bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative study of unsaturated transport of glycerol through aquaglyceroporin that has high affinity for glycerol
Authors: Rodriguez Roberto A. , Chan Ruth , Liang Huiyun , Chen Liao Y. 
Published: June 2020

Graphical AbstractABSTRACTThe structures of several aquaglyceroporins have been resolved to atomic resolution showing two or more glycerols bound inside a channel and confirming a glycerol-facilitator’s affinity for its substrate glycerol. However, the kinetics data of glycerol transport experiments all point to unsaturated transport that is characteristic of low substrate affinity in terms of the Michaelis-Menten kinetics. In this article, we present anin silico-in vitroresearch focused on AQP3, one of the human aquaglyceroporins that is natively expressed in the abundantly available erythrocytes. We conducted 2.1 μsin silicosimulations of AQP3 embedded in a model erythrocyte membrane with intracellular-extracellular asymmetries in leaflet lipid compositions and compartment salt ions. From the equilibrium molecular dynamics (MD), we elucidated the mechanism of glycerol transport at high substrate concentrations. From the steered MD simulations, we computed the Gibbs free-energy profile throughout the AQP3 channel. From the free-energy profile, we quantified the kinetics of glycerol transport that is unsaturated due to glycerol-glycerol interaction mediated by AQP3 resulting in the concerted movement of two glycerol molecules for the transport of one glycerol molecule across the cell membrane. We conductedin vitroexperiments on glycerol uptake into human erythrocytes for a wide range of substrate concentrations and various temperatures. The experimental data quantitatively validated our theoretical-computational conclusions on the unsaturated glycerol transport through AQP3 that has high affinity for glycerol.
A palette of fluorophores that are differentially accumulated by wild-type and mutant strains ofEscherichia coli: surrogate ligands for bacterial membrane transporters
Authors: Salcedo-Sora Jesus Enrique , Jindal Srijan , O’Hagan Steve , Kell Douglas B. 
Published: June 2020

AbstractOur previous work had demonstrated that two commonly used fluorescent dyes that were accumulated by wild-typeE. coliMG1655 were accumulated differentially in single-gene knockout strains, and also that they might be used as surrogates in flow cytometric transporter assays. We summarise the desirable properties of such stains, and here survey 143 candidate dyes. We triage them eventually (on the basis of signal, accumulation levels, and cost) to a palette of 39 commercially available and affordable fluorophores that are accumulated significantly by wild-type cells of the ‘Keio’ strain BW25113, as measured flow cytometrically. Cheminformatic analyses indicate both their similarities and their (much more considerable) structural differences. We describe the effects of pH and of the efflux pump inhibitor chlorpromazine on the accumulation. Even the ‘wild-type’ MG1655 and BW25113 strains can differ significantly in their ability to take up such dyes. We illustrate the highly differential uptake of our dyes into strains with particular lesions in, or overexpressed levels of, three particular transporters or transporter components (yhjV, yihN, andtolC). The relatively small collection of dyes described offers a rapid, inexpensive, convenient and valuable approach to the assessment of microbial physiology and transporter function.
Empirical and Computational Evaluation of Hemolysis in a Microfluidic Extracorporeal Membrane Oxygenator (ECMO) Prototype
Authors: Imtiaz Nayeem , Poskus Matthew , Stoddard William A. , Gaborski Thomas R. , Day Steven W. 
Published: June 2020

