bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes
Authors: Mostajo Berrospi Nelly , Lataretu Marie , Krautwurst Sebastian , Mock Florian , Desirò Daniel , Lamkiewicz Kevin , Collatz Maximilian , Schoen Andreas , Weber Friedemann , Marz Manja , Hölzer Martin 
Published: August 2019

ABSTRACTAlthough bats are increasingly becoming the focus of scientific studies due to their unique properties, these exceptional animals are still among the least studied mammals. Assembly quality and completeness of bat genomes vary a lot and especially non-coding RNA (ncRNA) annotations are incomplete or simply missing. Accordingly, standard bioinformatics pipelines for gene expression analysis often ignore ncRNAs such as microRNAs or long antisense RNAs. The main cause of this problem is the use of incomplete genome annotations. We present a complete screening for ncRNAs within 16 bat genomes. NcRNAs affect a remarkable variety of vital biological functions, including gene expression regulation, RNA processing, RNA interference and, as recently described, regulatory processes in viral infections. Within all investigated bat assemblies we annotated 667 ncRNA families including 162 snoRNAs and 193 miRNAs as well as rRNAs, tRNAs, several snRNAs and IncRNAs, and other structural ncRNA elements. We validated our ncRNA candidates by six RNA-Seq data sets and show significant expression patterns that have never been described before in a bat species on such a large scale. Our annotations will be usable as a resource (Electronic Supplement) for deeper studying of bat evolution, ncRNAs repertoire, gene expression and regulation, ecology, and important host-virus interactions.Supplementary informationis available at rna.uni-jena.de/supplements/bats, the Open Science Framework (doi.org/10.17605/OSF.IO/4CMDN), and GitHub (github.com/rnajena/bats_ncrna).
Automatic Spatial Estimation of White Matter Hyperintensities Evolution in Brain MRI using Disease Evolution Predictor Deep Neural Networks
Authors: Rachmadi Muhammad Febrian , del C. Valdés-Hernández Maria , Makin Stephen , Wardlaw Joanna , Komura Taku 
Published: August 2019

AbstractPrevious studies have indicated that white matter hyperintensities (WMH), the main radiological feature of small vessel disease, may evolve (i.e., shrink, grow) or stay stable over a period of time. Predicting these changes are challenging because it involves some unknown clinical risk factors that leads to a non-deterministic prediction task. In this study, we propose a deep learning model to predict the evolution of WMH from baseline to follow-up (i.e., 1-year later), namely “Disease Evolution Predictor” (DEP) model, which can be adjusted to become a non-deterministic model. The DEP model receives a baseline image as input and produces a map called “Disease Evolution Map” (DEM), which represents the evolution of WMH from baseline to follow-up. Two DEP models are proposed, namely DEP-UResNet and DEP-GAN, which are representatives of the supervised (i.e., need expert-generated manual labels to generate the output) and unsupervised (i.e., do not require manual labels produced by experts) deep learning algorithms respectively. To simulate the non-deterministic and unknown parameters involved in WMH evolution, we modulate a Gaussian noise array to the DEP model as auxiliary input. This forces the DEP model to imitate a wider spectrum of alternatives in the prediction results. The alternatives of using other types of auxiliary input instead, such as baseline WMH and stroke lesion loads are also proposed and tested. Based on our experiments, the fully supervised machine learning scheme DEP-UResNet regularly performed better than the DEP-GAN which works in principle without using any expert-generated label (i.e., unsupervised). However, a semi-supervised DEP-GAN model, which uses probability maps produced by a supervised segmentation method in the learning process, yielded similar performances to the DEP-UResNet and performed best in the clinical evaluation. Furthermore, an ablation study showed that an auxiliary input, especially the Gaussian noise, improved the performance of DEP models compared to DEP models that lacked the auxiliary input regardless of the model’s architecture. To the best of our knowledge, this is the first extensive study on modelling WMH evolution using deep learning algorithms, which deals with the non-deterministic nature of WMH evolution.
Single Cell Transcriptional Signatures of the Human Placenta in Term and Preterm Parturition
Authors: Pique-Regi Roger , Romero Roberto , L.Tarca Adi , Sendler Edward D. , Xu Yi , Garcia-Flores Valeria , Leng Yaozhu , Luca Francesca , Hassan Sonia S. , Gomez-Lopez Nardhy 
Published: August 2019

