bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the road to percent accuracy: non-linear reaction of the matter power spectrum to dark energy and modified gravity
Authors: Cataneo M , Lombriser L , Heymans C , Mead A J , Barreira A , Bose S , Li B 
Published: July 2019

ABSTRACT
We present a general method to compute the non-linear matter power spectrum for dark energy (DE) and modified gravity scenarios with per cent-level accuracy. By adopting the halo model and non-linear perturbation theory, we predict the reaction of a lambda cold dark matter (ΛCDM) matter power spectrum to the physics of an extended cosmological parameter space. By comparing our predictions to N-body simulations we demonstrate that with no-free parameters we can recover the non-linear matter power spectrum for a wide range of different w0–wa DE models to better than 1 per cent accuracy out to k ≈ 1 $h \,{\rm Mpc}^{-1}$. We obtain a similar performance for both DGP and f(R) gravity, with the non-linear matter power spectrum predicted to better than 3 per cent accuracy over the same range of scales. When including direct measurements of the halo mass function from the simulations, this accuracy improves to 1 per cent. With a single suite of standard ΛCDM N-body simulations, our methodology provides a direct route to constrain a wide range of non-standard extensions to the concordance cosmology in the high signal-to-noise non-linear regime.
Observational properties of ultra-diffuse galaxies in low-density environments: field UDGs are predominantly blue and star forming
Authors: Prole D J , van der Burg R F J , Hilker M , Davies J I 
Published: July 2019

Abstract
While we have learnt much about ultradiffuse galaxies (UDGs) in groups and clusters, relatively little is known about them in less dense environments. More isolated UDGs are important for our understanding of UDG formation scenarios because they form via secular mechanisms, allowing us to determine the relative importance of environmentally driven formation in groups and clusters. We have used the public Kilo-Degree Survey together with the Hyper Suprime-Cam Subaru Strategic Program to constrain the abundance and properties of UDGs in the field, targeting sources with low surface brightness (24.0 ≤ $\bar{\mu }_{\mathrm{ e},r}$ ≤ 26.5) and large apparent sizes (3.0 arcsec ≤ $\bar{r}_{\mathrm{ e},r}$ ≤ 8.0 arcsec). Accounting for several sources of interlopers in our selection based on canonical scaling relations, and using an empirical UDG model based on measurements from the literature, we show that a scenario in which cluster-like red-sequence UDGs occupy a significant number of field galaxies is unlikely, with most field UDGs being significantly bluer and showing signs of localized star formation. An immediate conclusion is that UDGs are much more efficiently quenched in high-density environments. We estimate an upper limit on the total field abundance of UDGs of 8 ± 3 × 10−3 cMpc−3 within our selection range. We also compare the total field abundance of UDGs to a measurement of the abundance of H i-rich UDGs from the literature, suggesting that they occupy at least one-fifth of the overall UDG population. The mass formation efficiency of UDGs implied by this upper limit is similar to what is measured in groups and clusters.
A complex suite of loci and elements in eukaryotic type II topoisomerases determine selective sensitivity to distinct poisoning agents
Authors: Blower Tim R , Bandak Afif , Lee Amy S Y , Austin Caroline A , Nitiss John L , Berger James M 
Published: July 2019

AbstractType II topoisomerases catalyze essential DNA transactions and are proven drug targets. Drug discrimination by prokaryotic and eukaryotic topoisomerases is vital to therapeutic utility, but is poorly understood. We developed a next-generation sequencing (NGS) approach to identify drug-resistance mutations in eukaryotic topoisomerases. We show that alterations conferring resistance to poisons of human and yeast topoisomerase II derive from a rich mutational ‘landscape’ of amino acid substitutions broadly distributed throughout the entire enzyme. Both general and discriminatory drug-resistant behaviors are found to arise from different point mutations found at the same amino acid position and to occur far outside known drug-binding sites. Studies of selected resistant enzymes confirm the NGS data and further show that the anti-cancer quinolone vosaroxin acts solely as an intercalating poison, and that the antibacterial ciprofloxacin can poison yeast topoisomerase II. The innate drug-sensitivity of the DNA binding and cleavage region of human and yeast topoisomerases (particularly hTOP2β) is additionally revealed to be significantly regulated by the enzymes’ adenosine triphosphatase regions. Collectively, these studies highlight the utility of using NGS-based methods to rapidly map drug resistance landscapes and reveal that the nucleotide turnover elements of type II topoisomerases impact drug specificity.
Specificity of protein–DNA interactions in hypersaline environment: structural studies on complexes of Halobacterium salinarum oxidative stress-dependent protein hsRosR
Authors: Kutnowski Nitzan , Shmulevich Fania , Davidov Geula , Shahar Anat , Bar-Zvi Dudy , Eichler Jerry , Zarivach Raz , Shaanan Boaz 
Published: July 2019

