bluuebunny/crossref_metadata_2025_split huggingface dataset:
Real-Time Topic Detection with Dynamic Windows
Authors: Su Na , Ji Shujuan , Liu Jimin 
Published: April 2019

Abstract
Microblog is a popular social network in which hot topics propagate online rapidly. Real-time topic detection can not only understand public opinion well but also bring high commercial value. We design a method for real-time microblog data analysis in order to detect popular long lasting events as well as emerging events. Firstly, a mining frequent items algorithm on microblog data stream is proposed to count approximate word frequency. This mining frequent items algorithm can find the frequent words for some time. Secondly, the windows size of the monitored words is adjusted dynamically according to the duration time and the evolution of events. Lastly, new topics and trends of existing topics can be detected by using dynamic clustering algorithm based on vector space model. Experimental results show that the proposed algorithms can improve performance in terms of running time and accuracy.
piRDisease v1.0: a manually curated database for piRNA associated diseases
Authors: Muhammad Azhar , Waheed Ramay , Khan Nauman Ali , Jiang Hong , Song Xiaoyuan 
Published: April 2019

Abstract
In recent years, researches focusing on PIWI-interacting RNAs (piRNAs) have increased rapidly. It has been revealed that piRNAs have strong association with a wide range of diseases; thus, it becomes very important to understand piRNAs’ role(s) in disease diagnosis, prognosis and assessment of treatment response. We searched more than 2500 articles using keywords, such as `PIWI-interacting RNAs’ and `piRNAs’, and further scrutinized the articles to collect piRNAs-disease association data. These data are highly complex and heterogeneous due to various types of piRNA idnetifiers (IDs) and different reference genome versions. We put considerable efforts into removing redundancy and anomalies and thus homogenized the data. Finally, we developed the piRDisease database, which incorporates experimentally supported data for piRNAs’ relationship with wide range of diseases. The piRDisease (piRDisease v1.0) is a novel, comprehensive and exclusive database resource, which provides 7939 manually curated associations of experimentally supported 4796 piRNAs involved in 28 diseases. piRDisease facilitates users by providing detailed information of the piRNA in respective disease, explored by experimental support, brief description, sequence and location information. Considering piRNAs’ role(s) in wide range of diseases, it is anticipated that huge amount of data would be produced in the near future. We thus offer a submitting page, on which users or researches can contribute in to update our piRDisease database.
Cloning and analysis of Ophiocordyceps xuefengensis mating type (MAT) loci
Authors: Zou Juan , Zeng Ting-Ting , He Zheng-Mi , Zhang Ping , Chen Zuo-Hong 
Published: April 2019

ABSTRACT
The entomopathogenic fungus Ophiocordyceps xuefengensis, a recently described species and identified as the sister taxon of Ophiocordyceps sinensis, is a desirable alternative to O. sinensis. The mating systems of fungi play a vitally important role in the regulation of sexual reproduction and evolution, but the mating type loci of O. xuefengensis were completely unknown. In this study, the mating systems of O. xuefengensis were analyzed. The conserved α-box region of the MAT1-1-1 and HMG-box of MAT1-2-1 were successfully obtained by PCR amplification. The distribution of both mating types in different tissues of wild and cultivated O. xuefengensis growth was detected and analyzed. The results showed that the asci always harbored both mating types, whereas the sclerotium, the stipe and each isolated strain of wild O. xuefengensis always had only one idiomorph, either MAT1-1 or MAT1-2, which confirmed that O. xuefengensis is heterothallic. The MAT1-1 locus of O. xuefengensis harbors MAT1-1-1, MAT1-1-2 and MAT1-1-3, and MAT1-2 contains the MAT1–2-1 gene. Southern blot analysis showed the MAT-1-1-1 and MAT-1-2-1 genes were single-copy in O. xuefengensis. These results will help to understand its life cycle and support artificial cultivation of O. xuefengensis.
The Cryptococcus neoformans monocarboxylate transporter Jen4 is responsible for increased 3-bromopyruvate sensitivity
Authors: Niedźwiecka Katarzyna , Ribas David , Casal Margarida , Ułaszewski Stanisław 
Published: April 2019

