bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated Machine Learning Approach to Identify Metabolome Fingerprints of Pathological Stages Following Heart Failure Treatment
Authors: Choi Howard , Mirza Bilal , Liem David A. , Wang Ding , Deng Mario C. , Wang Wei , Ping Peipei 
Published: April 2020

IntroductionPathologic cardiac remodeling from a healthy to diseased state is characterized by an intricate and coordinated multitude of alterations among various biomolecules over time. Conversely, mechanical circulatory support devices (MCSD) are a promising strategy for unloading the heart and reversing this process. Understanding the molecular drivers of remodeling and reverse remodeling would inform new mechanistic insights and more nuanced diagnostics, prognostics, and therapeutics for hypertrophy and/or heart failure (HF). Plasma metabolomics holds great promise for the temporal profiling and characterization of healthy and diseased phenotypes, but large‐scale technological platforms with machine learning (ML) pipelines for clinical temporal metabolomics profiling are still lacking.MethodsIn this study, we established a Multiple Reaction Monitoring (MRM)‐based MS quantitative platform and a corresponding ML‐based computational workflow to unravel the metabolomics fingerprints of healthy humans, HF patients, and a mouse model. Accordingly, we quantified the plasma levels of 610 metabolites, and identified those exhibiting high correlation to phenotypic changes using feature selection algorithms following random forest‐based missing data imputation.ResultsIn summary, a total of 30 metabolites were significantly altered during the cardiac remodeling: 12 metabolites were continuously upregulated during ISO‐treatment, belonging to the biological categories of amino acids and sphingomyelin (SM). In parallel, 18 metabolites were downregulated, consisting of 10 free fatty acids (FFA), 6 ceramides, and 2 phosphatidylcholine (PC). Among these FFAs, we identified 3 saturated FFAs, 6 monounsaturated FFAs (with 1 double bond) and 5 polyunsaturated fatty acids (PUFA). Importantly, we have identified 4 driver metabolites that are significantly associated with changes in HW/BW ratio, all of which are FFAs: C14:0 (Myristic acid), cis‐C16:1w7 (Palmitoleic acid), cis‐C18:1w9 (Oleic acid), and cis‐C18:3w3 (α‐Linolenic acid, ALA).SummaryOur study highlights a novel ML workflow that, in conjunction with benchmark datasets, will facilitate future biomarker discovery.Support or Funding InformationNIH/NHLBI T32 Postdoctoral Fellowship, T32HL139450
Modulation of GPCR Function by Membrane Lipids and Water
Authors: Weerasinghe Nipuna , Fried Steven D.E. , Eitel Anna R. , Mann Helen F. , Cosgriff Emily L. , Struts Andrey V. , Perera Suchithranga M.D.C. , Brown Michael F. 
Published: April 2020

G‐protein‐coupled receptors (GPCRs) are integral membrane proteins that regulate a wide range of normal and disease‐related physiological processes. Our understanding of the role of soft matter such as membrane lipids and cellular water on activation and regulation of the GPCR function remains incomplete. In the standard biochemical model, GPCRs behave as primarily agonist dependent bimodal switches, with little influence of the surrounding medium. However, using the visual receptor rhodopsin as a model GPCR, we show that water drives rhodopsin to a partially disordered, solvent‐swollen conformational ensemble upon light absorption, rendering the standard model obsolete
[1],
[2]. We placed rhodopsin under varying degrees of osmotic stress using polyethylene glycol solutes and investigated the activation equilibrium response using UV‐Visible spectroscopy. Our results show a flood of ~ 80 water molecules into the rhodopsin interior during photoactivation, a result supported by atomistic molecular dynamics simulations
[3]. Furthermore, the osmolyte effects on rhodopsin activation are size dependent: large osmolytes back shift the equilibrium to inactive metarhodopsin‐I (MI), while small osmolytes forward‐shift the equilibrium to active metarhodopsin‐II (MII). We attribute these size effects to varying degrees of osmolyte penetration into the rhodopsin core. Large polymers behave similarly to ideal osmolytes and dehydrate rhodopsin, while smaller polymers wriggle into the rhodopsin interior and stabilize the open MII conformation of rhodopsin. Besides osmotic pressure, the application of hydrostatic pressure also back shifts the metarhodopsin equilibrium but for fundamentally different reasons. Integrating the two force‐based methods together with neutron scattering experiments indicates that the active state of rhodopsin is more hydrated yet simultaneously more structurally collapsed
[4]. At the same time, the active GPCR undergoes dynamic volume fluctuations and solvent coupling, which give rise to greater thermal volume. Our results necessitate a new understanding of GPCR activation in which the surrounding soft matter is paramount in governing conformational energy landscapes.Support or Funding InformationNSF (MCB 11817862 and CHE 1904125) and US NIH (EY012049 and EY02604)
Mitochondrial ROS production in lung microvascular endothelial cells sensitizes the transient receptor potential vanilloid‐4 (TRPV4) channel to physical and chemical stimuli.
Authors: Philip Nicolas , Servinsky Laura , Jiang Haiyang , Huetsch John , Damarla Mahendra , Shimoda Larissa , Suresh Karthik 
Published: April 2020

