bluuebunny/crossref_metadata_2025_split huggingface dataset:
Online data repositories as educational resources? A learning environment covering formal and informal inferential statistics ideas in scientific inquiry
Authors: Schubatzky Thomas , Haagen-Schützenhöfer Claudia 
Published: May 2019

Abstract
Statistical ideas play a vital role in scientific investigations. For students enrolling in physics-related courses at university, the need to interpret data is set from the start. Analysing graphical representations of data is seen as one way to acquaint students with statistical thinking without relying on pre-knowledge about formal statistics for applying more sophisticated methods like multiple regression. We designed a learning environment, which supports students in understanding the exploratory analysis of multivariate datasets as well as the concept of multiple regression. For phase one of the learning path, we work with exploratory data analysis using the software TinkerPlots, which has several major advantages in contrast to conventional software. Only in phase two formal inferential statistics is applied. We have chosen a context-oriented approach for this learning environment, using the particulate matter concentration in an Austrian city as topic. By providing data from online data repositories in a simplified way, students get the opportunity to work with real data. The amount of this data exceeds the number of measurements collected in typical training labs in an authentic and feasible way. In this article, the design of the intervention and a range of results originating from the triggered learning paths will be presented and discussed. To sum it up, we illustrate advantages and opportunities of the use of innovative software, online data repositories and informal statistics for a first introduction of methods of formal statistics like multiple regression.
Quantum point spread function for imaging trapped few-body systems with a quantum gas microscope
Authors: Pyzh Maxim , Krönke Sven , Weitenberg Christof , Schmelcher Peter 
Published: May 2019

Abstract
Quantum gas microscopes, which image the atomic occupations in an optical lattice, have opened a new avenue to the exploration of many-body lattice systems. Imaging trapped systems after freezing the density distribution by ramping up a pinning lattice leads, however, to a distortion of the original density distribution, especially when its structures are on the scale of the pinning lattice spacing. We show that this dynamics can be described by a filter, which we call in analogy to classical optics a quantum point spread function. Using a machine learning approach, we demonstrate via several experimentally relevant setups that a suitable deconvolution allows for the reconstruction of the original density distribution. These findings are both of fundamental interest for the theory of imaging and of immediate importance for current quantum gas experiments.
WITHDRAWN: A novel searching method of fault chains for power system Cascading outages based on quantitative analysis of dynamic interaction between system and components
Authors: She Jintao 
Published: May 2019

Abstract
This article has been withdrawn by IOP Publishing following a notification from the author post-publication that they did not have permission to publish some of the data present in it.
To ensure compliance with the national regulations for sharing the data, this article has been withdrawn from IOPscience.
multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
Authors: Ecale Zhou Carol L , Malfatti Stephanie , Kimbrel Jeffrey , Philipson Casandra , McNair Katelyn , Hamilton Theron , Edwards Robert , Souza Brian 
Published: May 2019

Abstract

Summary
To address the need for improved phage annotation tools that scale, we created an automated throughput annotation pipeline: multiple-genome Phage Annotation Toolkit and Evaluator (multiPhATE). multiPhATE is a throughput pipeline driver that invokes an annotation pipeline (PhATE) across a user-specified set of phage genomes. This tool incorporates a de novo phage gene calling algorithm and assigns putative functions to gene calls using protein-, virus- and phage-centric databases. multiPhATE’s modular construction allows the user to implement all or any portion of the analyses by acquiring local instances of the desired databases and specifying the desired analyses in a configuration file. We demonstrate multiPhATE by annotating two newly sequenced Yersinia pestis phage genomes. Within multiPhATE, the PhATE processing pipeline can be readily implemented across multiple processors, making it adaptable for throughput sequencing projects. Software documentation assists the user in configuring the system.

Availability and implementation
multiPhATE was implemented in Python 3.7, and runs as a command-line code under Linux or Unix. multiPhATE is freely available under an open-source BSD3 license from https://github.com/carolzhou/multiPhATE. Instructions for acquiring the databases and third-party codes used by multiPhATE are included in the distribution README file. Users may report bugs by submitting to the github issues page associated with the multiPhATE distribution.

