bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the saturation of acoustic mode frequencies at high solar activity
Authors: Rabello Soares M Cristina 
Published: April 2019

ABSTRACT
Acoustic mode frequencies obtained by applying spherical harmonic decomposition to HMI, MDI, and GONG observations were analysed throughout the solar cycle. Evidence of a deviation from a linear relation with solar radio flux was found indicating a saturation effect at high solar activity. The Gompertz model, which is one of the most frequently used sigmoid functions to fit growth data, is used. It is shown that its fitting to MDI and GONG data are statistically significant and a median saturation of 400 sfu is estimated. This saturation level is 50 per cent larger than any obtained in the last century, hence the small effect observed in the minimum-to-maximum frequency shift. However, as shown here, it should not be disregarded.
Data-driven characterization of molecular phenotypes across heterogeneous sample collections
Authors: Mehtonen Juha , Pölönen Petri , Häyrynen Sergei , Dufva Olli , Lin Jake , Liuksiala Thomas , Granberg Kirsi , Lohi Olli , Hautamäki Ville , Nykter Matti , Heinäniemi Merja 
Published: April 2019

Abstract
Existing large gene expression data repositories hold enormous potential to elucidate disease mechanisms, characterize changes in cellular pathways, and to stratify patients based on molecular profiles. To achieve this goal, integrative resources and tools are needed that allow comparison of results across datasets and data types. We propose an intuitive approach for data-driven stratifications of molecular profiles and benchmark our methodology using the dimensionality reduction algorithm t-distributed stochastic neighbor embedding (t-SNE) with multi-study and multi-platform data on hematological malignancies. Our approach enables assessing the contribution of biological versus technical variation to sample clustering, direct incorporation of additional datasets to the same low dimensional representation, comparison of molecular disease subtypes identified from separate t-SNE representations, and characterization of the obtained clusters based on pathway databases and additional data. In this manner, we performed an integrative analysis across multi-omics acute myeloid leukemia studies. Our approach indicated new molecular subtypes with differential survival and drug responsiveness among samples lacking fusion genes, including a novel myelodysplastic syndrome-like cluster and a cluster characterized with CEBPA mutations and differential activity of the S-adenosylmethionine-dependent DNA methylation pathway. In summary, integration across multiple studies can help to identify novel molecular disease subtypes and generate insight into disease biology.
Improved Perinatal and Postpartum Human Immunodeficiency Virus Outcomes After Use of a Perinatal Care Coordination Team
Authors: Hackett Stephanie , Badell Martina L , Meade Christina M , Davis Jennifer M , Blue Jeronia , Curtin Lisa , Camacho-Gonzalez Andres , Chahroudi Ann , Chakraborty Rana , Nguyen Minh Ly T , Palmore Melody P , Sheth Anandi N 
Published: April 2019

AbstractIn a high-volume clinic in the Southeastern United States, pregnant women living with human immunodeficiency virus (HIV) had improved HIV outcomes up to 6 months after delivery following the introduction of a multidisciplinary perinatal care coordination team.
Microarray results as an indicator of sexual abuse
Authors: Russell Vanessa , Nikkel Sarah M , Ward Michelle G K 
Published: April 2019

Abstract
This case report illustrates the unexpected identification of intrafamilial sexual abuse of a young mother through genetic testing of her child. The child’s genome was found to have a relatively common chromosomal condition with congruent clinical manifestations, but the microarray also suggested a close biological relationship between the parents because of a high degree of homozygosity. This prompted a child protection investigation as the mother had been a minor at the time of conception, and intrafamilial sexual abuse was confirmed. Both the intended and unintended results of microarray should be considered with respect to the health and social context of the child and their biological parents. This becomes particularly important for young mothers and raises protection concerns when significant amounts of homozygosity (consanguinity) are detected.
A Motor Learning Paradigm Combining Technology and Associative Learning to Assess Prone Motor Learning in Infants
Authors: Tripathi Tanya , Dusing Stacey , Pidcoe Peter E , Xu Yaoying , Shall Mary Snyder , Riddle Daniel L 
Published: April 2019

Abstract

Background
Associative learning is the ability to discover a relationship between two or more events. We combined principles of learning and technology to develop a paradigm to assess associative learning in prone.

Purpose
The purpose of this study was to determine whether 3- to 6-month-old infants can demonstrate: (1) short-term learning of an association between their upper body movements in prone and activation of a toy, and (2) retention of the association learned on day 1, 24 hours later.

Methods
Twenty-eight infants who were 3 to 6 months of age and who were typically developing were tested for 2 consecutive days in an instrumented play gym. Both days of testing had a baseline and 4 acquisition phases (2 minutes each). During the acquisition phase, the toy activated for a maximum of 10 seconds when the infant's head was above a threshold. A criterion was set a priori to distinguish infants as short-term learners and retainers of the association learned on day 1.

