bluuebunny/crossref_metadata_2025_split huggingface dataset:
Segmentation of the Zebrafish Brain Vasculature from Light Sheet Fluorescence Microscopy Datasets
Authors: Kugler Elisabeth C. , Rampun Andrik , Chico Timothy J.A. , Armitage Paul A. 
Published: July 2020

AbstractLight sheet fluorescent microscopy allows imaging of zebrafish vascular development in great detail. However, interpretation of data often relies on visual assessment and approaches to validate image analysis steps are broadly lacking. Here, we compare different enhancement and segmentation approaches to extract the zebrafish cerebral vasculature, provide comprehensive validation, study segmentation robustness, examine sensitivity, apply the validated method to quantify embryonic cerebrovascular volume, and examine applicability to different transgenic reporter lines. The best performing segmentation method was used to train different deep learning networks for segmentation. We found that U-Net based architectures outperform SegNet. While there was a slight overestimation of vascular volume using the U-Net methodologies, variances were low, suggesting that sensitivity to biological changes would still be obtained.HighlightsGeneral filtering is less applicable than Sato enhancement to enhance zebrafish cerebral vessels.Biological data sets help to overcome the lack of segmentation gold-standards and phantom models.Sato enhancement followed by Otsu thresholding is highly accurate, robust, and sensitive.Direct generalization of the segmentation approach to transgenics, other than the one optimized for, should be treated with caution.Deep learning based segmentation is applicable to the zebrafish cerebral vasculature, with U-Net based architectures outperforming SegNet architectures.Graphical Abstract
Response of soil microbial communities to mixed forests of European beech and conifers: Variations with site conditions
Authors: Lu Jing-Zhong , Scheu Stefan 
Published: July 2020

AbstractTree - soil interactions depend on environmental conditions. Planting trees may strongly impact microorganisms in particular at unfavorable site conditions, compromising the functioning of soil microorganisms. To understand the effects of tree species composition on soil microorganisms, we quantified structural and functional responses of soil microorganisms to forest types across environmental conditions using substrate-induced respiration and phospholipid fatty acid analyses. Five forest types were studied including pure stands of native European beech (Fagus sylvatica), range expanding Norway spruce (Picea abies), and non-native Douglas-fir (Pseudotsuga menziesii), as well as the two conifer - beech mixtures. We found that microbial functioning strongly depends on site conditions, in particular on soil nutrients. At nutrient-poor sites, soil microorganisms were more stressed in pure and mixed coniferous forests, especially in Douglas-fir, compared to beech forests. By contrast, microbial structure and functional indicators in beech forests varied little with site conditions, likely because beech provided high amounts of root-derived resources for microbial growth. Since soil microbial communities are sensitive to Douglas-fir, planting Douglas-fir may compromise ecosystem functioning in particular at nutrient-poor sites. Overall, root-derived resources are important for determining the structure and functioning of soil microbial communities, and soil microorganisms sensitively respond to plantations containing tree species that may differ in the provisioning of these resources.
Comparison of long read sequencing technologies in resolving bacteria and fly genomes
Authors: Tvedte Eric S. , Gasser Mark , Sparklin Benjamin C. , Michalski Jane , Zhao Xuechu , Bromley Robin , Tallon Luke J. , Sadzewicz Lisa , Rasko David A. , Dunning Hotopp Julie C. 
Published: July 2020

ABSTRACTBackgroundThe newest generation of DNA sequencing technology is highlighted by the ability to sequence reads hundreds of kilobases in length, and the increased availability of long read data has democratized the genome sequencing and assembly process. PacBio and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. Released in 2019, the PacBio Sequel II platform advertises substantial enhancements over previous PacBio systems.ResultsWe used whole-genome sequencing data produced by two PacBio platforms (Sequel II and RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteriaEscherichia coliand the fruit flyDrosophila ananassae. Sequel II assemblies had higher contiguity and consensus accuracy relative to other methods, even after accounting for differences in sequencing throughput. ONT RAPID libraries had the fewest chimeric reads in addition to superior quantification ofE. coliplasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assemblies or combined ONT and Sequel II libraries for eukaryotic genome assemblies. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of knownE. colimethyltransferase recognition motifs in addition to undocumentedD. ananassaemotifs.ConclusionsThe ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined.
Evaluating tank acclimation and trial length for shuttle box temperature preference assays
Authors: Harman Adam Alexander , Fuzzen Meghan , Stoa Lisa , Boreham Douglas , Manzon Richard , Somers Christopher M. , Wilson Joanna Yvonne 
Published: July 2020

