bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hemocyte-targeted gene expression in the female malaria mosquito using thehemolectinpromoter fromDrosophila
Authors: Pondeville Emilie , Puchot Nicolas , Parvy Jean-Philippe , Carrissimo Guillaume , Poidevin Mickael , Waterhouse Robert M. , Marois Eric , Bourgouin Catherine 
Published: December 2019

AbstractHemocytes, the immune cells in mosquitoes, participate in immune defenses against pathogens including malaria parasites. Mosquito hemocytes can also be infected by arthropod-borne viruses but the pro- or anti-viral nature of this interaction is unknown. Although there has been progress on hemocyte characterization during pathogen infections in mosquitoes, the specific contribution of hemocytes to immune responses and the hemocyte-specific functions of immune genes and pathways remain unresolved due to the lack of genetic tools to manipulate gene expression in these cells specifically. Here, we used the Gal4-UAS system to characterize the activity of theDrosophilahemocyte-specifichemolectinpromoter in the adults ofAnopheles gambiae, the malaria mosquito. We established anhml-Gal4 driver line that we further crossed to a fluorescent UAS responder line, and examined the expression pattern in the adult progeny driven by thehmlpromoter. We show that thehmlregulatory region drives hemocyte-specific transgene expression in a subset of hemocytes, and that transgene expression is triggered after a blood meal. Thehmlpromoter drives transgene expression in differentiating prohemocytes as well as in differentiated granulocytes. Analysis of different immune markers in hemocytes in which thehmlpromoter drives transgene expression revealed that this regulatory region could be used to study phagocytosis as well as melanization. Finally, thehmlpromoter drives transgene expression in hemocytes in which o’nyong’nyong virus replicates. Altogether, thehmlpromoter constitutes a good tool to drive transgene expression in hemocyte only and to analyze the function of these cells and the genes they express during pathogen infection inAnopheles gambiae.
An Alignment-free Method for Phylogeny Estimation using Maximum Likelihood
Authors: Zahin Tasfia , Abrar Md. Hasin , Rahman Mizanur , Tasnim Tahrina , Bayzid Md. Shamsuzzoha , Rahman Atif 
Published: December 2019

AbstractWhile alignment has traditionally been the primary approach for establishing homology prior to phylogenetic inference, alignment-free methods offer a simplified alternative, particularly beneficial when handling genome-wide data involving long sequences and complex events such as rearrangements. Moreover, alignment-free methods become crucial for data types like genome skims, where assembly is impractical. However, despite these benefits, alignment-free techniques have not gained widespread acceptance since they lack the accuracy of alignment-based techniques, primarily due to their reliance on simplified models of pairwise distance calculation. Here, we present a likelihood based alignment-free technique for phylogenetic tree construction. We encode the presence or absence ofk-mers in genome sequences in a binary matrix, and estimate phylogenetic trees using a maximum likelihood approach. We analyze the performance of our method on seven real datasets and compare the results with the state of the art alignment-free methods. Results suggest that our method is competitive with existing alignment-free tools. This indicates that maximum likelihood based alignment-free methods may in the future be refined to outperform alignment-free methods relying on distance calculation as has been the case in the alignment-based setting. A likelihood based alignment-free method for phylogeny estimation is implemented for the first time in a software named Peafowl, which is available at:https://github.com/hasin-abrar/Peafowlrepo.
The effect of feeding behavior ofMonochamus alternatus(Coleoptera: Cerambycidae) on the departure of pine wood nematode,Bursaphelenchus xylophilus(Nematoda: Aphelenchoididae)
Authors: Wang Yang , Chen Fengmao , Wang Lichao , Zhou Lifeng , Song Juan 
Published: December 2019