AbstractMore than 135 million births occur each year; yet, the molecular underpinnings of human parturition in gestational tissues, and in particular the placenta, are still poorly understood. The placenta is a complex heterogeneous organ including cells of both maternal and fetal origin, and insults that disrupt the maternal-fetal dialogue could result in adverse pregnancy outcomes such as preterm birth. There is limited knowledge of the cell type composition and transcriptional activity of the placenta and its compartments during physiologic and pathologic parturition. To fill this knowledge gap, we used scRNA-seq to profile the placental villous tree, basal plate, and chorioamniotic membranes of women with or without labor at term and those with preterm labor. Significant differences in cell type composition and transcriptional profiles were found among placental compartments and across study groups. For the first time, two cell types were identified: 1) lymphatic endothelial decidual cells in the chorioamniotic membranes, and 2) non-proliferative interstitial cytotrophoblasts in the placental villi. Maternal macrophages from the chorioamniotic membranes displayed the largest differences in gene expression (e.g. NFKB1) in both processes of labor; yet, specific gene expression changes were also detected in preterm labor. Importantly, several placental scRNA-seq transcriptional signatures were modulated with advancing gestation in the maternal circulation, and specific immune cell type signatures were increased with labor at term (NK-cell and activated T-cell) and with preterm labor (macrophage, monocyte, and activated T-cell). Herein, we provide a catalogue of cell types and transcriptional profiles in the human placenta, shedding light on the molecular underpinnings and non-invasive prediction of the physiologic and pathologic parturition.One sentence summaryThe common molecular pathway of parturition for both term and preterm spontaneous labor is characterized using single cell gene expression analysis of the human placenta.
Metabolic response to point mutations reveals principles of modulation of in vivo enzyme activity and phenotype
Authors: Bhattacharyya Sanchari , Bershtein Shimon , Adkar Bharat V. , Woodard Jaie , Shakhnovich Eugene I. 
Published: August 2019

AbstractThe relationship between sequence variation and phenotype is poorly understood. Here we use metabolomic analysis to elucidate the molecular mechanism underlying the filamentous phenotype of E. coli strains that carry destabilizing mutations in Dihydrofolate Reductase (DHFR). We find that partial loss of DHFR activity causes reversible filamentation despite SOS response indicative of DNA damage, in contrast to thymineless death (TLD) achieved by complete inhibition of DHFR activity by high concentrations of antibiotic Trimethoprim. This phenotype is triggered by a disproportionate drop in intracellular dTTP, which could not be explained by drop in dTMP based on the Michaelis-Menten like in vitro activity curve of Thymidylate Kinase (Tmk), a downstream enzyme that phosphorylates dTMP to dTDP. Instead, we show that a highly cooperative (Hill coefficient 2.5) in vivo activity of Tmk is the cause of suboptimal dTTP levels. dTMP supplementation rescues filamentation and restores in vivo Tmk kinetics to Michaelis-Menten. Overall, this study highlights the important role of cellular environment in sculpting enzymatic kinetics with system level implications for bacterial phenotype.
A major locus controls a biologically active pheromone component inHeliconius melpomene
Authors: Byers Kelsey J.R.P. , Darragh Kathy , Musgrove Jamie , Almeida Diana Abondano , Garza Sylvia Fernanda , Warren Ian A. , Rastas Pasi M. , Kučka Marek , Chan Yingguang Frank , Merrill Richard M. , Schulz Stefan , McMillan W. Owen , Jiggins Chris D. 
Published: August 2019

AbstractUnderstanding the production, response, and genetics of signals used in mate choice can inform our understanding of the evolution of both intraspecific mate choice and reproductive isolation. Sex pheromones are important for courtship and mate choice in many insects, but we know relatively little of their role in butterflies. The butterflyHeliconius melpomeneuses a complex blend of wing androconial compounds during courtship. Electroantennography inH. melpomeneand its close relativeH. cydnoshowed that responses to androconial extracts were not species-specific. Females of both species responded equally strongly to extracts of both species, suggesting conservation of peripheral nervous system elements across the two species. Individual blend components provoked little to no response, with the exception of octadecanal, a major component of theH. melpomeneblend. Supplementing octadecanal on the wings of octadecanal-richH. melpomenemales led to an increase in the time until mating, demonstrating the bioactivity of octadecanal inHeliconius.Using quantitative trait locus (QTL) mapping, we identified a single locus on chromosome 20 responsible for 41% of the parental species’ difference in octadecanal production. This QTL does not overlap with any of the major wing color or mate choice loci, nor does it overlap with known regions of elevated or reducedFST. A set of 16 candidate fatty acid biosynthesis genes lies underneath the QTL. Pheromones inHeliconiuscarry information relevant for mate choice and are under simple genetic control, suggesting they could be important during speciation.
The etiological classification of the epilepsies: A brain network underpinning?
Authors: Slinger Geertruida , Otte Willem M. , Noorlag Lotte , Jansen Floor E. , Braun Kees P.J. , van Diessen Eric 
Published: August 2019