RationaleIncreased proliferation of lung microvascular endothelial cells (MVECs) is a known feature of pulmonary arterial hypertension (PAH). We have previously shown that increased mitochondrial reactive oxygen species (mtROS) and basal intracellular calcium ([Ca2+]i) are associated with increased proliferation and migration in MVECs isolated from animals undergoing experimental PAH (Sugen Hypoxia model; SuHx‐MVECs) compared to MVECs isolated from normoxic controls (N‐MVECs). In these studies, we observed that quenching mtROS in SuHx‐MVECs attenuated TRPV4 activity, basal [Ca2+]i, migration and proliferation in SuHx‐MVECs. However, whether induction of mtROS production alone, in N‐MVECs, was sufficient to activate TRPV4 was unclear.MethodsTo measure [Ca2+]i in MVECs, cells were incubated on glass coverslips with the calcium‐sensing dye FURA‐2 AM and transferred to a temperature‐controlled flow chamber set at baseline to 37 degrees and flow rate of 0.1 dynes/cm2. Cells were perfused with freshly‐prepared Krebs buffer. TRPV4 inhibition was achieved with HC‐067047 (HC) treatment. mtROS production was induced using treatment with antimycin A (AA) or Mito‐Paraquat (MPQ). TRPV4 was activated using either the chemical agonist GSK1016790A (GSK) or by increasing chamber and perfusate temperature to 40 degrees (since heat is a known activator of this channel).ResultsTreatment of N‐MVECs with antimycin A (AA) increased basal [Ca2+]i. GSK‐induced Ca2+ influx was also significantly higher in AA‐treated N‐MVECs. Both increased basal Ca2+ and increased GSK‐induced Ca2+ influx were attenuated with HC pre‐treatment (i.e. TRPV4 inhibition). Using temperature as a TRPV4 stimulus, we observed greater heat‐induced Ca2+ in AA‐treated N‐MVECs. Since AA may have off‐target effects, we repeated our GSK‐induced Ca2+ experiments following treatment with MitoPQ, a redox cycler also known to increase mtROS. Similarly to AA, Mito‐PQ treatment increased basal [Ca2+]i and GSK‐induced calcium influx.ConclusionThese data suggest that, in N‐MVECs, mitochondrial ROS elevate basal intracellular calcium levels and both activate TRPV4 and sensitize the channel to subsequent activation by either chemical or physical stimuli.Support or Funding InformationThis work was supported by by the National Heart, Lung and Blood Institute Grants F32HL124930 and K08HL132055 (KS), R01HL073859, R25HL084762 and R01HL126514 (LAS), F32HL124727, and K08HL133475 (JH) and T32HL007534 (KS and JH).
Understanding the Role of the G Protein‐Coupled Estrogen Receptor (GPR30/GPER‐1) in Neurodevelopment
Authors: DeLeon Chelsea , Pemberton Kyle , Xu Fenglian , Arnatt Christopher 
Published: April 2020

Several studies have commented on the effects of 17β‐estradiol(E2) on neurodevelopment. These studies have primarily focused on the classical nuclear estrogen receptors, ERα and ERβ. It has been established that E2 has the ability to activate rapid, non‐genomic signaling through the G Protein‐Coupled Estrogen Receptor (GPR30/GPER‐1). Few studies have examined the neurodevelopmental effects of selectively targeting GPER‐1. Previously, our group synthesized novel, selective GPER‐1 agonists. During biological evaluation, the pharmacology associated with the novel agonists appeared to differ from known GPER‐1 agonist, G‐1. Treatment with the beta‐gamma subunit inhibitor, galein, revealed a significant attenuation in signal for the synthesized agonists but not for G‐1 at concentrations above 1μM. Additionally, the efficacy of eliciting neurite outgrowth in rat hippocampal E18 neurons was greater for the synthesized agonists than G‐1. To further understand the observed differences in signaling between the synthesized compounds and G‐1, rat hippocampal E18 neurons and neural progenitor cells (NPCs) originating from healthy humans were studied. RNA sequencing was utilized to reveal the presence of changes in gene expression in response to GPER‐1 compounds in rat hippocampal E18 neurons, excitatory NPCs, and inhibitory NPCs. These results provide information regarding opportunities associated with targeting GPER‐1 in neurodevelopment as well as information related to the cell‐signaling pathway that may be leveraged in the design of new therapeutic lead compounds.Support or Funding InformationSaint Louis University
Optogenetic control of the Sphingosine‐1‐phosphate receptor 1 enables light‐mediated regulation of endothelial permeability and angiogenesis
Authors: Kang Hojin , Matsche Jacob , Karginov Andrei 
Published: April 2020

