bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep learning-based chest X-ray age serves as a novel biomarker for cardiovascular aging
Authors: Ieki Hirotaka , Ito Kaoru , Saji Mike , Kawakami Rei , Nagatomo Yuji , Koyama Satoshi , Matsunaga Hiroshi , Miyazawa Kazuo , Ozaki Kouichi , Onouchi Yoshihiro , Katsushika Susumu , Matsuoka Ryo , Shinohara Hiroki , Yamaguchi Toshihiro , Kodera Satoshi , Higashikuni Yasutomi , Fujiu Katsuhito , Akazawa Hiroshi , Isobe Mitsuaki , Yoshikawa Tsutomu , Komuro Issei 
Published: March 2021

AbstractChest X-ray (CXR) is one of the most commonly performed medical imaging tests. Although aging, sex and disease status have been known to cause changes in CXR findings, the extent of these effects has not been fully characterized. Here, we present a deep neural network (DNN) model trained using more than 100,000 CXRs to estimate the patient’s age and sex solely from CXRs. Our DNN exhibited high performance in terms of estimating age and sex, with Pearson’s correlation coefficient between the actual and estimated age of above 0.9 and an area under the ROC curve of 0.98 for sex estimation. The difference between the actual and estimated age is large in CXRs with abnormal findings, suggesting that the estimated age (“CXR age”) can be a biomarker for disease status. Furthermore, by applying our DNN to CXRs of consecutive 1,562 hospitalized heart failure patients, we demonstrated that an elevated CXR age is not only associated with aging-related diseases, such as hypertension and atrial fibrillation, but also a worse outcome of heart failure. Given these results, our new concept “CXR age” serves as a novel biomarker for cardiovascular aging and can help clinicians to predict, prevent, and manage cardiovascular diseases.
Germ plasm anchors at tight junctions in the early zebrafish embryo
Authors: Rostam Nadia , Goloborodko Alexander , Riemer Stephan , Hertel Andres , Klein Sabine , Riedel Dietmar , Vorbrüggen Gerd , Dosch Roland 
Published: March 2021

AbstractThe zebrafish germline is specified during early embryogenesis by inherited maternal RNAs and proteins collectively called germ plasm. Only the cells containing germ plasm will become part of the germline, whereas other cells will commit to somatic cell fates. Therefore, proper localization of germ plasm is key for germ cell specification and its removal is critical for the development of soma. The molecular mechanism underlying this process in vertebrates is largely unknown. Here we show that germ plasm localization in zebrafish is similar toXenopusand amniotes but distinct fromDrosophila. We identified non muscle myosin II (NMII) and tight junction (TJ) components as interaction candidates of Bucky ball (Buc), which is the germ plasm organizer in zebrafish. Remarkably, we also found that TJ protein ZO1 colocalizes with germ plasm and electron microscopy (EM) of zebrafish embryos uncovered TJ like structures at early cleavage furrows. In addition, injection of the TJ-receptor Claudin-d (Cldn-d) produced extra germ plasm aggregates. Our findings discover for the first time a role of TJs in germ plasm localization.
Honeybee dance-followers respond similarly to dances regardless of their spatial information content
Authors: Hasenjager Matthew J. , Hoppitt William , Leadbeater Ellouise 
Published: March 2021

AbstractHoneybees famously use waggle dances to communicate foraging locations to nestmates in the hive, thereby recruiting them to those sites. The decision to dance is governed by rules that, when operating collectively, are assumed to direct foragers to the most profitable locations with little input from potential recruits, who are presumed to respond similarly to any dance regardless of its information content. Yet variation in receiver responses can qualitatively alter collective outcomes. Here, we use network-based diffusion analysis to compare the collective influence of dance information during recruitment to feeders at different distances. We further assess how any such effects might be achieved at the individual level by dance-followers either persisting with known sites when novel targets are distant and/or seeking more accurate spatial information to guide long-distance searches. Contrary to predictions, we found no evidence that dance-followers’ responses depended on target distance. While dance information was always key to feeder discovery, its importance did not vary with feeder distance, and bees were in fact quicker to abandon previously rewarding sites for distant alternatives. These findings provide empirical support for the longstanding assumption that self-organized foraging by honeybee colonies relies heavily on signal performance rules with limited input from recipients.
A cationic lipid site at the outward transmembrane face of a pentameric ligand-gated ion channel
Authors: Sridhar Akshay , Lummis Sarah C.R. , Pasini Diletta , Mehregan Aujan , Brams Marijke , Kambara Kumiko , Bertrand Daniel , Lindahl Erik , Howard Rebecca J. , Ulens Chris 
Published: March 2021

