bluuebunny/crossref_metadata_2025_split huggingface dataset:
Migration dynamics of an important rice pest: the brown planthopper (Nilaparvata lugens) across Asia – insights from population genomics
Authors: Hereward J. P. , Cai X.H. , Matias A. M. , Walter G. H. , Xu C. X. , Wang Y. 
Published: March 2020

AbstractBrown planthoppers (Nilaparvata lugens) are the most serious insect pests of rice, one of the world’s most important staple crops. They reproduce year-round in the tropical parts of their distribution, but cannot overwinter in the temperate areas where they occur, and invade seasonally from elsewhere. Decades of research has not revealed their source unambiguously. We therefore sequenced the genomes of brown planthopper populations from across temperate and tropical parts of their distribution and show that the Indochinese peninsula is the major source of migration into temperate China. The Philippines, once considered a key source, is not significant, with little evidence for their migration into China. We find support for immigration from the west of China contributing to these regional dynamics. The lack of connectivity between the Philippines and mainland China explains the different evolution of Imidacloprid resistance in these populations. This study highlights the promise of whole genome sequence data to understand migration when gene flow is high – a situation that has been difficult to resolve using traditional genetic markers.
Plasmodiumoocysts respond with dormancy to crowding and nutritional stress
Authors: Habtewold Tibebu , Sharma Aayushi A. , Wyer Claudia A.S. , Masters Ellen K.G. , Windbichler Nikolai , Christophides George K. 
Published: March 2020

AbstractMalaria parasites develop and grow as oocysts in the mosquito for several days before being able to infect another human. During this time, mosquitoes take regular bloodmeals to replenish their nutrient and energy reserves needed for flight and reproduction. We hypothesized that supplemental bloodmeals are critical for oocyst growth and that experimental infection protocols, typically involving a single bloodmeal, cause nutritional stress to developing oocysts. Therefore, enumerating oocysts independently of their growth and differentiation state may lead to erroneous conclusions regarding the efficacy of malaria transmission blocking interventions. We tested this hypothesis inAnopheles coluzziimosquitoes infected with human and rodent parasitesPlasmodium falciparumandPlasmodium berghei, respectively. We find that oocyst growth rates decrease at late developmental stages as infection intensities increase; an effect exacerbated at very high infection intensities. Oocyst growth and differentiation can be restored by supplemental bloodmeals even at high infection intensities. We show that high infection intensities as well as starvation conditions reduce RNA Polymerase III activity in oocysts unless supplemental bloodmeals are provided. Our data suggest that oocysts respond to crowding and nutritional stress by employing a dormancy-like strategy and urge development of alternative methods to assess the efficacy of transmission blocking interventions.
Contamination of Currency Notes with Kanamycin ResistantShigella flexneri
Authors: Al-Hajj Ebrahim Mohammed , Mohamed Malik Suliman , Abd Alfadil Noha A. , Altayb Hisham N. , Idris Abeer Babiker , El-Zaki Salah-Eldin , Hassan Mohamed A. 
Published: March 2020

AbstractShigella flexneriis the main causative agent of shigellosis commonly distributed in developing countries with high morbidity and mortality rates. This study aimed to examine the presence ofShigellaspecies in Sudanese currency notes using both traditional and molecular techniques. One hundred thirty five currency notes were collected and their contaminants were isolated and identified conventionally and genetically using 16S rRNA gene amplification and sequencing. Eight isolates were identified asShigellaspecies in different notes, and 3 of them were resistant to penicillin, kanamycin and nitrofurantoin. OneS. flexneriisolate has insertion mutation of guanine nucleotide at position 730 of life’s essential gene 16S rRNA which known evolutionarily to be stable gene. Banknotes are highly circulating items and therefore, appropriate measures such as regular replacement of the dirty notes with new papers are necessary to protect peoples from being infected with drug resistant pathogens.
Structure and function of virion RNA polymerase of crAss-like phage
Authors: Drobysheva Arina V. , Panafidina Sofia A. , Kolesnik Matvei V. , Klimuk Evgeny I. , Minakhin Leonid , Yakunina Maria V. , Borukhov Sergei , Nilsson Emelie , Holmfeldt Karin , Yutin Natalya , Makarova Kira S. , Koonin Eugene V. , Severinov Konstantin V. , Leiman Petr G. , Sokolova Maria L. 
Published: March 2020

