bluuebunny/crossref_metadata_2025_split huggingface dataset:
Position-wise binding preference is important for miRNA target site prediction
Authors: Talukder Amlan , Li Xiaoman , Hu Haiyan 
Published: March 2020

Abstract

Motivation
It is a fundamental task to identify microRNAs (miRNAs) targets and accurately locate their target sites. Genome-scale experiments for miRNA target site detection are still costly. The prediction accuracies of existing computational algorithms and tools are often not up to the expectation due to a large number of false positives. One major obstacle to achieve a higher accuracy is the lack of knowledge of the target binding features of miRNAs. The published high-throughput experimental data provide an opportunity to analyze position-wise preference of miRNAs in terms of target binding, which can be an important feature in miRNA target prediction algorithms.

Results
We developed a Markov model to characterize position-wise pairing patterns of miRNA–target interactions. We further integrated this model as a scoring method and developed a dynamic programming (DP) algorithm, MDPS (Markov model-scored Dynamic Programming algorithm for miRNA target site Selection) that can screen putative target sites of miRNA-target binding. The MDPS algorithm thus can take into account both the dependency of neighboring pairing positions and the global pairing information. Based on the trained Markov models from both miRNA-specific and general datasets, we discovered that the position-wise binding information specific to a given miRNA would benefit its target prediction. We also found that miRNAs maintain region-wise similarity in their target binding patterns. Combining MDPS with existing methods significantly improves their precision while only slightly reduces their recall. Therefore, position-wise pairing patterns have the promise to improve target prediction if incorporated into existing software tools.

Availability and implementation
The source code and tool to calculate MDPS score is available at http://hulab.ucf.edu/research/projects/MDPS/index.html.

Supplementary information
Supplementary data are available at Bioinformatics online.
Sequence comparisons of cytochrome P450 aromatases from Australian animals predict differences in enzymatic activity and/or efficiency†
Authors: Fatima Anam , Holien Jessica K , Tiwari Chandni , Parker Michael W , Rodgers Raymond J , Martin Lisandra L 
Published: March 2020

Abstract
Aromatase (P450arom, CYP19A1) is the terminal enzyme in the synthesis of the steroid hormone family of estrogens. Not surprisingly, this enzyme has structural similarities between the limited number of species studied thus far. This study examined the structure of aromatases from four diverse Australian species including a marsupial (tammar wallaby; Macropus eugenii), monotreme (platypus; Ornithorhynchus anatinus), ratite (emu; Dromaius novaehollandiae) and lizard (bearded dragon; Pogona vitticeps). We successfully built homology models for each species, using the only crystallographically determined structure available, human aromatase. The amino acid sequences showed high amino acid sequence identity to the human aromatase: wallaby 81%, platypus 73%, emu 75% and bearded dragon at 74%. The overall structure was highly conserved among the five species, although there were non-secondary structures (loops and bends) that were variable and flexible that may result in some differences in catalytic activity. At the N-terminal regions, there were deletions and variations that suggest that functional distinctions may be found. We found that the active sites of all these proteins were identical, except for a slight variation in the emu. The electrostatic potential across the surfaces of these aromatases highlighted likely variations to the protein-protein interactions of these enzymes with both redox partner cytochrome P450 reductase and possibly homodimerization in the case of the platypus, which has been postulated for the human aromatase enzyme. Given the high natural selection pressures on reproductive strategies, the relatively high degree of conservation of aromatase sequence and structure across species suggests that there is biochemically very little scope for changes to have evolved without the loss of enzyme activity.
Genetic Contributions to Multivariate Data-Driven Brain Networks Constructed via Source-Based Morphometry
Authors: Rodrigue Amanda L , Alexander-Bloch Aaron F , Knowles Emma E M , Mathias Samuel R , Mollon Josephine , Koenis Marinka M G , Perrone-Bizzozero Nora I , Almasy Laura , Turner Jessica A , Calhoun Vince D , Glahn David C 
Published: March 2020