AbstractPentameric ligand-gated ion channels (pLGICs) are crucial mediators of electrochemical signal transduction from bacteria to humans. Lipids play an important role in regulating pLGIC function, yet the structural basis for specific pLGIC-lipid interactions remains poorly understood. The bacterial channel ELIC recapitulates several properties of eukaryotic pLGICs, including activation by the neurotransmitter GABA and sensitivity to lipids, offering a simplified model system for structure-function studies. In this study, functional effects of non-canonical amino acid substitution of W206 at the top of the M1-helix, combined with detergent interactions observed in recent X-ray structures, are consistent with this region being the location of a lipid binding site on the outward face of the ELIC transmembrane domain. Coarse-grained and atomistic molecular dynamics simulations revealed preferential binding of lipids containing a positive charge, particularly involving interactions with residue W206 consistent with cation-π binding. Polar contacts from the principal subunit, particularly M3 residue Q264, further supported lipid binding via headgroup ester linkages. Aromatic residues were identified at analogous sites in a handful of eukaryotic family members, including the human GABAAreceptor subunit ɛ, suggesting conservation of relevant interactions in other evolutionary branches. Further mutagenesis experiments indicated that mutations at this site in ɛ-containing GABAAreceptors can change the apparent affinity of the agonist response to GABA, consistent with a potential role of this site in channel gating. In conclusion, this work is a detailed case study in type-specific lipid interactions at an evolutionarily distinctive pLGIC site, with implications for lipid modulation and lipophilic drug design.
The ratio of cytotoxic lymphocytes to M2-like macrophages is prognostic in immunogenic tumors
Authors: Mezheyeuski Artur , Backman Max , Mattsson Johanna , Martín-Bernabé Alfonso , Larsson Chatarina , Hrynchyk Ina , Hammarström Klara , Ström Simon , Ekström Joakim , Mauchanski Siarhei , Khelashvili Salome , Agnarsdóttir Margrét , Edqvist Per-Henrik , Huvila Jutta , Segersten Ulrika , Malmström Per-Uno , Botling Johan , Nodin Björn , Hedner Charlotta , Borg David , Brändstedt Jenny , Sartor Hanna , Leandersson Karin , Glimelius Bengt , Portyanko Anna , Ponten Fredrik , Jirström Karin , Micke Patrick , Sjöblom Tobias 
Published: March 2021

AbstractImmune cells in the microenvironment shape tumor development and progression. The prognostic value of T-cell-based immune scores exceeds those of clinical parameters in colon cancer, but reflects only a part of the anti-tumor immune response. Here, we assessed 15 distinct immune cell classes and identified a simple prognostic signature based on pro- and anti-tumoral immune cells in the tumor microenvironment. The ratio of cytotoxic lymphocytes to tumor supportive macrophages predicted survival better than the state-of-art immune score in colon cancer and had the highest relative contribution to survival prediction when compared to established clinical parameters. This signature was prognostic also in other cancers with high mutation burden, such as those of the lung, bladder, esophagus, and melanomas, supporting broad clinical applicability.One Sentence SummaryThe CD8/M2 ratio in tumor tissue defines prognosis in immunogenic cancers
Long-Term Metabolomics Reference Material
Authors: Gouveia Goncalo J. , Shaver Amanda O. , Garcia Brianna M. , Morse Alison M. , Andersen Erik C. , Edison Arthur S. , McIntyre Lauren M. 
Published: March 2021

AbstractThe use of quality control samples in metabolomics ensures data quality, reproducibility and comparability between studies, analytical platforms and laboratories. Long-term, stable and sustainable reference materials (RMs) are a critical component of the QA/QC system, however, the limited selection of currently available matrix matched RMs reduce their applicability for widespread use. To produce a RM in any context, for any matrix that is robust to changes over the course of time we developed IBAT (IterativeBatchAveraging meThod). To illustrate this method, we generated 11 independently grownE. colibatches and made a RM over the course of 10 IBAT iterations. We measured the variance of these materials by NMR and showed that IBAT produces a stable and sustainable RM over time. ThisE. coliRM was then used as food source to produce aC. elegansRM for a metabolomics experiment. The metabolite extraction of this material alongside 41 independently grown individualC. eleganssamples of the same genotype, allowed to estimate the proportion of sample variation in pre-analytical steps. From the NMR data, we found that 40% of the metabolite variance is due to the metabolite extraction process and analysis and 60% is due to sample-to-sample variance. The availability of RMs in untargeted metabolomics is one of the predominant needs of the metabolomics community that reach beyond quality control practices. IBAT addresses this need by facilitating the production of biologically relevant RMs and increasing their widespread use.
Full scale structural, mechanical and dynamical properties of HIV-1 liposomes
Authors: Bryer Alexander J. , Reddy Tyler , Lyman Edward , Perilla Juan R. 
Published: March 2021

