bluuebunny/crossref_metadata_2025_split huggingface dataset:
ExBoX: a simple Boolean exclusion strategy to drive expression in neurons
Authors: Ubina Teresa , Vahedi-Hunter Tyler , Agnew-Svoboda Will , Wong Wenny , Gupta Akshay , Santhakumar Vijayalakshmi , Riccomagno Martin M. 
Published: July 2020

AbstractThe advent of modern single-cell biology has revealed the striking molecular diversity of cell populations once thought to be more homogeneous. This newly appreciated complexity has made intersectional genetic approaches essential to understanding and probing cellular heterogeneity at the functional level. Here we build on previous knowledge to develop a simple AAV-based approach to define specific subpopulations of cells by Boolean exclusion logic (AND NOT). This Expression by Boolean Exclusion (ExBoX) system encodes for a gene of interest which is turned On by a particular recombinase (Cre or FlpO) and turned Off by another. ExBoX allows for the specific transcription of a gene of interest in cells expressing only the activating recombinase, but not in cells expressing both. We show the ability of the ExBoX system to tightly regulate expression of fluorescent reportersin vitroandin vivo, and further demonstrate the adaptability of the system by achieving expression of a variety of virally-delivered coding sequences in the mouse brain. This simple strategy will expand the molecular toolkit available for cell- and time-specific gene expression in a variety of systems.Summary statementUbina et al. describe the generation of a novel AAV-based intersectional approach to define and target specific subpopulations of cells in time and space via Expression by Boolean Exclusion (ExBoX).
Global drivers of obligate mycorrhizal symbionts diversification
Authors: Perez-Lamarque Benoît , Öpik Maarja , Maliet Odile , Afonso Silva Ana C. , Selosse Marc-André , Martos Florent , Morlon Hélène 
Published: July 2020

AbstractAnalyzing diversification dynamics is key to understanding the past evolutionary history of clades that led to present-day biodiversity patterns. While such analyses are widespread in well-characterized groups of species, they are much more challenging in groups which diversity is mostly known through molecular techniques. Here, we use the largest global database on the small subunit (SSU) rRNA gene of Glomeromycotina, a subphylum of microscopic arbuscular mycorrhizal fungi that provide mineral nutrients to most land plants by forming one of the oldest terrestrial symbioses, to analyze the diversification dynamics of this clade in the past 500 million years (Myr). We perform a range of sensitivity analyses and simulations to control for potential biases linked to the nature of the data. We find that Glomeromycotina tend to have low speciation rates compared to other eukaryotes. After a peak of speciations between 200 and 100 Myr ago, they experienced an important decline in speciation rates toward the present. Such a decline could be at least partially related to a shrinking of their mycorrhizal niches and to their limited ability to colonize new niches. Our analyses identify patterns of diversification in a group of obligate symbionts of major ecological and evolutionary importance and illustrate that short molecular markers combined with intensive sensitivity analyses can be useful for studying diversification dynamics in microbial groups.
Parallel genetics of regulatory sequencesin vivo
Authors: Froehlich Jonathan , Uyar Bora , Herzog Margareta , Theil Kathrin , Glažar Petar , Akalin Altuna , Rajewsky Nikolaus 
Published: July 2020

AbstractUnderstanding how regulatory sequences control gene expression is fundamental to explain how phenotypes arise in health and disease. Traditional reporter assays inform about function of individual regulatory elements, typically in isolation. However, regulatory elements must ultimately be understood by perturbing them within their genomic environment and developmental- or tissue-specific contexts. This is technically challenging; therefore, few regulatory elements have been characterizedin vivo. Here, we used inducible Cas9 and multiplexed guide RNAs to create hundreds of mutations in enhancers/promoters and 3′ UTRs of 16 genes inC. elegans. To quantify the consequences of mutations on expression, we developed a targeted RNA sequencing strategy across hundreds of mutant animals. We were also able to systematically and quantitatively assign fitness cost to mutations. Finally, we identified and characterized sequence elements that strongly regulate phenotypic traits. Our approach enables highly parallelized, functional analysis of regulatory sequencesin vivo.
Effects of Kappa Opioid Receptor Agonists on Fentanyl vs. Food Choice in Male and Female Rats: Contingent vs. Non-Contingent Administration
Authors: Townsend E. Andrew 
Published: July 2020

