bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigating Transfusion-related Sepsis Using Culture-Independent Metagenomic Sequencing
Authors: Crawford Emily , Kamm Jack , Miller Steve , Li Lucy M , Caldera Saharai , Lyden Amy , Yokoe Deborah , Nichols Amy , Tran Nam K , Barnard Sarah E , Conner Peter M , Nambiar Ashok , Zinter Matt S , Moayeri Morvarid , Serpa Paula Hayakawa , Prince Brian C , Quan Jenai , Sit Rene , Tan Michelle , Phelps Maira , Derisi Joseph L , Tato Cristina M , Langelier Charles 
Published: September 2019

Abstract

Background
Transfusion-related sepsis remains an important hospital infection control challenge. Investigation of septic transfusion events is often restricted by the limitations of bacterial culture in terms of time requirements and low yield in the setting of prior antibiotic administration.

Methods
In 3 gram-negative septic transfusion cases, we performed metagenomic next-generation sequencing (mNGS) of direct clinical blood specimens in addition to standard culture-based approaches utilized for infection control investigations. Pathogen detection leveraged IDSeq, a new open-access microbial bioinformatics portal. Phylogenetic analysis was performed to assess microbial genetic relatedness and understand transmission events.

Results
mNGS of direct clinical blood specimens afforded precision detection of pathogens responsible for each case of transfusion-related sepsis and enabled discovery of a novel Acinetobacter species in a platelet product that had become contaminated despite photochemical pathogen reduction. In each case, longitudinal assessment of pathogen burden elucidated the temporal sequence of events associated with each transfusion-transmitted infection. We found that informative data could be obtained from culture-independent mNGS of residual platelet products and leftover blood specimens that were either unsuitable or unavailable for culture or that failed to grow due to prior antibiotic administration. We additionally developed methods to enhance accuracy for detecting transfusion-associated pathogens that share taxonomic similarity to contaminants commonly found in mNGS library preparations.

Conclusions
Culture-independent mNGS of blood products afforded rapid and precise assessment of pathogen identity, abundance, and genetic relatedness. Together, these challenging cases demonstrated the potential for metagenomics to advance existing methods for investigating transfusion-transmitted infections.
Resilience and Urban Capabilities in Denise Mina’s Garnethill Trilogy
Authors: Rodríguez González Carla 
Published: September 2019

AbstractThis essay examines Denise Mina’s Garnethill trilogy from the standpoint of spatial and capabilities studies. It analyzes the representation of spaces of resilience and their role in the gendered redistribution of urban and domestic power portrayed in the narratives. In order to do so, it contextualizes these books within the framework of contemporary Scottish crime fiction and subsequently studies the contraposition and subversion of emotional spaces in Glasgow and London in the process of recovery from the trauma of the child sexual abuse their protagonist has undergone.
Parsimonious Eurolung risk models to predict cardiopulmonary morbidity and mortality following anatomic lung resections: an updated analysis from the European Society of Thoracic Surgeons database
Authors: Brunelli Alessandro , Cicconi Silvia , Decaluwe Herbert , Szanto Zalan , Falcoz Pierre Emmanuel 
Published: September 2019

Abstract

OBJECTIVES
To develop a simplified version of the Eurolung risk model to predict cardiopulmonary morbidity and 30-day mortality after lung resection from the ESTS database.

METHODS
A total of 82 383 lung resections (63 681 lobectomies, 3617 bilobectomies, 7667 pneumonectomies and 7418 segmentectomies) recorded in the ESTS database (January 2007–December 2018) were analysed. Multiple imputations with chained equations were performed on the predictors included in the original Eurolung models. Stepwise selection was then applied for determining the best logistic model. To develop the parsimonious models, different models were tested eliminating variables one by one starting from the less significant. The models’ prediction power was evaluated estimating area under curve (AUC) with the 10-fold cross-validation technique.

RESULTS
Cardiopulmonary morbidity model (Eurolung1): the best parsimonious Eurolung1 model contains 5 variables. The logit of the parsimonious Eurolung1 model was as follows: −2.852 + 0.021 × age + 0.472 × male −0.015 × ppoFEV1 + 0.662×thoracotomy + 0.324 × extended resection. Pooled AUC is 0.710 [95% confidence interval (CI) 0.677–0.743]. Mortality model (Eurolung2): the best parsimonious model contains 6 variables. The logit of the parsimonious Eurolung2 model was as follows: −6.350 + 0.047 × age + 0.889 × male −0.055 × BMI −0.010 × ppoFEV1 + 0.892 × thoracotomy + 0.983 × pneumonectomy. Pooled AUC is 0.737 (95% CI 0.702–0.770). An aggregate parsimonious Eurolung2 was also generated by repeating the logistic regression after categorization of the numeric variables. Patients were grouped into 7 risk classes showing incremental risk of mortality (P < 0.0001).