AbstractMicrofluidic devices promise to overcome the limitations of conventional hemodialysis and oxygenation technologies by incorporating novel membranes with ultrahigh permeability into portable devices with low blood volume. However, the characteristically small dimensions of these devices contribute to both non-physiologic shear that could damage blood components and laminar flow that inhibits transport. While many studies have applied empirical and computational models of hemolysis to medical devices, such as valves and blood pumps, little is known about blood damage in the microfluidic flow regime. In this study, four design variants of a microfluidic membrane-based oxygenator and two controls (positive and negative) are introduced and modeled using a Computational Fluid Dynamics (CFD) model to predict hemolysis. The simulations were performed in ANSYS Fluent for nine shear stress-based Power Law hemolysis model variants. Empirical testing of the devices in a recirculating loop revealed levels of hemolysis significantly lower (3 ppm hemolysis for pump, tube, and device combined) than the hemolysis ranges (>10 ppm) observed in conventional oxygenators. We found that most of the nine tested hemolysis models overpredict (5× to 10×) hemolysis compared to empirical experiments. However, two models demonstrated higher predictive accuracy for hemolysis values in devices characterized by low shear conditions, while another set of three models exhibited better performance for devices operating under higher shear conditions. Our study highlights the limitations of combining hemolysis models with computational fluid dynamics models for a priori in silico device-induced hemolysis. Nevertheless, with a judicious selection of hemolysis models based on the shear ranges of the test device, we propose that computational modeling can complement empirical testing in the development of novel micro-dialyzers or oxygenators, allowing for a more efficient iterative design process. Furthermore, the low device-induced hemolysis (< 2 ppm) measured in our study at physiologically relevant flow rates is promising for the future development of microfluidic dialyzers and oxygenators.
An Organoid for Woven Bone
Authors: Akiva Anat , Melke Johanna , Ansari Sana , Liv Nalan , van der Meijden Robin , van Erp Merijn , Zhao Feihu , Stout Merula , Nijhuis Wouter H. , de Heus Cilia , Muñiz Ortera Claudia , Fermie Job , Klumperman Judith , ito Keita , Sommerdijk Nico , Hofmann Sandra 
Published: June 2020

AbstractBone formation (osteogenesis) is a complex process in which cellular differentiation and the generation of a mineralized organic matrix are synchronized to produce a hybrid hierarchical architecture. To study the mechanisms of osteogenesis in health and disease, there is a great need for functional model systems that capture in parallel both cellular and matrix formation processes. Stem cell-based organoids are promising as functional, self-organizing 3Din vitromodels for studying the physiology and pathology of various tissues. However, for human bone, no such functional model system is yet available.This study reports thein vitrodifferentiation of human bone marrow stromal cells into a functional 3D self-organizing co-culture of osteoblasts and osteocytes, creating an organoid for early stage bone (woven bone) formation. It demonstrates the formation of an organoid where osteocytes are embedded within the collagen matrix that is produced by the osteoblasts and mineralized under biological control. Alikein vivoosteocytes the embedded osteocytes show network formation and communication via expression of sclerostin. The current system forms the most complete 3D livingin vitromodel system to investigate osteogenesis, both in physiological and pathological situations, as well as under influence of external triggers (mechanical stimulation, drug administration).
Devaluation-sensitive responding to preconditioned cues requires orbitofrontal cortex during initial cue-cue learning
Authors: Hart Evan E , Sharpe Melissa J , Gardner Matthew PH , Schoenbaum Geoffrey 
Published: June 2020

AbstractThe orbitofrontal cortex (OFC) is necessary for value inference in tests of model-based reasoning. This ability could be accounted for by either representation of value or by representation of broader associative structure. Our lab recently reported correlates of both value and of valueless associative structure in OFC using single-unit recording (Sadacca et al., 2018). This incidental stimulus-stimulus representation was surprising since OFC was thought to be involved only when items of biological significance were driving responses. However, we did not assess whether this activity was necessary for encoding the associative information that would contribute to value inference during probe testing. Here, we used optogenetic OFC inhibition during sensory preconditioning to test this. We found that OFC inhibition during preconditioning impaired value inference during the probe test, demonstrating that the correlates we previously observed are not simply downstream readouts of sensory processing and instead contribute to encoding valueless sensory associative information.
PKIS Deep Dive Yields a Chemical Starting Point for Dark Kinases and a Cell Active BRSK2 Inhibitor
Authors: Tamir Tigist Y. , Drewry David H. , Wells Carrow , Major M. Ben , Axtman Alison D. 
Published: June 2020