AbstractRationaleStrategies are needed to decrease the abuse liability of mu opioid receptor (MOR) agonists. One strategy under consideration is to combine MOR agonists with kappa opioid receptor (KOR) agonists.ObjectivesThe effects of KOR-agonists (U50488, nalfurafine) on fentanyl-versus-food choice were compared under conditions where the KOR agonists were added to the self-administered fentanyl (contingent delivery) or administered as pretreatments (non-contingent delivery) in male and female rats. The effects of increasing and decreasing the magnitude of the alternative food reinforcer were also determined.MethodsRats were trained to respond under a concurrent schedule of fentanyl (0, 0.32-10 μg/kg/infusion) and food reinforcement. In Experiment 1, U50488 and nalfurafine were co-administered with fentanyl as fixed-proportion mixtures (contingent administration). In Experiment 2, U50488 (1-10 mg/kg) and nalfurafine (3.2-32 μg/kg) were administered as acute pretreatments (non-contingent administration). nor-BNI (32 mg/kg) was administered prior to contingent and non-contingent KOR-agonist treatment in Experiment 3. Experiment 4 evaluated the effects of increasing and decreasing the magnitude of the non-drug reinforcer.ResultsBoth U50488 and nalfurafine decreased fentanyl choice when administered contingently, demonstrating that KOR agonists punish opioid choice. Non-contingent U50488 and nalfurafine administration decreased rates of fentanyl and food self-administration without altering fentanyl choice. Both contingent and non-contingent U50488 and nalfurafine effects on fentanyl choice were attenuated by nor-BNI. Fentanyl choice was sensitive to increases and decreases in the magnitude of the non-drug reinforcer.ConclusionsThese results demonstrate that the effects of KOR agonists on fentanyl reinforcement are dependent upon the contingencies under which they are administered.
Biogeochemical and omic evidence for paradoxical methane production via multiple co-occurring mechanisms in aquatic ecosystems
Authors: Perez-Coronel Elisabet , Beman J. Michael 
Published: July 2020

AbstractAquatic ecosystems are globally significant sources of the greenhouse gas methane (CH4) to the atmosphere. However, CH4is produced ‘paradoxically’ in oxygenated water via poorly understood mechanisms, fundamentally limiting our understanding of overall CH4production. Here we resolve paradoxical CH4production mechanisms through CH4measurements,δ13CH4analyses, 16S rRNA sequencing, and metagenomics/metatranscriptomics applied to freshwater incubation experiments with multiple time points and treatments (addition of a methanogenesis inhibitor, dark, high-light). We captured significant paradoxical CH4production, as well as consistent metabolism of methylphosphonate by abundant bacteria—resembling observations from marine ecosystems. Metatranscriptomics andδ13CH4analyses applied to experimental treatments identified an additional CH4production mechanism associated with (bacterio)chlorophyll metabolism and photosynthesis by Cyanobacteria, and especially by Proteobacteria. Both mechanisms occured together within metagenome-assembled genomes, and appear widespread in freshwater. Our results indicate that multiple, co-occurring, and broadly-distributed bacterial groups and metabolic pathways produce CH4in aquatic ecosystems.
Discovery of a Novel, Selective and Short-Acting Skeletal Myosin II Inhibitor
Authors: Radnai Laszlo , Surman Matthew , Hafenbreidel Madalyn , Young Erica J. , Stremel Rebecca F. , Lin Li , Pasetto Paolo , Jin Xiaomin , Geedy Mackenzie , Partridge Joni-Rae , Patel Aagam , Conlon Michael , Sellers James R. , Cameron Michael D. , Rumbaugh Gavin , Griffin Patrick R. , Kamenecka Theodore M. , Miller Courtney A. 
Published: July 2020