AbstractThermal preferenda are largely defined by optimal growth temperature for a species and describe the range of temperatures an organism will occupy when given a choice. Assays for thermal preferenda require at least 24 hours, which includes a long acclimation to the tank, limits throughput and thus impacts replication in the study. Three different behavioral assay experimental designs were tested to determine the effect of tank acclimation and trial length (12:12, 0:12, 2:2; hours of tank acclimation: behavioral trial) on the temperature preference of juvenile lake whitefish, using a shuttle box system. Average temperature preferences for the 12:12, 0:12, and 2:2 experimental designs were 16.10 ± 1.07 °C, 16.02 ± 1.56 °C, 16.12 ± 1.59°C respectively, with no significant differences between the experimental designs (p= 0.9337). Ultimately, length of acclimation time and trial length had no significant impact, suggesting that all designs were equally useful for studies of temperature preference.
Predicting cancer prognosis and drug response from the tumor microbiome
Authors: Hermida Leandro C. , Gertz E. Michael , Ruppin Eytan 
Published: July 2020

AbstractTumor gene expression is predictive of patient prognosis in some cancers. However, RNA- seq and whole genome sequencing data contain not only reads from host tumor and normal tissue, but also reads from the tumor microbiome, which can be used to infer the microbial abundances in each tumor. Here, we show that tumor microbial abundances, alone or in combination with tumor gene expression data, can predict cancer prognosis and drug response to some extent – microbial abundances are significantly less predictive of prognosis than gene expression, although remarkably, similarly as predictive of drug response, but in mostly different cancer-drug combinations. Thus, it appears possible to leverage existing sequencing technology, or develop new protocols, to obtain more non-redundant information about prognosis and drug response from RNA-seq and whole genome sequencing experiments than could be obtained from tumor gene expression or genomic data alone.
The untapped potential of conservation journals to promote freshwater biodiversity
Authors: He Fengzhi , Jähnig Sonja C. , Wetzig Annett , Langhans Simone D. 
Published: July 2020

AbstractFreshwater ecosystems are amongst the most diverse ecosystems on the planet. They are subject to intense and increasing threats and have a higher proportion of threatened and extinct species than terrestrial or marine realms. Concurrently, freshwater ecosystems are largely underrepresented in both conservation research and actions arguably as a consequence of less popularity and promotion. To test this assumption, we used cover images as a proxy of exposure and promotion opportunities provided by conservation journals. We collected information on cover images of 18 conservation journals from 1997 to 2016 and data on citations and Altmetric scores of papers published in them. We found that freshwater ecosystems (10.4%) were featured less often than marine (15.2%) or terrestrial (74.4%) ecosystems on covers of these journals. All 15 most featured species are from terrestrial or marine ecosystems, with 14 of them being large vertebrates such as elephants, big cats, rhinos, polar bears, and marine turtles. None of the 95 species featured more than once on the covers of conservation journals spend their whole life history in fresh waters, i.e. they are at least partly associated with terrestrial or marine ecosystems. Our results indicated that cover-featured studies received more attention from academia and the general public, i.e. showed higher citations and Altmetric scores, than non-featured ones within the same issue. By featuring freshwater species and habitats on covers, therewith providing more exposure opportunities, conservation journals hold the potential to promote biodiversity conservation in fresh waters. Scientists can help that endeavour by submitting freshwater-related photos together with their manuscripts for review, therewith providing more options for editors to portray freshwater species and habitats and to ultimately raise awareness and appreciation of freshwater life.
Inhibitors of L-type calcium channels show therapeutic potential for treating SARS-CoV-2 infections by preventing virus entry and spread
Authors: Straus Marco R. , Bidon Miya K. , Tang Tiffany , Jaimes Javier A. , Whittaker Gary R. , Daniel Susan 
Published: July 2020

