bluuebunny/crossref_metadata_2025_split huggingface dataset:
A dark matter profile to model diverse feedback-induced core sizes of ΛCDM haloes
Authors: Lazar Alexandres , Bullock James S , Boylan-Kolchin Michael , Chan T K , Hopkins Philip F , Graus Andrew S , Wetzel Andrew , El-Badry Kareem , Wheeler Coral , Straight Maria C , Kereš Dušan , Faucher-Giguère Claude-André , Fitts Alex , Garrison-Kimmel Shea 
Published: July 2020

ABSTRACT
We analyse the cold dark matter density profiles of 54 galaxy haloes simulated with Feedback In Realistic Environments (FIRE)-2 galaxy formation physics, each resolved within $0.5{{\ \rm per\ cent}}$ of the halo virial radius. These haloes contain galaxies with masses that range from ultrafaint dwarfs ($M_\star \simeq 10^{4.5}\, \mathrm{M}_{\odot }$) to the largest spirals ($M_\star \simeq 10^{11}\, \mathrm{M}_{\odot }$) and have density profiles that are both cored and cuspy. We characterize our results using a new, analytic density profile that extends the standard two-parameter Einasto form to allow for a pronounced constant density core in the resolved innermost radius. With one additional core-radius parameter, rc, this three-parameter core-Einasto profile is able to characterize our feedback-impacted dark matter haloes more accurately than other three-parameter profiles proposed in the literature. To enable comparisons with observations, we provide fitting functions for rc and other profile parameters as a function of both M⋆ and M⋆/Mhalo. In agreement with past studies, we find that dark matter core formation is most efficient at the characteristic stellar-to-halo mass ratio M⋆/Mhalo ≃ 5 × 10−3, or $M_{\star } \sim 10^9 \, \mathrm{M}_{\odot }$, with cores that are roughly the size of the galaxy half-light radius, rc ≃ 1−5 kpc. Furthermore, we find no evidence for core formation at radii $\gtrsim 100\ \rm pc$ in galaxies with M⋆/Mhalo &lt; 5 × 10−4 or $M_\star \lesssim 10^6 \, \mathrm{M}_{\odot }$. For Milky Way-size galaxies, baryonic contraction often makes haloes significantly more concentrated and dense at the stellar half-light radius than DMO runs. However, even at the Milky Way scale, FIRE-2 galaxy formation still produces small dark matter cores of ≃ 0.5−2 kpc in size. Recent evidence for a ∼2 kpc core in the Milky Way’s dark matter halo is consistent with this expectation.
Parameter inference for weak lensing using Gaussian Processes and MOPED
Authors: Mootoovaloo Arrykrishna , Heavens Alan F , Jaffe Andrew H , Leclercq Florent 
Published: July 2020

ABSTRACT
In this paper, we propose a Gaussian Process (GP) emulator for the calculation both of tomographic weak lensing band powers, and of coefficients of summary data massively compressed with the MOPED algorithm. In the former case cosmological parameter inference is accelerated by a factor of ∼10–30 compared with Boltzmann solver class applied to KiDS-450 weak lensing data. Much larger gains of order 103 will come with future data, and MOPED with GPs will be fast enough to permit the Limber approximation to be dropped, with acceleration in this case of ∼105. A potential advantage of GPs is that an error on the emulated function can be computed and this uncertainty incorporated into the likelihood. However, it is known that the GP error can be unreliable when applied to deterministic functions, and we find, using the Kullback–Leibler divergence between the emulator and class likelihoods, and from the uncertainties on the parameters, that agreement is better when the GP uncertainty is not used. In future, weak lensing surveys such as Euclid, and the Legacy Survey of Space and Time, will have up to ∼104 summary statistics, and inference will be correspondingly more challenging. However, since the speed of MOPED is determined not the number of summary data, but by the number of parameters, MOPED analysis scales almost perfectly, provided that a fast way to compute the theoretical MOPED coefficients is available. The GP provides such a fast mechanism.
Eukaryote-Conserved Methylarginine Is Absent in Diplomonads and Functionally Compensated inGiardia
Authors: Emery-Corbin Samantha J , Hamey Joshua J , Ansell Brendan R E , Balan Balu , Tichkule Swapnil , Stroehlein Andreas J , Cooper Crystal , McInerney Bernie V , Hediyeh-Zadeh Soroor , Vuong Daniel , Crombie Andrew , Lacey Ernest , Davis Melissa J , Wilkins Marc R , Bahlo Melanie , Svärd Staffan G , Gasser Robin B , Jex Aaron R 
Published: July 2020