AbstractObjectivethe current epilepsy classification is primarily clinical driven and lacks a mechanistic basis. A mechanistic basis of the classification, and within the classification especially the etiology layer, may help to better understand epilepsy and the associated comorbidities. It may also be helpful in guiding epilepsy treatment. With this study we aimed to investigate if there is a modelled mechanistic underpinning for the etiological epilepsy classification by assessing the association between epilepsy etiology and brain network topology.Methodsto that aim we assessed the association between epilepsy etiology and brain network topology. We included children referred to our outpatient first seizure clinic with suspected epilepsy who had a standard interictal EEG recording. From these EEGs, functional networks were constructed based on eyes-closed resting state time-series. Networks were characterized using measures of segregation, integration, centrality, and network strength. Principal component analyses were used to assess whether patients with epilepsy of similar etiology cluster together based on their functional brain network topology.Resultsin total, 228 children with epilepsy were included. Another 402 children served as control subjects. We were not able to detect a correlation between epilepsy etiology and functional brain network topology. We also did not find a difference in brain network topology between the controls and patients with epilepsy.Conclusionsour results do not support the presence of a brain network underpinning for the etiological epilepsy classification. This may support the hypothesis that brain network abnormalities in epilepsy are a result of ongoing seizure activity rather than the epilepsy etiology itself. Further in-depth analyses of network measures and longitudinal studies are needed to confirm this hypothesis.
Synchrotron in situ studies of mechanical activation treatment and γ-radiation impact on structural-phase transitions and high-temperature synthesis parameters during the formation of γ-(TiAl) compound
Authors: Loginova Marina , Sobachkin Alexey , Sitnikov Alexander , Yakovlev Vladimir , Filimonov Valeriy , Myasnikov Andrey , Sharafutdinov Marat , Tolochko Boris , Gradoboev Alexander 
Published: August 2019

In situ synchrotron studies of structure and phase formation dynamics in mechanically activated (t = 7 min, power density 40 g) and mechanically activated with subsequent irradiation by γ-quanta 60Co powder mixture (Ti 64 wt% + Al) during high-temperature synthesis by the method of thermal explosion using induction heating are described. In situ high-temperature synthesis was carried out on the created experimental complex adapted for synchrotron X-ray diffraction methods. The sequence of formation and time–temperature interval of the metastable and main phases were determined. The impact of preliminary mechanical activation and of γ-irradiation on the macrokinetic parameters of the synthesis were studied experimentally in situ. It has been established that the impact of γ-irradiation on the mechanically activated powder mixture of the composition Ti 64 wt% + Al leads to a change in the thermal parameters of combustion: the maximum synthesis temperature and the burning rate decrease. The heating rate for the non-irradiated mixture is 204.8 K s−1 and that for the irradiated mixture is 81.6 K s−1. The dependences of mass fractions of the synthesized compounds on time and temperature were calculated from the stage of preheating until completion of the thermal explosion. A single-phase equilibrium product of the composition γ-(TiAl) is formed in γ-irradiated mechanically activated mixture when the system reaches maximum temperature. The synthesized product of the mechanically activated mixture without γ-irradiation contains 72% γ-(TiAl); TiAl3 (26%) and residual Ti (2%) are also observed.
Efficient and reliable surge prevention algorithm for centrifugal compressor
Authors: Liśkiewicz Grzegorz 
Published: August 2019

Purpose
The paper aims to present an outline of the technology of the active anti-surge algorithm based on high-frequency pressure measurement. The presented system is fast, inexpensive and reliable and does not limit the machine-operating range. Many contemporary anti-surge systems are based on theoretical surge margin. This solution limits machine operating range by about 10-15 per cent in the region of the highest pressure ratios. It is also often sensitive to change in external conditions such as temperature or density, as the system reacts to limits calculated theoretically.

Design/methodology/approach
This paper presents results of pressure measurements obtained on the low-speed centrifugal blower DP1.12. The pressure signals were presented in the form of phase diagrams, and conclusions were drawn from their phase portraits to develop the surge indication parameter.

Findings
The presented safety system uses the signal to develop the so-called (rate of derivative fluctuation) RDF parameter. In nominal working conditions, this parameter keeps the value close to 1. When RDF reaches values over 3, the anti-surge procedure should be implemented. Experimental studies have shown that this algorithm assures enough time to incur actions suppressing unstable phenomena.