Results
Of 28 infants, 22 and 14 infants completed all phases of the testing on day 1 and day 2, respectively. Fourteen (50%) of the infants met the criteria for short-term learners. On day 2, there was an analyzable sample of 9 short-term learners. Three of the 12 short-term learners (25%) demonstrated retention on day 2.

Conclusion
Consistent with prior infant motor learning research, half of the infants demonstrated associative learning in this novel assessment in prone; however, based on study criteria, the infants had limited retention of the association on day 2.
ASSESSMENT OF NATURALLY OCCURRING RADIONUCLIDES IN MALAYSIA’S BUILDING MATERIALS
Authors: Abdullahi Shittu , Ismail Aznan Fazli , Samat Supian 
Published: April 2019

Abstract
The activity concentrations of 226Ra, 232Th and 40K radionuclides from common building materials used by Malaysian people for construction purposes were studied using High-Purity Germanium (HPGe) detector. The measured activity concentrations of the aforementioned radionuclides range from 10 ± 1 Bq kg−1 (limestone) to 155 ± 61 Bq kg−1 (feldspar), 12 ± 3 Bq kg−1 (limestone) to 274 ± 8 Bq kg−1 (kaolin) and 62 ± 19 Bq kg−1 (limestone) to 1114 ± 20 Bq kg−1 (pottery stone) for 226Ra, 232Th and 40K, respectively. The measured activity concentrations of the natural radionuclides reported herein were found to be in accordance with other previous studies. In general, the activity concentration of the natural radionuclides revealed that all the determined values were below the recommended limit.
Defence spending and women in research: A cross-country comparison
Authors: Saxon Tyler , Weiler Stephan 
Published: April 2019

AbstractThis article explores whether greater levels of national defence spending effectively push women away from research careers in science and engineering due to the biases that defence spending can foster in research and development (R&D) institutions. Defence R&D spending shapes the orientation of R&D both through the direct subsidisation of R&D, as well as through procurement, which creates demand for military technologies. These biases created by defence spending potentially alter and shape career tracks in ways that may be more antithetical to feminine gender norms and job values than those of men, thus reducing women’s participation in research careers and reducing gender diversity among developers of new technology. We evaluate this gender asymmetry empirically through a panel dataset of thirty-three nations. Our findings indicate that greater levels of defence spending are indeed associated with lower participation of women in research careers, particularly in government and higher education.
The Dutch foundation—changes to governance and other Dutch legal and tax headlines
Authors: van Steensel Martijn , van der Velden Rick 
Published: April 2019

Abstract
The Dutch foundation is a very flexible, multipurpose legal entity. The level of supervision within the foundation is largely dependent on the design of (the articles of association of) the foundation and its internal governance. Recently, the Dutch government introduced a bill to parliament that aims to modernize and harmonize the legal framework on management and supervision of all legal entities, including the foundation. In this article, the effect of this legislative proposal on the governance of Dutch foundations is discussed, in addition to other Dutch law developments in the Netherlands affecting Dutch foundations.
Implications of common reporting standard for Liechtenstein foundations and trusts—taking stock
Authors: Arnold Hannes , Herdina Sophie 
Published: April 2019

Abstract
Three years after the implementation of the common reporting standard (CRS), it is time to take stock and assess the impact that the CRS had on Liechtenstein’s financial centre, in particular on the approximately 15,000 foundations and trusts located in the Principality. Especially the particularities in transposition, eg the interpretation regarding the requirements of the managed by test, as well as the manner of information procurement, which is closely linked to the reporting obligations under the CRS, are of special interest in this regard.
Elevated temperature differently affects growth, photosynthetic capacity, nutrient absorption and leaf ultrastructure of Abies faxoniana and Picea purpurea under intra- and interspecific competition
Authors: Yu Lei , Song Mengya , Xia Zhichao , Korpelainen Helena , Niinemets Ülo , Li Chunyang 
Published: April 2019

AbstractThere is a limited understanding of the impacts of global warming on intra- and interspecific plant competition. Resolving this knowledge gap is important for predicting the potential influence of global warming on forests, particularly on high-altitude trees, which are more sensitive to warming. In the present study, effects of intra- and interspecific competition on plant growth and associated physiological, structural and chemical traits were investigated in Abies faxoniana and Picea purpurea seedlings under control (ambient temperature) and elevated temperature (ET, 2 °C above ambient temperature) conditions for 2 years. We found that A. faxoniana and P. purpurea grown under intra- and interspecific competition showed significant differences in dry matter accumulation (DMA), photosynthetic capacity, nutrient absorption, non-structural carbohydrate (NSC) contents and leaf ultrastructure under ET conditions. ET increased leaf, stem and root DMA of both conifers under both competition patterns. Moreover, under ET and interspecific competition, P. purpurea had overall superior competitive capacity characterized by higher organ (leaf, stem and root) and total DMA, height growth rate, net photosynthetic rate, specific leaf area, water use efficiency (δ13C), leaf and root N and NSC concentrations and greater plasticity for absorption of different soil N forms. Thus, the growth of P. purpurea benefitted from the presence of A. faxoniana under ET. Our results demonstrated that ET significantly affects the asymmetric competition patterns in subalpine conifer species. Potential alteration of plant competitive interactions by global warming can influence the composition, structure and functioning of subalpine coniferous forests.
VIII Renaissance Drama: Excluding Shakespeare
Authors: McEvilla Joshua , Sharrett Elizabeth , Cryar Jennifer , Ragni Cristiano , Equestri Alice 
Published: April 2019