AbstractMyosin IIs, actin-based motors that utilize the chemical energy of ATP to generate force, have potential as therapeutic targets. Their heavy chains differentiate the family into muscle (skeletal [SkMII], cardiac, smooth) and nonmuscle myosin IIs. Despite therapeutic potential for muscle disorders, no SkMII-specific inhibitor has been reported and characterized. Here we present the discovery, synthesis and characterization of “skeletostatins”, novel derivatives of the pan-myosin II inhibitor blebbistatin, with selectivity within the myosin IIs for SkMII. In addition, the skeletostatins bear improved potency, solubility and photostability, without cytotoxicity. Based on its optimalin vitroprofile, Skeletostatin 1’sin vivotolerability, efficacy and pharmacokinetics were determined. Skeletostatin 1 was well-tolerated in mice, impaired motor performance, and had an excellent muscle to plasma ratio. Skeletostatins are useful probes for basic research and a strong starting point for drug development.
Intradermal-delivered DNA vaccine provides anamnestic protection in a rhesus macaque SARS-CoV-2 challenge model
Authors: Patel Ami , Walters Jewell , Reuschel Emma L. , Schultheis Katherine , Parzych Elizabeth , Gary Ebony N. , Maricic Igor , Purwar Mansi , Eblimit Zeena , Walker Susanne N. , Guimet Diana , Bhojnagarwala Pratik , Doan Arthur , Xu Ziyang , Elwood Dustin , Reeder Sophia M. , Pessaint Laurent , Kim Kevin Y. , Cook Anthony , Chokkalingam Neethu , Finneyfrock Brad , Tello-Ruiz Edgar , Dodson Alan , Choi Jihae , Generotti Alison , Harrison John , Tursi Nicholas J. , Andrade Viviane M. , Dia Yaya , Zaidi Faraz I. , Andersen Hanne , Lewis Mark G. , Muthumani Kar , Kim J Joseph , Kulp Daniel W. , Humeau Laurent M. , Ramos Stephanie , Smith Trevor R.F. , Weiner David B. , Broderick Kate E. 
Published: July 2020

SummaryCoronavirus disease 2019 (COVID-19), caused by the SARS-CoV-2 virus, has had a dramatic global impact on public health, social, and economic infrastructures. Here, we assess immunogenicity and anamnestic protective efficacy in rhesus macaques of the intradermal (ID)-delivered SARS-CoV-2 spike DNA vaccine, INO-4800. INO-4800 is an ID-delivered DNA vaccine currently being evaluated in clinical trials. Vaccination with INO-4800 induced T cell responses and neutralizing antibody responses against both the D614 and G614 SARS-CoV-2 spike proteins. Several months after vaccination, animals were challenged with SARS-CoV-2 resulting in rapid recall of anti-SARS-CoV-2 spike protein T and B cell responses. These responses were associated with lower viral loads in the lung and with faster nasal clearance of virus. These studies support the immune impact of INO-4800 for inducing both humoral and cellular arms of the adaptive immune system which are likely important for providing durable protection against COVID-19 disease.
Cell-to-cell Mathematical Modeling of Arrhythmia Phenomena in the Heart
Authors: Garza Gabriel López , Nicolás Mata A. , Román Alonso G. , Godínez Fernández J. F. , Castro García M. A. 
Published: July 2020

