bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementation of a Novel Adherence Monitoring Strategy in a Phase III, Blinded, Placebo-Controlled, HIV-1 Prevention Clinical Trial
Authors: Husnik Marla J. , Brown Elizabeth R. , Marzinke Mark , Livant Edward , Palanee-Phillips Thesla , Hendrix Craig W. , Matovu Kiweewa Flavia , Nair Gonasagrie , Soto-Torres Lydia E. , Schwartz Katie , Hillier Sharon L. , Baeten Jared M. ,   for the MTN-020 ASPIRE Study Team
Published: July 2017

Background:
Placebo-controlled HIV-1 prevention trials of pre-exposure prophylaxis (PrEP) have not generally used concurrent measurement of adherence because of the potential risk of unblinding. However, several pre-exposure prophylaxis trials for HIV-1 prevention among women failed to show effectiveness because of low product adherence. Evaluation of product adherence objectively during a study provides the opportunity for strengthening adherence activities at sites having low adherence.

Methods:
During MTN-020/ASPIRE, a phase III, placebo-controlled trial of the dapivirine intravaginal ring, we implemented an adherence monitoring system. Monitoring began in quarter 1 (Q1) 2013 and continued through the conclusion of the trial. Blood plasma was collected quarterly and tested for dapivirine concentrations while maintaining blinding among study team members involved in participant management. Dapivirine concentrations >95 pg/mL, reflecting >8 hours of continuous use, were assessed as signaling product use. Study leadership monitored results on a monthly basis and provided feedback to site investigators. Experiences were shared across sites to motivate staff and counsel participants to strive toward higher adherence levels.

Results:
An upward trend in adherence was observed (P < 0.0001); the proportion of samples from subjects in the active arm with dapivirine >95 pg/mL increased from 63% in Q1 2013 to 84% by Q1 2015.

Conclusions:
Ongoing drug level testing as a marker of adherence in MTN-020/ASPIRE demonstrates the feasibility of real-time adherence monitoring while maintaining study blinding at the level of participants, sites, and study leadership. This approach is novel for large-scale effectiveness studies for HIV-1 prevention.
Pollen tube growth and guidance: Occam’s razor sharpened on a molecular AGP Rosetta Stone
Authors: Lamport Derek T. A. , Tan Li , Held Michael , Kieliszewski Marcia J. 
Published: July 2017

ABSTRACTOccam’s Razor suggests a new model of pollen tube tip growth based on a novel Hechtian oscillator that integrates: (1) a periplasmic AGP-Ca2+calcium capacitor with tip-localised arabinogalactan glycoproteins (AGPs); (2) tip-focussed cytosolic Ca2+oscillations; (3) Hechtian strands evidence of adhesion between the plasma membrane and the cell wall of the growing tip. Thus Hechtian adhesion, as a piconewton force transducer, couples the internal stress of a rapidly growing wall to the plasma membrane. Such Hechtian transduction via stretch-activated Ca2+channels and H+-ATPase proton efflux dissociating periplasmic AGP-Ca2+, creates a Ca2+influx that activates exocytosis of wall precursors. In effect a highly simplified primary cell wall regulates its own synthesis and a Hechtian growth oscillator regulates overall tip growth. By analogy with the Rosetta Stone that translates trilingual inscriptions as a single identical proclamation, the Hechtian Hypothesis translates classical AGPs and their roles as a Ca2+capacitor, pollen tube guide and wall plasticiser into a simple but widely applicable model of tip growth. Even wider ramifications of the Hechtian oscillator may implicate AGPs in osmosensing or gravisensing and other tropisms, leading us yet further towards the Holy Grail of plant growth.
The cytoplasmic DNA sensor cGAS promotes mitotic cell death
Authors: Zierhut Christian , Funabiki Hironori 
Published: July 2017