AbstractMethylation is a common posttranslational modification of arginine and lysine in eukaryotic proteins. Methylproteomes are best characterized for higher eukaryotes, where they are functionally expanded and evolved complex regulation. However, this is not the case for protist species evolved from the earliest eukaryotic lineages. Here, we integrated bioinformatic, proteomic, and drug-screening data sets to comprehensively explore the methylproteome of Giardia duodenalis—a deeply branching parasitic protist. We demonstrate that Giardia and related diplomonads lack arginine-methyltransferases and have remodeled conserved RGG/RG motifs targeted by these enzymes. We also provide experimental evidence for methylarginine absence in proteomes of Giardia but readily detect methyllysine. We bioinformatically infer 11 lysine-methyltransferases in Giardia, including highly diverged Su(var)3-9, Enhancer-of-zeste and Trithorax proteins with reduced domain architectures, and novel annotations demonstrating conserved methyllysine regulation of eukaryotic elongation factor 1 alpha. Using mass spectrometry, we identify more than 200 methyllysine sites in Giardia, including in species-specific gene families involved in cytoskeletal regulation, enriched in coiled-coil features. Finally, we use known methylation inhibitors to show that methylation plays key roles in replication and cyst formation in this parasite. This study highlights reduced methylation enzymes, sites, and functions early in eukaryote evolution, including absent methylarginine networks in the Diplomonadida. These results challenge the view that arginine methylation is eukaryote conserved and demonstrate that functional compensation of methylarginine was possible preceding expansion and diversification of these key networks in higher eukaryotes.
MtDNA sequence features associated with ‘selfish genomes’ predict tissue-specific segregation and reversion
Authors: Røyrvik Ellen C , Johnston Iain G 
Published: July 2020

AbstractMitochondrial DNA (mtDNA) encodes cellular machinery vital for cell and organism survival. Mutations, genetic manipulation, and gene therapies may produce cells where different types of mtDNA coexist in admixed populations. In these admixtures, one mtDNA type is often observed to proliferate over another, with different types dominating in different tissues. This ‘segregation bias’ is a long-standing biological mystery that may pose challenges to modern mtDNA disease therapies, leading to substantial recent attention in biological and medical circles. Here, we show how an mtDNA sequence’s balance between replication and transcription, corresponding to molecular ‘selfishness’, in conjunction with cellular selection, can potentially modulate segregation bias. We combine a new replication-transcription-selection (RTS) model with a meta-analysis of existing data to show that this simple theory predicts complex tissue-specific patterns of segregation in mouse experiments, and reversion in human stem cells. We propose the stability of G-quadruplexes in the mtDNA control region, influencing the balance between transcription and replication primer formation, as a potential molecular mechanism governing this balance. Linking mtDNA sequence features, through this molecular mechanism, to cellular population dynamics, we use sequence data to obtain and verify the sequence-specific predictions from this hypothesis on segregation behaviour in mouse and human mtDNA.
Characterizing and classifying neuroendocrine neoplasms through microRNA sequencing and data mining
Authors: Nanayakkara Jina , Tyryshkin Kathrin , Yang Xiaojing , Wong Justin J M , Vanderbeck Kaitlin , Ginter Paula S , Scognamiglio Theresa , Chen Yao-Tseng , Panarelli Nicole , Cheung Nai-Kong , Dijk Frederike , Ben-Dov Iddo Z , Kim Michelle Kang , Singh Simron , Morozov Pavel , Max Klaas E A , Tuschl Thomas , Renwick Neil 
Published: July 2020