ABSTRACT
In the last decades, 3-bromopyruvate (3BP) has been intensively studied as a promising anticancer and antimicrobial agent. The transport of this drug inside the cell is a critical step for its toxicity in cancer and microorganisms. The Cryptococcus neoformans is the most sensitive species of microorganisms toward 3BP. Its cells exhibit the highest uptake rate of 3BP among all tested fungal strains. In Saccharomyces cerevisiae cells, the Jen1 transporter was found to be responsible for 3BP sensitivity. The deletion of Jen1 resulted in the abolishment of 3BP mediated transport. We functionally characterized the Jen4 protein, a Jen1 homologue of C. neoformans, and its role in the phenotypic 3BP sensitivity. The deletion of the CNAG_04704 gene, which encodes Jen4, was found to impair the mediated transport of 3BP and decrease 3BP sensitivity. Further heterologous expression of Jen4 in the S. cerevisiae jen1Δ ady2Δ strain restored the mediated transport of 3BP. The application of a green fluorescent protein fusion tag with the CNAG_04704, revealed the Jen4 labeled on the plasma membrane. The identification of 3BP transporters in pathogen cells is of great importance for understanding the mechanisms of 3BP action and to anticipate the application of this compound as an antimicrobial drug.
A draft nuclear-genome assembly of the acoel flatworm Praesagittifera naikaiensis
Authors: Arimoto Asuka , Hikosaka-Katayama Tomoe , Hikosaka Akira , Tagawa Kuni , Inoue Toyoshige , Ueki Tatsuya , Yoshida Masa-aki , Kanda Miyuki , Shoguchi Eiichi , Hisata Kanako , Satoh Noriyuki 
Published: April 2019

Abstract

Background
Acoels are primitive bilaterians with very simple soft bodies, in which many organs, including the gut, are not developed. They provide platforms for studying molecular and developmental mechanisms involved in the formation of the basic bilaterian body plan, whole-body regeneration, and symbiosis with photosynthetic microalgae. Because genomic information is essential for future research on acoel biology, we sequenced and assembled the nuclear genome of an acoel, Praesagittifera naikaiensis.

Findings
To avoid sequence contamination derived from symbiotic microalgae, DNA was extracted from embryos that were free of algae. More than 290x sequencing coverage was achieved using a combination of Illumina (paired-end and mate-pair libraries) and PacBio sequencing. RNA sequencing and Iso-Seq data from embryos, larvae, and adults were also obtained. First, a preliminary ~17–kilobase pair (kb) mitochondrial genome was assembled, which was deleted from the nuclear sequence assembly. As a result, a draft nuclear genome assembly was ~656 Mb in length, with a scaffold N50 of 117 kb and a contig N50 of 57 kb. Although ~70% of the assembled sequences were likely composed of repetitive sequences that include DNA transposons and retrotransposons, the draft genome was estimated to contain 22,143 protein-coding genes, ~99% of which were substantiated by corresponding transcripts. We could not find horizontally transferred microalgal genes in the acoel genome. Benchmarking Universal Single-Copy Orthologs analyses indicated that 77% of the conserved single-copy genes were complete. Pfam domain analyses provided a basic set of gene families for transcription factors and signaling molecules.

Conclusions
Our present sequencing and assembly of the P. naikaiensis nuclear genome are comparable to those of other metazoan genomes, providing basic information for future studies of genic and genomic attributes of this animal group. Such studies may shed light on the origins and evolution of simple bilaterians.
Genome sequence of the corn leaf aphid (Rhopalosiphum maidis Fitch)
Authors: Chen Wenbo , Shakir Sara , Bigham Mahdiyeh , Richter Annett , Fei Zhangjun , Jander Georg 
Published: April 2019

Abstract

Background
The corn leaf aphid (Rhopalosiphum maidis Fitch) is the most economically damaging aphid pest on maize (Zea mays), one of the world's most important grain crops. In addition to causing direct damage by removing photoassimilates, R. maidis transmits several destructive maize viruses, including maize yellow dwarf virus, barley yellow dwarf virus, sugarcane mosaic virus, and cucumber mosaic virus.