Abstract
This chapter has three sections: 1. Editions and Textual Matters; 2. Theatre History; 3. Criticism. Section 1 is by Joshua McEvilla; section 2 is by Elizabeth Sharrett; section 3(a) is by Jennifer Cryar; section 3(b) is by Cristiano Ragni; section 3(c) is by Alice Equestri.
Human mitochondrial variant annotation with HmtNote
Authors: Preste R. , Clima R. , Attimonelli M. 
Published: April 2019

AbstractHmtNote is a Python package to annotate human mitochondrial variants from VCF files.Variants are annotated using a wide range of information, which are grouped into basic, cross-reference, variability and prediction subsets so that users can either select specific annotations of interest or use them altogether.Annotations are performed using data from HmtVar, a recently published database of human mitochondrial variations, which collects information from several online resources as well as offering in-house pathogenicity predictions.HmtNote also allows users to download a local annotation database, that can be used to annotate variants offline, without having to rely on an internet connection.HmtNote is a free and open source package, and can be downloaded and installed from PyPI (https://pypi.org/project/hmtnote) or GitHub (https://github.com/robertopreste/HmtNote).
A network-based data-mining approach to investigate indole-related microbiota-host co-metabolism
Authors: Neves Ana Luisa , Rodriguez-Martinez Andrea , Ayala Rafael , Posma Joram M , Abellona U MR , Chilloux Julien , Nicholson Jeremy K , Dumas Marc-Emmanuel , Hoyles Lesley 
Published: April 2019

AbstractMotivationIndoles have been shown to play a significant role in cardiometabolic disorders. While some individual bacterial species are known to produce indole-adducts, to our best knowledge no studies have made use of publicly available genome data to identify prokaryotes, specifically those associated with the human gut microbiota, contributing to the indole metabolic network.ResultsHere, we propose a computational strategy, comprising the integration of KEGG and BLAST, to identify prokaryote-specific metabolic reactions relevant for the production of indoles, as well as to predict new members of the human gut microbiota potentially involved in these reactions. By identifying relevant prokaryotic species for further validation studiesin vitro, this strategy represents a useful approach for those interrogating the metabolism of other gut-derived microbial metabolites relevant to human health.AvailabilityAll R scripts and files (gut microbial dataset, FASTA protein sequences, BLASTP output files) are available fromhttps://github.com/AndreaRMICL/Microbial_networks.ContactARM:andrea.rodriguez-martinez13@imperial.ac.uk; LH:lesley.hoyles@ntu.ac.uk.
Quantification and selection of ictogenic zones in epilepsy surgery
Authors: Laiou Petroula , Avramidis Eleftherios , Lopes Marinho A. , Abela Eugenio , Müller Michael , Akman Ozgur E. , Richardson Mark P. , Rummel Christian , Schindler Kaspar , Goodfellow Marc 
Published: April 2019

AbstractNetwork models of brain dynamics provide valuable insight into the healthy functioning of the brain and how this breaks down in disease. A pertinent example is the use of network models to understand seizure generation (ictogenesis) in epilepsy. Recently, computational models have emerged to aid our understanding of seizures and to predict the outcome of surgical perturbations to brain networks. Such approaches provide the opportunity to quantify the effect of removing regions of tissue from brain networks and thereby search for the optimal resection strategy.Here, we use computational models to elucidate how sets of nodes contribute to the ictogenicity of networks. In small networks we fully elucidate the ictogenicity of all possible sets of nodes and demonstrate that the distribution of ictogenicity across sets depends on network topology. However, the full elucidation is a combinatorial problem that becomes intractable for large networks. Therefore, we develop a global optimisation approach to search for minimal sets of nodes that contribute significantly to ictogenesis. We demonstrate the potential applicability of these methods in practice by identifying optimal sets of nodes to resect in networks derived from 20 individuals who underwent resective surgery for epilepsy.
Within-family studies for Mendelian randomization: avoiding dynastic, assortative mating, and population stratification biases
Authors: Brumpton Ben , Sanderson Eleanor , Hartwig Fernando Pires , Harrison Sean , Vie Gunnhild Åberge , Cho Yoonsu , Howe Laura D , Hughes Amanda , Boomsma Dorret I , Havdahl Alexandra , Hopper John , Neale Michael , Nivard Michel G , Pedersen Nancy L , Reynolds Chandra A , Tucker-Drob Elliot M , Grotzinger Andrew , Howe Laurence , Morris Tim , Li Shuai ,   MR within-family Consortium, Chen Wei-Min , Bjørngaard Johan Håkon , Hveem Kristian , Willer Cristen , Evans David M , Kaprio Jaakko , Åsvol Bjørn Olav , Smith George Davey , Åsvold Bjørn Olav , Hemani Gibran , Davies Neil M 
Published: April 2019