AbstractCrAss-like phages are a recently described family-level group of viruses that includes the most abundant virus in the human gut1,2. Genomes of all crAss-like phages encode a large virion-packaged protein2,3that contains a DFDxD sequence motif, which forms the catalytic site in cellular multisubunit RNA polymerases (RNAPs)4. UsingCellulophaga balticacrAss-like phage phi14:2 as a model system, we show that this protein is a novel DNA-dependent RNAP that is translocated into the host cell along with the phage DNA and transcribes early phage genes. We determined the crystal structure of this 2,180-residue enzyme in a self-inhibited, likely pre-virion-packaged state. This conformation is attained with the help of a Cleft-blocking domain that interacts with the active site motif and occupies the RNA-DNA hybrid binding grove. Structurally, phi14:2 RNAP is most similar to eukaryotic RNAPs involved in RNA interference5,6, although most of phi14:2 RNAP structure (nearly 1,600 residues) maps to a new region of protein folding space. Considering the structural similarity, we propose that eukaryal RNA interference polymerases take their origin in a phage, which parallels the emergence of the mitochondrial transcription apparatus7.
A neural m6A/YTHDF pathway is required for learning and memory inDrosophila
Authors: Kan Lijuan , Ott Stanislav , Joseph Brian , Park Eun Sil , Dai Crystal , Kleiner Ralph , Claridge-Chang Adam , Lai Eric C. 
Published: March 2020

AbstractThe roles of epitranscriptomic modifications in mRNA regulation have recently received substantial attention, with appreciation growing for their phenotypically selective impacts within the animal. We adoptedDrosophila melanogasteras a model system to study m6A, the most abundant internal modification of mRNA. Here, we report proteomic and functional analyses of fly m6A-binding proteins, confirming nuclear (YTHDC) and cytoplasmic (YTHDF) YTH domain proteins as the major m6A binders. Since all core m6A pathway mutants are viable, we assessedin vivorequirements of the m6A pathway in cognitive processes. Assays of short term memory revealed an age-dependent requirement of m6A writers working via YTHDF, but not YTHDC, comprising the first phenotypes assigned toDrosophilamutants of the cytoplasmic m6A reader. These factors promote memory via neural-autonomous activities, and are required in the mushroom body, the center for associative learning. To inform their basis, we mapped m6A from wild-type andmettl3null mutant heads, allowing robust discrimination of Mettl3-dependent m6A sites. In contrast to mammalian m6A, which is predominant in 3’ UTRs,Drosophilam6A is highly enriched in 5’ UTRs and occurs in an adenosine-rich context. Genomic analyses demonstrate thatDrosophilam6A does not directionally affect RNA stability, but is preferentially deposited on genes with low translational efficiency. However, functional tests indicate a role for m6A in translational activation, since we observe reduced nascent protein synthesis inmettl3-KOcells. Finally, we show that ectopic YTHDF can increase m6A target reporter output in an m6A-binding dependent manner, and that this activity is required forin vivoneural function of YTHDF in memory. Altogether, we provide the first tissue-specific m6A maps in this model organism and reveal selective behavioral and translational defects for m6A/YTHDF mutants.
Antibiotic-induced disturbances of the gut microbiota result in accelerated breast tumour growth via a mast cell-dependent pathway
Authors: Kirkup Benjamin M. , McKee Alastair M. , Madgwick Matthew , Price Christopher A , Dreger Sally A , Makin Kate A , Caim Shabhonam , Gall Gwenaelle Le , Paveley Jack , Leclaire Charlotte , Dalby Matthew , Alcon-Giner Cristina , Andrusaite Anna , Modica Martina Di , Triulzi Tiziana , Tagliabue Elda , Milling Simon WF , Weilbaecher Katherine N , Korcsmáros Tamas , Hall Lindsay J , Robinson Stephen D 
Published: March 2020