AbstractThe cyclic GMP-AMP (cGAMP) synthase cGAS counteracts infections by detecting and binding foreign cytoplasmic DNA1. DNA-induced synthesis of cGAMP activates innate immune signalling and apoptosis through the cGAMP receptor STING and the downstream effector IRF31–7. During interphase the nuclear envelope protects chromosomal self-DNA from cGAS, but the consequences of exposing chromosomes to cGAS following mitotic nuclear envelope disassembly are unknown. Here we demonstrate that cGAS associates with chromosomes during mitosis and binds nucleosomes with even higher affinity than naked DNA in vitro. Nucleosomes nevertheless competitively inhibit the DNA-dependent stimulation of cGAS, and accordingly, chromosomal cGAS does not affect mitotic progression under normal conditions. This suggests that nucleosomes prevent the inappropriate activation of cGAS during mitosis by acting as a signature of self-DNA. During prolonged mitotic arrest, however, cGAS becomes activated to promote cell death, limiting the fraction of cells that can survive and escape mitotic arrest induced by the chemotherapeutic drug taxol. Induction of mitotic cell death involves cGAMP synthesis by cGAS, as well as signal transduction to IRF3 by STING. We thus propose that cGAS plays a previously unappreciated role in guarding against mitotic errors, promoting cell death during prolonged mitotic arrest. Our data also indicate that the cGAS pathway, whose activity differs widely among cell lines, impacts cell fate determination upon treatment with taxol and other anti-mitotic drugs. Thus, we propose the innate immune system may be harnessed to selectively target cells with mitotic abnormalities.
FaStore – a space-saving solution for raw sequencing data
Authors: Roguski Łukasz , Ochoa Idoia , Hernaez Mikel , Deorowicz Sebastian 
Published: July 2017

AbstractThe affordability of DNA sequencing has led to the generation of unprecedented volumes of raw sequencing data. These data must be stored, processed, and transmitted, which poses significant challenges. To facilitate this effort, we introduce FaStore, a specialized compressor for FASTQ files. The proposed algorithm does not use any reference sequences for compression, and permits the user to choose from several lossy modes to improve the overall compression ratio, depending on the specific needs. We demonstrate through extensive simulations that FaStore achieves a significant improvement in compression ratio with respect to previously proposed algorithms for this task. In addition, we perform an analysis on the effect that the different lossy modes have on variant calling, the most widely used application for clinical decision making, especially important in the era of precision medicine. We show that lossy compression can offer significant compression gains, while preserving the essential genomic information and without affecting the variant calling performance.
AKT isoforms have distinct hippocampal expression and roles in synaptic plasticity
Authors: Levenga Josien , Wong Helen , Milstead Ryan A. , Keller Bailey N. , Laplante Lauren E. , Hoeffer Charles A. 
Published: July 2017

ABSTRACTAKT is a kinase that regulates numerous cellular processes in the brain and mutations inAKTare known to affect brain function. AKT is indirectly implicated in synaptic plasticity, but its direct role has not been studied. Moreover, three highly related AKT isoforms are expressed in the brain, but their individual roles are poorly understood. We find that each AKT isoform has a unique expression pattern in the hippocampus, with AKT1 and AKT3 primarily in neurons but displaying local differences, while AKT2 is in astrocytes. We also find isoform-specific roles for AKT in multiple paradigms of hippocampal synaptic plasticity. AKT1, but not AKT2 or AKT3, is required for L-LTP through regulating activity-induced protein synthesis. Interestingly, AKT activity inhibits mGluR-LTD, with overlapping functions for AKT1 and AKT3. In summary, our studies identify distinct expression patterns and roles in synaptic plasticity for AKT isoforms in the hippocampus.
Objective, Quantitative, Data-Driven Assessment of Chemical Probes
Authors: Antolin Albert A. , Tym Joe E. , Komianou Angeliki , Collins Ian , Workman Paul , Al-Lazikani Bissan 
Published: July 2017

ABSTRACTChemical probes are essential tools for understanding biological systems and for target validation, yet selecting tools for biomedical research is largely biased and subjective. Here we describe the Probe Miner: Chemical Probes Objective Assessment resource – capitalising on the plethora of public medicinal chemistry data to empower quantitative, objective, Big Data-driven assessment of chemical probes. We assess >1.8m compounds for their suitability as chemical tools against 2,220 human targets and dissect their biases and limitations.
Production, biophysical characterization and crystallization ofPseudomonas putidaGraA and its complexes with GraT and thegraTAoperator
Authors: Talavera Ariel , Tamman Hedvig , Ainelo Andres , Hadži San , Garcia-Pino Abel , Hõrak Rita , Konijnenberg Albert , Loris Remy 
Published: July 2017