AbstractCOVID-19 is caused by a novel coronavirus, severe acute respiratory syndrome coronavirus (CoV)-2 (SARS-CoV-2). The virus is responsible for an ongoing pandemic and concomitant public health crisis around the world. While vaccine development is proving to be highly successful, parallel drug development approaches are also critical in the response to SARS-CoV-2 and other emerging viruses. Coronaviruses require Ca2+ions for host cell entry and we have previously shown that Ca2+modulates the interaction of the viral fusion peptide with host cell membranes. In an attempt to accelerate drug development, we tested a panel of L-type calcium channel blocker (CCB) drugs currently developed for other conditions, to determine whether they would inhibit SARS-CoV-2 infection in cell culture. All the CCBs tested showed varying degrees of inhibition, with felodipine and nifedipine strongly limiting SARS-CoV-2 entry and infection in epithelial lung cells at concentrations where cell toxicity was minimal. Further studies with pseudo-typed particles displaying the SARS-CoV-2 spike protein suggested that inhibition occurs at the level of virus entry. Overall, our data suggest that certain CCBs have potential to treat SARS-CoV-2 infections and are worthy of further examination for possible treatment of COVID-19.
Experience-dependent plasticity in an innate social behavior is mediated by hypothalamic LTP
Authors: Stagkourakis Stefanos , Spigolon Giada , Liu Grace , Anderson David J. 
Published: July 2020

AbstractAll animals can perform certain survival behaviors without prior experience, suggesting a “hard wiring” of underlying neural circuits. Experience, however, can alter the expression of innate behaviors. Where in the brain and how such plasticity occurs remains largely unknown. Previous studies have established the phenomenon of “aggression training,” in which the repeated experience of winning successive aggressive encounters across multiple days leads to increased aggressiveness. Here we show that this procedure also leads to long-term potentiation (LTP) at an excitatory synapse, derived from the Anterior Hippocampus/Posterior Medial amygdala (AHiPM), onto estrogen receptor 1-expressing (Esr1+) neurons in the ventrolateral subdivision of the ventromedial hypothalamus (VMHvl). We demonstrate further that the optogenetic induction of such LTPin vivofacilitates, while optogenetic long-term depression (LTD) diminishes, the behavioral effect of aggression training, implying a causal role for potentiation at AHiPM➔VMHvlEsr1synapses in mediating the effect of this training. Interestingly, ∼25% of inbred C57BL/6 mice fail to respond to aggression training. We show that these individual differences are correlated both with lower levels of testosterone, relative to mice that respond to such training, and with a failure to exhibit LTPin vivoafter aggression training. Administration of exogenous testosterone to such non-aggressive mice restores both behavioral and physiological plasticityin vivo. Together, these findings reveal that LTP at a hypothalamic circuit node mediates a form of experience-dependent plasticity in an innate social behavior, and a potential hormone-dependent basis for individual differences in such plasticity among genetically identical mice.Significance StatementModification of instinctive behaviors occurs through experience, yet the mechanisms through which this happens have remained largely unknown. Recent studies have shown that potentiation of aggression, an innate behavior, can occur through repeated winning of aggressive encounters. Here we show that synaptic plasticity at a specific excitatory input to a hypothalamic cell population is correlated with, and required for, the expression of increasingly higher levels of aggressive behavior following successful aggressive experience. We additionally show that the amplitude and persistence of long-term potentiation at this synapse are influenced by serum testosterone, administration of which can normalize individual differences among genetically identical inbred mice, in the expression of intermale aggression.
Drosophila p53isoforms have overlapping and distinct functions in germline genome integrity and oocyte quality control
Authors: Chakravarti Ananya , Thirimanne Heshani N. , Calvi Brian R. 
Published: July 2020