AbstractThe diverse community of commensal microbes that comprise the gut microbiota is known to play an integral role in human health, not least through its ability to regulate host immune responses and metabolic pathways. Alterations to the homeostasis of this community, including through the use of broad-spectrum antibiotics, have already been associated with the progression of several cancers, namely melanoma and liver. The aggressive nature of breast cancer (BrCa), largely due to its ability to metastasize early, has ranked the disease with the second highest mortality rate of all cancers globally. Yet the body of research into the complex relationship between the microbiota and BrCa is still limited. This study found that a depletion of the microbiota, through the administration of antibiotics, significantly increased the rate of primary tumour progression in mouse BrCa models. We show that antibiotic-induced microbiota disturbances lead to changes in behaviour of a relatively obscure tumour-immune cell population: mast cells. We observed increases in tumour stroma-associated mast cells in antibiotic treated animals. Moreover, inhibition of mast cell degranulation, via cromolyn, slowed tumour progression in antibiotic treated animals but not in control animals. Thus, it appears that a perturbed microbiota drives stroma-associated mast cell recruitment and activation, which in turn promotes primary tumour growth through an as yet unknown mechanism.One Sentence Summary:We show that breast cancer progression is accelerated through a unique/novel immune response involving mast cells as a result of an antibiotic induced perturbation of the gut microbiota in a mouse model.
Meta-transcriptomic analysis of virus diversity in urban wild birds with paretic disease
Authors: Chang Wei-Shan , Eden John-Sebastian , Hall Jane , Shi Mang , Rose Karrie , Holmes Edward C. 
Published: March 2020

AbstractWild birds are major natural reservoirs and potential dispersers of a variety of infectious diseases. As such, it is important to determine the diversity of viruses they carry and use this information to help understand the potential risks of spill-over to humans, domestic animals, and other wildlife. We investigated the potential viral causes of paresis in long-standing, but undiagnosed disease syndromes in wild Australian birds. RNA from diseased birds was extracted and pooled based on tissue type, host species and clinical manifestation for metagenomic sequencing. Using a bulk and unbiased meta-transcriptomic approach, combined with careful clinical investigation and histopathology, we identified a number of novel viruses from the familiesAstroviridae, Picornaviridae, Polyomaviridae, Paramyxoviridae, Parvoviridae, Flaviviridae,andCircoviridaein common urban wild birds including Australian magpies, magpie lark, pied currawongs, Australian ravens, and rainbow lorikeets. In each case the presence of the virus was confirmed by RT-PCR. These data revealed a number of candidate viral pathogens that may contribute to coronary, skeletal muscle, vascular and neuropathology in birds of theCorvidaeandArtamidaefamilies, and neuropathology in members of thePsittaculidae. The existence of such a diverse virome in urban avian species highlights the importance and challenges in elucidating the etiology and ecology of wildlife pathogens in urban environments. This information will be increasingly important for managing disease risks and conducting surveillance for potential viral threats to wildlife, livestock and human health. More broadly, our work shows how meta-transcriptomics brings a new utility to pathogen discovery in wildlife diseases.ImportanceWildlife naturally harbor a diverse array of infectious microorganisms and can be a source of novel diseases in domestic animals and human populations. Using unbiased RNA sequencing we identified highly diverse viruses in native birds in Australian urban environments presenting with paresis. This investigation included the clinical investigation and description of poorly understood recurring syndromes of unknown etiology: clenched claw syndrome, and black and white bird disease. As well as identifying a range of potentially disease-causing viral pathogens, this study describes methods that can effectively and efficiently characterize emergent disease syndromes in free ranging wildlife, and promotes further surveillance for specific potential pathogens of potential conservation and zoonotic concern.
A causal role for pulvinar in coordinating task independent cortico-cortical interactions
Authors: Eradath Manoj K. , Pinsk Mark A. , Kastner Sabine 
Published: March 2020