AbstractThe Published Kinase Inhibitor Set (PKIS) is a publicly-available chemogenomic library distributed to more than 300 laboratories by GlaxoSmithKline (GSK) between 2011–2015 and by SGC-UNC from 2015–2017. Screening this library of well-annotated, published kinase inhibitors has yielded a plethora of data in diverse therapeutic and scientific areas, funded applications, publications, and provided impactful pre-clinical results. Based on kinome-wide screening results, we report a thorough investigation of one PKIS compound, GW296115, as an inhibitor of several members of the Illuminating the Druggable Genome (IDG) list of understudied dark kinases. Specifically, GW296115 validates as a potent lead chemical tool that inhibits six IDG kinases with IC50values less than 100nM. Focused studies establish that GW296115 is cell active, and directly engages BRSK2. Further evaluation showed that GW296115 downregulates BRSK2-driven phosphorylation and downstream signaling.Summary StatementGW296115 inhibits understudied kinases, including BRSK2, with IC50values less than 100nM.
Improving oligo-conjugated antibody signal in multimodal single-cell analysis
Authors: Buus Terkild Brink , Herrera Alberto , Ivanova Ellie , Mimitou Eleni , Cheng Anthony , Herati Ramin Sedaghat , Papagiannakopoulos Thales , Smibert Peter , Ødum Niels , Koralov Sergei B. 
Published: June 2020

AbstractSimultaneous measurement of surface proteins and gene expression within single cells using oligo-conjugated antibodies offers high resolution snapshots of complex cell populations. Signal from oligo-conjugated antibodies is quantified by high-throughput sequencing and is highly scalable and sensitive. In this study, we investigated the response of oligo-conjugated antibodies towards four variables: Concentration, staining volume, cell number at staining, and tissue. We find that staining with recommended antibody concentrations cause unnecessarily high background and that concentrations can be drastically reduced without loss of biological information. Reducing volume only affects antibodies targeting abundant epitopes used at low concentrations and is counteracted by reducing cell numbers. Adjusting concentrations increases signal, lowers background and reduces costs. Background signal can account for a major fraction of the total sequencing and is primarily derived from antibodies used at high concentrations. Together, this study provides new insight into the titration response and background of oligo-conjugated antibodies and offers concrete guidelines on how such panels can be improved.Impact statementOligo-conjugated antibodies are a powerful tool but require thorough optimization to reduce background signal, increase sensitivity, and reduce sequencing costs.
Plasticity in parental effects confers rapid larval thermal tolerance inNematostella vectensis
Authors: Rivera Hanny E. , Chen Cheng-Yi , Gibson Matthew C. , Tarrant Ann M. 
Published: June 2020

AbstractParental effects can prepare offspring for different environments and facilitate survival across generations. We exposed parental populations of the estuarine anemone,Nematostella vectensis, from Massachusetts to elevated temperatures and quantified larval mortality across a temperature gradient. We find that parental exposure to elevated temperatures results in a consistent increase in larval thermal tolerance (mean ΔLT50: 0.3°C), and larvae from subsequent spawns return to baseline thermal thresholds when parents are returned to normal temperatures. Histological analyses of gametogenesis in females suggests these dynamic shifts in larval thermal tolerance may be facilitated by maternal effects in non-overlapping gametic cohorts. We also compared larvae from North Carolina (a genetically distinct population with higher baseline thermal tolerance) and Massachusetts parents, and found larvae from heat-exposed Massachusetts parents have thermal thresholds comparable to larvae from unexposed North Carolina parents. North Carolina parents also increased larval thermal tolerance under the same high-temperature regime, suggesting plasticity in parental effects is an inherent trait forN. vectensis. Overall, we find larval thermal tolerance inN. vectensisshows both a strong genetic basis and phenotypic plasticity. Further understanding the mechanisms behind these shifts can elucidate the fate of thermally sensitive ectotherms in a rapidly changing thermal environment.
A self-supervised domain-general learning framework for human ventral stream representation
Authors: Konkle Talia , Alvarez George A. 
Published: June 2020