Sphingosine‐1‐phosphate receptor 1 (S1PR1) is critical regulator of endothelial cell (EC) migration, cytoskeletal structure, capillary‐network formation, sprouting angiogenesis, and vascular maturation. Here we developed a strategy for controlling endothelial barrier function and sprouting angiogenesis using an engineered photo activatable (PA)‐S1PR1 receptor. Regulation of signaling and cell function by PA‐S1PR1 was demonstrated in human pulmonary arterial endothelial cells (HPAECs). Following illumination with blue light, PA‐S1PR1 induced activation of known downstream signaling pathways (AKT, Erk1/2 and FAK). The kinetic and the extent of activation correlated with what was observed in HPAECs treated with 1μM S1P. Furthermore, activation of PA‐S1PR1 lead to enhancement of endothelial barrier and stimulation of sprouting angiogenesis in vitro. Thus, these findings suggest that engineered PA‐S1PR1 can be used to mimic its function in living cells and dissect S1P signaling with precise temporal and spatial resolution.Support or Funding InformationThis work was supported in part by American Heart Association Scientist Development Grant 17SDG33700146 to H. K., and R21CA159179 and CBC Pilot Grant to A.V.K.
Primary Endothelial Cells from Seals Mount a Rapid and Sustained Response to Acute Hypoxia
Authors: Allen Kaitlin , Vázquez-Medina José Pablo 
Published: April 2020

Marine mammals tolerate repeated bouts of hypoxemia while diving, with up to 90% of blood oxygen stores depleted in some species. Accordingly, tissues such as the endothelium experience acute fluctuations in oxygen availability. In terrestrial mammals, hypoxia/reoxygenation events of similar magnitude contribute to inflammatory signaling, reactive oxygen species (ROS) generation, and endothelial dysfunction in pathological settings. Marine mammals, however, appear well protected against oxidant stress and inflammation despite repeated exposure to hypoxia/reoxygenation, though the specific cellular mechanisms driving this protection remain unknown. We isolated endothelial cells (ECs) from placental arteries from northern elephant seals (Mirounga angustirostris), a pinniped species noted for its extreme diving capacity. Seal primary EC cultures proliferate, express the canonical EC markers PECAM‐1 and VE‐cadherin, and take up acetylated LDL. Seal ECs are metabolically active in adherent culture and respond to mitochondrial inhibition and uncoupling and pharmacological NADPH oxidase activation, demonstrating utility as a live, functionally relevant system in which to study the biochemical drivers of hypoxia/reoxygenation tolerance in diving seals.
Seal ECs exposed to 1% O
2 for up to 6 hours upregulated HIF‐1α protein, with maximal expression occurring within 15 minutes (68‐fold increase over normoxic levels). Human ECs matched this magnitude (73‐fold increase) though not until 1 hour, after which expression of HIF‐1α rapidly and progressively declined (22‐fold above normoxic levels at 6 hours). In contrast, seal ECs maintained elevated HIF‐1α protein expression (52‐fold) at 6 hours. Pharmacological stimulation with menadione, an inducer of redox cycling, significantly increased oxidant generation in human (5‐fold, p=0.027) but not seal ECs (2.5‐fold, p=0.18), as did
acute exposure to hypoxia/reoxygenation. Together, our data show that seal ECs mount a rapid, sustained response to hypoxia
/reoxygenation events, and that these cells are a functional system in which to study the mechanisms underlying innate hypoxia and oxidative stress tolerance in diving mammals.Support or Funding InformationNational Science Foundation GRFP
Deletion of Mouse Sf3b4 in Neural Crest Cells Causes Craniofacial Abnormalities
Authors: Kumar Shruti , Alam Sabrina Shameen , Beauchamp Marie-Claude , Majewski Jacek , Jerome-Majewska Loydie 
Published: April 2020