AbstractWith an aperiodic, self-similar distribution of two-dimensional arrangement of atrial cells, it is possible to simulate such phenomena as Fibrillation, Fluttering, and a sequence of Fibrillation-Fluttering. The topology of a network of cells may facilitate the initiation and development of arrhythmias such as Fluttering and Fibrillation. Using a GPU parallel architecture, two basic cell topologies were considered in this simulation, an aperiodic, fractal distribution of connections among 462 cells, and a chessboard-like geometry of 60×60 and 600×600 cells. With a complex set of initial conditions, it is possible to produce tissue behavior that may be identified with arrhythmias. Finally, we found several sets of initial conditions that show how a mesh of cells may exhibit Fibrillation that evolves into Fluttering.
Infection of human lymphomononuclear cells by SARS-CoV-2
Authors: Pontelli Marjorie C , Castro Italo A , Martins Ronaldo B , Veras Flávio P , Serra Leonardo La , Nascimento Daniele C , Cardoso Ricardo S , Rosales Roberta , Lima Thais M , Souza Juliano P , Caetité Diego B , de Lima Mikhael H F , Kawahisa Juliana T , Giannini Marcela C , Bonjorno Letícia P , Lopes Maria I F , Batah Sabrina S , Siyuan Li , Assad Rodrigo L , Almeida Sergio C L , Oliveira Fabiola R , Benatti Maíra N , Pontes Lorena L F , Santana Rodrigo C , Vilar Fernando C , Martins Maria A , Cunha Thiago M , Calado Rodrigo T , Alves-Filho José C , Zamboni Dario S , Fabro Alexandre , Louzada-Junior Paulo , Oliveira Rene D R , Cunha Fernando Q , Arruda Eurico 
Published: July 2020

AbstractAlthough SARS-CoV-2 severe infection is associated with a hyperinflammatory state, lymphopenia is an immunological hallmark, and correlates with poor prognosis in COVID-19. However, it remains unknown if circulating human lymphocytes and monocytes are susceptible to SARS-CoV-2 infection. In this study, SARS-CoV-2 infection of human peripheral blood mononuclear cells (PBMCs) was investigated bothin vitroandin vivo. We found thatin vitroinfection of whole PBMCs from healthy donors was productive of virus progeny. Results revealed that monocytes, as well as B and T lymphocytes, are susceptible to SARS-CoV-2 active infection and viral replication was indicated by detection of double-stranded RNA. Moreover, flow cytometry and immunofluorescence analysis revealed that SARS-CoV-2 was frequently detected in monocytes and B lymphocytes from COVID-19 patients, and less frequently in CD4+T lymphocytes. The rates of SARS-CoV-2-infected monocytes in PBMCs from COVID-19 patients increased over time from symptom onset. Additionally, SARS-CoV-2-positive monocytes and B and CD4+T lymphocytes were detected by immunohistochemistry in post mortem lung tissue. SARS-CoV-2 infection of blood circulating leukocytes in COVID-19 patients may have important implications for disease pathogenesis, immune dysfunction, and virus spread within the host.
Corticosteroid Use in Severely Hypoxemic COVID-19 Patients: An Observational Cohort Analysis of Dosing Patterns and Outcomes in the Early Phase of the Pandemic
Authors: Rahman Omar , Trigonis Russell A. , Craft Mitchell K. , Kruer Rachel M. , Miller Emily M. , Terry Colin L. , Persaud Sarah A. , Kapoor Rajat 
Published: July 2020