CONCLUSIONS
We were able to develop simplified and updated versions of the Eurolung risk models retaining the predictive ability of the full original models. They represent a more user-friendly tool designed to inform the multidisciplinary discussion and shared decision-making process of lung resection candidates.
New High-Quality Draft Genome of the Brown Rot Fungal Pathogen Monilinia fructicola
Authors: De Miccolis Angelini Rita Milvia , Romanazzi Gianfranco , Pollastro Stefania , Rotolo Caterina , Faretra Francesco , Landi Lucia 
Published: September 2019

Abstract
Brown rot is a worldwide fungal disease of stone and pome fruit that is caused by several Monilinia species. Among these, Monilinia fructicola can cause severe preharvest and postharvest losses, especially for stone fruit. Here, we present a high-quality draft genome assembly of M. fructicola Mfrc123 strain obtained using both Illumina and PacBio sequencing technologies. The genome assembly comprised 20 scaffolds, including 29 telomere sequences at both ends of 10 scaffolds, and at a single end of 9 scaffolds. The total length was 44.05 Mb, with a scaffold N50 of 2,592 kb. Annotation of the M. fructicola assembly identified a total of 12,118 genes and 13,749 proteins that were functionally annotated. This newly generated reference genome is expected to significantly contribute to comparative analysis of genome biology and evolution within Monilinia species.
Article 101 TFEU: Substantive Appraisal
Authors: Jones Alison , Sufrin Brenda , Dunne Niamh 
Published: September 2019

Abstract
This chapter examines the relationship between Article 101(1) and Article 101(3). It looks at the central question of which agreements, decisions and concerted practices have as their object or effect the prevention, restriction or distortion of competition for the purposes of Article 101(1) and at the issue of which agreements are held to infringe Article 101(1) but meet the critera for exemption from the prohibition set out in Article 101(3). The chapter looks at the way in which the interpretation of ‘object or effect the prevention, restriction or distortion of competition’ has changed since the early days of EEC competition law and at the problems of identifying which agreements are restrictive by object and which restrictive by effect. It examines the recent and controversial case law on this matter and the difficulties which remain including the doctrine of ancillary restraints. It then focuses on the analysis of the effect of agreements which are not restrictive by object, including the concept of appreciability and the de minimis notice. The chapter then considers the matter of which restrictive agreements may neverthess escape the prohibition in Article 101(1) because they meet the criteria in Article 101(3) in that they improve the production or distribution of goods or the promotion of technical or economic progress, how this criterion is distinguished from the agreement not having restrictive effects that bring it within Article 101(1) in the first place, and whether the Article 101(3) criteria can encompass socio-political or public policy matters. The chapter considers the application of the Article 101(3) criteria, the shifting of the burden of proof between Article 101(1) and 101(3), and the existence and importance of block exemptions.
Private Enforcement
Authors: Jones Alison , Sufrin Brenda , Dunne Niamh 
Published: September 2019

Abstract
This chapter focuses on the private civil enforcement of EU antitrust rules through claims made by private litigants in the national courts and tribunals of the individual Member States. The discussions cover the principle of direct effect and national procedural autonomy, mechanisms for cooperation between the Commission and national courts, the obligations of national courts when dealing with cases that raise the issue of whether a contract in violation of Article 101 or Article 102 is enforceable and whether, and if so when, damages and injunctions should be available to remedy such violations. It also considers wy historically there was relatively little antitrust litigation in the EU; the relationship between public and private enforcement; the Commission's policy towards private enforcement, the package of measures the Commission has taken to encourage private litigation, especially the 2014 Damages Directive and its likely impact.
‘Getting our voices out there’: acceptability of a mental health participation programme for young people with out of home care experience in Australia
Authors: Rafeld Jessie , Moeller-Saxone Kristen , Cotton Sue , Rice Simon , Monson Katherine , Harvey Carol , Herrman Helen 
Published: September 2019