AbstractIn order to study the causes of pine wood nematode (PWN) departure fromMonochamus alternatus, the effects of the feeding behavior ofM. alternatuson the start date of the departure of PWN were studied. The start date of the departure of PWN carried by the directly fedM. alternatuswas 5—13 d after beetle emergence, mainly concentrated within 6—10 d, with a mean (±SD) of 8.02 ± 1.96 d. The start date of the departure of PWN carried by theM. alternatusfed after starvation was 5—14 d after beetle emergence, mainly concentrated within 6—9 d, with a mean of 7.76 ± 2.28 d. The results show that there was no significant difference in the start departure date of PWN between the two treatments. This shows that the feeding behavior ofM. alternatusis not the trigger for PWN departure. At the same time, it was found that the motility of the PWN carried byM. alternatusat 8 d after emergence was significantly greater than that of the PWN carried by the newly emergedM. alternatus.And the PWN carried byM. alternatusat 8 d after emergence was extracted more easily than the PWN carried by newly emerged beetles. These results show that greater motility was associated with easier departure of PWN fromM. alternatus.In addition, transcriptome sequencing found that the level of oxidative phosphorylation metabolism of PWN carried by beetles at 8 d after emergence was significantly higher than that in the PWN carried by newly emerged beetle. High oxidative phosphorylation was associated with increased energy production and motility by the PWN and were the internal cause of the start of nematode departure.
Deriving Ranges of Optimal Estimated Transcript Expression Due to Non-identifiability
Authors: Zheng Hongyu , Ma Cong , Kingsford Carl 
Published: December 2019

AbstractCurrent expression quantification methods suffer from a fundamental but under-characterized type of error: the most likely estimates for transcript abundances are not unique. This means multiple estimates of transcript abundances generate the observed RNA-seq reads with equal likelihood, and the underlying true expression cannot be determined. This problem is called non-identifiability for probabilistic models, and is further exacerbated by incomplete reference transcriptome. That is, reads may be sequenced from unannotated expressed transcripts. Graph quantification is a generalization to transcript quantification, accounting for the reference incompleteness by allowing exponentially many unannotated transcripts to express reads. We propose methods to calculate a “confidence range of expression” for each transcript, representing its possible abundance across equally optimal estimates for both quantification models. This range informs both whether a transcript has potential estimation error due to non-identifiability and the extent of the error. Applying our methods to the Human Body Map data, we observe 35%–50% of transcripts potentially suffer from inaccurate quantification caused by non-identifiability. When comparing the expression between isoforms in one sample, we find that the degree of inaccuracy of 20%–47% transcripts can be so large that the ranking of expression between the transcript and its sibling isoforms cannot be determined. When comparing the expression of a transcript between two groups of RNA-seq samples in differential expression analysis, we observe that the majority of detected differentially expressed transcripts are reliable with a few exceptions after considering the ranges of the optimal expression estimates. The code for computing the range of expression is available athttps://github.com/Kingsford-Group/subgraphquant. The code for the involved analyses is available athttps://github.com/Kingsford-Group/subgraphquantanalysis.
SEC is an anti-angiogenic virulence factor that promotesStaphylococcus aureusInfective Endocarditis Independent of Superantigen Activity
Authors: Kinney Kyle J. , Tang Sharon S. , Wu Xiao-Jun , Tran Phuong M. , Bharadwaj Nikhila S. , Gibson-Corley Katherine N. , Forsythe Ana N. , Kulhankova Katarina , Gumperz Jenny E. , Salgado-Pabón Wilmara 
Published: December 2019

AbstractThe superantigen staphylococcal enterotoxin C (SEC) is critical forStaphylococcus aureusinfective endocarditis (SAIE) in rabbits. Superantigenicity, its hallmark function, was proposed to be a major underlying mechanism driving SAIE but was not directly tested. With the use ofS. aureusMW2 expressing SEC toxoids, we show that superantigenicity does not sufficiently account for vegetation growth, myocardial inflammation, and acute kidney injury in the rabbit model of native valve SAIE. These results highlight the critical contribution of an alternative function of superantigens to SAIE. In support of this, we provide evidence that SEC exerts anti-angiogenic effects by inhibiting branching microvessel formation in anex vivorabbit aortic ring model and by inhibiting endothelial cell expression of one of the most potent mediators of angiogenesis, VEGF-A. SEC’s ability to interfere with tissue re-vascularization and remodeling after injury serves as a mechanism to promote SAIE and its life-threatening systemic pathologies.
Ecological drivers of African swine fever virus persistence in wild boar populations: insight for control
Authors: Pepin Kim M. , Golnar Andrew J. , Abdo Zaid , Podgórski Tomasz 
Published: December 2019