Abstractp53 gene family members in humans and other organisms encode a large number of protein isoforms whose functions are largely undefined. UsingDrosophilaas a model, we find that a p53B isoform is expressed predominantly in the germline where it colocalizes with p53A into subnuclear bodies. It is only p53A, however, that mediates the apoptotic response to ionizing radiation in the germline and soma. In contrast, p53A and p53B both respond to meiotic DNA breaks and are required during oogenesis to prevent persistent germline DNA breaks, an activity that is more crucial when meiotic recombination is defective. We find that in oocytes with persistent DNA breaks p53A is required to activate a meiotic pachytene checkpoint. Our findings indicate thatDrosophilap53 isoforms have DNA lesion and cell type-specific functions, with parallels to the functions of mammalian p53 family members in the genotoxic stress response and oocyte quality control.
cDC1 Coordinate Innate and Adaptive Responses in the Omentum required for T cell Priming and Memory
Authors: Christian David A. , Adams Thomas A. , Smith Tony E. , Shallberg Lindsey A. , Theisen Derek J. , Phan Anthony T. , Abraha Mosana , Perry Joseph , Ruthel Gordon , Clark Joseph T. , Murphy Kenneth M. , Kedl Ross M. , Hunter Christopher A. 
Published: July 2020

ABSTRACTThe omentum in the peritoneal cavity contains fat associated lymphoid clusters (FALCs) whose role in the response to microbial challenge are poorly understood. After intraperitoneal immunization withToxoplasma gondii, type I dendritic cells (cDC1) were critical to induce innate sources of IFN-γ required to recruit monocytes to the FALCs. The migration of infected peritoneal macrophages into T and B cell rich areas of the FALCs allowed the TCR-induced activation of parasite-specific T cells. Unexpectedly, cDC1 were not required for T cell priming but rather supported the expansion of parasite-specific CD8+T cells. An agent-based mathematical model predicted that the lack of cDC1 would impact the early proliferative burst, and we confirmed that cDC1 were required for optimal T cell expression of nutrient uptake receptors and cell survival. These studies highlight that cDC1 in the FALCs have distinct roles in the co-ordination of the innate and adaptive responses to microbial challenge.
Understanding the antiviral effects of RNAi-based therapy on chronic hepatitis B infection
Authors: Kadelka Sarah , Dahari Harel , Ciupe Stanca M 
Published: July 2020

AbstractReaching hepatitis B surface antigen (HBsAg) loss (called functional cure) with approved treatment with pegylated interferon-α(IFN) and/or nucleos(t)ide analogues (NAs) in chronic hepatitis B virus (HBV) infected patients is suboptimal. The RNA interference (RNAi) drug ARC-520 was shown to be effective in reducing serum HBV DNA, HBsAg and hepatitis B e antigen (HBeAg) in chimpanzees and small animals. A recent clinical study (Heparc-2001) showed reduction of serum HBV DNA, HBeAg and HBsAg in HBeAg-positive patients treated with a single dose of ARC-520 and daily NA (entecavir). To provide insights into HBV dynamics under ARC-520 treatment and its efficacy in blocking HBV DNA, HBsAg, and HBeAg production we developed a a multi-compartmental pharmacokinetic-pharamacodynamic model and calibrated it with measured HBV data. We showed that the time-dependent ARC-520 efficacies in blocking HBsAg and HBeAg are more than 96% effective around day 1, and slowly wane to 50% in 1-4 months. The combined ARC-520 and entecavir effect on HBV DNA is constant over time, with efficacy of more than 99.8%. HBV DNA loss is entecavir mediated and the strong but transient HBsAg and HBeAg decays are solely ARC-520 mediated. We added complexity to the model in order to reproduce current long-term therapy outcomes with NAs by considering the tradeoff between hepatocyte loss and hepatocyte division, and used it to makein-silicolong-term predictions for virus, HBsAg and HBeAg titer dynamics. These results may help assess ongoing RNAi drug development for hepatitis B virus infection.Author summaryWith about 300 million persons infected worldwide and 800,000 deaths annually, chronic infection with hepatitis B virus (HBV) is a major public health burden with high endemic areas around the world. Current treatment options focus on removing circulating HBV DNA but are suboptimal in removing hepatitis B s- and e-antigens. ARC-520, a RNA interference drug, had induced substantial hepatitis B s- and e- antigen reductions in animals and patients receiving therapy. We study the effect of ARC-520 on hepatitis B s- and e-antigen decline by developing mathematical models for the dynamics of intracellular and serum viral replication, and compare it to patient HBV DNA, hepatitis B s- and e-antigen data from a clinical trial with one ARC-520 injection and daily nucleoside analogue therapy. We examine biological parameters describing the different phases of HBV DNA, s-antigen and e-antigen decline and rebound after treatment initiation, and estimate treatment effectiveness. Such approach can inform the RNA interference drug therapy.
dN/dSdynamics quantify tumour immunogenicity and predict response to immunotherapy
Authors: Zapata Luis , Caravagna Giulio , Williams Marc J , Lakatos Eszter , AbdulJabbar Khalid , Werner Benjamin , Graham Trevor A , Sottoriva Andrea 
Published: July 2020