AbstractYouth with experience of out-of-home-care (OoHC) typically have poorer mental health than their peers in the general population, and lack opportunities to contribute to service planning. Promoting mental health through leadership training may improve young people’s mental health and facilitate system change. The Bounce Project is a pilot youth-leadership mental health training programme co-designed with young people who have experienced OoHC. In this study, we evaluated the Bounce Project from the young people’s perspectives to explore the acceptability, successes and limitations of the training to promote the participant’s mental health and their contribution to system level change. Thirteen young people aged 18–26 years old who had experienced OoHC and participated in the Bounce Project were interviewed. Semi-structured interviews were conducted and thematically analysed. Four major themes were thereby identified: making their mark; opportunities for growth; redefining roles and pitfalls of research participation. Participants valued the opportunity to have their voices heard, participate in research and learn about mental health. Perceived negative aspects included infrequent participation opportunities, interpersonal difficulties and frustration about the limitations of research including pressure to recruit and restrictive deadlines. Participating in the Bounce Project was a mostly positive experience, but young people also encountered barriers to meaningful participation. Youth with lived experience need more avenues to participate in research and leadership, but research programmes require specific designs that take into consideration the needs of participants and create opportunities for effective and meaningful participation.
Staging of Schizophrenia With the Use of PANSS: An International Multi-Center Study
Authors: Fountoulakis Konstantinos N , Dragioti Elena , Theofilidis Antonis T , Wikilund Tobias , Atmatzidis Xenofon , Nimatoudis Ioannis , Thys Erik , Wampers Martien , Hranov Luchezar , Hristova Trayana , Aptalidis Daniil , Milev Roumen , Iftene Felicia , Spaniel Filip , Knytl Pavel , Furstova Petra , From Tiina , Karlsson Henry , Walta Maija , Salokangas Raimo K R , Azorin Jean-Michel , Bouniard Justine , Montant Julie , Juckel Georg , Haussleiter Ida S , Douzenis Athanasios , Michopoulos Ioannis , Ferentinos Panagiotis , Smyrnis Nikolaos , Mantonakis Leonidas , Nemes Zsófia , Gonda Xenia , Vajda Dora , Juhasz Anita , Shrivastava Amresh , Waddington John , Pompili Maurizio , Comparelli Anna , Corigliano Valentina , Rancans Elmars , Navickas Alvydas , Hilbig Jan , Bukelskis Laurynas , Injac Stevovic Lidija , Vodopic Sanja , Esan Oluyomi , Oladele Oluremi , Osunbote Christopher , Rybakowski Janusz Κ , Wojciak Pawel , Domowicz Klaudia , Figueira Maria Luisa , Linhares Ludgero , Crawford Joana , Panfil Anca-Livia , Smirnova Daria , Izmailova Olga , Lecic-Tosevski Dusica , Temmingh Henk , Howells Fleur , Bobes Julio , Garcia-Portilla Maria Paz , García-Alvarez Leticia , Erzin Gamze , Karadağ Hasan , De Sousa Avinash , Bendre Anuja , Hoschl Cyril , Bredicean Cristina , Papava Ion , Vukovic Olivera , Pejuskovic Bojana , Russell Vincent , Athanasiadis Loukas , Konsta Anastasia , Stein Dan , Berk Michael , Dean Olivia , Tandon Rajiv , Kasper Siegfried , De Hert. Marc 
Published: September 2019

Abstract

Introduction
A specific clinically relevant staging model for schizophrenia has not yet been developed. The aim of the current study was to evaluate the factor structure of the PANSS and develop such a staging method.

Methods
Twenty-nine centers from 25 countries contributed 2358 patients aged 37.21 ± 11.87 years with schizophrenia. Analysis of covariance, Exploratory Factor Analysis, Discriminant Function Analysis, and inspection of resultant plots were performed.

Results
Exploratory Factor Analysis returned 5 factors explaining 59% of the variance (positive, negative, excitement/hostility, depression/anxiety, and neurocognition). The staging model included 4 main stages with substages that were predominantly characterized by a single domain of symptoms (stage 1: positive; stages 2a and 2b: excitement/hostility; stage 3a and 3b: depression/anxiety; stage 4a and 4b: neurocognition). There were no differences between sexes. The Discriminant Function Analysis developed an algorithm that correctly classified &gt;85% of patients.