Originality/value
The system reacts to real machine working conditions and is hence reliable. The RDF algorithm could also be used to identify local flow instabilities, as well as off-design operation.
Accounting changes and beyond budgeting principles (BBP) in the public sector
Authors: Alsharari Nizar Mohammad 
Published: August 2019

PurposeThe purpose of this paper is to explain the process of accounting changes and beyond budgeting principles (BBP) in the public sector as influenced by the institutional framework. It also looks beyond the outcomes of implementing budgeting changes to take into account the complexities of the factors that drive and shape the cumulative processes of accounting change.Design/methodology/approachThe study presents the results of an interpretive case study in the Jordan Customs (JC) as good evidence from developing countries. It uses the triangulation of data collection methods including interviews, observations, and documents and archival records.FindingsThe paper found that JC changes to their accounting systems were influenced by the BBP, with the new budgeting systems implemented based on reconsideration and re-enacting of theoretical accounting bases and procedures. As a result, the accounting changes were managed by modifying the laws and regulations. Among the accounting changes included in the Beyond Budgeting (BB) approach in JC was relative performance evaluation, as an alternative to fixed budget targets. Rolling forecasts were prepared the BB and were employed in JC’s revenues section and the technical aspects of preparing those relied on E-views software. Most BBP were successfully implemented as values, controls, teams, goals, rewards, resources, coordination and governance. Other BBP have faced some resistance in areas of transparency, trust and accountability.Research limitations/implicationsThe paper uses the case study approach that yielded insightful lessons. It reveals the organizational interaction with the external environment and how BBP is influenced and shaped by isomorphic pressures. It also shows the successful and unsuccessful BBP with-(out) resistance in the public sector. This paper has important implications for change dynamics that can emerge from a BBP approach at the institutional level. It also explains the interaction between the “external” origins and “internal” accounts, which identified that accounting is both shaped by and shaping socio-economic and political processes. This broad sensitivity to the nature of accounting has important implications for how accounting change along with BBP is studied.Originality/valueThe paper is one of the few case studies in the accounting literature on organizations that change budgeting practice by adopting BBP. The study provides a detailed explanation of the dynamics of accounting changes through BBP in the public sector. It also provides pieces of evidence about the IPSAS and public accounting reforms in developing countries.
Public management systems, accounting education, and compliance with international public sector accounting standards in sub-Saharan Africa
Authors: Sellami Yosra Mnif , Gafsi Yosra 
Published: August 2019

Purpose
The purpose of this paper is to examine the transparency and completeness of government financial reporting in sub-Saharan African countries by assessing the extent of compliance with IPSAS disclosures and to investigate the impact of the strength of public management systems (SPMS) and accounting education on this level.

Design/methodology/approach
This research develops a self-constructed disclosure index from content analysis and applies panel regressions for a sample of 60 sub-Saharan African government entities during the period 2014–2017.

Findings
The study results indicate that IPSAS disclosure levels significantly vary across sub-Saharan African governments. They reveal a positive effect of the SPMS and accounting education on the extent of compliance with IPSAS in this region.

Practical implications
The study findings are of interest to practitioners, researchers, government policy makers, supervisory authorities and professional bodies. By focusing on the effect of the SPMS and accounting education on IPSAS disclosure level, this paper leaves room for future research to investigate other relevant factors associated with the compliance with these standards whether in sub-Saharan Africa or in other parts of the world.

Originality/value
This paper gives new insights into the assessment of the quality and transparency of government financial reporting in sub-Saharan Africa by examining the extent of compliance with IPSAS in this region. It is the first to investigate the impact of the SPMS and accounting education on this level.
Determinants of digital learning acceptance behavior
Authors: Kaushik Mohit Kant , Verma Deepak 
Published: August 2019

Purpose
The purpose of this paper is to review existing literature on users’ digital learning acceptance behavior and to identify gaps in the current body of knowledge and suggest future research directions. The paper also includes identification of motivating as well as inhibiting factors previously explored by academicians in the acceptance of digital learning.

Design/methodology/approach
The systematic literature review based on PRISMA methodology was conducted, and 200 articles from peer-reviewed journals on digital learning acceptance behavior using technology adoption theories were examined.

Findings
The study found an overall rise in the number of papers published yearly during 2002–2017. Most of the studies were published in two journals, i.e. Computers & Education and Computers in Human Behaviour and were carried out in Asia followed by Europe, North America, Africa, Oceania and South America. It was also noted that most of the studies have used the technology acceptance model and were empirical in nature. The study also found that prominently students’ digital learning acceptance behavior was investigated. The review also indicates a lack of qualitative and mixed method (qualitative and quantitative) approaches to study digital learning acceptance behavior.

Practical implications
The study identified gaps in the current body of knowledge by reviewing published articles that will suggest future directions for further research. The top three determinants of digital learning acceptance that have been analyzed were the behavioral intention, perceived usefulness and perceived ease of use, followed by attitude and user behavior. The study articulates the implications for providers in marketing digital learning products, for higher education institution in expanding digital content, for students seeking digital education tools, for educators in motivating students to accept digital learning and for governments in delivering cost-effective public education by utilizing digital learning.

Originality/value
The paper analyzes 200 publications on digital learning acceptance through technology adoption theories. To the best of the authors’ knowledge, this is the first initiative to provide systematic and exhaustive summarization of the knowledge in this subject. It further explores the various factors influencing digital learning adoption behavior and provides avenues for future research. The paper is useful for researchers working on digital learning acceptance behavior.