bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inability to make facial expressions dampens emotion perception
Authors: Japee Shruti , Jordan Jessica , Licht Judith , Lokey Savannah ,   Moebius Syndrome Research Consortium, Chen Gang , Snow Joseph , Jabs Ethylin Wang , Webb Bryn D , Engle Elizabeth C , Manoli Irini , Baker Chris , Ungerleider Leslie G. 
Published: October 2022

ABSTRACTHumans rely heavily on facial expressions for social communication to convey their thoughts and emotions and to understand them in others. One prominent but controversial view is that humans learn to recognize the significance of facial expressions by mimicking the expressions of others. This view predicts that an inability to make facial expressions (e.g., facial paralysis) would result in reduced perceptual sensitivity to others’ facial expressions. To test this hypothesis, we developed a diverse battery of sensitive emotion recognition tasks to characterize emotion perception in individuals with Moebius Syndrome (MBS), a congenital neurological disorder that causes facial palsy. Using computer-based emotion detection tasks we systematically assessed emotion perception thresholds for static and dynamic face and body expressions. We found that while MBS individuals were able to perform challenging perceptual control tasks, they were less efficient at extracting emotion from facial expressions, compared to matched controls. Exploratory analyses of fMRI data from a small group of MBS participants suggested potentially reduced engagement of the amygdala in MBS participants during expression processing relative to matched controls. Collectively, these results support the role of facial mimicry and consequent facial feedback and motor experience in the perception of others’ expressions.
Optical Genome and Epigenome Mapping of Clear Cell Renal Cell Carcinoma
Authors: Margalit Sapir , Tulpová Zuzana , Michaeli Yael , Detinis Zur Tahir , Deek Jasline , Louzoun-Zada Sivan , Nifker Gil , Grunwald Assaf , Scher Yuval , Schütz Leonie , Weinhold Elmar , Gnatek Yehudit , Omer Dorit , Dekel Benjamin , Friedman Eitan , Ebenstein Yuval 
Published: October 2022

ABSTRACTCancer cells display complex genomic aberrations that include large-scale genetic rearrangements and epigenetic modulation that are not easily characterized by short-read sequencing. We present a method for simultaneous profiling of long-range genetic/epigenetic changes in matched cancer samples. Clear cell renal cell carcinoma (ccRCC) is the most common subtype of kidney cancer. Most ccRCC cases demonstrate somatic genomic alterations involving the short arm of chromosome 3 (3p), most often targeting the von Hippel–Lindau (VHL) gene. Aiming to identify somatic alterations that characterize early stage ccRCC, we performed comprehensive genetic, cytogenetic and epigenetic analyses comparing ccRCC tumor to adjacent non-tumorous tissue. Optical genome mapping identified genomic aberrations such as structural and copy number variations, complementing exome-sequencing results. Single-molecule methylome and hydroxymethylome mapping revealed multiple differential regions, some of them known to be associated with ccRCC pathogenesis. Among them, metabolic pathways were significantly enriched. Moreover, significant global epigenetic differences were detected between the tumor and the adjacent non-tumorous tissue, and a correlation between epigenetic signals and gene expression was found. This is the first reported comparison of a human tumor and a matched tissue by optical genome/epigenome mapping, revealing well-established and novel somatic aberrations.
Coevolution of species colonization rates controls food-chain length in spatially structured food webs
Authors: Calcagno Vincent , David Patrice , Jarne Philippe , Massol François 
Published: October 2022

AbstractThe complexity of food webs and how it depends on environmental variables is a long-standing question in ecology. Food-chain length depends on many factors, such as productive space, disturbance and spatial processes. It is not clear though how food-chain length should vary with adaptive evolutionary changes of the constitutive species. Assuming that each trophic level is subject to a competition-colonization trade-off, we model the adaptive evolution of their colonization rates and its consequences on equilibrium occupancies and food-chain length. When colonization rates are allowed to evolve, longer food chains can persist. Extinction, perturbation and habitat loss all affect the evolutionary-stable colonization rates, but trade-off strength (costs of dispersal) has a major role: weaker trade-offs yield longer chains. Our results suggest a strong link between within-trophic level competition, spatial occupancies and food-chain length. Although these eco-evo dynamics partly alleviate the constraint on food-chain length in metacommunities, we show it is no magic bullet: the highest, most vulnerable, trophic levels are also those that least benefit from evolution. Our model generates qualitative predictions regarding how trait evolution affects the response of communities to disturbance and habitat loss. This highlights the importance of eco-evolutionary dynamics at metacommunity level in determining food-chain length.
Virulence Network of Interacting Influenza-Host Protein Domains
Authors: Ng Teng Ann , Rashid Shamima , Kwoh Chee Keong 
Published: October 2022