AbstractIdentifying genetic factors underlying neuroanatomical variation has been difficult. Traditional methods have used brain regions from predetermined parcellation schemes as phenotypes for genetic analyses, although these parcellations often do not reflect brain function and/or do not account for covariance between regions. We proposed that network-based phenotypes derived via source-based morphometry (SBM) may provide additional insight into the genetic architecture of neuroanatomy given its data-driven approach and consideration of covariance between voxels. We found that anatomical SBM networks constructed on ~ 20 000 individuals from the UK Biobank were heritable and shared functionally meaningful genetic overlap with each other. We additionally identified 27 unique genetic loci that contributed to one or more SBM networks. Both GWA and genetic correlation results indicated complex patterns of pleiotropy and polygenicity similar to other complex traits. Lastly, we found genetic overlap between a network related to the default mode and schizophrenia, a disorder commonly associated with neuroanatomic alterations.
Susceptibility to Hepatitis A Virus Infection in the United States, 2007–2016
Authors: Yin Shaoman , Barker Laurie , Ly Kathleen N , Kilmer Greta , Foster Monique A , Drobeniuc Jan , Jiles Ruth B 
Published: March 2020

Abstract

Background
Despite national immunization efforts, including universal childhood hepatitis A (HepA) vaccination recommendations in 2006, hepatitis A virus (HAV)–associated outbreaks have increased in the United States. Unvaccinated or previously uninfected persons are susceptible to HAV infection, yet the susceptibility in the US population is not well known.

Methods
Using National Health and Nutrition Examination Survey 2007–2016 data, we estimated HAV susceptibility prevalence (total HAV antibody negative) among persons aged ≥2 years. Among US-born adults aged ≥20 years, we examined prevalence, predictors, and age-adjusted trends of HAV susceptibility by sociodemographic characteristics. We assessed HAV susceptibility and self-reported nonvaccination to HepA among risk groups and the “immunization cohort” (those born in or after 2004).

Results
Among US-born adults aged ≥20 years, HAV susceptibility prevalence was 74.1% (95% confidence interval, 72.9–75.3%) during 2007–2016. Predictors of HAV susceptibility were age group 30–49 years, non-Hispanic white/black, 130% above the poverty level, and no health insurance. Prevalences of HAV susceptibility and nonvaccination to HepA, respectively, were 72.9% and 73.1% among persons who reported injection drug use, 67.5% and 65.2% among men who had sex with men, 55.2% and 75.1% among persons with hepatitis B or hepatitis C, and 22.6% and 25.9% among the immunization cohort. Susceptibility and nonvaccination decreased over time among the immunization cohort but remained stable among risk groups.

Conclusions
During 2007–2016, approximately three-fourths of US-born adults remained HAV susceptible. Enhanced vaccination efforts are critically needed, particularly targeting adults at highest risk for HAV infection, to mitigate the current outbreaks.
Phạm Duy Khiêm, classical reception, and colonial subversion in early 20th century Vietnam and France
Authors: Nguyen Kelly 
Published: March 2020

AbstractThe tradition of the Vietnamese reception of classical literature has not yet been examined, and this article is the first to venture into this intersection between Classics and Vietnamese studies. In this article, I focus on Phạm Duy Khiêm (1908–74) and his use of Classics to translate and mediate his Vietnamese heritage to his French audience. Phạm lived during a particularly turbulent time in Vietnamese history: he experienced Vietnam as a French protectorate called Annam, he witnessed his compatriots defy French rule and win independence for Vietnam, and he saw the civil war that challenged that new independence. Throughout these changing political contexts, Phạm navigated the politics of polarity that separated the colonizer from the colonized as he struggled to make sense of these supposedly irreconcilable differences between the two, which contested his own intercultural identity. In this article, I argue that Phạm used his classical education and its cultural capital not only to explain Vietnamese culture to his French audience, but also to elevate it as equal, and perhaps even superior, to that of the French and their supposed classical inheritance.
Educational Transitions and Educational Inequality: A Multiple Pathways Sequential Logit Model Analysis of Finnish Birth Cohorts 1960–1985
Authors: Härkönen Juho , Sirniö Outi 
Published: March 2020