Discussion
This study elaborates a 5-factor solution and a clinical staging method for patients with schizophrenia. It is the largest study to address these issues among patients who are more likely to remain affiliated with mental health services for prolonged periods of time.
Projection of Costs of Polio Eradication Compared to Permanent Control
Authors: Zimmermann Marita , Hagedorn Brittany , Lyons Hil 
Published: September 2019

Abstract
Despite increased efforts and spending toward polio eradication, it has yet to be eliminated worldwide. We aimed to project economic costs of polio eradication compared to permanent control. We used historical Financial Resource Requirements from the Global Polio Eradication Initiative, as well as vaccination and population data from publicly available sources, to project costs for routine immunization, immunization campaigns, surveillance and laboratory resources, technical assistance, social mobilization, treatment, and overhead. We found that cumulative spending for a control strategy would exceed that for an eradication strategy in 2032 (range, 2027–2051). Eradication of polio would likely be cost-saving compared to permanent control.
A maximum likelihood approach to electronic health record phenotyping using positive and unlabeled patients
Authors: Zhang Lingjiao , Ding Xiruo , Ma Yanyuan , Muthu Naveen , Ajmal Imran , Moore Jason H , Herman Daniel S , Chen Jinbo 
Published: September 2019

AbstractObjectivePhenotyping patients using electronic health record (EHR) data conventionally requires labeled cases and controls. Assigning labels requires manual medical chart review and therefore is labor intensive. For some phenotypes, identifying gold-standard controls is prohibitive. We developed an accurate EHR phenotyping approach that does not require labeled controls.Materials and MethodsOur framework relies on a random subset of cases, which can be specified using an anchor variable that has excellent positive predictive value and sensitivity independent of predictors. We proposed a maximum likelihood approach that efficiently leverages data from the specified cases and unlabeled patients to develop logistic regression phenotyping models, and compare model performance with existing algorithms.ResultsOur method outperformed the existing algorithms on predictive accuracy in Monte Carlo simulation studies, application to identify hypertension patients with hypokalemia requiring oral supplementation using a simulated anchor, and application to identify primary aldosteronism patients using real-world cases and anchor variables. Our method additionally generated consistent estimates of 2 important parameters, phenotype prevalence and the proportion of true cases that are labeled.DiscussionUpon identification of an anchor variable that is scalable and transferable to different practices, our approach should facilitate development of scalable, transferable, and practice-specific phenotyping models.ConclusionsOur proposed approach enables accurate semiautomated EHR phenotyping with minimal manual labeling and therefore should greatly facilitate EHR clinical decision support and research.
Bridging the Process-Pattern Divide to Understand the Origins and Early Stages of Adaptive Radiation: A Review of Approaches With Insights From Studies of Anolis Lizards
Authors: Stroud James T , Losos Jonathan B 
Published: September 2019

AbstractUnderstanding the origins and early stages of diversification is one of the most elusive tasks in adaptive radiation research. Classical approaches, which aim to infer past processes from present-day patterns of biological diversity, are fraught with difficulties and assumptions. An alternative approach has been to study young clades of relatively few species, which may represent the putative early stages of adaptive radiation. However, it is difficult to predict whether those groups will ever reach the ecological and morphological disparity observed in the sorts of clades usually referred to as adaptive radiations, thereby making their utility in informing the early stages of such radiations uncertain. Caribbean Anolis lizards are a textbook example of an adaptive radiation; anoles have diversified independently on each of the 4 islands in the Greater Antilles, producing replicated radiations of phenotypically diverse species. However, the underlying processes that drove these radiations occurred 30–65 million years ago and so are unobservable, rendering major questions about how these radiations came to be difficult to tackle. What did the ancestral species of the anole radiation look like? How did new species arise? What processes drove adaptive diversification? Here, we review what we have learned about the cryptic early stages of adaptive radiation from studies of Anolis lizards, and how these studies have attempted to bridge the process-pattern divide of adaptive radiation research. Despite decades of research, however, fundamental questions linking eco-evolutionary processes to macroevolutionary patterns in anoles remain difficult to answer.
Association between Small Dense Low-Density Lipoproteins and High-Density Phospolipid Content in Patients with Coronary Artery Disease with or without Diabetes
Authors: Aoua Hanene , Nkaies Ymène , Ben Khalfallah Ali , Sakly Mohsen , Aouani Ezzedine , Attia Nebil 
Published: September 2019