AbstractInteractions between proteins and DNA are crucial for all biological systems. Many studies have shown the dependence of protein–DNA interactions on the surrounding salt concentration. How these interactions are maintained in the hypersaline environments that halophiles inhabit remains puzzling. Towards solving this enigma, we identified the DNA motif recognized by the Halobactrium salinarum ROS-dependent transcription factor (hsRosR), determined the structure of several hsRosR–DNA complexes and investigated the DNA-binding process under extreme high-salt conditions. The picture that emerges from this work contributes to our understanding of the principles underlying the interplay between electrostatic interactions and salt-mediated protein–DNA interactions in an ionic environment characterized by molar salt concentrations.
Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes
Authors: Stadlbauer Petr , Kührová Petra , Vicherek Lukáš , Banáš Pavel , Otyepka Michal , Trantírek Lukáš , Šponer Jiří 
Published: July 2019

AbstractGuanine quadruplexes (G4s) are non-canonical nucleic acids structures common in important genomic regions. Parallel-stranded G4 folds are the most abundant, but their folding mechanism is not fully understood. Recent research highlighted that G4 DNA molecules fold via kinetic partitioning mechanism dominated by competition amongst diverse long-living G4 folds. The role of other intermediate species such as parallel G-triplexes and G-hairpins in the folding process has been a matter of debate. Here, we use standard and enhanced-sampling molecular dynamics simulations (total length of ∼0.9 ms) to study these potential folding intermediates. We suggest that parallel G-triplex per se is rather an unstable species that is in local equilibrium with a broad ensemble of triplex-like structures. The equilibrium is shifted to well-structured G-triplex by stacked aromatic ligand and to a lesser extent by flanking duplexes or nucleotides. Next, we study propeller loop formation in GGGAGGGAGGG, GGGAGGG and GGGTTAGGG sequences. We identify multiple folding pathways from different unfolded and misfolded structures leading towards an ensemble of intermediates called cross-like structures (cross-hairpins), thus providing atomistic level of description of the single-molecule folding events. In summary, the parallel G-triplex is a possible, but not mandatory short-living (transitory) intermediate in the folding of parallel-stranded G4.
Single-molecule detection of deoxyribonucleoside triphosphates in microdroplets
Authors: Breiner Boris , Johnson Kerr , Stolarek Magdalena , Silva Ana-Luisa , Negrea Aurel , Bell Neil M , Isaac Tom H , Dethlefsen Mark , Chana Jasmin , Ibbotson Lindsey A , Palmer Rebecca N , Bush James , Dunning Alexander J , Love David M , Pachoumi Olympia , Kelly Douglas J , Shibahara Aya , Wu Mei , Sosna Maciej , Dear Paul H , Tolle Fabian , Petrini Edoardo , Amasio Michele , Shelford Leigh R , Saavedra Monica S , Sheridan Eoin , Kuleshova Jekaterina , Podd Gareth J , Balmforth Barnaby W , Frayling Cameron A 
Published: July 2019