ABSTRACTINTRODUCTIONHypoxemia in Severe Acute Respiratory Syndrome due to Novel Coronavirus of 2019 (SARS-CoV-2) is mediated by severe inflammation that may be mitigated by corticosteroids. We evaluated pattern and effects of corticosteroid use in these patients during an early surge of the pandemic.METHODSObservational study of 136 SARS-CoV-2 patients admitted to the Intensive care Unit between March 1 and April 27, 2020 at a tertiary care hospital in Indianapolis, USA.Statistical comparison between cohorts and dosing pattern analysis was done. Outcome measures included number of patients requiring intubation, duration of mechanical ventilation, length of ICU stay and inpatient mortality.RESULTSOf 136 patients, 72 (53%) received corticosteroids. Groups demographics: Age (60.5 vs. 65; p .083), sex (47% male vs. 39% female; p .338) and comorbidities were similar. Corticosteroid group had increased severity of illness: PaO2/FiO2 (113 vs. 130; p .014) and SOFA (8 vs. 5.5; p < .001). Overall mortality (21% vs. 30%; p .234) or proportion of patients intubated (78 vs. 64%; p .078) was similar. Mortality was similar among mechanically ventilated (27% vs. 15%; p .151) however there were no deaths among patients who were not mechanically ventilated and received corticosteroids (0% vs. 57%; p <.001). Early administration (within 48 hours) showed decrease in proportion of intubation (66% vs. 87 vs. 100%; p.045), ICU days (6 vs., 16 vs. 18; p <.001), and ventilator days (3 vs. 12 & 14; p <.001). 45% received methylprednisolone.CONCLUSIONCorticosteroids were used more frequently in SARS CoV-2 patients with higher severity of illness. Early administration of corticosteroids improved survival in non-mechanically ventilated patients; decreased ICU stay and may have prevented intubation.
Nest records, Nest Site selection ofGyps bengalensisWhite-rumped Vulture and the role of Feeding Station in Kangra, Himachal Pradesh
Authors: Sehgal Archi , Kumar Krishan , Rajan Rubina , Hore Upmanyu 
Published: July 2020

AbstractActive nests ofGyps bengalensisWhite-rumped Vulture depends on elevation and aspects for nest site selection, while feeding station plays a significant role for determining the position of the nesting sites.This study attempted to record nest count for the breeding period 2018, identify key variables for the nest site selection and understand the role of feeding station in the nest site selection. Nest counts were conducted during the breeding period, each nest was categorized into active and inactive nest based on assesment of different components. Simultaneously, different variables (tree height, tree species, elevation and aspect) were recorded for each nest. Aerial distance was used to determine the role of feeding station for selecting the nesting sites. From the 24 nesting sites, 352 active nests were recorded, and a significant Pearson’s correlation for elevation and aspect were drawn. We found, vulture prefer single tree species for nesting. We also found that, 71% (n = 17) nesting sites located within radial distance of 20 km of the feeding station. High congregration of active nests within short radial distance from feeding station, signify the positive impact of management of feeding station by the wildlife wing of Forest department since 2008, for the ex-situ conservation of critically endangeredGyps bengalensisWhite-rumped Vulture
MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes
Authors: Yao Guocai , Zhang Wenliang , Yang Minglei , Yang Huan , Wang Jianbo , Zhang Haiyue , Wei Lai , Xie Zhi , Li Weizhong 
Published: July 2020

AbstractMicrobes play important roles in human health and disease. The interaction between microbes and hosts is a reciprocal relationship, which remains largely under-explored. Current computational resources lack manually and consistently curated data to connect metagenomic data to pathogenic microbes, microbial core genes, and disease phenotypes. We developed the MicroPhenoDB database by manually curating and consistently integrating microbe-disease association data. MicroPhenoDB provides 5677 non-redundant associations between 1781 microbes and 542 human disease phenotypes across more than 22 human body sites. MicroPhenoDB also provides 696,934 relationships between 27,277 unique clade-specific core genes and 685 microbes. Disease phenotypes are classified and described using the Experimental Factor Ontology (EFO). A refined score model was developed to prioritize the associations based on evidential metrics. The sequence search option in MicroPhenoDB enables rapid identification of existing pathogenic microbes in samples without running the usual metagenomic data processing and assembly. MicroPhenoDB offers data browsing, searching and visualization through user-friendly web interfaces and web service application programming interfaces. MicroPhenoDB is the first database platform to detail the relationships between pathogenic microbes, core genes, and disease phenotypes. It will accelerate metagenomic data analysis and assist studies in decoding microbes related to human diseases. MicroPhenoDB is available throughhttp://www.liwzlab.cn/microphenodbandhttp://lilab2.sysu.edu.cn/microphenodb.
Automatic segmentation of dentate nuclei for microstructure assessment: example of application to temporal lobe epilepsy patients
Authors: Gaviraghi Marta , Savini Giovanni , Castellazzi Gloria , Palesi Fulvia , Rolandi Nicolò , Sacco Simone , Pichiecchio Anna , Mariani Valeria , Tartara Elena , Tassi Laura , Vitali Paolo , D’Angelo Egidio , Gandini Wheeler-Kingshott Claudia A.M. 
Published: July 2020

