bluuebunny/crossref_metadata_2025_split huggingface dataset:
RImmPort: an R/Bioconductor package that enables ready-for-analysis immunology research data
Authors: Shankar Ravi D , Bhattacharya Sanchita , Jujjavarapu Chethan , Andorf Sandra , Wiser Jeffery A , Butte Atul J 
Published: November 2016

Abstract

Summary
Open access to raw clinical and molecular data related to immunological studies has created a tremendous opportunity for data-driven science. We have developed RImmPort that prepares NIAID-funded research study datasets in ImmPort (immport.org) for analysis in R. RImmPort comprises of three main components: (i) a specification of R classes that encapsulate study data, (ii) foundational methods to load data of a specific study and (iii) generic methods to slice and dice data across different dimensions in one or more studies. Furthermore, RImmPort supports open formalisms, such as CDISC standards on the open source bioinformatics platform Bioconductor, to ensure that ImmPort curated study datasets are seamlessly accessible and ready for analysis, thus enabling innovative bioinformatics research in immunology.

Availability and Implementation
RImmPort is available as part of Bioconductor (bioconductor.org/packages/RImmPort).

Supplementary information
Supplementary data are available at Bioinformatics online.
DNABarcodes: an R package for the systematic construction of DNA sample tags
Authors: Buschmann Tilo 
Published: November 2016

Abstract

Motivation
DNA barcodes are commonly used for counting and discriminating purposes in molecular and cell biology. Not every set of DNA sequences is equally suitable for this goal. There is a growing demand for more sophisticated barcode designs, with only few tools available. We prepared an R package that combines known algorithms and innovative methods for the efficient, flexible and near-optimal generation of robust barcode sets.

Results
Our R-software package ‘DNABarcodes’ generates sets of DNA barcodes from a few basic input parameters (e.g. length, distance metric, minimum distance, chemical properties). It satisfies the specifics of most particular experimental demands in de novo design of barcodes. Additionally, the package allows analysing existing sets of DNA barcodes as well as the generation of subsets of those existing sets to improve their error correction and detection properties. ‘DNABarcodes’ was designed for speed, versatility, provable correctness and large set sizes.

Availability and Implementation
The DNABarcodes R package is available from Bioconductor at http://bioconductor.org/packages/DNABarcodes under the GPL-2 license.

Supplementary information
Supplementary data are available at Bioinformatics online.
Parameter estimation for dynamical systems with discrete events and logical operations
Authors: Fröhlich Fabian , Theis Fabian J , Rädler Joachim O , Hasenauer Jan 
Published: November 2016

Abstract

Motivation
Ordinary differential equation (ODE) models are frequently used to describe the dynamic behaviour of biochemical processes. Such ODE models are often extended by events to describe the effect of fast latent processes on the process dynamics. To exploit the predictive power of ODE models, their parameters have to be inferred from experimental data. For models without events, gradient based optimization schemes perform well for parameter estimation, when sensitivity equations are used for gradient computation. Yet, sensitivity equations for models with parameter- and state-dependent events and event-triggered observations are not supported by existing toolboxes.

Results
In this manuscript, we describe the sensitivity equations for differential equation models with events and demonstrate how to estimate parameters from event-resolved data using event-triggered observations in parameter estimation. We consider a model for GFP expression after transfection and a model for spiking neurons and demonstrate that we can improve computational efficiency and robustness of parameter estimation by using sensitivity equations for systems with events. Moreover, we demonstrate that, by using event-outputs, it is possible to consider event-resolved data, such as time-to-event data, for parameter estimation with ODE models. By providing a user-friendly, modular implementation in the toolbox AMICI, the developed methods are made publicly available and can be integrated in other systems biology toolboxes.

Availability and Implementation
We implement the methods in the open-source toolbox Advanced MATLAB Interface for CVODES and IDAS (AMICI, https://github.com/ICB-DCM/AMICI).