ABSTRACTThere exist several databases that provide virus-host protein interactions. While most provide curated records of interacting virus-host protein pairs, information on the strain-specific virulence factors or protein domains involved, is lacking. Some databases offer incomplete coverage of Influenza strains because of the need to sift through vast amounts of literature (including those of major viruses including HIV and Dengue, besides others). None have offered complete, strain specific protein-protein interaction records for the Influenza A group of viruses.In this paper, we present a comprehensive network of predicted domain-domain interaction(s) (DDI) between Influenza A virus (IAV) and mouse host proteins, that will allow the systematic study of disease factors by taking the virulence information (lethal dose) into account. From a previously published dataset of lethal dose studies of IAV infection in mice, we constructed an interacting domain network of mouse and viral protein domains as nodes with weighted edges. The edges were scored with the Domain Interaction Statistical Potential (DISPOT) to indicate putative DDI.The virulence network can be easily navigated via a web browser, with the associated virulence information (LD50values) prominently displayed. The network will aid Influenza A disease modeling by providing strain-specific virulence levels with interacting protein domains. It can possibly contribute to computational methods for uncovering Influenza infection mechanisms mediated through protein domain interactions between viral and host proteins.
Remodeling of yeast vacuole membrane lipidomes from the log (1-phase) to stationary stage (2-phases)
Authors: Reinhard John , Leveille Chantelle L. , Cornell Caitlin E. , Merz Alexey J. , Klose Christian , Ernst Robert , Keller Sarah L. 
Published: October 2022

ABSTRACTUpon nutrient limitation, budding yeast ofSaccharomyces cerevisiaeshift from fast growth (the log stage) to quiescence (the stationary stage). This shift is accompanied by liquid-liquid phase separation in the membrane of the vacuole, an endosomal organelle. Recent work indicates that the resulting micron-scale domains in vacuole membranes enable yeast to survive periods of stress. An outstanding question is which molecular changes might cause this membrane phase separation. Here, we conduct lipidomics of vacuole membranes in both the log and stationary stages. Isolation of pure vacuole membranes is challenging in the stationary stage, when lipid droplets are in close contact with vacuoles. Immuno-isolation has previously been shown to successfully purify log-stage vacuole membranes with high organelle specificity, but it was not previously possible to immuno-isolate stationary stage vacuole membranes. Here, we develop Mam3 as a bait protein for vacuole immuno-isolation, and demonstrate low contamination by non-vacuolar membranes. We find that stationary stage vacuole membranes contain surprisingly high fractions of phosphatidylcholine lipids (∼50%), roughly twice as much as log-stage membranes. Moreover, in the stationary stage these lipids have higher melting temperatures, due to longer and more saturated acyl chains. Another surprise is that no significant change in sterol content is observed. These results fit within the predominant view that phase separation in membranes requires at least three types of molecules to be present: lipids with high melting temperatures, lipids with low melting temperatures, and sterols.SIGNIFICANCE STATEMENTWhen budding yeast shift from growth to quiescence, the membrane of one of their organelles (the vacuole) undergoes liquid-liquid phase separation. What changes in the membrane’s lipids cause this phase transition? Here, we conduct lipidomics of immuno-isolated vacuole membranes. We analyze our data in the context of lipid melting temperatures, inspired by observations that liquid-liquid phase separation in model membranes requires a mixture of lipids with high melting temperatures, lipids with low melting temperatures, and sterols. We find that phase-separated vacuole membranes have higher concentrations of PC lipids, and that those lipids have higher melting temperatures. To conduct our experiments, we developed a tagged version of a protein (Mam3) for immuno-isolation of vacuole membranes.
Photodynamic therapy in colorectal cancer using photosensitizers functionalized by arene-ruthenium complexes
Authors: Massoud Jacquie , Pinon Aline , Gallardo-Villagran Manuel , Paulus Lucie , Antoun Sayed , Diab-Assaf Mona , Therrien Bruno , Liagre Bertrand 
Published: October 2022