Supplementary information
Supplementary data are available at Bioinformatics online.
When Postcolonial Studies Interrupts Media Studies†
Authors: Shome Raka 
Published: May 2019

AbstractThis article utilizes a postcolonial theoretical framework to challenge and unsettle the ways in which media has been historicized in media studies where the time of the North Atlantic West is taken to be an unspoken normative assumption through which we chart media’s development. Further, this article attempts to move us to the Global South by calling attention to media objects and the mediated lives that function through those objects, that have not received any place in media history. Nor are they recognized as a media object. The basic questions that this article raises are: (a) what happens to our understanding of media’s development when we complicate the temporality (North Atlantic Western) through which we narrate the history of media, and (b) What happens to our understanding of what media is when 24/7 electrification is not taken as a norm in our recognition of a media or technology object. What other media objects and mediated lives might then become visible?
Hydrogen technologies and developments in Japan
Authors: Iida Shigeki , Sakata Ko 
Published: May 2019

Abstract
The successful development of hydrogen-energy technologies has several advantages and benefits. Hydrogen-energy development could prevent global warming as well as ensure energy security for countries without adequate energy resources. The successful development of hydrogen would provide energy for transportation and electric power. It is a unique energy carrier, as it can be produced from various energy sources such as wind, fossil fuels and biomass and, when it is combusted, it emits no CO2 emissions. The other advantage is the wide distribution of resources globally that can be used to produce hydrogen. In Japan, the Ministry of Economy, Trade and Industry (METI) published a ‘Strategic Roadmap for Hydrogen and Fuel Cells’ in 2014, with a revised update published in March 2016. The goal of the roadmap is to achieve a hydrogen society. The roadmap aims to resolve technical problems and secure economic efficiency. The roadmap has been organized into the following three phases: Phase 1—Installation of fuel cells; Phase 2—Hydrogen power plant/mass supply chain; Phase 3—CO2-free hydrogen. This paper reports on the current status of fuel cells and fuel-cell vehicles in Japan and gives a description and status of the R&D programmes along with the results of global energy model study towards 2050.
Validated Liquid Chromatographic Method for the Determination of (Canagliflozin, Dapagliflozin or Empagliflozin) and Metformin in the Presence of (1-Cyanoguanidine)
Authors: Hassib Sonia T , Taha Elham A , Elkady Ehab F , Barakat Ghada H 
Published: May 2019

Abstract
A simple and accurate liquid chromatographic method has been developed and validated for the determination of either canagliflozin, dapagliflozin propandiol monohydrate or empagliflozin and metformin in presence of metformin major degradation product;1-cyanoguanidine. The Liquid Chromatographic (LC) method was based on isocratic elution on Prontosil (Lichrosorb 100-5-NH2) column using a mobile phase consisting of NaH2PO4 buffer (10 mM, pH 2.8):acetonitrile (18.5:81.5, v/v), at a flow rate of 2 mL/min−1. Quantitation was achieved with UV detection at 225 nm. The validation of the method was assessed according to International Conference on Harmonization (ICH) guidelines. Linearity, accuracy and precision were satisfactory over the concentration ranges of 12.5–100, 3.75–30, 0.3075–2.46, and 0.3125–2.5 μg/mL for metformin HCl, canagliflozin, dapagliflozin propandiol monohydrate and empagliflozin, respectively. Limits of detection and quantitation were found to be 0.068, 0.135, 0.077 and 0.069 μg/mL and 0.206, 0.410, 0.233 and 0.210 μg/mL for metformin HCl, canagliflozin, dapagliflozin propandiol monohydrate and empagliflozin, respectively. The developed method is suitable for the quality control and routine analysis of the cited drugs separately or in combinations.
Thermal performance of fish is explained by an interplay between physiology, behaviour and ecology
Authors: Neubauer Philipp , Andersen Ken H 
Published: May 2019