AbstractPulvinar is the largest nucleus in the primate thalamus and has topographically organized connections with multiple cortical areas, thereby forming extensive cortico-pulvino-cortical input-output loops. Neurophysiological studies have provided evidence for a role of these transthalamic pathways in regulating information transmission between cortical areas. However, a causal role of pulvinar in regulating cortico-cortical interactions has not yet been demonstrated. In particular, it is not known whether pulvinar’s influences on cortical networks are task-dependent or reflect more basic large-scale network properties that maintain functional connectivity across a network regardless of active task demands. In the current study, under a passive viewing condition, we conducted simultaneous electrophysiological recordings from interconnected ventral (area V4) and dorsal (LIP) nodes of the macaque visual system while reversibly inactivating the dorsal part of lateral pulvinar (dPL), which shares common anatomical connectivity with V4 and LIP. Our goal was to probe a causal role of pulvinar in regulating cortico-cortical interactions in the absence of any active task demands. Our results show a significant reduction in local field potential phase coherence between LIP and V4 in low frequencies (4-15 Hz) following muscimol -a potent GABAAagonist -injection into dPL. At the local level, no significant changes in firing rates or LFP power were observed in LIP or in V4 following dPL inactivation. These results indicate a causal role for pulvinar in synchronizing neural activity between interconnected cortical nodes of a large-scale network, even in the absence of an active task state.Significance StatementPulvinar, the largest nucleus of the primate thalamus, has been implicated in several cognitive functions. The extensive cortico-pulvino-cortical loops formed by pulvinar are suggested to be regulating information transmission between interconnected cortical areas. However, a causal evidence for pulvinar’s role in cortico-cortical interactions in the absence of active task demands is not yet clear. We conducted simultaneous recordings from nodes of macaque visual system (areas V4 and LIP) while inactivating the dorsal part of the lateral pulvinar (dPL) under a passive viewing condition. Our results show a significant reduction in local field phase coherence between LIP and V4 in low frequencies (4-15 Hz) following inactivation of dPL, thus providing evidence for a causal role of pulvinar in regulating cortico-cortical interactions even in the absence of an active task state.
ProGen: Language Modeling for Protein Generation
Authors: Madani Ali , McCann Bryan , Naik Nikhil , Keskar Nitish Shirish , Anand Namrata , Eguchi Raphael R. , Huang Po-Ssu , Socher Richard 
Published: March 2020

AbstractGenerative modeling for protein engineering is key to solving fundamental problems in synthetic biology, medicine, and material science. We pose protein engineering as an unsupervised sequence generation problem in order to leverage the exponentially growing set of proteins that lack costly, structural annotations. We train a 1.2B-parameter language model, ProGen, on ∼280M protein sequences conditioned on taxonomic and keyword tags such as molecular function and cellular component. This provides ProGen with an unprecedented range of evolutionary sequence diversity and allows it to generate with fine-grained control as demonstrated by metrics based on primary sequence similarity, secondary structure accuracy, and conformational energy.
mbImpute: an accurate and robust imputation method for microbiome data
Authors: Jiang Ruochen , Li Wei Vivian , Li Jingyi Jessica 
Published: March 2020

AbstractMicrobiome studies have gained increased attention since many discoveries revealed connections between human microbiome compositions and diseases. A critical challenge in microbiome research is that excess non-biological zeros distort taxon abundances, complicate data analysis, and jeopardize the reliability of scientific discoveries. To address this issue, we propose the first imputation method, mbImpute, to identify and recover likely non-biological zeros by borrowing information jointly from similar samples, similar taxa, and optional metadata including sample covariates and taxon phylogeny. Comprehensive simulations verified that mbImpute achieved better imputation accuracy under multiple measures than five state-of-the-art imputation methods designed for non-microbiome data. In real data applications, we demonstrate that mbImpute improved the power and reproducibility of identifying disease-related taxa from microbiome data of type 2 diabetes and colorectal cancer.
Effects of attapulgite on the worn surface and fretting wear resistance property of UHMWPE composites
Authors: Meng Zhaojie , Wang Yunxia , Xin Xiaocui , Liu Hao , Yan Yunfeng , Yan Fengyuan 
Published: March 2020

Purpose
The purpose of this study is to examine the fretting wear property of ultra-high molecular weight polyethylene (UHMWPE)-based composites reinforced by different content of attapulgite.