ABSTRACTAnterior regions of the ventral visual stream encode substantial information about object categories. Are top-down category-level forces critical for arriving at this representation, or can this representation be formed purely through domain-general learning of natural image structure? Here we present a fully self-supervised model which learns to represent individual images, rather than categories, such that views of the same image are embedded nearby in a low-dimensional feature space, distinctly from other recently encountered views. We find (i) category information implicitly emerges in the local similarity structure of this feature space, and (ii) these models learn hierarchical features which capture the structure of brain responses across the human ventral visual stream, on par with category-supervised models. These results provide computational support for a domain-general framework guiding the formation of visual representation, where the proximate goal is not explicitly about category information, but is instead to learn unique, compressed descriptions of the visual world.
Spatial context of trait variation: morphology of spotted salamanders (Ambystoma maculatum) varies more within ponds than between ponds
Authors: Green Elizabeth T. , Dell Anthony I. , Crawford John A. , Biro Elizabeth G. , Daversa David R. 
Published: June 2020

AbstractThe influence of intraspecific trait variation on species interactions makes trait-based approaches critical to understanding eco-evolutionary processes. Because species occupy habitats that are patchily distributed in space, advancement in trait-based ecology hinges on understanding how trait variation is distributed within and between habitat patches. We sampled larval spotted salamanders (Ambystoma maculatum) across spatially discrete ponds to quantify within- and between-pond variation in mass, length, and their allometric relationship. Between-pond variation explained 7-35% of total observed variation in the length and shape of salamander larvae, depending on the body segment measured (i.e., head, body, or tail). Salamander tail morphology was more variable and exhibited more between-pond variation than head or body morphology. Salamander mass was highly variable and strongly correlated with total length. Allometric analysis revealed that the slopes of mass-length relationships were similar across ponds, but that intercepts differed across ponds. Preliminary evidence hinted that newly constructed ponds were a driver of the observed differences in mass-length relationships. Pond construction may therefore bolster trait diversity across the broader landscape, and in so doing instil more adaptive potential of salamander populations under current and future environmental change.
Citrulline supplementation improves spatial memory in a murine model for Alzheimer’s disease
Authors: Martínez-González Katia , Serrano-Cuevas Leonor , Almeida-Gutiérrez Eduardo , Flores-Chavez Salvador , Mejía-Aranguré Juan Manuel , Garcia-delaTorre Paola 
Published: June 2020

BackgroundAlzheimer’s disease (AD) correlates with the dysfunction of metabolic pathways that translates into neurological symptoms. An arginine deficiency, a precursor of nitric oxide (NO), has been reported for AD patients.ObjectiveWe aimed to evaluate the effect of citrulline oral supplementation on cognitive decline in an AD murine model.MethosThree-month citrulline or water supplementation was blindly given to male and female wild type and 3xTg-AD mice trained and tested in the Morris Water Maze (MWM). Cerebrospinal fluid and brain tissue were collected. Ultra Performance Liquid Chromatography was used for arginine determinations while the Griess method was used for NO.ResultsEight-month-old male 3xTg-AD mice supplemented with citrulline performed significantly better in the MWM task; arginine levels increased in cerebrospinal fluid although no changes were seen in brain tissue and only a tendency of increase of NO was observed.ConclusionsCitrulline oral administration is a viable treatment for memory improvement in the early stages of AD pointing to NO as a viable, efficient target for memory dysfunction in AD.
Metagenomic characterization of soil microbial communities in the Luquillo experimental forest (Puerto Rico) and implications for nitrogen cycling
Authors: Karthikeyan Smruthi , Orellana Luis H. , Johnston Eric R. , Hatt Janet K. , Löffler Frank E. , Ayala-del-Río Héctor L. , González Grizelle , Konstantinidis Konstantinos T 
Published: June 2020