ThegraTAoperon fromPseudomonas putidaencodes a toxin–antitoxin module with an unusually moderate toxin. Here, the production, SAXS analysis and crystallization of the antitoxin GraA, the GraTA complex and the complex of GraA with a 33 bp operator fragment are reported. GraA forms a homodimer in solution and crystallizes in space groupP21, with unit-cell parametersa= 66.9,b = 48.9,c= 62.7 Å, β = 92.6°. The crystals are likely to contain two GraA dimers in the asymmetric unit and diffract to 1.9 Å resolution. The GraTA complex forms a heterotetramer in solution. Crystals of the GraTA complex diffracted to 2.2 Å resolution and are most likely to contain a single heterotetrameric GraTA complex in the asymmetric unit. They belong to space groupP41orP43, with unit-cell parametersa=b= 56.0,c= 128.2 Å. The GraA–operator complex consists of a 33 bp operator region that binds two GraA dimers. It crystallizes in space groupP31orP32, with unit-cell parametersa=b= 105.6,c= 149.9 Å. These crystals diffract to 3.8 Å resolution.
Methylation, crystallization and SAD phasing of the Csu pilus CsuC–CsuE chaperone–adhesin subunit pre-assembly complex from Acinetobacter baumannii
Authors: Pakharukova Natalia , Tuittila Minna , Paavilainen Sari , Zavialov Anton 
Published: July 2017

Acinetobacter baumannii is one of the most difficult Gram-negative bacteria to control and treat. This pathogen forms biofilms on hospital surfaces and medical devices using Csu pili assembled via the archaic chaperone–usher pathway. To uncover the mechanism of bacterial attachment to abiotic surfaces, it was aimed to determine the crystal structure of the pilus tip adhesin CsuE. The CsuC–CsuE chaperone–subunit pre-assembly complex was purified from the periplasm of Escherichia coli overexpressing CsuC and CsuE. Despite the high purity of the complex, no crystals could be obtained. This challenge was solved by the methylation of lysine residues. The complex was crystallized in 0.1 M bis-tris pH 5.5, 17% PEG 3350 using the hanging-drop vapour-diffusion method. The crystals diffracted to a resolution of 2.31 Å and belonged to the triclinic space group P1, with unit-cell parameters a = 53.84, b = 63.85, c = 89.25 Å, α = 74.65, β = 79.65, γ = 69.07°. Initial phases were derived from a single anomalous diffraction experiment using a selenomethionine derivative.
An investigation of corrosion resistance of HVOF coated ASME SA213 T91 boiler steel in an actual boiler environment
Authors: Sidhu Varinder Pal Singh , Goyal Khushdeep , Goyal Rakesh 
Published: July 2017

Purpose
This paper aims to use the high-velocity oxy fuel (HVOF) spraying process for depositing 93(WC–Cr3C2)–7Ni, 75Cr3C2–25NiCr, 83WC–17CO and 86WC–10CO–4Cr coatings on ASME SA213 T91 to study the corrosion resistance of these coatings in an actual boiler environment.

Design/methodology/approach
The HVOF spraying process was used for depositing 93(WC–Cr3C2)–7Ni, 75Cr3C2–25NiCr, 83WC–17CO and 86WC–10CO–4Cr coatings on ASME SA213 T91. All the coatings obtained are found to be uniform, dense and having thickness between 200 and 250 μm. All the coatings were exposed in an actual boiler environment at 900°C temperature for 10 cycles. Each cycle consisted of 100 h heating followed by 1 h cooling at ambient conditions. X-ray diffraction, scanning electron microscopy and energy-dispersive spectroscopy techniques were used to analyse corrosion products.

Findings
All the coated samples were found to be having higher corrosion resistance than the uncoated samples. Among coated specimens, 93(WC–Cr3C2)–7Ni coating has shown maximum and 75Cr3C2–25NiCr coating has shown minimum resistance to corrosion.

Originality/value
This paper is original research.
Characterization and hot corrosion behavior of D-gun sprayed Cr2O3-75% Al2O3 coated ASTM-SA210-A1 boiler steel in molten salt environment
Authors: Rani Amita , Bala Niraj , Gupta C.M. 
Published: July 2017

Purpose
Hot corrosion is the major degradation mechanism of failure of boiler and gas turbine components. The present work aims to investigate the hot corrosion resistance of detonation gun sprayed (D-gun) Cr2O3-75 per cent Al2O3 ceramic coating on ASTM-SA210-A1 boiler steel.