AbstractColorectal cancer (CRC) is one of the most frequently diagnosed cancers worldwide and one of the main causes of cancer deaths in the global population. First-line treatment usually includes surgical procedures followed by combination chemotherapy. Despite the improvements in CRC treatments, the mortality rate remains very high, leading consequently to conventional treatment resistance. Several therapies were enrolled to this content in a way to find the best solutions for this disease. Photodynamic therapy (PDT) using photosensitizers (PS) presents itself as an original innovative therapeutic strategy that strongly limits the undesirable side effects of conventional treatment. However, low physiological solubility and a lack of selectivity of PS towards tumor sites are the principal restrictions of their current clinical use. Indeed, drug delivery systems are currently a key issue in cancer therapy. To overcome the problem of solubility and stability of PS such as porphyrins and their derivatives, metallic assemblies based on arene-ruthenium (Ru) units have begun to attract considerable attention as PS delivery systems. The purpose of this study was to demonstrate firstly the interest in the vectorization of tetrapyridylporphin (TPyP-arene-Ru) and Zn-tetrapyridylporphin arene-ruthenium (Zn-TPyP-arene-Ru) metallacages to increase their solubility in biological media and then, consequently their anticancer efficacy in PDT. Secondly, to elucidate the anticancer mechanism as well as identify the cell death process mediated by these new vectorized PS. The results showed that the two PS-arene-Ru complexes have a strong photocytotoxic effect after photoactivation on human HCT116 and HT-29 colorectal cancer cell lines. TPyP-arene-Ru-PDT induced outstanding cytotoxicity when compared to the Zn-TPyP-arene-Ru analogue. The two complexes show no significant effect on proliferation in the dark. In addition, results demonstrated that these two PS-arene-Ru complexes-PDT induce an apoptotic process through the appearance of a sub-G1 peak, phosphatidylserines externalization, poly-ADP ribose polymerase (PARP) cleavage and DNA fragmentation. Thus, our data contribute to highlighting that the incorporation of porphyrins in Ru-based assemblies could be an efficient vectorized system to treat CRC by PDT.
SARS-CoV2 associated secretion of nanoLuciferase reports on virus and Virus-Like Particle production
Authors: Gullberg Rebekah C. , Frydman Judith 
Published: October 2022

AbstractSARS-CoV2 is a positive-strand RNA virus in theCoronaviridaefamily that has caused world-wide morbidity and mortality. While much progress has been made we still need expanded rapid anti-virals. The top advanced antiviral candidates all target stages of RNA replication, leaving virus assembly an unexplored avenue of antiviral research. To address this gap, and explore the biochemical and cell biological features of viral assembly, we have employed an improved virus-like particle (VLP) system. We exploited the small nanoLuciferase protein for enhanced signal and surprisingly found that the protein itself appears to be packaged into both SARS CoV2 VLPs and virions and secreted from cells. Interestingly, nLuc is not co-secreted with dengue or Zika infection, suggesting the large virion of Coronavirus can encaspidate and secrete a cellularly expressed reporter protein. Our findings open the way for powerful new approaches to measure viral particle production, egress and viral entry mechanisms.
Tripartite interactions between filamentous Pf4 bacteriophage,Pseudomonas aeruginosa, and bacterivorous nematodes
Authors: Schwartzkopf Caleb M. , Robinson Autumn J. , Ellenbecker Mary , Faith Dominick R. , Brooks Diane M. , Lewerke Lincoln , Voronina Ekaterina , Dandekar Ajai A. , Secor Patrick R. 
Published: October 2022