Supplementary information
Supplementary data are available at Bioinformatics online.
GC Content Heterogeneity Transition of Conserved Noncoding Sequences Occurred at the Emergence of Vertebrates
Authors: Hettiarachchi Nilmini , Saitou Naruya 
Published: November 2016

Abstract
Conserved non-coding sequences (CNSs) of Eukaryotes are known to be significantly enriched in regulatory sequences. CNSs of diverse lineages follow different patterns in abundance, sequence composition, and location. Here, we report a thorough analysis of CNSs in diverse groups of Eukaryotes with respect to GC content heterogeneity. We examined 24 fungi, 19 invertebrates, and 12 non-mammalian vertebrates so as to find lineage specific features of CNSs. We found that fungi and invertebrate CNSs are predominantly GC rich as in plants we previously observed, whereas vertebrate CNSs are GC poor. This result suggests that the CNS GC content transition occurred from the ancestral GC rich state of Eukaryotes to GC poor in the vertebrate lineage due to the enrollment of GC poor transcription factor binding sites that are lineage specific. CNS GC content is closely linked with the nucleosome occupancy that determines the location and structural architecture of DNAs.
Towards ecosystem-based management: identifying operational food-web indicators for marine ecosystems
Authors: Tam Jamie C. , Link Jason S. , Rossberg Axel G. , Rogers Stuart I. , Levin Philip S. , Rochet Marie-Joëlle , Bundy Alida , Belgrano Andrea , Libralato Simone , Tomczak Maciej , van de Wolfshaar Karen , Pranovi Fabio , Gorokhova Elena , Large Scott I. , Niquil Nathalie , Greenstreet Simon P. R. , Druon Jean-Noel , Lesutiene Jurate , Johansen Marie , Preciado Izaskun , Patricio Joana , Palialexis Andreas , Tett Paul , Johansen Geir O. , Houle Jennifer , Rindorf Anna 
Published: November 2016

Abstract
Modern approaches to Ecosystem-Based Management and sustainable use of marine resources must account for the myriad of pressures (interspecies, human and environmental) affecting marine ecosystems. The network of feeding interactions between co-existing species and populations (food webs) are an important aspect of all marine ecosystems and biodiversity. Here we describe and discuss a process to evaluate the selection of operational food-web indicators for use in evaluating marine ecosystem status. This process brought together experts in food-web ecology, marine ecology, and resource management, to identify available indicators that can be used to inform marine management. Standard evaluation criteria (availability and quality of data, conceptual basis, communicability, relevancy to management) were implemented to identify practical food-web indicators ready for operational use and indicators that hold promise for future use in policy and management. The major attributes of the final suite of operational food-web indicators were structure and functioning. Indicators that represent resilience of the marine ecosystem were less developed. Over 60 potential food-web indicators were evaluated and the final selection of operational food-web indicators includes: the primary production required to sustain a fishery, the productivity of seabirds (or charismatic megafauna), zooplankton indicators, primary productivity, integrated trophic indicators, and the biomass of trophic guilds. More efforts should be made to develop thresholds-based reference points for achieving Good Environmental Status. There is also a need for international collaborations to develop indicators that will facilitate management in marine ecosystems used by multiple countries.
Constitutional Statutes
Authors: Ahmed Farrah , Perry Adam 
Published: November 2016

Abstract
In recent years, British courts have treated constitutional statutes differently from ordinary statutes. This article sets outs to explain: (i) how courts have treated constitutional statutes differently from ordinary statutes; (ii) what a constitutional statute is; and (iii) why constitutional statutes should be treated differently from ordinary statutes. Courts have made it harder for ordinary statutes to repeal constitutional statutes by implication, and easier for constitutional statutes to repeal ordinary statutes by implication. A constitutional statute is a statute which regulates state institutions, and which possesses importance of a particular type that we describe. The nature of a constitutional statute largely—but not entirely—justifies the special treatment they have been given. These conclusions have wider implications, including for proposals to codify the British constitution.
A Pilot Comparison of a Smartphone App With or Without 2-Way Messaging Among Chronic Pain Patients
Authors: Jamison Robert N. , Jurcik Dylan C. , Edwards Robert R. , Huang Chuan-Chin , Ross Edgar L. 
Published: November 2016

Objectives:
The overall aim of this study was to determine the effect of introducing a smartphone pain application (app), for both Android and iPhone devices that enables chronic pain patients to assess, monitor, and communicate their status to their providers.