Findings
The genome of a parthenogenetically reproducing R. maidis clone was assembled with a combination of Pacific Biosciences (207-fold coverage) and Illumina (83-fold coverage) sequencing. The 689 assembled contigs, which have an N50 size of 9.0 megabases (Mb) and a low level of heterozygosity, were clustered using Phase Genomics Hi-C interaction maps. Consistent with the commonly observed 2n = 8 karyotype of R. maidis, most of the contigs (473 spanning 321 Mb) were successfully oriented into 4 scaffolds. The genome assembly captured the full length of 95.8% of the core eukaryotic genes, indicating that it is highly complete. Repetitive sequences accounted for 21.2% of the assembly, and a total of 17,629 protein-coding genes were predicted with integrated evidence from ab initio and homology-based gene predictions and transcriptome sequences generated with both Pacific Biosciences and Illumina. An analysis of likely horizontally transferred genes identified 2 from bacteria, 7 from fungi, 2 from protozoa, and 9 from algae. Repeat elements, transposons, and genes encoding likely detoxification enzymes (cytochrome P450s, glutathione S-transferases, carboxylesterases, uridine diphosphate–glucosyltransferases, and ABC transporters) were identified in the genome sequence. Other than Buchnera aphidicola (642,929 base pairs, 602 genes), no endosymbiont bacteria were found in R. maidis.

Conclusions
A high-quality R. maidis genome was assembled at the chromosome level. This genome sequence will enable further research related to ecological interactions, virus transmission, pesticide resistance, and other aspects of R. maidis biology. It also serves as a valuable resource for comparative investigation of other aphid species.
On the robustness of attenuation measurements on teleseismic P waves: insights from micro-array analysis of the 2017 North Korean nuclear test
Authors: Bezada M J , Byrnes J , Eilon Z 
Published: April 2019

SUMMARY
Despite their importance as a fundamental constraint on Earth properties, regional-scale measurements of body-wave seismic attenuation are scarce. This is partially a result of the difficulty in producing robust estimates of attenuation. In this paper, we focus on measuring differential attenuation on records of teleseismic P waves. We examine a unique data set of five records of the North Korean nuclear test of 2017 measured at five broad-band seismic stations deployed within a few metres of each other but using different installation procedures. Given their extreme proximity, we expect zero differential intrinsic attenuation between the different records. However, we find that different attenuation measurement methods and implementation parameters in fact produce significant apparent differential attenuation (Δt*). Frequency-domain methods yield a wide range of Δt* estimates between stations, depending on measurement bandwidth and nuances of signal processing. This measurement instability increases for longer time windows. Time domain methods are largely insensitive to the frequency band being considered but are sensitive to the time window that is chosen. We determine that signal-generated noise can affect measurements in both the frequency and time domain. In some cases, the range of results amounts to a significant fraction of the range of differential attenuation across the conterminous United States as determined by a recent study. We suggest some approaches to manage the inherent instability in these measurements and recommend best practices to confidently estimate body wave attenuation.
Value and effectiveness of National Immunization Technical Advisory Groups in low- and middle-income countries: a qualitative study of global and national perspectives
Authors: Bell Sadie , Blanchard Laurence , Walls Helen , Mounier-Jack Sandra , Howard Natasha 
Published: April 2019

Abstract
The Global Vaccine Action Plan proposes that every country establish or have access to a National Immunization Technical Advisory Group (NITAG) by 2020. The NITAG role is to produce evidence-informed recommendations that incorporate local context, to guide national immunization policies and practice. This study aimed to explore the value and effectiveness of NITAGs in low- and middle-income countries (LMICs), identifying areas in which NITAGs may require further support to improve their functionality and potential barriers to global investment. A multi-methods study design was used, comprising 134 semi-structured interviews and 82 literature review sources that included 38 countries. Interviews were conducted with 53 global/regional and 81 country-level participants able to provide insight into NITAG effectiveness, including NITAG members, national immunization programme staff, and global agency representatives (e.g. the World Health Organisation, the Bill and Melinda Gates Foundation, Gavi the Vaccine Alliance). The review, including published and unpublished sources on NITAGs in LMICs, was conducted to supplement and corroborate interview findings. Data were analysed thematically. NITAGs were described as valuable in promoting evidence-informed vaccination decision-making, with NITAG involvement enhancing national immunization programme strength and sustainability. Challenges to NITAG effectiveness included: (1) unreliable funding; (2) insufficient diversity of member expertise; (3) inadequate conflicts of interest management procedures; (4) insufficient capacity to access and use evidence; (5) lack of transparency; and (6) limited integration with national decision-making processes that reduced the recognition and incorporation of NITAG recommendations. LMIC NITAGs have developed significantly in the past decade. Well-functioning NITAGs were trusted national resources that enhanced country ownership of immunization provision. However, many LMIC NITAGs require additional technical and funding support to strengthen quality and effectiveness, while maintaining impartiality and ensuring sufficient integration with national decision-making processes. Barriers to sustainable global support need to be addressed for LMIC NITAGs to both continue and develop further.
Emergence of NDM-1-producing Klebsiella pneumoniae in Greece: evidence of a widespread clonal outbreak
Authors: Politi Lida , Gartzonika Konstantina , Spanakis Nicholas , Zarkotou Olympia , Poulou Aggeliki , Skoura Lemonia , Vrioni Georgia , Tsakris Athanasios 
Published: April 2019