ABSTRACTThe phylogenetic and functional diversity of microbial communities in tropical rainforests, and how these differ from temperate communities remain poorly described but are directly related to the increased fluxes of greenhouse gases such as nitrous oxide (N2O) from the tropics. Towards closing these knowledge gaps, we analyzed replicated shotgun metagenomes representing distinct life zones from four locations in the Luquillo Experimental Forest (LEF), Puerto Rico. These soils had a distinct microbial community composition and lower species diversity when compared to temperate grasslands or agricultural soils. Unlike temperate soils, LEF soils showed little stratification with depth in the first 0-30cm, with ~45% of community composition differences explained solely by location. The relative abundances and nucleotide sequences of N2O reductases (nosZ) were highly similar between tropical forest and temperate soils. However, respiratory NO reductase (norB) was 2-fold more abundant in the tropical soils, which might be relatable to their greater N2O emissions. Nitrogen fixation (nifH) also showed higher relative abundance in rainforest compared to temperate soils (20% vs. 0.1-0.3% of bacterial genomes in each soil type harbored the gene, respectively). Collectively, these results advance our understanding of spatial diversity and metabolic repertoire of tropical rainforest soil communities, and should facilitate future ecological modeling efforts.ImportanceTropical rainforests are the largest terrestrial sinks of atmospheric CO2and the largest natural source of N2O emissions, two critical greenhouse gases for the climate. The microbial communities of rainforest soils that directly or indirectly, through affecting plant growth, contribute to these fluxes remain poorly described by cultured-independent methods. To close this knowledge gap, the present study applied shotgun metagenomics to samples selected from 3 distinct life zones within the Puerto Rico rainforest. The results advance our understanding of microbial community diversity in rainforest soils and should facilitate future studies of natural or manipulated perturbations of these critical ecosystems.
Utility of Lung Ultrasound in COVID-19: A Systematic Scoping Review
Authors: Trauer Michael M , Matthies Ashley , Mani Nick , Mcdermott Cian , Jarman Robert 
Published: June 2020

ABSTRACTLung ultrasound (LUS) has an established evidence base and has proven useful in previous viral epidemics. An understanding of the utility of LUS in COVID-19 is crucial to determine its most suitable role based on local circumstances. A scoping review was thus undertaken to explore the utility of LUS in COVID-19 and guide future research.33 studies were identified which represent a rapidly expanding evidence base for LUS in COVID-19. The quality of the included studies was relatively low. However LUS appears to be a highly sensitive and fairly specific test for COVID-19 in all ages and in pregnancy and is almost certainly more sensitive than CXR. The precise diagnostic accuracy of LUS may be influenced by various factors including disease severity, pre-existing lung disease, scanning protocol, operator experience, disease prevalence and the reference standard.High quality research is needed in various fields including: diagnostic accuracy in undifferentiated patients; triage and prognostication; monitoring progression and guiding interventions; persistence of residual LUS findings; inter-observer agreement; and the role of contrast-enhanced LUS.
Complement and tissue factor-enriched neutrophil extracellular traps are key drivers in COVID-19 immunothrombosis
Authors: Skendros Panagiotis , Mitsios Alexandros , Chrysanthopoulou Akrivi , Mastellos Dimitrios C. , Metallidis Simeon , Rafailidis Petros , Ntinopoulou Maria , Sertaridou Eleni , Tsironidou Victoria , Tsigalou Christina , Tektonidou Maria , Konstantinidis Theocharis , Papagoras Charalampos , Mitroulis Ioannis , Germanidis Georgios , Lambris John D. , Ritis Konstantinos 
Published: June 2020

AbstractEmerging data indicate that complement and neutrophils are involved in the maladaptive host immune response that fuels hyper-inflammation and thrombotic microangiopathy increasing the mortality rate in coronavirus disease 2019 (COVID-19). Here, we investigated the interaction between complement and the platelet/neutrophil extracellular traps (NETs)/thrombin axis, using COVID-19 clinical samples, cell-based inhibition studies and NETs/human aortic endothelial cell (HAEC) co-cultures. Increased plasma levels of NETs, TF activity and sC5b-9 were detected in patients. Neutrophils yielded high tissue factor (TF) expression and released NETs carrying functionally active TF. Confirming our ex vivo findings, treatment of control neutrophils with COVID-19 platelet-rich plasma generated TF-bearing NETs that induced thrombotic activity of HAEC. Thrombin or NETosis inhibition or C5aR1 blockade attenuated platelet-mediated NET-driven thrombogenicity. Serum isolated from COVID-19 patients induces complement activation in vitro, which is consistent with high complement activity in clinical samples. Complement inhibition at the level of C3 with compstatin Cp40 disrupted TF expression in neutrophils. In conclusion, we provide a mechanistic basis that reveals the pivotal role of complement and NETs in COVID-19 immmunothrombosis. This study supports emerging strategies against SARS-CoV-2 infection that exploit complement therapeutics or NETosis inhibition.