Design/methodology/approach
The coating exhibits nearly uniform, adherent and dense microstructure with porosity less than 0.8 per cent. Thermogravimetry technique is used to study the high temperature hot corrosion behavior of bare and coated boiler steel in molten salt environment (Na2SO4-60 per cent V2O5) at high temperature 900°C for 50 cycles. The corrosion products are analyzed by using X-ray diffraction, scanning electron microscopy (SEM) and field emission scanning electron microscope/energy-dispersive analysis (EDAX) to reveal their microstructural and compositional features for elucidating the corrosion mechanisms.

Findings
During investigations, it was found that the Cr2O3-75 per cent Al2O3 coating on Grade A-1 boiler steel is found to be very effective in decreasing the corrosion rate in the molten salt environment at 900°C. The coating has shown lesser weight gains along with better adhesiveness of the oxide scales with the substrate till the end of the experiment. Thus, coatings serve as an effective diffusion barrier to preclude the diffusion of oxygen from the environment into the substrate boiler steel.

Research limitations/implications
Therefore, it is concluded that the better hot corrosion resistance of the coating is due to the formation of desirable microstructural features such as very low porosity, uniform fine grains and the flat splat structures in the coating; as compared to the bare substrate under cyclic conditions.

Practical implications
This research is useful for coal-fired boilers and other power plant boilers.

Social implications
This research is useful for power generation plants.

Originality/value
There is no reported literature on hot corrosion behavior of Cr2O3-75 per cent Al2O3 coating deposited on the selected substrates by D-gun spray technique. The present work has been focused to study the influence of the Cr2O3-75 per cent Al2O3 coating developed with D-gun spraying technique on high temperature corrosion behavior of ASTM-SA210-A-1 boiler steel in an aggressive environment of Na2SO4-60 per cent V2O5 molten salt at 900°C under cyclic conditions.
Adsorption and corrosion inhibition behavior of aluminium by 2,6-di methyl pyridine in distilled water
Authors: Padash Rahman , Jamalizadeh Effat , Jafari Abdol Hamid 
Published: July 2017

Purpose
Chemical and electrochemical measurements were used to study the corrosion inhibition of aluminium in distilled water using one of pyridine derivatives as corrosion inhibitor.

Design/methodology/approach
Corrosion inhibition of aluminum in distilled water was investigated in the absence and presence of different concentrations of 2,6-di methyl pyridine (DMP). Potentiodynamic polarization, open circuit potential and Fourier Transform Infrared Spectroscopy were employed.

Findings
Inhibition efficiency of 86 per cent is reached with 0.0187 M of DMP at 25°C. Potentiodynamic polarization showed that DMP behaves as mixed type inhibitor. The inhibitor obeyed the Langmuir adsorption isotherm. The value of ΔG°ads suggests physico-chemical adsorption of the inhibitor molecule on the aluminium surface.

Originality/value
This paper indicates DMP could be used as corrosion inhibitor to prevent the corrosion of aluminium in in distilled water.
Making the mission visible: altmetrics and nontraditional publishing
Authors: Bonnet Jennifer L. , Méndez-Brady Marisa 
Published: July 2017

PurposeWhereas traditional book and journal publishing remain the gold standard for many post-secondary institutions, nontraditional publishing is just as prolific at the flagship university in Maine. The university has strong land and sea grant missions that drive a broad research agenda, with an emphasis on community outreach and engagement. However, the impact of researchers’ contributions outside of academe is unlikely to be accurately reflected in promotion, tenure or review processes. Thus, the authors designed a series of altmetrics workshops aimed at seeding conversations around novel ways to track the impact of researchers’ diverse scholarly and creative outputs.

Design/methodology/approachThis paper presents a case study of the instructional approach taken at the University of Maine library to facilitate discussions of alternative impact assessments that reach beyond traditional publications.