AbstractThe opportunistic pathogenPseudomonas aeruginosaPAO1 is infected by the filamentous bacteriophage Pf4. Pf4 virions promote biofilm formation, protect bacteria from antibiotics, and modulate animal immune responses in ways that promote infection. Furthermore, strains cured of their Pf4 infection (ΔPf4) are less virulent in animal models of infection. Consistently, we find that strain ΔPf4 is less virulent in aCaenorhabditis elegansnematode infection model. However, our data indicate that PQS quorum sensing is activated and production of the pigment pyocyanin, a potent virulence factor, is enhanced in strain ΔPf4. The reduced virulence of ΔPf4 despite high levels of pyocyanin production may be explained by our finding thatC. elegansmutants unable to sense bacterial pigments through the aryl hydrocarbon receptor are more susceptible to ΔPf4 infection compared to wild-typeC. elegans. Collectively, our data support a model where suppression of quorum-regulated virulence factors by Pf4 allowsP. aeruginosato evade detection by innate host immune responses.Author SummaryPseudomonas aeruginosais an opportunistic bacterial pathogen that infects wounds, lungs, and medical hardware.P. aeruginosastrains are often themselves infected by a filamentous virus (phage) called Pf. At sites of infection, filamentous Pf virions are produced that promote bacterial colonization and virulence. Here, we report that strains ofP. aeruginosacured of their Pf infection are less virulent in aCaenorhabditis elegansnematode infection model. We also report that PQS quorum sensing and production of the virulence factor pyocyanin are enhanced inP. aeruginosastrains cured of their Pf infection. Compared to wild-typeC. elegans, nematodes unable to detect bacterial pigments via the aryl hydrocarbon receptor AhR were more susceptible to infection by Pf-freeP. aeruginosastrains that over-produce pyocyanin. Collectively, this study supports a model where Pf phage suppressP. aeruginosaPQS quorum sensing and reduce pyocyanin production, allowingP. aeruginosato evade AhR-mediated immune responses inC. elegans.
Discovering hub genes involved in the pathophysiological impact of COVID-19 on diabetes kidney disease by differential gene expression and interactome analysis
Authors: Osuna-Martínez Ulises , Aviña-Padilla Katia , Olimón-Andalón Vicente , Angulo-Rojo Carla , Guadrón-Llanos Alma , Rivas-Ferreira José Carlos , Urrea Francisco , Calderon-Zamora Loranda 
Published: October 2022

AbstractDiabetic kidney disease (DKD) is a frequently chronic kidney pathology derived from diabetes comorbidity. This condition has irreversible damage, and its risk factor increases with SARS-CoV-2 infection. The prognostic outcome for diabetic patients with COVID-19 is dismal, even with intensive medical treatment. However, there is still scarce information on critical genes involved in the pathophysiological impact of COVID-19 on DKD. Herein, we characterize differential expression gene (DEG) profiles and determine hub genes undergoing transcriptional reprogramming in both disease conditions. Out of 995 DEGs, we identified 42 DEGs shared with COVID-19 pathways. Enrichment analysis elucidated that they are significantly induced with implications for immune and inflammatory responses. By performing a protein-protein interaction (PPI) network and applying topological methods, we determine the following five hub genesSTAT1, IRF7, ISG15, MX1, andOAS1. Then, by network deconvolution, we determine their co-expressed gene modules. Moreover, we validate the conservancy of their upregulation using the Coronascape database (DB). Finally, tissue-specific regulation of the five predictive hub genes indicates thatOAS1andMX1expression levels are lower in healthy kidney tissue. Altogether, our results suggest that these genes could play an essential role in developing severe outcomes of COVID-19 in DKD patients.
Real-time surveillance of international SARS-CoV-2 prevalence using systematic traveller arrival screening
Authors: Kucharski Adam J , Chung Kiyojiken , Aubry Maite , Teiti Iotefa , Teissier Anita , Richard Vaea , Russell Timothy W , Bos Raphaëlle , Olivier Sophie , Cao-Lormeau Van-Mai 
Published: October 2022