AbstractObjectiveTo evaluate the phospholipid profile in total plasma, non–high-density lipoprotein (HDL), and HDL fractions. We tried to correlate the phospholipid profile to low-density lipoprotein (LDL) size, as reflected by cholesterol content in each LDL subclass.MethodsWe measured small dense LDL-C levels after heparin-magnesium precipitation and measured high-density lipoprotein phospholipid (HDL-P) levels using a colorimetric enzymatic method.ResultsThe correlation of the phospholipid profile to small dense LDL-C (sdLDL-C) in patients with coronary problems showed a negative association between small dense low-density lipoprotein (sdLDL) and HDL-P (r = −0.73; P = .02). Moreover, a strong positive correlation was detected between TG and the ratio HDL-P/HDL-C (r = 0.83; P &lt;.001).ConclusionsHDL phospholipid has an antiatherogenic effect in coronary artery disease with or without diabetes. Further, large LDL modulation seems to be associated with diabetes rather than coronaropathy.
Testing the warmness of dark matter
Authors: Kumar Suresh , Nunes Rafael C , Yadav Santosh Kumar 
Published: September 2019

ABSTRACT
Dark matter (DM) as a pressureless perfect fluid provides a good fit of the standard Λ cold dark matter (ΛCDM) model to the astrophysical and cosmological data. In this paper, we investigate two extended properties of DM: a possible time dependence of the equation of state of DM via Chevallier–Polarski–Linder parametrization, wdm = wdm0 + wdm1(1 − a), and the constant non-null sound speed $\hat{c}^2_{\rm s,dm}$. We analyse these DM properties on top of the base ΛCDM model by using the data from Planck cosmic microwave background (CMB) temperature and polarization anisotropy, baryonic acoustic oscillations (BAOs), and the local value of the Hubble constant from the Hubble Space Telescope (HST). We find new and robust constraints on the extended free parameters of DM. The most tight constraints are imposed by CMB+BAO data, where the three parameters wdm0, wdm1, and $\hat{c}^2_{\rm s,dm}$ are, respectively, constrained to be less than 1.43 × 10−3, 1.44 × 10−3, and 1.79 × 10−6 at 95 per cent CL. All the extended parameters of DM show consistency with zero at 95 per cent CL, indicating no evidence beyond the CDM paradigm. We notice that the extended properties of DM significantly affect several parameters of the base ΛCDM model. In particular, in all the analyses performed here, we find significantly larger mean values of H0 and lower mean values of σ8 in comparison to the base ΛCDM model. Thus, the well-known H0 and σ8 tensions might be reconciled in the presence of extended DM parameters within the ΛCDM framework. Also, we estimate the warmness of DM particles as well as its mass scale, and find a lower bound: ∼500 eV from our analyses.
GHASP: an H α kinematical survey of spiral galaxies – XIII. Distribution of luminous and dark matter in spiral and irregular nearby galaxies using H α and H i rotation curves and WISE photometry
Authors: Korsaga M , Epinat B , Amram P , Carignan C , Adamczyk P , Sorgho A 
Published: September 2019

Abstract
We present the mass models of 31 spiral and irregular nearby galaxies obtained using hybrid rotation curves (RCs) combining high-resolution GHASP Fabry–Perot H α RCs and extended WHISP H i ones together with 3.4 $\mu$m WISE photometry. The aim is to compare the dark matter (DM) halo properties within the optical radius using only H α RCs with the effect of including and excluding the mass contribution of the neutral gas component, and when using H i or hybrid RCs. Pseudo-isothermal (ISO) core and Navarro–Frenk–White (NFW) cuspy DM halo profiles are used with various fiducial fitting procedures. Mass models using H α RCs including or excluding the H i gas component provide compatible disc M/L. The correlations between DM halo and baryon parameters do not strongly depend on the RC. Clearly, the differences between the fitting procedures are larger than between the different data sets. Hybrid and H i RCs lead to higher M/L values for both ISO and NFW best-fitting models but lower central densities for ISO haloes and higher concentration for NFW haloes than when using H α RCs only. The agreement with the mass model parameters deduced using hybrid RCs, considered as a reference, is better for H i than for H α RCs. ISO density profiles better fit the RCs than the NFW ones, especially when using H α or hybrid RCs. Halo masses at the optical radius determined using the various data sets are compatible even if they tend to be overestimated with H α RCs. Hybrid RCs are thus ideal to study the mass distribution within the optical radius.