Abstract
Neuroendocrine neoplasms (NENs) are clinically diverse and incompletely characterized cancers that are challenging to classify. MicroRNAs (miRNAs) are small regulatory RNAs that can be used to classify cancers. Recently, a morphology-based classification framework for evaluating NENs from different anatomical sites was proposed by experts, with the requirement of improved molecular data integration. Here, we compiled 378 miRNA expression profiles to examine NEN classification through comprehensive miRNA profiling and data mining. Following data preprocessing, our final study cohort included 221 NEN and 114 non-NEN samples, representing 15 NEN pathological types and 5 site-matched non-NEN control groups. Unsupervised hierarchical clustering of miRNA expression profiles clearly separated NENs from non-NENs. Comparative analyses showed that miR-375 and miR-7 expression is substantially higher in NEN cases than non-NEN controls. Correlation analyses showed that NENs from diverse anatomical sites have convergent miRNA expression programs, likely reflecting morphological and functional similarities. Using machine learning approaches, we identified 17 miRNAs to discriminate 15 NEN pathological types and subsequently constructed a multilayer classifier, correctly identifying 217 (98%) of 221 samples and overturning one histological diagnosis. Through our research, we have identified common and type-specific miRNA tissue markers and constructed an accurate miRNA-based classifier, advancing our understanding of NEN diversity.
The Dream Catcher experiment: blinded analyses failed to detect markers of dreaming consciousness in EEG spectral power
Authors: Wong William , Noreika Valdas , Móró Levente , Revonsuo Antti , Windt Jennifer , Valli Katja , Tsuchiya Naotsugu 
Published: July 2020

Abstract
The Dream Catcher test defines the criteria for a genuine discovery of the neural constituents of phenomenal consciousness. Passing the test implies that some patterns of purely brain-based data directly correspond to the subjective features of phenomenal experience, which would help to bridge the explanatory gap between consciousness and brain. Here, we conducted the Dream Catcher test for the first time in a step-wise and simplified form, capturing its core idea. The Dream Catcher experiment involved a Data Team, which measured participants’ brain activity during sleep and collected dream reports, and a blinded Analysis Team, which was challenged to predict, based solely on brain measurements, whether or not a participant had a dream experience. Using a serial-awakening paradigm, the Data Team prepared 54 1-min polysomnograms of non-rapid eye movement sleep—27 of dreamful sleep and 27 of dreamless sleep (three of each condition from each of the nine participants)—redacting from them all associated participant and dream information. The Analysis Team attempted to classify each recording as either dreamless or dreamful using an unsupervised machine learning classifier, based on hypothesis-driven, extracted features of electroencephalography (EEG) spectral power and electrode location. The procedure was repeated over five iterations with a gradual removal of blindness. At no level of blindness did the Analysis Team perform significantly better than chance, suggesting that EEG spectral power could not be utilized to detect signatures specific to phenomenal consciousness in these data. This study marks the first step towards realizing the Dream Catcher test in practice.
The role of activin: the other side of chronic kidney disease–mineral bone disorder?
Authors: Cianciolo Giuseppe , La Manna Gaetano , Capelli Irene , Gasperoni Lorenzo , Galassi Andrea , Ciceri Paola , Cozzolino Mario 
Published: July 2020

Abstract
Chronic kidney disease–mineral bone disorder (CKD-MBD) plays a pivotal role in the excess of cardiovascular morbidity and mortality associated with CKD. There is now a growing awareness that pathways involved in CKD-MBD, like canonical Wnt signalling, are activated from the earliest stages of CKD, playing a role in the development of adynamic bone disease with unknown consequences on vasculature. These changes occur before the classic changes in mineral metabolism: secondary hyperparathyroidism, calcitriol deficiency and hyperphosphataemia. Furthermore, vascular calcification is frequently associated and evolves with decreased bone mineral density and deranged bone turnover, while bone and arterial mineralization share common pathways. Therefore, results of clinical trials focused on mineral bone disorder, aimed at preserving bone and cardiovascular health, are considered unsatisfactory. In order to identify more effective therapeutic strategies, it is necessary to clarify the pathways modulating the cross-talk between bone and vasculature and identify new mediators involved in the pathogenesis of CKD-MBD. Much attention has been paid recently to the role of the transforming growth factor-beta superfamily members in renal disease, and in particular of activin A (ActA). Preclinical studies demonstrate an upgrade of ActA signalling in kidney, skeleton, vasculature and heart during CKD. This supports the idea that an endocrine factor produced in the kidney during renal disease, in addition to promoting the progression of kidney damage, deranges other organs’ homoeostasis and participates in CKD-MBD. In this review, we analyse the contribution of ActA to kidney fibrosis and inflammation as well as its role in the development of CKD-MBD.
Updated review of reported cases of reactive airways dysfunction syndrome
Authors: Walters G I , Huntley C C 
Published: July 2020

Abstract

Background
A previous systematic review of the diagnosis of reactive airways dysfunction syndrome (RADS), undertaken from 1985 to 2004, found a lack of standardization of case reporting, thus misattribution of symptoms can occur.