AbstractDentate nuclei (DNs) segmentation is helpful for assessing their potential involvement in neurological diseases. Once DNs have been segmented, it becomes possible to investigate whether DNs they are microstructurally affected, through analysis of quantitative MRI parameters, such as the ones derived from diffusion weighted imaging (DWI). This study, therefore, aimed to develop a fully automated segmentation method using the non-DWI (b0) images from a DWI dataset to obtain DN masks inherently registered with parameter maps.Three different automatic methods were applied to healthy subjects in order to segment the DNs: registration to SUIT (a spatially unbiased atlas template of the cerebellum and brainstem), OPAL (Optimized Patch Match for Label fusion) and CNN (Convolutional Neural Network). DNs manual segmentation was considered the gold standard. Results show that the segmentation obtained with SUIT has an average Dice Similarity Coefficient (DSC) of 0.4907±0.0793 between the automatic SUIT masks and the gold standard. A comparison with manual masks was also performed for OPAL (DSC = 0.7624 ± 0.1786) and CNN (DSC = 0.8658 ± 0.0255), showing a better performance when using CNN.OPAL and CNN were optimised on heathy subjects’ data with high spatial resolution from the Human Connectome Project. The three methods were further used to segment the DNs of a subset of subjects affected by Temporal Lobe Epilepsy (TLE). This subset was derived from a 3T MRI research study which included DWI data acquired with a coarser resolution. In TLE dataset, SUIT performed similarly to using the HCP dataset, with a DSC = 0.4145 ± 0.1023. Using TLE data, OPAL performed worse than using HCP data: after changing the probability threshold the DSC was 0.4522 ± 0.1178.CNN was able to extract the DNs using the TLE data without need for retraining and with a good DSC = 0.7368 ± 0.0799. Statistical comparison of quantitative parameters derived from DWI analysis, as well as volumes of each DN, revealed altered and lateralised changes in TLE patients compared to healthy controls.The proposed CNN is therefore a viable option for accurate extraction of DNs from b0 images of DWI data with different resolutions and acquired at different sites.
NK cells integrate signals over large areas when building immune synapses but require local stimuli for degranulation
Authors: Verron Quentin , Forslund Elin , Brandt Ludwig , Leino Mattias , Frisk Thomas W. , Olofsson Per E. , Önfelt Björn 
Published: July 2020

AbstractImmune synapses are large-scale, transient molecular assemblies that serve as platforms for antigen presentation to B and T cells, and target recognition by cytotoxic T cells and natural killer (NK) cells. The formation of an immune synapse is a tightly regulated, stepwise process where the cytoskeleton, cell-surface receptors and signaling proteins rearrange into supramolecular activation clusters (SMACs). Here we use a reductionist system of microcontact-printed artificial immune synapses (AIS) shaped as hallmark SMAC structures to show that the spatial distribution of activating ligands influences the formation, stability and outcome of NK cell synapses. Organizing ligands into donut-shaped AIS resulted in fewer long-lasting, symmetrical synapses compared to dot-shaped AIS. NK cells spreading evenly over either AIS exhibited similar arrangement of the lytic machinery, however degranulation was only possible in regions allowing local signaling. Our results demonstrate that the macroscopic organization of ligands in the synapse can affect its outcome, which could be exploited by target cells as an escape mechanism.