Abstract
We developed a multiple pathways sequential logit model for analysing social background inequality in completed education and applied it to analyse educational inequality in Finland (birth cohorts 1960–1985). Our model builds on the sequential logit model for educational transitions, originally presented by Robert D. Mare and later extended by Maarten Buis, which disaggregates inequality in completed education into the weighted sum of inequalities in the transitions leading to it. Although the educational transitions framework is popular among educational stratification researchers, its applications have almost exclusively focused on analysing inequalities in separate educational transitions. Buis presented a unifying model of inequalities in educational transitions and completed education, which gives a substantive interpretation to the weights that link them. We applied this to an educational system in which the same educational outcomes can be reached through multiple pathways. Our analysis of Finnish register data shows that intergenerational educational persistence increased, particularly among women. The main reasons are increased inequality in academic upper-secondary (gymnasium) completion and gymnasium expansion that increased the weight of this transition as well as of the transition to university. We discuss the integration of structural and allocative mechanisms in educational stratification research.
Impacts of copper and lead exposure on prokaryotic communities from contaminated contrasted coastal seawaters: the influence of previous metal exposure
Authors: Coclet Clément , Garnier Cédric , Durrieu Gaël , D'onofrio Sébastien , Layglon Nicolas , Briand Jean-François , Misson Benjamin 
Published: March 2020

ABSTRACT
Our understanding of environmental factors controlling prokaryotic community is largely hampered by the large environmental variability across spatial scales (e.g. trace metal contamination, nutrient enrichment and physicochemical variations) and the broad diversity of bacterial pre-exposure to environmental factors. In this article, we investigated the specific influence of copper (Cu) and lead (Pb) on prokaryotic communities from the uncontaminated site, using mesocosm experiments. In addition, we studied how pre-exposure (i.e. life history) affects communities, with reference to previous metal exposure on the response of three prokaryotic communities to similar Cu exposition. This study showed a stronger influence of Cu contamination than Pb contamination on prokaryotic diversity and structure. We identified 12 and 34 bacterial families and genera, respectively, contributing to the significant differences observed in community structure between control and spiked conditions. Taken altogether, our results point toward a combination of direct negative responses to Cu contamination and indirect responses mediated by interaction with phytoplankton. These identified responses were largely conditioned by the previous exposure of community to contaminants.
Investigating bifidobacteria and human milk oligosaccharide composition of lactating mothers
Authors: Lugli Gabriele Andrea , Duranti Sabrina , Milani Christian , Mancabelli Leonardo , Turroni Francesca , Alessandri Giulia , Longhi Giulia , Anzalone Rosaria , Viappinai Alice , Tarracchini Chiara , Bernasconi Sergio , Yonemitsu Chloe , Bode Lars , Goran Michael I , Ossiprandi Maria Cristina , van Sinderen Douwe , Ventura Marco 
Published: March 2020

ABSTRACT
Human milk is known to carry its own microbiota, of which the precise origin remains obscure. Breastfeeding allows mother-to-baby transmission of microorganisms as well as the transfer of many other milk components, such as human milk oligosaccharides (HMOs), which act as metabolizable substrates for particular bacteria, such as bifidobacteria, residing in infant intestinal tract. In the current study, we report the HMO composition of 249 human milk samples, in 163 of which we quantified the abundance of members of the Bifidobacterium genus using a combination of metagenomic and flow cytometric approaches. Metagenomic data allowed us to identify four clusters dominated by Bifidobacterium adolescentis and Bifidobacterium pseudolongum, Bifidobacterium crudilactis or Bifidobacterium dentium, as well as a cluster represented by a heterogeneous mix of bifidobacterial species such as Bifidobacterium breve and Bifidobacterium longum. Furthermore, in vitro growth assays on HMOs coupled with in silico glycobiome analyses allowed us to elucidate that members of the Bifidobacterium bifidum and B. breve species exhibit the greatest ability to degrade and grow on HMOs. Altogether, these findings indicate that the bifidobacterial component of the human milk microbiota is not strictly correlated with their ability to metabolize HMOs.
Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions
Authors: St. James Andrew R , Richardson Ruth E 
Published: March 2020