AbstractImmunoediting is a major force during cancer evolution that selects for clones with low immunogenicity (adaptation), or clones with mechanisms of immune evasion (escape). However, quantifying immunogenicity in the cancer genome and how the tumour-immune coevolutionary dynamics impact patient outcomes remain unexplored. Here we show that the ratio of nonsynonymous to synonymous mutations (dN/dS) in the immunopeptidome quantifies tumor immunogenicity and differentiates between adaptation and escape. We analysed 8,543 primary tumors from TCGA and validated immune dN/dS as a measure of selection associated with immune infiltration in immune-adapted tumours. In a cohort of 308 metastatic patients that received immunotherapy, pre-treatment lesions in non-responders showed increased immune selection (dN/dS<1), whereas responders did not and instead harboured a higher proportion of genetic escape mechanisms. Ultimately, these findings highlight the potential of evolutionary genomic measures to predict clinical response to immunotherapy.
Flagellar perturbations activate adhesion through two distinct pathways inCaulobacter crescentus
Authors: Hershey David M. , Fiebig Aretha , Crosson Sean 
Published: July 2020

AbstractBacteria carry out sophisticated developmental programs to colonize exogenous surfaces. The rotary flagellum, a dynamic machine that drives motility, is a key regulator of surface colonization. The specific signals recognized by flagella and the pathways by which those signals are transduced to coordinate adhesion remain subjects of debate. Mutations that disrupt flagellar assembly in the dimorphic bacteriumCaulobacter crescentusstimulate the production of a polysaccharide adhesin called the holdfast. Using a genome-wide phenotyping approach, we compared surface adhesion profiles in wild-type and flagellar mutant backgrounds ofC. crescentus. We identified a diverse set of flagellar mutations that enhance adhesion by inducing a hyper-holdfast phenotype and discovered a second set of mutations that suppress this phenotype. Epistasis analysis of theflagellar signaling suppressor(fss) mutations demonstrated that the flagellum stimulates holdfast production via two genetically distinct pathways. The developmental regulator PleD contributes to holdfast induction in mutants disrupted at both early and late stages of flagellar assembly. Mutants disrupted at late stages of flagellar assembly, which assemble an intact rotor complex, induce holdfast production through an additional process that requires the MotAB stator and its associated diguanylate cyclase, DgcB. We have assigned a subset of thefssgenes to either the stator- orpleD-dependent networks and characterized two previously unidentified motility genes that regulate holdfast production via the stator complex. We propose a model through which the flagellum integrates mechanical stimuli into theC. crescentusdevelopmental program to coordinate adhesion.ImportanceUnderstanding how bacteria colonize solid surfaces is of significant clinical, industrial and ecological importance. In this study, we identified genes that are required forCaulobacter crescentusto activate surface attachment in response to signals from a macromolecular machine called the flagellum. Genes involved in transmitting information from the flagellum can be grouped into separate pathways, those that control theC. crescentusmorphogenic program and those that are required for flagellar motility. Our results support a model in which a developmental and a mechanical signaling pathway operate in parallel downstream of the flagellum and converge to regulate adhesion. We conclude that the flagellum serves as a signaling hub by integrating internal and external cues to coordinate surface colonization and emphasize the role of signal integration in linking complex sets of environmental stimuli to individual behaviors.