AbstractA new approach to single-molecule DNA sequencing in which dNTPs, released by pyrophosphorolysis from the strand to be sequenced, are captured in microdroplets and read directly could have substantial advantages over current sequence-by-synthesis methods; however, there is no existing method sensitive enough to detect a single nucleotide in a microdroplet. We have developed a method for dNTP detection based on an enzymatic two-stage reaction which produces a robust fluorescent signal that is easy to detect and process. By taking advantage of the inherent specificity of DNA polymerases and ligases, coupled with volume restriction in microdroplets, this method allows us to simultaneously detect the presence of and distinguish between, the four natural dNTPs at the single-molecule level, with negligible cross-talk.
The medical necessity of advanced molecular testing in the diagnosis and treatment of brain tumor patients
Authors: Horbinski Craig , Ligon Keith L , Brastianos Priscilla , Huse Jason T , Venere Monica , Chang Susan , Buckner Jan , Cloughesy Timothy , Jenkins Robert B , Giannini Caterina , Stupp Roger , Nabors L Burt , Wen Patrick Y , Aldape Kenneth J , Lukas Rimas V , Galanis Evanthia , Eberhart Charles G , Brat Daniel J , Sarkaria Jann N 
Published: July 2019

AbstractAccurate pathologic diagnoses and molecularly informed treatment decisions for a wide variety of cancers depend on robust clinical molecular testing that uses genomic, epigenomic, and transcriptomic-based tools. Nowhere is this more essential than in the workup of brain tumors, as emphasized by the incorporation of molecular criteria into the 2016 World Health Organization classification of central nervous system tumors and the updated official guidelines of the National Comprehensive Cancer Network. Despite the medical necessity of molecular testing in brain tumors, access to and utilization of molecular diagnostics is still highly variable across institutions, and a lack of reimbursement for such testing remains a significant obstacle. The objectives of this review are (i) to identify barriers to adoption of molecular testing in brain tumors, (ii) to describe the current molecular tools recommended for the clinical evaluation of brain tumors, and (iii) to summarize how molecular data are interpreted to guide clinical care, so as to improve understanding and justification for their coverage in the routine workup of adult and pediatric brain tumor cases.
Sovereignty
Authors: Heller Hermann 
Published: July 2019

Abstract
This 1927 work addresses the paradox of sovereignty, that is, how the sovereign can be both the highest authority and subject to law. Unlike Kelsen and Schmitt who seek to dissolve the paradox, this text sees the tensions that the paradox highlights as an essential part of a society ruled by law. Sovereignty, in the sense of national sovereignty, is often perceived in liberal democracies today as being under threat, or at least “in transition,” as power devolves from nation states to international bodies. This threat to national sovereignty is at the same time considered a threat to a different idea of sovereignty, popular sovereignty—the sovereignty of “the people”—as important decisions seem increasingly to be made by institutions outside of a country’s political system or by elite-dominated institutions within. This text was written in 1927 amidst the very similar tensions of the Weimar Republic. In an exploration of history, constitutional and political theory, and international law, it shows that democrats must defend a legal idea of sovereignty suitable for a pluralistic world.
Good Governance
Authors: Addink Henk 
Published: July 2019

Abstract
The pivotal aim of this book is to explain the creation, development, and impact of good governance from a conceptual, principal perspective and in the context of national administrative law. Three lines of reasoning have been worked out: developing the concept of good governance; specification of this concept by developing principles of good governance; and implementation of these principles of good governance on the national level. In this phase of further development of good governance, it is important to have a clear concept of good governance, presented in this book as the third cornerstone of a modern state, alongside the concepts of the rule of law and democracy. That is a rather new national administrative law perspective which is influenced by regional and international legal developments; thus, we can speak about good governance as a multilevel concept. But the question is: how is this concept of good governance further developed? Six principles of good governance (which in a narrower sense also qualify as principles of good administration) have been further specified in a systematic way, from a legal perspective. These are the principles of properness, transparency, participation, effectiveness, accountability, and human rights. Furthermore, the link has been made with integrity standards. The important developments of each of these principles are described on the national level in Europe, but also in countries outside Europe (such as Australia, Canada, and South Africa). This book gives a systematic comparison of the implementation of the principles of good governance between countries.
Comparative Company Law
Authors: Gerner-Beuerle Carsten , Schillig Michael Anderson 
Published: July 2019