AbstractEnvironmental sources of infection can play a primary role in shaping epidemiological dynamics, however the relative impact of environmental transmission on host-pathogen systems is rarely estimated. We developed and fit a spatially-explicit model of African swine fever virus (ASFV) in wild boar to estimate what proportion of carcass-based transmission is contributing to the low-level persistence of ASFV in Eastern European wild boar. Our model was developed based on ecological insight and data from field studies of ASFV and wild boar in Eastern Poland. We predicted that carcass-based transmission would play a substantial role in persistence, especially in low-density host populations where contact rates are low. By fitting the model to outbreak data using Approximate Bayesian Computation, we inferred that between 53 to 66% of transmission events were carcass-based – i.e., transmitted through contact of a live host with a contaminated carcass. Model fitting and sensitivity analyses showed that the frequency of carcass-based transmission increased with decreasing host density, suggesting that management policies should emphasize the removal of carcasses and consider how reductions in host densities may drive carcass-based transmission. Sensitivity analyses also demonstrated that carcass-based transmission is necessary for the autonomous persistence of ASFV under realistic parameters. Autonomous persistence through direct transmission alone required high host densities; otherwise re-introduction of virus periodically was required for persistence when direct transmission probabilities were moderately high. We quantify the relative role of different persistence mechanisms for a low-prevalence disease using readily collected ecological data and viral surveillance data. Understanding how the frequency of different transmission mechanisms vary across host densities can help identify optimal management strategies across changing ecological conditions.
Unexpected diversity of CRISPR unveils some evolutionary patterns of repeated sequences inMycobacterium tuberculosis
Authors: Refrégier Guislaine , Sola Christophe , Guyeux Christophe 
Published: December 2019

AbstractDiversity of the CRISPR locus ofMycobacterium tuberculosiscomplex has been studied since 1997 for molecular epidemiology purposes. By targeting solely the 43 spacers present in the two first sequenced genomes (H37Rv and BCG), it gave a biased idea of CRISPR diversity and ignored diversity in the neighbouringcas-genes.We set up tailored pipelines to explore the diversity of CRISPR-cas locus in Short Reads. We analyzed data from a representative set of 198 clinical isolates as evidenced by well-characterized SNPs.We found a relatively low diversity in terms of spacers: we recovered only the 68 spacers that had been described in 2000. We found no partial or global inversions in the sequences, letting always the Direct Variant Repeats (DVR) in the same order. In contrast, we found an unexpected diversity in the form of: SNPs in spacers and in Direct Repeats, duplications of various length, and insertions at various locations of the IS6110insertion sequence, as well as blocks of DVR deletions. The diversity was in part specific to lineages. When reconstructing evolutionary steps of the locus, we found no evidence for SNP reversal. DVR deletions were linked to recombination between IS6110insertions or between Direct Repeats.This work definitively shows that CRISPR locus ofM. tuberculosisdid not evolve by classical CRISPR adaptation (incorporation of new spacers) since the last most recent common ancestor of virulent lineages. The evolutionary mechanisms that we discovered could be involved in bacterial adaptation but in a way that remains to be identified.
Comparison of mechanical sorting and DNA metabarcoding for diet analysis with degraded wolf scats
Authors: Massey Aimee , Roffler Gretchen , Vermeul Tessa , Allen Jennifer , Levi Taal 
Published: December 2019