AbstractIncreasing temperatures under climate change are thought to affect individual physiology of fish and other ectotherms through increases in metabolic demands, leading to changes in species performance with concomitant effects on species ecology. Although intuitively appealing, the driving mechanism behind thermal performance is contested; thermal performance (e.g. growth) appears correlated with metabolic scope (i.e. oxygen availability for activity) for a number of species, but a substantial number of datasets do not support oxygen limitation of long-term performance. Whether or not oxygen limitations via the metabolic scope, or a lack thereof, have major ecological consequences remains a highly contested question. size and trait-based model of energy and oxygen budgets to determine the relative influence of metabolic rates, oxygen limitation and environmental conditions on ectotherm performance. We show that oxygen limitation is not necessary to explain performance variation with temperature. Oxygen can drastically limit performance and fitness, especially at temperature extremes, but changes in thermal performance are primarily driven by the interplay between changing metabolic rates and species ecology. Furthermore, our model reveals that fitness trends with temperature can oppose trends in growth, suggesting a potential explanation for the paradox that species often occur at lower temperatures than their growth optimum. Our model provides a mechanistic underpinning that can provide general and realistic predictions about temperature impacts on the performance of fish and other ectotherms and function as a null model for contrasting temperature impacts on species with different metabolic and ecological traits.
A simple, graphical approach to comparing multiple treatments
Authors: Thompson Brennan S , Webb Matthew D 
Published: May 2019

SummaryWe consider a graphical approach to comparing multiple treatments that allows users to easily infer differences between any treatment effect and zero, and between any pair of treatment effects. This approach makes use of a flexible, resampling-based procedure that asymptotically controls the familywise error rate (the probability of making one or more spurious inferences). We demonstrate the usefulness of this approach with three empirical examples.
PopNetD3—A Network-Based Web Resource for Exploring Population Structure
Authors: Zhang Javi , Parkinson John 
Published: May 2019

AbstractWe present PopNetD3, a web tool that provides an integrated approach for the network-based visualization of population structure based on the PopNet clustering framework. Users first submit a tab-delimited file that defines diversity of SNPs across the genome which is subsequently processed by the PopNet backend to define patterns of conservation at the chromosome level. The resulting population structure is visualized through a dedicated D3-based tool, allowing users to interactively examine chromosomal regions predicted to share ancestry. We illustrate the capabilities of PopNetD3 through an analysis of 16 strains of Neisseria gonorrhoeae. PopNetD3 is capable of processing population data sets consisting of hundreds of individuals and is publicly available online at: http://compsysbio.org/popnetd3 Last Accessed: May 17, 2019.
Towards inclusive priority-setting for global health research projects: recommendations for sharing power with communities
Authors: Pratt Bridget 
Published: May 2019

AbstractGlobal health research priority-setting is dominated by funders and researchers, often from high-income countries. Engaging communities that are considered disadvantaged and marginalized in priority-setting is essential to making their voices and concerns visible in global health research projects’ topics and questions. However, without attention to power dynamics, their engagement can often lead to presence without voice and voice without influence. Global health research priority-setting must be designed to share power with such communities to ensure that research projects’ topics and questions reflect the health care and system inequities they face. To better understand what sharing ‘power over’ priority-setting requires, 29 in-depth, semi-structured interviews and one focus group were undertaken with researchers, ethicists, community engagement practitioners and community-based organization staff. The study shows that, before moving ahead with priority-setting for global health research projects, it is vital to assess whether contextual factors necessary for meaningful engagement between researchers and marginalized communities are present or can be built in the research setting. Study findings describe several such contextual factors and 12 features of priority-setting that affect how processes are run, who participates in them, and who influences their outputs. During priority-setting for global health research projects, it is essential to implement ways of sharing power with communities in relation to these features. Study findings describe a multitude of such strategies that are employed in practice. After priority-setting, it is important to demonstrate respect and accountability to communities.
Non-self mutation: double-stranded RNA elicits antiviral pathogenic response in a Drosophila model of expanded CAG repeat neurodegenerative diseases
Authors: Eyk Clare L van , Samaraweera Saumya E , Scott Andrew , Webber Dani L , Harvey David P , Mecinger Olivia , O’Keefe Louise V , Cropley Jennifer E , Young Paul , Ho Joshua , Suter Catherine , Richards Robert I 
Published: May 2019