Abstract
This book provides an exposition of company law from a comparative perspective. It analyses important policy issues in the area of company law, including the emergence and nature of the business corporation, EU company law, incorporation and corporate representation, agency problems in the firm, rights of stakeholders and shareholders, minority shareholder protection in corporate control transactions, legal capital, and piercing the corporate veil, as well as corporate insolvency and restructuring law. The book’s main focus is the law of public and private companies in the common law sense (the law of partnerships is referred to and taken into account as necessary). The book’s analysis encompasses the corporate laws of the US, the UK, Germany, and France, as well as the legislative measures adopted by the EU and the relevant case law of the Court of Justice of the EU. It includes edited and, where necessary, translated extracts from leading company case law. The cases are discussed and interpreted in the context of the national and European regulatory frameworks and in light of economic and legal theory, as well as legal history.
Between relevance and excellence? Research impact agenda and the production of policy knowledge
Authors: Bandola-Gill Justyna 
Published: July 2019

AbstractThe recent moves towards incentivising ‘impact’ within the research funding system pose a growing challenge to academic research practices, charged with producing both scientific, and social impact. This article explores this tension by drawing on interviews with sixty-one UK academics and policymakers involved in publicly-funded knowledge exchange initiatives. The experiences of the interviewed academics point to a functional separation of academic practices into three distinct types: producing traditional research, translating research, and producing policy-oriented research. These three types of practices differ in terms of both the epistemic qualities of the produced knowledge and its legitimacy as valid academic work. Overall, the article argues that the relationship between relevance and excellence of research within the impact agenda is characterised by simultaneous contradiction and co-dependence, leading to hybridisation of academic knowledge production and expansion of the boundaries of policy expertise into the traditionally-academic spaces.
Household Debt and Children’s Risk of Food Insecurity
Authors: Brewer Mackenzie 
Published: July 2019

AbstractIn the United States, almost one in six households with children cannot access adequate food for a healthy and active lifestyle. Although food insecurity disproportionately affects lower-income households, it remains unclear why some lower-income families are more vulnerable to food insecurity than others. Household unsecured debt, such as debt incurred from credit cards and medical bills, may be an unexplored financial constraint associated with food insecurity. Using data from the 2014 Child Development Supplement (CDS) of the Panel Study of Income Dynamics (PSID), I assess whether unsecured debt, by amount and type of debt, is associated with food insecurity among lower-income households with children (N=1,319). Results indicate that medical debt increases odds of household food insecurity even after accounting for key sociodemographic and economic risk factors, while no relationship exists between other forms of unsecured debt and food insecurity. Moreover, although liquid assets decrease the risk of household food insecurity and attenuate the harmful effects associated with unpaid medical bills, few households have enough liquid assets to mitigate the risks associated with medical debt. Efforts to prevent medical debt may be essential for eliminating food insecurity among lower-income households with children.
Biochemical and Functional Analysis of Cyanobacterium Geitlerinema sp. LPS on Human Monocytes
Authors: Swanson-Mungerson Michelle , Williams Philip G , Gurr Joshua R , Incrocci Ryan , Subramaniam Vijay , Radowska Kinga , Hall Mary L , Mayer Alejandro M S 
Published: July 2019

Abstract
Cyanobacterial blooms are an increasing source of environmental toxins that affect both human and animals. After ingestion of cyanobacteria, such as Geitlerinema sp., toxins and lipopolysaccharide (LPS) from this organism induce fever, gastrointestinal illness, and even death. However, little is known regarding the effects of cyanobacterial LPS on human monocytes after exposure to LPS upon ingestion. Based on our previous data using Geitlerinema sp. LPS (which was previously named Oscillatoria sp., a genus belonging to the same order as Geitlerinema), we hypothesized that Geitlerinema sp. LPS would activate human monocytes to proliferate, phagocytose particles, and produce cytokines that are critical for promoting proinflammatory responses in the gut. Our data demonstrate that Geitlerinema sp. LPS induced monocyte proliferation and TNF-α, IL-1, and IL-6 production at high concentrations. In contrast, Geitlerinema sp. LPS is equally capable of inducing monocyte-mediated phagocytosis of FITC-latex beads when compared with Escherichia coli LPS, which was used as a positive control for our experiments. In order to understand the mechanism responsible for the difference in efficacy between Geitlerinema sp. LPS and E. coli LPS, we performed biochemical analysis and identified that Geitlerinema sp. LPS was composed of significantly different sugars and fatty acid side chains in comparison to E. coli LPS. The lipid A portion of Geitlerinema sp. LPS contained longer fatty acid side chains, such as C15:0, C16:0, and C18:0, instead of C12:0 found in E. coli LPS which may explain the decreased efficacy and toxicity of Geitlerinema sp. LPS in comparison to E. coli LPS.
Insomnia Increases Symptom Severity and Health Care Utilization in Patients With Fibromyalgia
Authors: Huang Chun-Jen , Huang Chin-Liang , Fan Yen-Chun , Chen Ting-Yu , Tsai Pei-Shan 
Published: July 2019