Aims
We aimed to update the systematic review, update the list of reported causes and see whether a more structured approach to reporting has been adopted.

Methods
We undertook a systematic literature review, using the databases EMBASE and Ovid MEDLINE, with search terms ‘reactive airways dysfunction syndrome’ or ‘asthma AND acute irritant’, and reported according to PRISMA guidelines. We included papers and abstracts published from January 2005 to September 2019, and articles were grouped by the presence or absence of diagnostic features: ‘definite’ RADS (met Brooks’ criteria) or ‘possible’ RADS (Brooks’ criteria not met or insufficient data). We collected demographic and diagnostic data for cases, where given.

Results
Eleven papers and six conference abstracts met the inclusion criteria, 13 of which were case series or reports, and comprised 752 cases in total; seven articles met Brooks’ criteria for RADS diagnosis. A variety of agents were implicated, with chlorine or chlorine-releasing molecules most frequently reported.

Conclusions
A lack of standardized reporting of RADS remains. The majority of published articles and conference abstracts either do not meet, or contain insufficient data to judge against, Brooks’ criteria, particularly in relation to onset of symptoms and bronchial hyper-reactivity or variability of airflow obstruction. Some novel agents are described, in keeping with recognized structural taxonomies.
Occupational health physicians as users of electronic health records
Authors: Nissinen S , Leino T , Tarvainen K , Soini S 
Published: July 2020

Abstract

Background
Electronic health records (EHRs)’ purpose is to facilitate the documentation of patient data and to improve the exchange of information between the professionals involved in a patient’s care.

Aims
To investigate occupational health (OH) physicians’ experiences of EHRs and the factors hampering work.

Methods
An electronic questionnaire was sent to physicians working in OH services in April 2017 and a total of 342 OH physicians participated in the study. The results were reported as quantities and percentages. The survey text was analysed using data-driven content analysis.

Results
The respondents considered their EHR stable in terms of technical features but the routine tasks with EHR were not straightforward. Also, the documentation of patient data for statistical purposes took an unreasonable amount of time and the access to patient data from other organizations was poor. Instead, a well-functioning feature of EHRs were electronic prescriptions. The factors, which hampered respondents’ work, were constant or frequent time pressure, too little time to do their job properly and a stress caused by uncompleted tasks.

Conclusions
This study showed that the usability problems of EHRs were the slowness, unexpected downtimes and difficulties in obtaining patient data. Also, respondents felt very often a lack of time in their work. OH physicians’ work is best supported by EHRs that consider their specific role in healthcare, i.e. the assessment of work ability, the co-ordination of care and rehabilitation and support for return to work.
Do Online Voter Guides Empower Citizens?
Authors: Munzert Simon , BarberÁ Pablo , Guess Andrew , Yang JungHwan 
Published: July 2020

AbstractVoting Advice Applications (VAAs), which provide citizens with information on the party that best represents their political preferences, are often cited as evidence of the empowering capabilities of digital tools. Aside from the informational benefits of these voter guides, observational studies have suggested a strong effect on political participation and vote choice. However, existing impact evaluations have been limited by a reliance on convenience samples, lack of random assignment, or both. This raises questions about self-selection and the precise mechanisms underlying how voters learn about politics. Here, we provide evidence from a field experiment with survey outcomes conducted with a sample of over 1,000 German citizens in the 2017 federal election campaign. Using linked panel survey and digital trace data combined with a randomized encouragement to complete a VAA, we assess respondents’ compliance with treatment and observe how the use of this tool affects political behavior, attitudes, media consumption, political knowledge, and even social media activity. Our findings reveal that the overwhelming consensus in favor of positive effects on turnout and vote choice should be treated with caution, as we find no such effects. Rather, the actual virtue of VAAs in a complex online information environment lies in increasing knowledge about parties’ positions on issues—exactly the kind of information these tools were designed to provide.
Maternal and foetal placental vascular malperfusion in pregnancies with anti-phospholipid antibodies
Authors: Spinillo Arsenio , Bellingeri Camilla , Cavagnoli Chiara , Maggio Irene De , Riceputi Greta , Ruspini Beatrice , Cesari Stefania , Beneventi Fausta 
Published: July 2020

Abstract

Objective
The objective of the study was to evaluate the rates of pathological placental lesions among pregnant subjects positive for aPL antibodies.