AbstractDNA metabarcoding has become a powerful technique for identifying species and profiling biodiversity with the potential to improve efficiency, reveal rare prey species, and correct mistaken identification error in diet studies. However, the extent to which molecular approaches agree with traditional approaches is unknown for many species. Here, we compare diets from wolf scats profiled using both mechanical sorting and metabarcoding of amplified vertebrate DNA sequences. Our objectives were: (1) compare findings from mechanical sorting and metabarcoding as a method of diet profiling and (2) use results to better understand diets of wolves on Prince of Wales Island, a population of conservation concern. We predicted metabarcoding would reveal both higher diversity of prey and identify rare species that are overlooked with mechanical sorting. We also posited that the relative contribution of Sitka black-tailed deer (Odocoileus hemionus sitkensis) and beaver (Castor canadensis) would be overestimated with mechanical sorting methods because of the failure to account for the full diet diversity of these wolves. We found that there was substantial overlap in the diets revealed using both methods, indicating that deer, beaver, and black bear (Ursus americanus) were the primary prey species. However, there was a large discrepancy in the occurrence of beaver in scats (54% and 24% from mechanical sorting and metabarcoding, respectively) explained by the high rate of false positives with mechanical sorting methods. Metabarcoding revealed more diet diversity than mechanical sorting, thus supporting our initial predictions. Prince of Wales Island wolves appear to have a more diverse diet with greater occurrence of rare species than previously described including 14 prey species that contribute to wolf diet. Metabarcoding is an effective method for profiling carnivore diet and enhances our knowledge concerning the full diversity of wolf diets, even in the extremely wet conditions of southeast Alaska, which can lead to DNA degradation. Given the increasingly efficient and cost-effective nature of collecting eDNA, we recommend incorporating these molecular methods into field-based projects to further examine questions related to increased use of alternate prey coinciding with changes in abundance of primary prey and habitat alteration.
Tuning shape and internal structure of protein droplets via biopolymer filaments
Authors: Scheff Danielle R. , Weirich Kimberly L. , Dasbiswas Kinjal , Patel Avinash , Vaikuntanathan Suriyanarayanan , Gardel Margaret L. 
Published: December 2019

AbstractMacromolecules can phase separate to form liquid condensates, which are emerging as critical compartments in fields as diverse as intracellular organization and soft materials design. A myriad of macromolecules, including the protein FUS, form condensates which behave as isotropic liquids. Here, we investigate the influence of filament dopants on the material properties of protein liquids. We find that the short, biopolymer filaments of actin spontaneously partition into FUS droplets to form composite liquid droplets. As the concentration of the filament dopants increases, the coalescence time decreases, indicating that the dopants control the relative surface tension to viscosity. The droplet shape is tunable ranging from spherical to tactoid as the filament length or concentration is increased. We find that the tactoids are well described by a model of a bipolar liquid crystal droplet, where nematic order from the anisotropic actin filaments competes with isotropic interfacial energy from the FUS, controlling droplet shape in a size-dependent manner. Our results demonstrate a versatile approach to construct tunable, anisotropic macromolecular liquids.
UniPath: A uniform approach for pathway and gene-set based analysis of heterogeneity in single-cell epigenome and transcriptome profiles
Authors: Chawla Smriti , Samydurai Sudhagar , Kong Say Li , Wang Zhenxun , Tam Wai Leong , Sengupta Debarka , Kumar Vibhor 
Published: December 2019

AbstractHere, we introduce UniPath, for representing single-cells using pathway and gene-set enrichment scores by a transformation of their open-chromatin or gene-expression profiles. Besides being robust to variability in dropout, UniPath provides consistency and scalability in estimating gene-set enrichment scores for every cell. UniPath’s approach of predicting temporal-order of single-cells using their gene-set activity score enables suppression of known covariates. UniPath based analysis of mouse cell atlas yielded surprising, albeit biologically-meaningful co-clustering of cell-types from distant organs and helped in annotating many unlabeled cells. By enabling unconventional analysis, UniPath also proves to be useful in inferring context-specific regulation in cancer cells.
Effects of nitrogen deposition on the spatial pattern of biocrusts and soil microbial activity in a semi‐arid Mediterranean shrubland
Authors: Benvenutto‐Vargas Verónica P. , Ochoa‐Hueso Raúl 
Published: December 2019

Abstract

Human activities have doubled, or even tripled, the amount of nitrogen (N) fixed globally, which alters the functioning and reduces the biodiversity of terrestrial ecosystems.

In this study, we used a 10‐year N addition experiment in a semi‐arid Mediterranean shrubland in central Spain to evaluate the effects of increased N deposition on biocrust cover, soil microbial enzymatic activity and their spatial patterns. We collected highly replicated, spatially explicit data to carry out Moran's I correlograms at the plot level and used linear mixed models to evaluate the effects of N addition on cover, microbial activity and Moran's I values for each distance class of correlograms.