AbstractObjectivesNDM-producing Enterobacteriaceae clinical isolates remain uncommon in the European region. We describe the emergence and broad dissemination of one successful NDM-1-producing Klebsiella pneumoniae clone in Greek hospitals.MethodsDuring a 4 year survey (January 2013–December 2016), 480 single-patient carbapenem non-susceptible K. pneumoniae isolates, phenotypically MBL positive, were consecutively recovered in eight Greek hospitals from different locations and subjected to further investigation. Antimicrobial susceptibility testing, combined-disc test, identification of resistance genes by PCR and sequencing, molecular fingerprinting by PFGE, plasmid profiling, replicon typing, conjugation experiments and MLST were performed.ResultsMolecular analysis confirmed the presence of the blaNDM-1 gene in 341 (71%) K. pneumoniae isolates. A substantially increasing trend of NDM-1-producing K. pneumoniae was noticed during the survey (R2 = 0.9724). Most blaNDM-1-carrying isolates contained blaCTX-M-15, blaOXA-1, blaOXA-2 and blaTEM-1 genes. PFGE analysis clustered NDM-1 producers into five distinct clonal types, with five distinct STs related to each PFGE clone. The predominant ST11 PFGE clonal type was detected in all eight participating hospitals, despite adherence to the national infection control programme; it was identical to that observed in the original NDM-1 outbreak in Greece in 2011, as well as in a less-extensive NDM-1 outbreak in Bulgaria in 2015. The remaining four ST clonal types (ST15, ST70, ST258 and ST1883) were sporadically detected. blaNDM-1 was located in IncFII-type plasmids in all five clonal types.ConclusionsThis study gives evidence of possibly the largest NDM-1-producing K. pneumoniae outbreak in Europe; it may also reinforce the hypothesis of an NDM-1 clone circulating in the Balkans.
Helicoverpa zea (Lepidoptera: Noctuidae) Preference for Plant Structures, and Their Location, Within Bt Cotton Under Different Nitrogen and Irrigation Regimes
Authors: Braswell Lewis R , Reisig Dominic D , Sorenson Clyde E , Collins Guy D 
Published: April 2019

Abstract
Helicoverpa zea Boddie is a common economic pest of cotton (Gossypium hirsutum L.), including transgenic cotton varieties that express Bacillus thuringiensis (Bt). Helicoverpa zea oviposition is similar in Bt and non-Bt cotton, but behavior of H. zea larvae can be different in the presence of Bt, with neonates moving away from terminals faster in single-toxin Bt than non-Bt cotton or avoiding Bt-treated diet in the lab. We quantified H. zea oviposition and larval distribution on structures within cotton plants in small plot experiments of Cry1Ac + Cry1F cotton for 2 yr under different irrigation and nitrogen treatments. More eggs were oviposited on plants receiving nitrogen application during 2016 and on leaves in the top section of irrigated plants during 2017, but other treatment effects on eggs or larvae were minimal. Helicoverpa zea eggs were most common on leaves in the top third of plants at position zero and middle section of cotton plants throughout the season, but some oviposition occurred on fruiting structures as well. First and second instars were more common on squares in the top section of plants during 2016 and bolls in the middle and lower sections during 2017 due to oviposition lower in the canopy during 2017. During both years, third through fifth instars were more common on bolls in the middle and lower section of plants closer to the main stem. These findings have resistance management implications as extended larval feeding on bolls could optimize nutrition, decrease Bt susceptibility, and potentially influence behavioral resistance.
A Microinjection Method for Infecting the Planthopper Sogatella furcifera (Hemiptera: Delphacidae) with the Southern Rice Black-Streaked Dwarf Virus
Authors: Hu Kui , Qiu Lin , Zhang Yurong , Du Yu , He Hualiang , Ding Wenbing , Li Youzhi 
Published: April 2019