Design/methodology/approach
A series of composites were prepared by a hot-pressing method. Fretting tests were carried out using an SRV-IV oscillating reciprocating friction wear tester with a load of 10 N and a frequency of 100 Hz. The morphology of the fracture structure and the worn surface was observed by field-emission scanning electron microscopy, X-ray diffraction and a non-contact three dimensional surface profiler.

Findings
With the addition of attapulgite, the microstructure of the composites become more regular, and their heat resistance improved. Furthermore, the friction coefficient and the specific wear rate of the composites with lower filler content reduced compared with that of neat UHMWPE, and the optimum filler content is 1 per cent.

Originality/value
The study investigated the fretting resistance mechanism of the attapulgite in the UHMWPE matrix. The results could help to provide some experimental evidence for the broader application of silicates on the fretting wear resistance of polymers.

Peer review
The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-10-2019-0420/
Demographics, natural history and treatment outcomes of non‐molar gestational choriocarcinoma: a UK population study
Authors: Savage P , Winter M , Parker V , Harding V , Sita‐Lumsden A , Fisher RA , Harvey R , Unsworth N , Sarwar N , Short D , Aguiar X , Tidy J , Hancock B , Coleman R , Seckl MJ 
Published: March 2020

ObjectiveTo investigate the demographics, natural history and treatment outcomes of non‐molar gestational choriocarcinoma.DesignA retrospective national population‐based study.SettingUK 1995–2015.PopulationA total of 234 women with a diagnosis of gestational choriocarcinoma, in the absence of a prior molar pregnancy, managed at the UKs two gestational trophoblast centres in London and Sheffield.MethodsRetrospective review of the patient’s demographic and clinical data. Comparison with contemporary UK birth and pregnancy statistics.Main outcomesIncidence statistics for non‐molar choriocarcinoma across the maternal age groups. Cure rates for patients by FIGO prognostic score group.ResultsOver the 21‐year study period, there were 234 cases of non‐molar gestational choriocarcinoma, giving an incidence of 1:66 775 relative to live births and 1:84 226 to viable pregnancies. For women aged under 20, the incidence relative to viable pregnancies was 1:223 494, for ages 30–34, 1:80 227, and for ages 40–45, 1:41 718. Treatment outcomes indicated an overall 94.4% cure rate. Divided by FIGO prognostic groups, the cure rates were low‐risk group 100%, high‐risk group 96% and ultra‐high‐risk group 80.5%.ConclusionsNon‐molar gestational choriocarcinoma is a very rare diagnosis with little prior detailed information on the demographics and natural history. The data in this study give age‐related incidence data based on a large national population study. The results also demonstrated the widely varying natural history of this rare malignancy and the marked correlation of disease incidence with rising maternal age.Tweetable abstractNational gestational choriocarcinoma database indicates a close association between increasing maternal age and incidence.
Long‐term consequences of being placed in disciplinary segregation†
Authors: Wildeman Christopher , Andersen Lars Højsgaard 
Published: March 2020

AbstractBeing placed in restrictive housing is considered one of the most devastating experiences a human can endure, yet a scant amount of research has been conducted to test how this experience affects core indicators of prisoner reentry such as employment and recidivism. In this article, we use Danish registry data, which allow for us to link penal conditions to postrelease outcomes, to show how the reentry outcomes of individuals placed in disciplinary segregation, which is placement in restrictive housing because of disciplinary infractions, compare with those sanctioned for in‐prison offenses but not placed in segregation. The results from matched difference‐in‐differences analyses show that Danish inmates placed in disciplinary segregation experience larger drops in employment and larger increases in the risk of being convicted of a new crime in the 3 years after release from a correctional facility than do Danish inmates who were sanctioned for a serious offense but not placed in disciplinary segregation as a result. Because being placed in disciplinary segregation, and restrictive housing more broadly, is so common, these results indicate that restrictive housing placement may be a key moderator of the effects of incarceration that merits more attention from criminologists, provided the associations shown here represent causal effects and generalize.