritici populations from across the sampled area. One older gene, Pm4b, also retained at least some efficacy across the sampled area. The B. graminis f. sp. tritici population sampled from Arkansas and Missouri, on the western edge of the eastern soft red winter wheat region, had virulence profiles more similar to other soft wheat mildew populations than to the geographically closer population from hard wheat fields in the Plains states of Oklahoma, Nebraska, and Kansas. The Plains population differed in that it was avirulent to several Pm genes long defeated in the soft-wheat-growing areas. Virulence complexity was greatest east of the Mississippi River, and diminished toward the west. Several recently introgressed Pm genes (Pm25, Pm34, Pm35, and NCA6) that are highly effective against mildew in the field in North Carolina were unexpectedly susceptible to eastern-U.S. B. graminis f. sp. tritici populations in detached-leaf tests. Sampled fields displayed a wide range of pathotype diversity and spatial distribution, suggesting that epidemics are caused by varying numbers of pathotypes in all regions. The research confirmed that most long-used Pm genes are defeated in the eastern United States, and the U.S. B. graminis f. sp. tritici population has different virulence profiles in the hard- and soft-wheat regions, which are likely maintained by host selection, isolation by distance, and west-to-east gene flow.
Exploring Parental and Staff Perceptions of the Family-Integrated Care Model
Authors: Broom Margaret , Parsons Georgia , Carlisle Hazel , Kecskes Zsuzsoka , Thibeau Shelley
Published: October 2017

Background:

Family-integrated care (FICare) is an innovative model of care developed at Mount Sinai Hospital, Canada, to better integrate parents into the team caring for their infant in the neonatal intensive care unit (NICU). The effects of FICare on neonatal outcomes and parental anxiety were assessed in an international multicenter randomized trial. As an Australian regional level 3 NICU that was randomized to the intervention group, we aimed to explore parent and staff perceptions of the FICare program in our dual occupancy NICU.

Subjects and Design:

This qualitative study took place in a level 3 NICU with 5 parent participants and 8 staff participants, using a post implementation review design.

Methods:

Parents and staff perceptions of FICare were explored through focus group methodology. Thematic content analysis was done on focus group transcripts.

Results:

Parents and staff perceived the FICare program to have had a positive impact on parental confidence and role attainment and thought that FICare improved parent-to-parent and parent-to-staff communication. Staff reported that nurses working with families in the program performed less hands-on care and spent more time educating and supporting parents.

Implications for Practice:

FICare may change current NICU practice through integrating and accepting parents as active members of the infant's care team. In addition, nurse's roles may transition from bedside carer to care coordinator, educating and supporting parents during their journey through the NICU.

Implications for Research:

Further research is needed to assess the long-term impact of FICare on neonates, parents, and staff.
Evaluation of a Postdischarge Call System Using the Logic Model
Authors: Frye Timothy C. , Poe Terri L. , Wilson Marisa L. , Milligan Gary
Published: October 2017

This mixed-method study was conducted to evaluate a postdischarge call program for congestive heart failure patients at a major teaching hospital in the southeastern United States. The program was implemented based on the premise that it would improve patient outcomes and overall quality of life, but it had never been evaluated for effectiveness. The Logic Model was used to evaluate the input of key staff members to determine whether the outputs and results of the program matched the expectations of the organization. Interviews, online surveys, reviews of existing patient outcome data, and reviews of publicly available program marketing materials were used to ascertain current program output. After analyzing both qualitative and quantitative data from the evaluation, recommendations were made to the organization to improve the effectiveness of the program.