AbstractEnveloped viruses are enclosed by a lipid membrane inside of which are all of the components necessary for the virus life cycle; viral proteins, the viral genome and metabolites. Viral envelopes are lipid bilayers that adopt morphologies ranging from spheres to tubes. The envelope is derived from the host cell during viral replication. Thus, the composition of the bilayer depends on the complex constitution of lipids from the host-cell’s organelle(s) where assembly and/or budding of the viral particle occurs. Here, molecular dynamics (MD) simulations of authentic, asymmetric HIV-1 liposomes are used to derive a unique level of resolution of its full-scale structure, mechanics and dynamics. Analysis of the structural properties reveal the distribution of thicknesses of the bilayers over the entire liposome as well as its global fluctuations. Moreover, full-scale mechanical analyses are employed to derive the global bending rigidity of HIV-1 liposomes. Finally, dynamical properties of the lipid molecules reveal important relationships between their 3D diffusion, the location of lipid-rafts and the asymmetrical composition of the envelope. Overall, our simulations reveal complex relationships between the rich lipid composition of the HIV-1 liposome and its structural, mechanical and dynamical properties with critical consequences to different stages of HIV-1’s life cycle.
Factors Associated with Emerging and Re-emerging of SARS-CoV-2 Variants
Authors: Spratt Austin N. , Kannan Saathvik R. , Woods Lucas T. , Weisman Gary A. , Quinn Thomas P. , Lorson Christian L. , Sönnerborg Anders , Byrareddy Siddappa N. , Singh Kamal 
Published: March 2021

AbstractGlobal spread of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has triggered unprecedented scientific efforts, as well as containment and treatment measures. Despite these efforts, SARS-CoV-2 infections remain unmanageable in some parts of the world. Due to inherent mutability of RNA viruses, it is not surprising that the SARS-CoV-2 genome has been continuously evolving since its emergence. Recently, four functionally distinct variants, B.1.1.7, B.1.351, P.1 and CAL.20C, have been identified, and they appear to more infectious and transmissible than the original (Wuhan-Hu-1) virus. Here we provide evidence based upon a combination of bioinformatics and structural approaches that can explain the higher infectivity of the new variants. Our results show that the greater infectivity of SARS-CoV-2 than SARS-CoV can be attributed to a combination of several factors, including alternate receptors. Additionally, we show that new SARS-CoV-2 variants emerged in the background of D614G in Spike protein and P323L in RNA polymerase. The correlation analyses showed that all mutations in specific variants did not evolve simultaneously. Instead, some mutations evolved most likely to compensate for the viral fitness.
High-throughput screen using fluorescence lifetime detects compounds that modulate myosin-binding protein C interactions with actin
Authors: Bunch Thomas A. , Guhathakurta Piyali , Lepak Victoria C. , Thompson Andrew R. , Kanassatega Rhye-Samuel , Wilson Anna , Thomas David D. , Colson Brett A. 
Published: March 2021