ABSTRACTThe anaerobic digestion of wastes is globally important in the production of methane (CH4) as a biofuel. When sulfate is present, sulfate-reducing bacteria (SRB) are stimulated, competing with methanogens for common substrates, which decreases CH4 production and results in the formation of corrosive, odorous hydrogen sulfide gas (H2S). Here, we show that a population of SRB within a methanogenic bioreactor fed only butyrate for years immediately (within hours) responded to sulfate availability and shifted the microbial community dynamics within the bioreactor. By mapping shotgun metatranscriptomes to metagenome-assembled genomes, we shed light on the transcriptomic responses of key community members in response to increased sulfate provision. We link these short-term transcriptional responses to long-term niche partitioning using comparative metagenomic analyses. Our results suggest that sulfate provision supports a syntrophic butyrate oxidation community that disfavors poly-β-hydroxyalkanoate storage and that hydrogenotrophic SRB populations effectively exclude obligately hydrogenotrophic, but not aceticlastic, methanogens when sulfate is readily available. These findings elucidate key ecological dynamics between SRB, methanogens and syntrophic butyrate-oxidizing bacteria, which can be applied to a variety of engineered and natural systems.
Reconstructing the Phylogeny of Corynebacteriales while Accounting for Horizontal Gene Transfer
Authors: Coimbra Nilson Da Rocha , Goes-Neto Aristoteles , Azevedo Vasco , Ouangraoua Aïda 
Published: March 2020

Abstract
Horizontal gene transfer is a common mechanism in Bacteria that has contributed to the genomic content of existing organisms. Traditional methods for estimating bacterial phylogeny, however, assume only vertical inheritance in the evolution of homologous genes, which may result in errors in the estimated phylogenies. We present a new method for estimating bacterial phylogeny that accounts for the presence of genes acquired by horizontal gene transfer between genomes. The method identifies and corrects putative transferred genes in gene families, before applying a gene tree-based summary method to estimate bacterial species trees. The method was applied to estimate the phylogeny of the order Corynebacteriales, which is the largest clade in the phylum Actinobacteria. We report a collection of 14 phylogenetic trees on 360 Corynebacteriales genomes. All estimated trees display each genus as a monophyletic clade. The trees also display several relationships proposed by past studies, as well as new relevant relationships between and within the main genera of Corynebacteriales: Corynebacterium, Mycobacterium, Nocardia, Rhodococcus, and Gordonia. An implementation of the method in Python is available on GitHub at https://github.com/UdeS-CoBIUS/EXECT (last accessed April 2, 2020).
Reference Data and T-Scores of Lumbar Skeletal Muscle Area and Its Skeletal Muscle Indices Measured by CT Scan in a Healthy Korean Population
Authors: Kim Eun Hee , Kim Kyung Won , Shin Yongbin , Lee Jiwoo , Ko Yousun , Kim Ye-Jee , Lee Min Jung , Bae Sung-Jin , Park Sung Won , Choe Jaewon , Kim Hong-Kyu 
Published: March 2020

Abstract

Background
Although computed tomography (CT) is considered the gold standard for investigating skeletal muscles, diagnostic cutoff points for sarcopenia have not been established. We therefore suggested clinically relevant diagnostic cutoff points for sarcopenia based on reference values of skeletal muscle area (SMA) measured by CT scan in a large-sized healthy Asian population.

Methods
This cross-sectional analysis included 11,845 subjects (7,314 men, 4,531 women) who underwent abdominal CT scans in South Korea. SMA including all muscles on the selected axial images of the L3 lumbar vertebrae level was demarcated using predetermined thresholds (−29 to +150 Hounsfield units). SMA indices (height-, weight-, and body mass index [BMI]-adjusted) were calculated.