Methods:
This study recruited 105 chronic pain patients to use a smartphone pain app and half of the patients (N=52) had 2-way messaging available through the app. All patients completed baseline measures and were asked to record their progress every day for 3 months, with the opportunity to continue for 6 months. All participants were supplied a Fitbit to track daily activity. Summary line graphs were posted to each of the patients’ electronic medical records and physicians were notified of their patient’s progress.

Results:
Ninety patients successfully downloaded the pain app. Average age of the participants was 47.1 (range, 18 to 72), 63.8% were female and 32.3% reported multiple pain sites. Adequate validity and reliability was found between the daily assessments and standardized questionnaires (r=0.50) and in repeated daily measures (pain, r=0.69; sleep, r=0.83). The app was found to be easily introduced and well tolerated. Those patients assigned to the 2-way messaging condition on average tended to use the app more and submit more daily assessments (95.6 vs. 71.6 entries), but differences between groups were not significant. Pain-app satisfaction ratings overall were high.

Discussion:
This study highlights some of the challenges and benefits in utilizing smartphone apps to manage chronic pain patients, and provides insight into those individuals who might benefit from mHealth technology.
GOLDEN anniversary of the acute respiratory distress syndrome: still much work to do!
Authors: Villar Jesús , Slutsky Arthur S. 
Published: November 2016

Purpose of review
Over the past 50 years, we have developed a conceptual model of the acute respiratory distress syndrome (ARDS), and have witnessed significant advances in the care of patients with ARDS. In this commentary, we will discuss recent published articles reporting or suggesting new conceptual models for diagnosis, classification, stratification, prevention, ventilatory management, pharmacologic treatment, and outcome prediction of ARDS.

Recent findings
This review is a tribute to all clinicians and investigators that have contributed to a better understanding of ARDS. However, we will mainly focus on publications from the last 24 months dealing with clinically relevant issues, and we briefly mention recent approaches in respiratory intensive care medicine that could improve ARDS outcome.

Summary
Because this year is the golden anniversary of the first clinical description of ARDS in 1967, we have used the acronym ‘G.O.L.D.E.N.’ to frame our review. It is clear that although much has been learned over the past 50 years, there is still much work to do to unravel and control this continuously surprising syndrome.
Limiting sedation for patients with acute respiratory distress syndrome – time to wake up
Authors: Shah Faraaz Ali , Girard Timothy D. , Yende Sachin 
Published: November 2016

Purpose of review
Critically ill patients with acute respiratory distress syndrome (ARDS) may require sedation in their clinical care. The goals of sedation in ARDS patients are to improve patient comfort and tolerance of supportive and therapeutic measures without contributing to adverse outcomes. This review discusses the current evidence for sedation management in patients with ARDS.

Recent findings
Deep sedation strategies should be avoided in the care of patients with ARDS because deep sedation has been associated with increased time on mechanical ventilation, longer ICU and hospital length of stay, and higher mortality in critically ill patients. Adoption of protocol-based, light-sedation strategies is preferred and improves patient outcomes. Although the optimal sedative agent for ARDS patients is unclear, benzodiazepines should be avoided because of associations with oversedation, delirium, prolonged ICU and hospital length of stay, and increased mortality. Minimizing sedation in patients with ARDS facilitates early mobilization and early discharge from the ICU, potentially aiding in recovery from critical illness. Strategies to optimize ventilation in ARDS patients, such as low tidal volume ventilation and high positive end-expiratory pressure can be employed without deep sedation; however, deep sedation is required if patients receive neuromuscular blockade, which may benefit some ARDS patients. Knowledge gaps persist as to whether or not prone positioning and extracorporeal membrane oxygenation can be tolerated with light sedation.