Abstract
Inflammation is activated prior to symptoms in neurodegenerative diseases, providing a plausible pathogenic mechanism. Indeed, genetic and pharmacological ablation studies in animal models of several neurodegenerative diseases demonstrate that inflammation is required for pathology. However, while there is growing evidence that inflammation-mediated pathology may be the common mechanism underlying neurodegenerative diseases, including those due to dominantly inherited expanded repeats, the proximal causal agent is unknown. Expanded CAG.CUG repeat double-stranded RNA causes inflammation-mediated pathology when expressed in Drosophila. Repeat dsRNA is recognized by Dicer-2 as a foreign or ‘non-self’ molecule triggering both antiviral RNA and RNAi pathways. Neither of the RNAi pathway cofactors R2D2 nor loquacious are necessary, indicating antiviral RNA activation. RNA modification enables avoidance of recognition as ‘non-self’ by the innate inflammatory surveillance system. Human ADAR1 edits RNA conferring ‘self’ status and when co-expressed with expanded CAG.CUG dsRNA in Drosophila the pathology is lost. Cricket Paralysis Virus protein CrPV-1A is a known antagonist of Argonaute-2 in Drosophila antiviral defense. CrPV-1A co-expression also rescues pathogenesis, confirming anti-viral-RNA response. Repeat expansion mutation therefore confers ‘non-self’ recognition of endogenous RNA, thereby providing a proximal, autoinflammatory trigger for expanded repeat neurodegenerative diseases.
Delayed Diagnosis of Respiratory Syncytial Virus Infections in Hospitalized Adults: Individual Patient Data, Record Review Analysis and Physician Survey in the United States
Authors: Lee Nelson , Walsh Edward E , Sander Ian , Stolper Robert , Zakar Jessica , Wyffels Veronique , Myers David , Fleischhackl Roman 
Published: May 2019

AbstractBackgroundDespite the prevalence of respiratory syncytial virus (RSV) in adults hospitalized with acute respiratory infections, guidelines for the diagnosis and management of RSV have not been established. This analysis evaluated the role and timeliness of RSV diagnostic testing and its potential impact on clinical outcomes.MethodsWe analyzed individual patient data from hospitalized adults with confirmed RSV infections during 2 North American RSV seasons. Participating physicians reported clinical, virologic diagnosis, and outcome variables using a standardized online case form.ResultsAcross 32 US states, 132 physicians reported 379 RSV cases. Polymerase chain reaction–based diagnostics were the most common type of test ordered (94.2%) with <5% ordered specifically to diagnose RSV. Most tests (67.6%) were ordered in hospital wards or intensive care units. Overall, 47.4%, 30.9%, and 21.7% of patients had RSV diagnosed <12, 12‒24, and >24 hours after hospital admission, respectively. Later diagnosis was associated with longer hospital stays (n = 145; R = +0.191; P < .05) and greater antibiotic use.ConclusionDiagnosis of RSV infection in hospitalized adults is often delayed, which may affect clinical management and outcomes. Our findings indicate the need to improve the diagnostic strategies in this patient population.
Overexpression of SmeGH contributes to the acquired MDR of Stenotrophomonas maltophilia
Authors: Li Li-Hua , Zhang Man-San , Wu Chao-Jung , Lin Yi-Tsung , Yang Tsuey-Ching 
Published: May 2019

Abstract

Background
Stenotrophomonas maltophilia displays high-level resistance to various antibiotics. Fluoroquinolone is among the few treatment options for S. maltophilia infection. Overexpression of SmeDEF, SmeVWX and SmQnr are the main mechanisms responsible for fluoroquinolone resistance in S. maltophilia.

Objectives
To reveal the unidentified fluoroquinolone resistance mechanisms in S. maltophilia.