The SF3B4 gene encodes a core component of the U2‐major spliceosome complex important during splicing of pre‐mRNA to mRNA. Recently, patients with two craniofacial disorders: Nager syndrome and Rodriguez syndrome were identified to carry rare mutations in this gene. The autosomal dominant nature of these syndromes indicates that this is due to haploinsufficiency for SF3B4. Both disorders affect the face as well as the limb including both hands and feet. Nager syndrome patients survive and exhibit smaller jaw bones, smaller cheek bones, cleft palate, hearing problems as well as downward slanted eyelids. However, Rodriguez syndrome is much more severe, and patients often die before or soon after birth. We hypothesized that craniofacial abnormalities associated with reduced SF3B4 levels is due to tissue‐specific expression and requirement of this gene in neural crest cells. Using in situ hybridization, we showed that in mouse embryos, Sf3b4 was expressed ubiquitously from embryonic day (E)9.5 – E12.5. From E10.5 – E12.5, enriched expression of this gene was found in the maxillomandibular region, limb and tail bud. To generate a conditional mutant mouse line for Sf3b4, we used CRISPR/Cas9 to insert LoxP sequences in intron 1 and 3 of this gene. To test our hypothesis, we mated Sf3b4 conditional mutant mice to Wnt1‐Cre2 transgenic mice to delete exons 2 and 3 specifically in neural crest cells. Heterozygous mutant embryos from these matings were normal. From E9.0 onwards, all homozygous mutant embryos had hypoplasia of the midbrain and pharyngeal arches. Homozygous mutant embryos died by E14.5. To examine neural crest cells and their derivatives in the head and craniofacial region, we used the Rosa26R lacZ reporter line. LacZ staining of mutant embryos showed a reduced number of neural crest cells in pharyngeal arches. Thus, our data suggests that craniofacial malformations due to mutations in SF3B4 are the result of reduced neural crest cells.Support or Funding InformationCanadian Institutes of Health Research (CIHR)
Re‐Defining the Specificity of Phosphoinositide‐Binding by Human PH Domain‐Containing Proteins
Authors: Singh Nilmani , Reyes-Ordonez Adriana , Compagnone Michael , Moreno Jesus , Yao Lucy , Chen Jie 
Published: April 2020

The human genome encodes over 250 PH domain containing proteins, all of which share an invariable structure. PH domains are presumed to mediate protein‐lipid interactions specifically to phosphoinositides (PIPs), and yet only a small fraction of PH domain‐containing proteins have been reported to bind PIPs with specificity. Most reported protein‐lipid interaction studies employ methods that either require purified proteins or utilize non‐physiological presentation of lipids, and rely on isolated PH domains rather than full‐length proteins. To circumvent these problems, we recently developed a total internal reflection fluorescence (TIRF) microscopy‐based single‐molecule pulldown (SiMPull) assay, called lipid‐SiMPull, to study protein‐lipid interactions using GFP‐tagged full‐length proteins in whole cell lysates and lipid vesicles. Here, we applied the lipid‐SiMPull assay to probe the lipid binding properties of 67 human PH domain proteins. We found that >50% of those full‐length proteins bound at least one of the phospholipids, with 44% of them displaying various levels of selectivity towards PIPs. About two‐thirds of those proteins had not been previously reported to bind PIPs with any specificity. Additionally, we examined lipid binding by 17 isolated PH domains and found that most of them did not behave like their full‐length counterparts. One of the proteins, XPLN (ARHGEF3), was found to bind specifically PI‐4,5‐P2 in lipid‐SiMPull. Further characterization revealed that PI‐4,5‐P2 binding was necessary for XPLN membrane association, activation of RhoA, and stimulation of stress fiber formation. Taken together, our findings suggest that specific PIP recognition by PH domain proteins is more prevalent than previously believed, and that full‐length proteins display lipid binding properties distinct from the isolated PH domains.Support or Funding InformationNIH NIGMS R01GM089771
Coordinated development of the mitochondrial reticulum in skeletal muscle
Authors: Kim Yuho , Lindberg Eric , Bleck Christopher K.E. , Glancy Brian 
Published: April 2020