Abstract
The southern rice black-streaked dwarf virus (SRBSDV) causes significant economic damage to rice crops. This virus is transmitted to rice plants by the planthopper Sogatella furcifera (Horváth) in a persistent, circular, and propagative manner. Researchers currently lack suitable methods for assaying the activity of SRBSDV in vitro and preserving the virus all year. We used a microinjection method to directly inject SRBSDV extracts into the hemocoel of S. furcifera nymphs. SRBSDV was subsequently detected by Reverse Transcription-Polymerase Chain Reaction in more than 56.7% of the insects after 5 d and 60% of healthy rice plants fed by these insects also became SRBSDV infected. Moreover, injecting planthopper with an extract of SRBSDV-infected rice plant that had been frozen at −80°C for 220 d caused 63.3% to become viruliferous. These results indicate that SRBSDV can be successfully transmitted to S. furcifera by microinjection, and that extracts of SRBSDV-infected rice plants frozen at −80°C for 220 d still contain sufficient active SRBSDV to infect S. furcifera. We provide a novel way to preserve SRBSDV all year by injecting S. furcifera with the SRBSDV extract.
Magnetic domains characterization of crystalline Fe3O4 under DC and AC magnetic field
Authors: Li Xiang , Zhu Xiaojuan , Pan Dong , Xue Yan , Jia Qingqing , Liu Fang , Li Zhenghua 
Published: April 2019

Abstract
Fe3O4 nanoparticles with crystallite sizes around 10 nm were synthesized by an emulsion method. X-ray diffractometer (XRD) shows that nanocrystalline Fe3O4 possesses face center cubic structure. The magnetic characteristics are investigated by magnetic force microscopy (MFM). Magnetic field directions were applied parallel and perpendicular to the Fe3O4 sample surface for magnetic measurements. Under the perpendicular magnetic field, the phase images of most magnetic nanoparticles exhibit bright or dark MFM contrast. In comparison, the parallel field phase images display a bright–dark dipole MFM contrast, with in-plane magnetic domain configurations. Furthermore, the investigation of strip domains inside Fe3O4 particles under altering magnetic fields indicates the existence of magnetic anisotropy energies, dipole energies as well as inter-grain coupling energies inside the clusters. This approach for probing magnetic responses on nanoscale magnetic domains can be further extended to the analysis of local physical features.
Cognitive Function in Sickle Cell Disease Across Domains, Cerebral Infarct Status, and the Lifespan: A Meta-Analysis
Authors: Prussien Kemar V , Jordan Lori C , DeBaun Michael R , Compas Bruce E 
Published: April 2019

Abstract

Objective
To provide a comprehensive quantitative review of neurocognitive function in sickle cell disease (SCD) across multiple domains, cerebral infarct status, and the lifespan.

Methods
One hundred and ten studies were identified in PubMed, MedLine, and PsycINFO involving 110 studies of 3,600 participants with SCD and 1,127 sibling or health controls.

Results
Meta-analytic findings indicate significant deficits across all neurocognitive domains, age groups, and infarct status. Significant deficits relative to the normative mean ranged from Hedges’ g = −.39 to g = −.63 in preschool children, g = −.83 to g = −1.18 in school-aged children and adolescents, and g = −.46 to g = −.86 in adults. Deficits in full scale IQ (FSIQ), verbal reasoning, perceptual reasoning, and executive function increased from preschool to school-aged samples. However, findings also showed that deficits were smaller in adult samples relative to school-aged samples, likely due to sampling bias in adult studies. Findings across infarct status in sickle cell anemia showed that deficits ranged from g = −.54 to g = −.65 in samples without infarcts, g = −.52 to g = −1.03 in samples with silent cerebral infarct, and g = −1.35 to g = −1.82 in samples with stroke. Deficits in each domain increased in magnitude from no infarct or stroke, to silent cerebral infarct, to overt stroke.

Conclusion
Individuals with SCD are at risk for cognitive deficits across domains, infarct status, and the lifespan. More research is necessary to determine unbiased effects for cognitive function in adults with SCD.