Results
When T-score &lt; −2.0 was used as the cutoff for defining sarcopenia, the sex-specific cutoff points of SMA, SMA/height2, SMA/weight, and SMA/BMI were 119.3 and 74.2 cm2, 39.8 and 28.4 cm2/m2, 1.65 and 1.38 cm2/kg, and 4.97 and 3.46 in men and women, respectively. In both sexes, the SMA/BMI values peaked in the 20s and decreased gradually. The SMA/BMI yielded the highest diagnostic rate of sarcopenia (4.2% in men, 8.7% in women), while SMA/height2 provided the lowest yield (2.8% in men, 1.0% in women).

Conclusions
This is the first study to report the reference values of SMA and skeletal muscle indices (SMIs) measured on CT scans and to suggest cutoff points for diagnosis of sarcopenia based on T-score in Asian subjects. BMI-adjusted index (SMA/BMI) was the best index of CT-measured SMA to reflect the age-related muscle changes and to maximize the diagnostic yield for sarcopenia.
Two main rupture stages during the 2018 magnitude 7.5 Sulawesi earthquake
Authors: Li Qi , Zhao Bin , Tan Kai , Xu Wenbin 
Published: March 2020

SUMMARYOn 28 September 2018, a Mw 7.5 strike-slip earthquake occurred in Sulawesi Island, Indonesia, and it unexpectedly triggered a tsunami. To clearly understand the spatiotemporal evolution process of source rupture, we collected the far-field body wave data and utilized the back-projection method together with finite fault inversion method to investigate the rupture kinematics of this earthquake. Results obtained with the two methods have good consistency and complementarity. We hold that the rupture expanded from the epicentre and propagated bilaterally towards the north and south along the strike direction during the first 24 s, and then to the south. Therefore, the whole rupture process consists of two main stages. For the second stage, the fault segment experienced most of the moment release between 0 and 15 km depth, while the fault plane tended to slip at greater depth (down to 20 km) in the first stage. The total length of the rupture was about 200 km and the seismic moment was ∼2.48 × 1020 Nm, which was equivalent to Mw 7.5. The surface rupture was evident and the maximum slip of 6.24 m was observed in the Palu basin, which was close to Palu city. The rupture was dominated by left-lateral strike-slip with both normal and thrust components as well. The normal slip exhibited in the shallow part of the fault on the north side of Palu bay together with the special geographical location of Palu bay likely favored tsunami genesis.
CorPhU: an algorithm based on phase closure for the correction of unwrapping errors in SAR interferometry
Authors: Benoit Angélique , Pinel-Puysségur Béatrice , Jolivet Romain , Lasserre Cécile 
Published: March 2020

SUMMARY
Interferometric Synthetic Aperture Radar (InSAR) is commonly used in Earth Sciences to study surface displacements or construct high resolution topographic maps. Recent satellites such as those of the Sentinel-1 constellation allow to derive dense deformation maps with millimetric precision with high revisit frequency. However, InSAR is still limited by interferometric coherence. Interferometric phase noise resulting from a loss of coherence, due to changes in scattering properties between repeated SAR acquisitions, may lead to unwrapping errors, which then in turn lead to centimetric errors in time-series reconstruction. We present an algorithm based on interferometric phase closure to automatically correct unwrapping errors. We describe the algorithm and highlight its performances with two case studies, in Lebanon with Envisat satellite data and in Central Turkey with Sentinel-1 data. The first data set is particularly affected by unwrapping errors because of long spatial (500 m) and temporal baseline interferograms (6 yr) and decorrelation due, in particular, to vegetation. The second data set contains unwrapping errors because of temporal changes in the scattering properties of the ground. For these two examples, the algorithm allows the correction of almost all detectable unwrapping errors, without requiring visual inspection or manual deletions. Our algorithm is efficient especially on large data sets, such as with Sentinel-1 constellation, where interferometric phase is redundant and improves eventually the reconstruction of time-series.