Methods
Fluoroquinolone-resistant spontaneous mutants were selected by spreading KJΔDEFΔ5, a SmeDEF- and SmeVWX-null double mutant, on ciprofloxacin- or levofloxacin-containing medium. Antibiotic susceptibility was assessed by the agar dilution method. Outer membrane protein profiles of fluoroquinolone-resistant mutants were assayed by SDS-PAGE and significant protein was characterized by LC-MS/MS. The expression of tolCsm, smeH, smeK, smeN, smeP, smeZ and smQnr was investigated by real-time quantitative PCR. The contribution of SmeGH overexpression to antibiotic resistance was verified by ΔsmeH mutant construction and smeGH complementation assay.

Results
Most fluoroquinolone-resistant mutants displayed MDR. The TolCsm protein and smeH transcript were concomitantly overexpressed in some MDR mutants. smeH deletion increased the susceptibility of the MDR mutants to fluoroquinolone, macrolide, chloramphenicol and tetracycline, and the resistance compromise was partially reversed by complementation with a plasmid containing smeGH. SmeGH overexpression was found in some fluoroquinolone-resistant clinical S. maltophilia isolates whose SmeDEF, SmeVWX and SmQnr proteins were not or were lowly expressed.

Conclusions
Overexpression of SmeGH contributes to the acquired resistance of S. maltophilia to fluoroquinolone, macrolide, chloramphenicol and tetracycline.
Leveraging Nordic links: South African labour’s role in regulating labour standards in wine global production networks
Authors: Hastings Thomas 
Published: May 2019

AbstractThere are established difficulties in upholding private standards within global production networks (GPNs) through the use of multi-stakeholder initiatives (MSIs). Taking the case of wine production in South Africa, the article examines labour’s role in leveraging new approaches to labour regulation in the interests of improved working standards and opportunities for labour organising. To do this, the paper adopts an extended take on the GPN framework which focuses on labour’s own networked capabilities. The role of worker agency in forging international connections and new relational geographies between unions and civil society organisations across wine GPNs (in particular between South Africa and Scandinavia) is explored. By applying pressure within and through these networks, workers are shown to encourage new approaches to private governance in the interests of improved worker rights on the ground.
The concerted actions of Tip1/CLIP-170, Klp5/Kinesin-8, and Alp14/XMAP215 regulate microtubule catastrophe at the cell end
Authors: Niu Xiaojia , Zheng Fan , Fu Chuanhai 
Published: May 2019

Abstract
Spatial regulation of microtubule catastrophe is important for controlling microtubule length and consequently contributes to the proper establishment of cell polarity and cell growth. The +TIP proteins including Tip1/CLIP-170, Klp5/Kinesin-8, and Alp14/XMAP215 reside at microtubule plus ends to regulate microtubule dynamics. In the fission yeast Schizosaccharomyces pombe, Tip1 and Alp14 serve as microtubule-stabilizing factors, while Klp5 functions oppositely as a catastrophe-promoting factor. Despite that Tip1 has been shown to play a key role in restricting microtubule catastrophe to the cell end, how Tip1 fulfills the role remains to be determined. Employing live-cell microscopy, we showed that the absence of Tip1 impairs the localization of both Klp5 and Alp14 at microtubule plus ends, but the absence of Klp5 prolongs the residence time of Tip1 at microtubule plus ends. We further revealed that Klp5 accumulates behind Tip1 at microtubule plus ends in a Tip1-dependent manner. In addition, artificially tethering Klp5 to microtubule plus ends promotes premature microtubule catastrophe, while tethering Alp14 to microtubule plus ends in the cells lacking Tip1 rescues the phenotype of short microtubules. These findings establish that Tip1 restricts microtubule catastrophe to the cell end likely by spatially restricting the microtubule catastrophe activity of Klp5 and stabilizing Alp14 at microtubule plus ends. Thus, the work demonstrates the orchestration of Tip1, Alp14, and Klp5 in ensuring microtubule catastrophe at the cell end.