Summary
Current evidence supports the use of protocol-based, light-sedation strategies in critically ill patients with ARDS. Further research into sedation management specifically in ARDS populations is needed.
The gut peptide neuropeptide Y and post-traumatic stress disorder
Authors: Rasmusson Ann M. 
Published: November 2016

Purpose of review
This article reviews the role of neuropeptide Y (NPY) in the pathophysiology of post-traumatic stress disorder (PTSD) and gastrointestinal disorders such as irritable bowel syndrome (IBS) with which PTSD is highly comorbid. NPY is low in the cerebrospinal fluid and plasma of male combat veterans with PTSD and correlates negatively with sympathetic nervous system (SNS) hyperreactivity, PTSD symptoms and time to recovery. NPY regulation has not yet been evaluated in women with PTSD.

Recent findings
NPY levels in bowel tissue are low in IBS with diarrhea (IBS-D) versus IBS with constipation. The density of ghrelin containing cells of the gastric oxyntic mucosa is markedly increased in IBS-D. PTSD-related SNS hyperreactivity may interact with this substrate to increase ghrelin release, which activates receptors in the lumbosacral spinal cord and basolateral amygdala to increase colonic motility and amygdala hyperreactivity, respectively. Loss of function gene polymorphisms in adrenergic α2-autoreceptors and increased corticotropin-releasing hormone, as observed in PTSD, are also thought to contribute to IBS-D.

Summary
Knowledge of shared underlying NPY system-related neurobiological factors that contribute to the comorbidity of PTSD and gastrointestinal disorders may help guide research, development and prescription of targeted and more effective individualized therapeutic interventions.
Signalling maps in cancer research: construction and data analysis
Authors: Kondratova Maria , Sompairac Nicolas , Barillot Emmanuel , Zinovyev Andrei , Kuperstein Inna 
Published: November 2016

AbstractGeneration and usage of high-quality molecular signalling network maps can be augmented by standardising notations, establishing curation workflows and application of computational biology methods to exploit the knowledge contained in the maps. In this manuscript, we summarize the major aims and challenges of assembling information in the form of comprehensive maps of molecular interactions. Mainly, we share our experience gained while creating the Atlas of Cancer Signalling Network. In the step-by-step procedure, we describe the map construction process and suggest solutions for map complexity management by introducing a hierarchical modular map structure. In addition, we describe the NaviCell platform, a computational technology using Google Maps API to explore comprehensive molecular maps similar to geographical maps, and explain the advantages of semantic zooming principles for map navigation. We also provide the outline to prepare signalling network maps for navigation using the NaviCell platform. Finally, several examples of cancer high-throughput data analysis and visualization in the context of comprehensive signalling maps are presented.
Coxsackievirus B3 protease 3C: expression, purification, crystallization and preliminary structural insights
Authors: Fili Stavroula , Valmas Alexandros , Christopoulou Magdalini , Spiliopoulou Maria , Nikolopoulos Nikos , Lichière Julie , Logotheti Souzana , Karavassili Fotini , Rosmaraki Eleftheria , Fitch Andrew , Wright Jonathan , Beckers Detlef , Degen Thomas , Nénert Gwilherm , Hilgenfeld Rolf , Papageorgiou Nicolas , Canard Bruno , Coutard Bruno , Margiolaki Irene 
Published: November 2016