Skeletal muscle cells form a mitochondrial network, or reticulum, in a fiber‐type specific manner with grid‐like and fiber‐perpendicular mitochondrial network configurations found in oxidative and glycolytic fibers, respectively. However, it is not well characterized how the networks form during postnatal muscle development. Using focused ion beam scanning electron microscopy (FIB‐SEM) and machine learning based 3D image segmentation and analysis, we have sought to understand the 3D mitochondrial development in oxidative (soleus) and glycolytic (gastrocnemius) muscles of mice at different postnatal days 1 (P1), 14 (P14), and 42 (P42). Both oxidative and glycolytic fibers show tortuous, parallel mitochondrial formations at P1. At P14, oxidative fibers have more elongated, fiber‐parallel mitochondria, while glycolytic fibers have a more grid‐like mitochondrial reticulum. To better understand the intra‐ and inter‐organelle interactions of the mitochondrial reticulum during development, we additionally assessed intermitochondrial junctions (IMJ) and mitochondrial interactions with lipid droplets (LD). During early maturation (P1‐P14), many IMJ in oxidative fibers are arranged in both diagonal (~40%) and parallel (~40%) directions, yet matured oxidative fibers have almost half (~50%) of IMJ in the perpendicular direction. In contrast, after having ~50% of IMJ along the parallel axis at P1, glycolytic fibers gradually change IMJ orientations more into both perpendicular and diagonal axis and IMJ are located in all directions at P42. Although mitochondria in glycolytic fibers maintain similar sizes of the IMJ contact sites between P1 and P14 and have smaller areas at P42, oxidative fibers have ~2‐fold larger IMJ areas at P14 as compared to early (P1) and matured (P42) fibers. Meanwhile, both oxidative and glycolytic fibers at P1 have many, big LD that sharply decrease in size during the course of postnatal development. In the matured muscles, oxidative fibers have few, tiny LD and glycolytic fibers have no LD. Both fibers maintain similar LD contract areas per mitochondrion across P1‐P42. Notably, mitochondria directly in contact with LD have volumes ~2–3‐fold larger than non‐LD‐contacted mitochondria at all time points. In addition, the LD‐contacted mitochondria have ~2‐fold bigger IMJ areas as compared to non‐contacted one, with the largest differences observed at P14. In conclusion, development of the muscle mitochondrial reticulum occurs in coordination with altered interactions among mitochondria and with LD. However, future studies are warranted to study possible interactive roles of calcium handling structures such as sarcoplasmic reticulum and t‐tubules.Support or Funding InformationThis study is supported by intramural programs within the National Heart, Lung, and Blood Institute and the National Institute of Arthritis and Musculoskeletal and Skin Diseases (grant 1ZIAHL006221‐02).
Medical Faculty’s Perception of the Use of Altmetrics
Authors: Brown Kirsten , Byram Jessica , Lazarus Michelle , Wilson Adam 
Published: April 2020

In recent years, Academia is increasingly engaging with online scholarly tools (e.g., Mendeley) and social media platforms (e.g., Twitter), providing potentially impactful alternative pathways for research dissemination and engagement. These platforms flatten access to knowledge with online platforms fostering easier access by both peers and the broader community alike. Termed altmetrics, or “alternative metrics”, these platforms carry with them novel methods for tracking scholarly impact and reach whose potential is not yet fully understood. These non‐traditional Altmetrics capture quantitative data indicative of social media shares, clicks and plays. The use of altmetrics as indicators of scholarly/societal impact is garnering increased attention over the last decade. However, the degree to which faculty demographics, career stage, professional roles, and areas of research focus influence perceptions and use of altmetrics within academia is yet to be characterized. This study examined the perceptions of medical faculty regarding their use of altmetrics, exploring how factors, such as career focus and social media use, influence these opinions.Medical faculty responded to a Qualtrics survey distributed through social media platforms and organizational listservs. The survey collected demographic information, and data on social media usage, the likelihood of disseminating altmetric outcomes in academic documents (e.g., CV), and perceptions on the value/utility of altmetrics.Of the 48 respondents, 23 were male and most were from North America or Oceania (81%). All age groups and career levels were represented. While only 17% indicated their institution endorses altmetrics, slightly more than half (54%) indicated altmetrics were ‘moderately’ to ‘extremely valuable’. A Pearson’s correlation revealed that frequent social media usage was strongly and positively correlated with favorable perceptions of altmetrics (r=0.512, p<0.001). Neither age range, career level, nor years of experience explained one’s level of social media usage (p>0.402) or one’s favorable perceptions of altmetrics (p>0.200). Irrespective of respondents’ primary professional roles, areas of research focus, or whether their institution endorsed altmetrics, no significant differences (p>0.05) in social media usage or altmetric perceptions scores were detected.This study suggests that more favorable perceptions of altmetrics are associated with higher social media use. Even though institutions may not endorse altmetrics for promotion and tenure purposes, many medical faculty still regard them to be valuable. These results also indicate that favorable perceptions of altmetrics traverse career level, age ranges, and years of experiences, supporting a more universal appreciation for these non‐traditional evaluations of impact. Future work will explore, through qualitative inductive interviews, motivations for those engaging (or not) in social media platforms and altmetrics.