AbstractBackgroundEffective COVID-19 response relies on good knowledge of infection dynamics, but owing to under-ascertainment and delays in symptom-based reporting, obtaining reliable infection data has typically required large dedicated local population studies. Although many countries implemented SARS-CoV-2 testing among travellers, interpretation of arrival testing data has typically been challenging because arrival testing data were rarely reported systematically, and pre-departure testing was often in place as well, leading to non-representative infection status among arrivals.MethodsIn French Polynesia, testing data were reported systematically with enforced pre-departure testing type and timing, making it possible to adjust for non-representative infection status among arrivals. Combining statistical models of PCR positivity with data on international travel protocols, we reconstructed estimates of prevalence at departure using only testing data from arrivals. We then applied this estimation approach to the USA and France, using data from over 220,000 tests from travellers arriving into French Polynesia between July 2020 and March 2022.FindingsWe estimated a peak infection prevalence at departure of 2.8% (2.3-3.6%) in France and 1.1% (0.81-3.1%) in the USA in late 2020/early 2021, with prevalence of 5.4% (4.8-6.1%) and 5.5% (4.6-6.6%) respectively estimated for the Omicron BA.1 waves in early 2022. We found that our infection estimates were a leading indicator of later reported case dynamics, as well as being consistent with subsequent observed changes in seroprevalence over time.InterpretationAs well as elucidating previously unmeasured infection dynamics in these countries, our analysis provides a proof-of-concept for scalable tracking of global infections during future pandemics.FundingWellcome (206250/Z/17/Z)
Cytosolic PCNA interacts with S100A8 and controls an inflammatory subset of neutrophils in COVID-19
Authors: de Oliveira Formiga Rodrigo , Pesenti Lucie , Ladjemi Maha Zohra , Frachet Philippe , Andrieu Muriel , Many Souganya , Karunanithy Vaarany , Bailly Karine , Dhôte Théo , Castel Manon , Rousseau Christophe , Starick Marick , da Rocha Edroaldo Lummertz , Lombardi Emilia Puig , Granger Vanessa , Chollet-Martin Sylvie , De Chaisemartin Luc , Mouthon Luc , Spiller Fernando , Hosmalin Anne , Hurtado-Nedelec Margarita , Martin Clémence , Pène Frédéric , Burgel Pierre-Regis , Tourneur Léa , Witko-Sarsat Véronique 
Published: October 2022

AbstractNeutrophils are key players in the hyperinflammatory response upon SARS-CoV-2 infection. We have previously described that cytosolic proliferating cell nuclear antigen (PCNA) controls neutrophil survival and NADPH oxidase-dependent ROS production. We here show that both PCNA and S100A8 expression and interaction were elevated in neutrophils from patients with COVID-19 compared to healthy donors and this was correlated with disease severity. Increased PCNA expression was accompanied by a decreased apoptosis and increased NADPH-oxidase activity in neutrophils from COVID-19 patients compared to healthy donors. These effects, as well as the interaction between PCNA and S100A8, were potently counteracted by T2 amino alcohol (T2AA), a PCNA inhibitor, demonstrating that the PCNA scaffold orchestrated neutrophil activation. Notably, the interaction between PCNA-S100A8 was more intense in the CD16high-CD62Llowactivated neutrophil subset. We propose that PCNA-S100A8 complex acts as potential driver for neutrophil dysregulation in COVID-19 and show for the first time that the PCNA scaffold is a decisive component of both neutrophil activation and heterogeneity.
Analysis of fatality among COVID-19 cases in Mexican pregnant women: a cross-sectional study
Authors: Padilla-Raygoza Nicolás , Gallardo-Luna María de Jesús , Flores-Vargas Gilberto , Navarro-Olivos Efrain , Magos-Vázquez Francisco J. , Lara-Lona Elia , Díaz-Martínez Daniel A. 
Published: October 2022

AbstractThis study aims to analyze the fatality of cases confirmed by COVID-19 among pregnant women in Mexico. It is a cross-sectional and analytical study. We used the registries from pregnant women available in the open database of the National Epidemiological Surveillance System from the General Directorate of Epidemiology. We showed descriptive statistics for all the variables. A suspected case of COVID-19 is any person who presented the following signs and symptoms: fever, headache, cough, and others. A confirmed case is any suspected case with a positive RT-PCR test result. We computed OR and 95% confidence intervals to estimate the effect of independent variables on dying from COVID-19. Also, it was calculated the Case Fatality Ratio (CFR) among pregnant women. The alpha value was fixed at 0.05 as a threshold to show statistical significance. The CFR was 1.09%. For confirmed cases, the average age among those who died was higher than among those who did not die (P <0.05). The average time between the onset of symptoms and registration in the system was higher for those who died (P <0.05). Among the deceased, 76.97% had pneumonia. For the 40-49 years age group, the effect on death was statistically significant (OR 4.97, CI95% 1.77 – 17.85). Outpatient care had a protective effect on dying (OR 0.04, CI95% 0.02 – 0.09). Pneumonia was highly associated with death (OR 8.68, CI95% 5.72 – 13.6). Co-morbidities did not affect dying while considering them in a multivariable logistic regression model. Among pregnant women, smoking has little effect on death by COVID-19. The CFR was low compared with the rest of the Mexican population. The co-morbidities had a low prevalence among pregnant women. Since the reproductive age span is young age, pregnant women have two protective factors for COVID-19 detected so far: being young and woman.