Methods
We performed a longitudinal case–control study including 27 subjects with primary APS, 51 with non-criteria APS, 24 with aPL antibodies associated with other well-known CTDs enrolled at the end of the first trimester of pregnancy and 107 healthy controls.

Results
Compared with controls and after correction for multiple comparisons, primary, non-criteria APS and aPL associated to CTD, subjects had lower placental weight, volume and area. After penalized logistic regression analysis to correct for potential confounders, placental lesions suggesting severe maternal vascular malperfusion (MVM) were more common among primary [odds ratio (OR) 11.7 (95% CI 1.3, 108)] and non-criteria APS [OR 8.5 (95% CI 1.6, 45.9)] compared with controls. The risk of foetal vascular malperfusion (FVM) was higher in primary APS [OR 4.5 (95% CI 1.2, 16.4)], aPL associated with CTDs [OR 3.1 (95% CI 1.5, 6.7)] and non-criteria APS [OR 5.9 (95% CI 1.7, 20.1)] compared with controls. Among clinical and laboratory criteria of APS, first trimester aCL IgG &gt;40 UI/ml [OR 4.4 (95% CI 1.3, 14.4)], LA positivity [OR 6.5 (95% CI 1.3, 33.3)] and a history of pre-eclampsia at &lt;34 weeks [OR 32.4 (95% CI 6.5, 161)] were the best independent first trimester predictors of severe MVM [area under the curve 0.74 (95% CI 0.6, 0.87)].

Conclusion
Compared with healthy controls, pregnant subjects with aPL antibodies have an increased risk of placental lesions, suggesting MVM and FVM. First-trimester variables such as aCL IgG &gt;40 UI/ml and a history of pre-eclampsia were significant predictors of both severe MVM and FVM.
BOLD activity during emotion reappraisal positively correlates with dietary self-control success
Authors: Maier Silvia U , Hare Todd A 
Published: July 2020

AbstractWe combined established emotion regulation and dietary choice tasks with fMRI to investigate behavioral and neural associations in self-regulation across the two domains in human participants. We found that increased BOLD activity during the successful reappraisal of positive and negative emotional stimuli was associated with dietary self-control success. This cross-task correlation was present in medial and lateral prefrontal cortex as well as the striatum. In contrast, BOLD activity during the food choice task was not associated with self-reported emotion regulation efficacy. These results suggest that neural processes utilized during the reappraisal of emotional stimuli may also facilitate dietary choices that override palatability in favor of healthfulness. In summary, our findings indicate that the neural systems supporting emotion reappraisal can generalize to other behavioral contexts that require reevaluation of rewarding stimuli and outcomes to promote choices that conform with the current goal.
Stakeholder perspectives and sustainability of an integrated care model for the prevention and management of obesity: the Childhood Obesity Research Demonstration (CORD) project
Authors: Lee Rebecca E , Parker Nathan H , Hallett Allen M , Kao Dennis , Modelska Maria J , Rifai Hanadi S , Soltero Erica G , O’Connor Daniel P 
Published: July 2020

Abstract
Although reliable strategies exist to promote healthy habits that reduce childhood obesity, the sustainability of these strategies remains an ongoing public health challenge. This study aimed to identify factors experienced in a large, multisite project aimed at reducing childhood obesity that might contribute to project sustainability. Hypothesized constructs underpinning sustainability included replicability, continuation of benefits, institutionalization, and community capacity. Key informants (n = 27) completed 60 min, in-depth interviews, which were audio recorded and transcribed. Transcripts were first coded using a combined deductive and inductive approach. Four major themes emerged (with numerous subthemes): developing partnerships, challenges to the sustainability of implemented programming, the importance of intervening in multiple settings, and ongoing implementation and evaluation strategies. Replicability of complex childhood obesity interventions is possible when there are strong partnerships. Benefits can continue to be conferred from programming, particularly when evidence-based strategies are used that employ best practices. Implementation is facilitated by institutionalization and policies that buffer challenges, such as staffing or leadership changes. Community capacity both enhances the sustainability of interventions and develops as a result of strengthening partnerships and policies that support childhood obesity programming.