Objective:
This study aimed to determine whether comorbid insomnia is associated with increased use of fibromyalgia-related medications and health resources in fibromyalgia (FM) patients.

Materials and Methods:
We analyzed data retrieved from the Longitudinal Health Insurance Database 2010, which contains claims data of 1 million beneficiaries randomly selected from Taiwan’s National Health Insurance program. Patients treated for FM (n=17,920) on 2 separate visits between 2000 and 2001 were selected and subsequently divided into 2 groups: patients with and without comorbid insomnia (n=5466 and 12,454, respectively). Insomnia was identified through diagnosis on 2 separate visits after the index FM date. FM-related pharmacotherapies and ambulatory care visits were tracked from the index date to the end of 2013.

Results:
Insomnia was associated with increased likelihood of future use of antidepressants (adjusted odds ratio [OR]=3.84, P<0.001), gabapentin (adjusted OR=1.67, P<0.001), pregabalin (adjusted OR=1.79, P=0.046), muscle relaxants (adjusted OR=3.05, P<0.001), and opioids and tramadol (adjusted OR=1.59, P<0.001) among FM patients compared with FM patients without insomnia. In addition, a diagnosis of insomnia was associated with an increased frequency of visits to ambulatory care services for both FM (β=1.79; 95% confidence interval, 1.57-2.02; P<0.001) and other conditions (β=108.51; 95% confidence interval, 103.14-113.89; P<0.001).

Discussion:
This study demonstrates the substantial burden of comorbid insomnia in patients with FM.
ZAP-VAP
Authors: Jacobs Pepin Breanna , Lesslie Debra , Berg Wendy , Spaulding Alicen B. , Pokora Thomas 
Published: July 2019

Background:
Ventilator-associated pneumonia (VAP) is the second most frequent hospital-acquired infection in neonatal intensive care units (NICUs) and significantly affects neonatal morbidity and mortality. The population most at risk for VAP are extremely preterm infants.

Purpose:
The objectives of this quality improvement project were to create and evaluate the effectiveness of a VAP prevention bundle (“ZAP-VAP”) in reducing VAP.

Methods:
The development of the ZAP-VAP bundle and creation of audit tools were documented. A targeted gestational age less than 29 weeks was selected for this study. Electronic medical record review was used to determine the preintervention baseline for patient outcomes. Patient medical record data were analyzed retrospectively to measure patient outcomes preimplementation. VAP rates (number of VAP cases per 1000 ventilator days) were calculated pre- and postintervention. After implementation, data were analyzed prospectively to measure patient outcomes between neonates who developed VAP and those who did not.

Results:
The VAP rate significantly decreased from 8.5 (2010-2011) to 2.5 (P= .0004) postintervention (2016). Median mechanical ventilation days decreased among VAP cases (47 vs 33 days) and slightly increased among non-VAP cases (19 vs 24 days) during the intervention period. Median length of stay decreased for VAP cases (136 vs 100 days) but remained unchanged for non-VAP cases (85 vs 84 days).

Implications for Practice:
The intervention was implemented from 2012 to 2016. The protocol was readily accepted by our neonatal intensive care unit (NICU) team through education and practice changes. ZAP-VAP is an effective and straightforward protocol that improved VAP outcomes in our level IIIB NICU. An interdisciplinary team successfully implemented this intervention for mechanically ventilated infants of all gestational ages in our unit and has been a model for these practice changes in other units and other hospitals.

Implications for Research:
Future studies should focus on how to create sustainable interventions to decrease VAP in NICUs and to expand the approaches to other units in our hospital and other hospitals in our city among patients at risk for VAP.