ABSTRACTCardiac myosin-binding protein C (cMyBP-C) interacts with actin and myosin to modulate cardiac contractility. These interactions are regulated by cMyBP-C phosphorylation. Heart failure patients often have decreased cMyBP-C phosphorylation and phosphorylation in model systems appears to be cardioprotective for heart failure. Therefore, cMyBP-C is a potential target for heart failure drugs that mimic phosphorylation and/or perturb its interactions with actin/myosin.We have used a novel fluorescence lifetime-based assay to identify small-molecule inhibitors of actin-cMyBP-C binding. Actin was labeled with a fluorescent dye (Alexa Fluor 568, AF568) near its cMyBP-C binding sites. When combined with cMyBP-C N-terminal fragment, C0-C2, the fluorescence lifetime of AF568-actin decreases. Using this reduction in lifetime as a readout of actin binding, a high-throughput screen of a 1280-compound library identified 3 reproducible Hit compounds that reduced C0-C2 binding to actin in the micromolar range. Binding of phosphorylated C0-C2 was also blocked by these compounds. That they specifically block binding was confirmed by a novel actin-C0-C2 time-resolved FRET (TR-FRET) binding assay. Isothermal titration calorimetry (ITC) and transient phosphorescence anisotropy (TPA) confirmed that the Hit compounds bind to cMyBP-C but not to actin. TPA results were also consistent with these compounds inhibiting C0-C2 binding to actin. We conclude that the actin-cMyBP-C lifetime assay permits detection of pharmacologically active compounds that affect cMyBP-C’s actin binding function. TPA, TR-FRET, and ITC can then be used to understand the mechanism by which the compounds alter cMyBP-C interactions with actin.
Convergent evolution of a novel blood-red nectar pigment in vertebrate-pollinated flowers
Authors: Roy Rahul , Moreno Nickolas , Brockman Stephen A. , Kostanecki Adam , Zambre Amod , Holl Catherine , Solhaug Erik M. , Minami Anzu , Snell-Rood Emilie , Hampton Marshall , Bee Mark A. , Chiari Ylenia , Hegeman Adrian D. , Carter Clay J. 
Published: March 2021

AbstractNesocodon mauritianus (Campanulaceae) produces a blood-red nectar that has been proposed to serve as a visual attractant for pollinator visitation. Here we show that the nectar’s red color is derived from a novel alkaloid termed nesocodin. The first nectar produced is acidic and pale yellow in color, but slowly becomes alkaline before taking on its characteristic red color. Three enzymes secreted into the nectar are either necessary or sufficient for pigment production, including (1) a carbonic anhydrase that creates an alkaline environment, (2) an aryl alcohol oxidase that generates sinapaldehyde, a pigment precursor, and (3) a ferritin-like catalase that protects nesocodin from degradation by hydrogen peroxide. Our findings demonstrate how these three enzymatic activities allow for the condensation of sinapaldehyde and proline to form a novel pigment with a stable imine bond, which in turn is attractive to Phelsuma geckos, the presumed pollinators of Nesocodon. We also identify nesocodin in the red nectar of the distantly related Jaltomata herrerae and provide evidence for convergent evolution of this trait. While the overall enzymatic activities required for red pigment formation in both Nesocodon and J. herrerae nectars are identical, the associated genes encoding the enzymes are not orthologous and, in the case of the aryl alcohol oxidase, even belong to different protein families. This work cumulatively identifies a novel, convergently evolved trait in two vertebrate-pollinated species, suggesting the red pigment is selectively favored and that only a limited number of compounds are likely to underlie this adaptation.SignificanceNearly 90% of flowering plants produce nectar to attract pollinators. Beyond sugars, many types of nectar solutes play important ecological roles; however, the molecular basis for the diversity of nectar composition across species is less explored. One rare trait among flowering plants is the production of colored nectar, which may function to attract and guide prospective pollinators. Our findings indicate convergent evolution of a red-colored nectar across two distantly related plant species. Behavioral data show that the red pigment attracts diurnal geckos, a presumed pollinator of one of these plants. These findings join a growing list of examples of distinct biochemical and molecular mechanisms underlying evolutionary convergence, and provide a fascinating system for testing how interactions across species drive the evolution of novel pigments in an understudied context.
CCR2 Regulates Vaccine-Induced Mucosal T-Cell Memory to Influenza A Virus
Authors: Lee Woojong , Kingstad-Bakke Brock , Kedl Ross M. , Kawaoka Yoshihiro , Suresh M. 
Published: March 2021