AbstractMendelian randomization (MR) is a widely-used method for causal inference using genetic data. Mendelian randomization studies of unrelated individuals may be susceptible to bias from family structure, for example, through dynastic effects which occur when parental genotypes directly affect offspring phenotypes. Here we describe methods for within-family Mendelian randomization and through simulations show that family-based methods can overcome bias due to dynastic effects. We illustrate these issues empirically using data from 61,008 siblings from the UK Biobank and Nord-Trøndelag Health Study. Both within-family and population-based Mendelian randomization analyses reproduced established effects of lower BMI reducing risk of diabetes and high blood pressure. However, while MR estimates from population-based samples of unrelated individuals suggested that taller height and lower BMI increase educational attainment, these effects largely disappeared in within-family MR analyses. We found differences between population-based and within-family based estimates, indicating the importance of controlling for family effects and population structure in Mendelian randomization studies.
Conserved DNA polymorphisms distinguish species in the eastern North American white oak syngameon: Insights from an 80-SNP oak DNA genotyping toolkit
Authors: Hipp Andrew L. , Whittemore Alan T. , Garner Mira , Hahn Marlene , Fitzek Elisabeth , Guichoux Erwan , Cavender-Bares Jeannine , Gugger Paul F. , Manos Paul S. , Pearse Ian S. , Cannon Charles H. 
Published: April 2019

AbstractThe eastern North American white oaks, a complex of approximately 16 potentially interbreeding species, have become a classic model for studying the genetic nature of species in a syngameon. Genetic work over the past two decades has demonstrated the reality of oak species, but gene flow between sympatric oaks raises the question of whether there are conserved regions of the genome that define oak species. Does gene flow homogenize the entire genome? Do the regions of the genome that distinguish a species in one part of its range differ from the regions that distinguish it in other parts of its range, where it grows in sympatry with different species? Or are there regions of the genome that are relatively conserved across species ranges? In this study, we revisit seven species of the eastern North American white oak syngameon using a set of 80 SNPs selected in a previous study because they show differences among, and consistency within, the species. We test the hypothesis that there exist segments of the genome that do not become homogenized by repeated introgression, but retain distinct alleles characteristic of each species. We undertake a rangewide sampling to investigate whether SNPs that appeared to be fixed based on a relatively small sample in our previous work are fixed or nearly fixed across the range of the species. Each of the seven species remains genetically distinct across its range, given our diagnostic set of markers, with relatively few individuals exhibiting admixture of multiple species. SNPs map back to all 12Quercuslinkage groups (chromosomes) and are separated from each other by an average of 7.47 million base pairs (± 8.74 million bp, s.d.), but are significantly clustered relative to a random null distribution, suggesting that our SNP toolkit reflects genome-wide patterns of divergence while potentially being concentrated in regions of the genome that reflect a higher-than-average history of among-species divergence. This application of a DNA toolkit designed for the simple problem of identifying species in the field has an important implication: the eastern North American white oak syngameon is composed of entities that most taxonomists would consider “good species,” and species in the syngameon retain their genetic cohesion because characteristic portions of the genome do not become homogenized despite a history of introgression.
Single-molecule analysis reveals the rapid effect of estradiol on the surface movement of AMPAR in live neurons
Authors: Godó Soma , Barabás Klaudia , Lengyel Ferenc , Ernszt Dávid , Kovács Tamás , Kecskés Miklós , Varga Csaba , Jánosi Tibor Z. , Kovács Gergely , Orsolits Barbara , Fujiwara Takahiro , Kusumi Akihiro , Ábrahám István M. 
Published: April 2019

AbstractThe gonadal steroid 17β-estradiol (E2) rapidly alters glutamatergic neurotransmission, but its direct effect on the AMPA receptor (AMPAR) remains unknown. Live-cell single-molecule imaging experiments revealed that E2 rapidly and dose-dependently alters the surface movement of AMPAR via membrane estrogen receptors with distinct effects on somas and neurites. The effect of E2 on the surface mobility of AMPAR depends on the integrity of the cortical actin network.