Viral proteases are proteolytic enzymes that orchestrate the assembly of viral components during the viral life cycle and proliferation. Here, the expression, purification, crystallization and preliminary X-ray diffraction analysis are presented of protease 3C, the main protease of an emerging enterovirus, coxsackievirus B3, that is responsible for many cases of viral myocarditis. Polycrystalline protein precipitates suitable for X-ray powder diffraction (XRPD) measurements were produced in the presence of 22–28%(w/v) PEG 4000, 0.1 MTris–HCl, 0.2 MMgCl2in a pH range from 7.0 to 8.5. A polymorph of monoclinic symmetry (space groupC2, unit-cell parametersa = 77.9,b= 65.7,c = 40.6 Å, β = 115.9°) was identifiedviaXRPD. These results are the first step towards the complete structural determination of the moleculeviaXRPD and a parallel demonstration of the accuracy of the method.
Mapping outcomes of four Queensland city futures initiatives
Authors: Russo Colin 
Published: November 2016

Purpose
The purpose of this paper is to map the outcomes of four influential South East Queensland city visioning and foresight initiatives conducted by the cities of Maroochy, Logan, Gold Coast and Brisbane.

Design/methodology/approach
This paper applies causal layered analysis to map the outcomes of four city visioning and foresight initiatives.

Findings
It is averred in this paper that cities need to map their experiences of past futures initiatives for what worked and what has resulted today, and for recommendations of futures actions and innovations.

Originality/value
This paper deepens the discussion about the critical features of the four initiatives by focusing on their outcomes and alternatives they could produce to influence the futures of their cities.
Sectoral entry-barriers for entrepreneurial activities – a Russian start-up between challenging global markets and local conservative path dependencies
Authors: Thurner Thomas , Proskuryakova Liliana 
Published: November 2016

Purpose
Sectoral foresight activities often identify technological opportunities but leave the question open who will pursue them. Entrepreneurial activities have become increasingly important for the introduction and commercialization of new technological solutions. The same is true for Russia’s oil and gas industry, which requires a major technological upscaling to stay competitive. Promising start-ups, however, often face high barriers and fail to commercialize superior technological solutions. The purpose of this study is to show how industry-specific entry barriers can hamper start-up activities.

Design/methodology/approach
This paper discusses the experiences of a Russian oilfield service start-up in commercializing a self-developed technology for increasing the productivity of oil wells.

Findings
The start-up faced conservatism from corporate decision-makers, declining oil prices and suboptimal protection of intellectual property rights. The company overcame most barriers through moving into other markets outside of Russia, as closing a deal with customers in the USA and Canada went much faster than the extended business cycles of national oil companies.

Originality/value
This paper connects sectoral foresight activities to the real-life experience of a start-up. The findings suggest that entry barriers need to be addressed by the planning process to really pave the way for a greater impact of entrepreneurial activity.
Robust strategies of climate change mitigation in interacting energy, economy and land use systems
Authors: Leimbach Marian , Labriet Maryse , Bonsch Markus , Dietrich Jan Philipp , Kanudia Amit , Mouratiadou Ioanna , Popp Alexander , Klein David 
Published: December 2016

PurposeBioenergy is a key component of climate change mitigation strategies aiming at low stabilization. Its versatility and capacity to generate negative emissions when combined with carbon capture and storage add degrees of freedom to the timing of emission reductions. This paper aims to explore the robustness of a bioenergy-based mitigation strategy by addressing several dimensions of uncertainty on biomass potential, bioenergy use and induced land use change emissions.Design/methodology/approachDifferent mitigation scenarios were explored by two different energy-economy optimization models coupled to the same land use model, which provides a common basis for the second generation bioenergy dynamics in the two energy-economy models.FindingsUsing bioenergy is found to be a robust mitigation strategy as demonstrated by high biomass shares in primary energy demand in both models and in all mitigation scenarios.Practical implicationsA variety of possible storylines about future uses of biomass exist. The comparison of the technology choices preferred by the applied models helps understand how future emission reductions can be achieved under alternative storylines.Originality/valueThe presented comparison-based assessment goes beyond other comparison studies because both energy-economy models are coupled to the same land use model.