FindingsEvaluations revealed an increased awareness of, and interest in, impact tracking tools that capture both traditional scholarship, like journal articles, and nontraditional scholarly and creative outputs, such as videos, podcasts and newsletters. The authors learned that altmetrics provides an entry point into a broader conversation about scholarly impact, and was best received by those whose scholarly output is not always captured by traditional metrics.

Practical implications Scholars are equipped with novel methods for describing the value of their work and discovering a broader audience for their research. Future initiatives will target the needs identified through initial conversations around altmetrics.

Originality/valueAltmetrics workshops provide spaces to explore the potential for new tools that capture a range of previously unconsidered measures of impact, and to discuss the implications of those measures.
Perceptions, preferences of scholarly publishing in Open Access journals
Authors: Bosah Gabriel , Okeji Chuma Clement , Baro Ebikabowei Emmanuel 
Published: July 2017

PurposeThe purpose of the study is to know the various factors librarians consider while selecting Open Access (OA) journal for publication and to identify the challenges librarians face with OA journal publishing.Design/methodology/approachOnline questionnaire was designed to collect data from 402 academic librarians in 87 universities in Africa using SurveyMonkey software.FindingsThe study found that academic librarians are aware of the “green” and “gold” routes but not familiar with the “diamond” route. The study revealed that a large number of the academic librarians have published only one paper in OA journals, followed by those who have not published any paper in OA journals. The study also revealed that reputation of journal and impact factor of journal were seen as very important among the factors that inform them of choosing OA. The majority of the respondents agreed that author fees, and lack of stable internet connectivity are the major barriers to publishing in OA journals.Practical implicationsThe study recommends that academic libraries in institutions of higher learning in Africa should organize seminars periodically on the need for their librarians to research and publish in OA journals.Social implicationsIdentifying factors involved in author decisions to publish in OA journals will help illuminate issues that may encourage or discourage author support of OA publishing models. Further understanding of these issues can assist the efforts to improve author perceptions of and confidence in OA publications.Originality/valueIt is believed that this study of African librarians publishing in OA journals is the first study in the region.
Implementing IT governance: a primer for informaticians
Authors: Cervone H. Frank 
Published: July 2017

PurposeThe purpose of this article is to explore the relevance of information technology (IT) governance to informaticians. In most organizations, informatics is part of the IT function. Therefore, an understanding of IT governance is of benefit to informaticians in their day-to-day work. In addition, while IT governance is not data governance, informaticians often are responsible for data governance efforts. Understanding the larger picture of IT governance can be useful to informaticians, as it provides a solid context and many models that can be used or adapted for data governance efforts.

Design/methodology/approachThis paper is a general review of IT governance based on industry best practice and the author’s experience.

FindingsIT governance is critical to success in IT as it helps ensure all stakeholders have a voice and appropriate decision-making rights in guiding the IT efforts across the organization. Implementing and maintaining an IT governance structure requires commitment from the organization at all levels and requires time and resources for management and implementation.

Originality/valueThis paper provides an overview and introduction to IT governance concepts specifically for the informatics professional.
Mapping the cybersecurity institutional landscape
Authors: Kuerbis Brenden , Badiei Farzaneh 
Published: July 2017

Purpose
There is growing contestation between states and private actors over cybersecurity responsibilities, and its governance is ever more susceptible to nationalization. The authors believe these developments are based on an incomplete picture of how cybersecurity is actually governed in practice and theory. Given this disconnect, this paper aims to attempt to provide a cohesive understanding of the cybersecurity institutional landscape.

Design/methodology/approach
Drawing from institutional economics and using extensive desk research, the authors develop a conceptual model and broadly sketch the activities and contributions of market, networked and hierarchical governance structures and analyze how they interact to produce and govern cybersecurity.

Findings
Analysis shows a robust market and networked governance structures and a more limited role for hierarchical structures. Ex ante efforts to produce cybersecurity using purely hierarchical governance structures, even buttressed with support from networked governance structures, struggle without market demand like in the case of secure internet identifiers. To the contrary, ex post efforts like botnet mitigation, route monitoring and other activities involving information sharing seem to work under a variety of combinations of governance structures.

Originality/value
The authors’ conceptual framework and observations offer a useful starting point for unpacking how cybersecurity is produced and governed; ultimately, we need to understand if and how these governance structure arrangements actually impact variation in observed levels of cybersecurity.