High N deposition (50 kg N ha−1 year−1) reduced the cover of the foliose lichen Cladonia foliacea, an important component of biocrusts, and generated significant alterations and losses of the spatial pattern of biocrusts and soil microbial enzymatic activity. Furthermore, we found indication that N addition altered the relationship between biocrust cover and microbial enzymatic activity, suggesting that the presence of well‐developed biocrust communities modulates the effects of high N deposition on soil microbial activity.

Synthesis. Overall, our study suggests that an increase in N deposition may have important consequences for the structure and functioning of Mediterranean ecosystems and that some of these consequences may be due to alterations in the way in which different soil communities (e.g. moss‐lichen biocrusts and soil microorganisms) interact with one another.

A free Plain Language Summary can be found within the Supporting Information of this article.
Neuropharmacological effects of Aconiti Lateralis Radix Praeparata
Authors: Zhao Lihong , Sun Zhihui , Yang Limin , Cui Ranji , Yang Wei , Li Bingjin 
Published: December 2019

AbstractAconiti Lateralis Radix Praeparata (Fuzi in Chinese), which are the lateral roots of Aconitum Carmichaelii Debx, is widely used in China to treat many neurological diseases. Fuzi, in its various forms, has many neuropharmacological effects. It can act as an analgesic and help with depression, epilepsy, and dementia. However, the neuropharmacological effects of Aconiti Lateralis Radix Praeparata are seldom comprehensively reviewed. In this review, the neuropharmacological activities of some components contained in Aconiti Lateralis Radix Praeparata are considered. These include aconitine, mesaconitine, hypaconitine, total alkaloid, polysaccharide‐1, benzoylmesaconine, fuziline, songorine, and napelline. We also specifically discuss the antidepressant effects of total alkaloids and polysaccharide‐1. This review may provide a theoretical basis for further utilization of Aconiti Lateralis Radix Praeparata for diseases that affect the central nervous system.
Agricultural and rural development in China during the past four decades: an introduction
Authors: Huang Jikun , Rozelle Scott , Zhu Xinkai , Zhao Shiji , Sheng Yu 
Published: December 2019

The past four decades have witnessed unprecedented economic growth and rapidly rising food demand in China. This paper provides an introduction to readers with useful information summarising the development of China’s agricultural sector and the transformation of its rural economy over the 40 years of economic reform. It is, however, impossible to cover all aspects of this recent and rich history in a single journal special issue. Nevertheless, we are of the view that these papers address the most fundamentally important and insightful topics including: land reform and rural development; technology progress and productivity growth; changing food consumption patterns; rural education and human capital accumulation; and poverty alleviation.
Effects of opting‐out from federal nurse anesthetists' supervision requirements on anesthesiologist work patterns
Authors: Baird Matthew , O'Donnell John M. , Martsolf Grant R. 
Published: December 2019

AbstractObjectiveTo estimate the impact of opting‐out from Medicare supervision requirements for certified registered nurse anesthetists (CRNAs) on anesthesiologists' work patterns.Data Sources/Study SettingSecondary data from two national surveys of anesthesiologists and the Area Health Resource File.Study DesignWe use a matching difference‐in‐difference regression which contrasts the change in work patterns for anesthesiologists in California, which dropped supervision requirements, to the change for similar anesthesiologists. Key outcome variables include the number of weekly hours worked, the type of work done, and type of care delivery teams.Data Collection/Extraction MethodsSelf‐reported national survey data drawn from members of the American Society of Anesthesiologists.Principal FindingsAnesthesiologists in California saw no change in time spent working or time spent supervising CRNAs. There was a decrease in direct care clinical work hours along with a shift in working more in intraoperative care, a decrease in postoperative care, and an increase in the percentage of cases supervising residents.ConclusionsAnesthesiologists had small but real responses to California’s decisions to opt‐out of the physician supervision requirement for CRNAs, doing more work in intraoperative care and less outside of the operating room. Total hours worked saw no change.