AbstractElicitation of lung tissue-resident memory CD8 T cells (TRMs) is a goal of T-cell based vaccines against respiratory viral pathogens such as influenza A virus (IAV). Chemokine receptor 2 (CCR2)-dependent monocyte trafficking plays an essential role in the establishment of CD8 TRMs in lungs of IAV-infected mice. Here, we used a combination adjuvant-based subunit vaccine strategy that evokes multifaceted (TC1/TC17/TH1/TH17) IAV nucleoprotein-specific lung TRMs, to determine whether CCR2 and monocyte infiltration are essential for vaccine-induced TRMdevelopment and protective immunity to IAV in lungs. Following intranasal vaccination, neutrophils, monocytes, conventional dendrtitic cells (DCs) and monocyte-derived DCs internalized and processed vaccine antigen in lungs. We also found that Basic Leucine Zipper ATF-Like Transcription Factor 3 (BATF-3)-dependent DCs were essential for eliciting T cell responses, but CCR2 deficiency enhanced the differentiation of CD127HI/KLRG-1LO, OX40+veCD62L+veand mucosally imprinted CD69+veCD103+veeffector and memory CD8 T cells in lungs and airways of vaccinated mice. Mechanistically, increased development of lung TRMs, induced by CCR2 deficiency was linked to dampened expression of T-bet, but not altered TCF-1 levels or T cell receptor signaling in CD8 T cells. T1/T17 functional programming, parenchymal localization of CD8/CD4 effector and memory T cells, recall T cell responses and protective immunity to a lethal IAV infection were unaffected in CCR2-deficient mice. Taken together, we identified a negative regulatory role for CCR2 and monocyte trafficking in mucosal imprinting and differentiation of vaccine-induced TRMs. Mechanistic insights from this study may aid the development of T-cell-based vaccines against respiratory viral pathogens including IAV and SARS-CoV-2.ImportanceWhile antibody-based immunity to influenza A virus (IAV) is type and sub-type specific, lung and airway-resident memory T cells that recognize conserved epitopes in the internal viral proteins are known to provide heterosubtypic immunity. Hence, broadly protective IAV vaccines need to elicit robust T-cell memory in the respiratory tract. We have developed a combination adjuvant-based IAV nucleoprotein vaccine that elicits strong CD4 and CD8 T cell memory in lungs and protects against H1N1 and H5N1 strains of IAV. In this study, we examined the mechanisms that control vaccine-induced protective memory T cells in the respiratory tract. We found that trafficking of monocytes into lungs might limit the development of anti-viral lung-resident memory T cells, following intranasal vaccination. These findings suggested that strategies that limit monocyte infiltration can potentiate vaccine-induced frontline T-cell immunity to respiratory viruses such as IAV and SARS-CoV-2.
Multiple forms of working memory emerge from synapse-astrocyte interactions
Authors: De Pittà Maurizio , Brunel Nicolas 
Published: March 2021

AbstractCompeting accounts propose that working memory (WM) is subserved either by persistent activity in single neurons, or by time-varying activity across a neural population, or by activity-silent mechanisms carried out by hidden internal states of the neural population. While WM is traditionally regarded to originate exclusively from neuronal interactions, cortical networks also include astrocytes that can modulate neural activity. We propose that different mechanisms of WM can be brought forth by astrocyte-mediated modulations of synaptic transmitter release. In this account, the emergence of different mechanisms depends on the network’s spontaneous activity and the geometry of the connections between synapses and astrocytes.
A robust SARS-CoV-2 replication model in primary human epithelial cells at the air liquid interface to assess antiviral agents
Authors: Dan Do Thuc Nguyen , Donckers Kim , Vangeel Laura , Chatterjee Arnab K. , Gallay Philippe A. , Bobardt Michael D. , Bilello John P. , Cihlar Tomas , De Jonghe Steven , Neyts Johan , Jochmans Dirk 
Published: March 2021

ABSTRACTThere are, besides remdesivir, no approved antivirals for the treatment of SARS-CoV-2 infections. To aid in the search for antivirals against this virus, we explored the use of human tracheal airway epithelial cells (HtAEC) and human small airway epithelial cells (HsAEC) grown at the air/liquid interface (ALI). These cultures were infected at the apical side with one of two different SARS-CoV-2 isolates. Each virus was shown to replicate to high titers for extended periods of time (at least 8 days) and, in particular an isolate with the D614G in the spike (S) protein did so more efficiently at 35°C than 37°C. The effect of a selected panel of reference drugs that were added to the culture medium at the basolateral side of the system was explored. Remdesivir, GS-441524 (the parent nucleoside of remdesivir), EIDD-1931 (the parent nucleoside of molnupiravir) and IFN (β1 and λ1) all resulted in dose-dependent inhibition of viral RNA and infectious virus titers collected at the apical side. However, AT-511 (the free base form of AT-527 currently in clinical testing) failed to inhibit viral replication in thesein vitroprimary cell models. Together, these results provide a reference for further studies aimed at selecting SARS-CoV-2 inhibitors for further preclinical and clinical development.