bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ocean acidification increases susceptibility to sub-zero air temperatures in ecosystem engineers (Mytilus sp.): a limit to poleward range shifts
Authors: Thyrring Jakob , MacLeod Colin D. , Marshall Katie E. , Kennedy Jessica , Tremblay Réjean , Harley Christopher D. G. 
Published: July 2022

AbstractOngoing climate change has caused rapidly increasing temperatures, and an unprecedented decline in seawater pH, known as ocean acidification. Increasing temperatures are redistributing species towards higher and cooler latitudes which are most affected by ocean acidification. Whilst the persistence of intertidal species in cold environments is related to their capacity to resist sub-zero air temperatures, studies have never considered the interacting impacts of ocean acidification and freeze stress on species survival and distribution. A full-factorial experiment was used to study whether ocean acidification increases mortality in Mytilus spp. following sub-zero air temperature exposure. We examined physiological processes behind variation in freeze tolerance using 1H NMR metabolomics, analyses of fatty acids, and amino acid composition. We show that low pH conditions (pH = 7.5) significantly decrease freeze tolerance in both intertidal and subtidal populations of Mytilus spp. Under current day pH conditions (pH = 7.9), intertidal M. trossulus were more freeze tolerant than subtidal M. trossulus and M. galloprovincialis. Opposite, under low pH conditions, subtidal M. trossulus was more freeze tolerant than the other groups. We observed a marked shift from negative to positive metabolite-metabolite correlations across species under low pH conditions, but there was no evidence that the concentration of individual metabolites or amino acids affected freeze tolerance. Finally, pH-induced changes in the composition of cell membrane phospholipid fatty acids had no effect on survival. These results suggest that ocean acidification can offset the poleward expanding facilitated by warming, and that reduced freeze tolerance could result in a niche squeeze if temperatures become lethal at the equatorward edge.
The changing landscape of respiratory viruses contributing to respiratory hospitalisations: results from a hospital-based surveillance in Quebec, Canada, 2012-13 to 2021-22
Authors: Gilca Rodica , Amini Rachid , Carazo Sara , Frenette Charles , Boivin Guy , Charest Hugues , Dumaresq Jeannot 
Published: July 2022

AbstractBackgroundA comprehensive description of the combined effect of SARS-CoV-2 and respiratory viruses (RV) other than SARS-CoV-2 (ORV) on hospitalisations is lacking.AimTo compare viral etiology of acute respiratory infections (ARI) hospitalisations before and during two pandemic years from a surveillance network in Quebec, Canada.MethodWe compared detection of ORV and SARS-CoV-2 during 2020-21 and 2021-22 to 8 pre-pandemic influenza seasons in patients hospitalised with ARI who were tested systematically by a multiplex PCR.ResultsDuring pre-pandemic influenza seasons, overall RV detection was 92.7% (1,493) (48.3% respiratory syncytial virus (RSV)) in children and 62.8% (4,339) (40.1% influenza) in adults. Overall RV detection in 2020-21 was 58.6% (29) in children (all ORV) and 43.7% (333) in adults (3.4% ORV, 40.3% SARS-CoV2, both including coinfections). In 2021-22 overall RV detection was 91.0% (201) in children (82.8% ORV, 8.1% SARS-CoV-2, both including coinfections) and 55.5% (527) in adults (14.1% ORV, 41.4% SARS-CoV-2, both including coinfections).Virtually no influenza was detected in 2020-21 and in 2021-22 up to epi-week 2022-9 presented here; no RSV was detected in 2020-21. In 2021-22, detection of RSV was comparable to pre-pandemic years but with an unusually early season. There were significant differences in ORV and SARS-CoV-2 detection between time periods and age groups.ConclusionSignificant continuous shifts in age distribution and viral etiology of ARI hospitalisations occurred during two pandemic years. This reflects evolving RV epidemiology and underscores the need for increased scrutiny of ARI hospitalisation etiology to inform tailored public health recommendations.
Glycolysis-enhancing α1-adrenergic antagonists modify cognitive symptoms related to Parkinson’s disease
Authors: Weber Matthew A. , Sivakumar Kartik , Tabakovic Ervina E. , Oya Mayu , Aldridge Georgina M. , Zhang Qiang , Simmering Jacob E. , Narayanan Nandakumar S. 
Published: July 2022

AbstractTerazosin is an α1-adrenergic receptor antagonist that enhances glycolysis and increases cellular ATP by binding to the enzyme phosphoglycerate kinase 1 (PGK1). Recent work has shown that terazosin is protective against motor dysfunction in rodent models of Parkinson’s disease (PD) and is associated with slowed motor symptom progression in PD patients. However, PD is also characterized by profound cognitive symptoms. We tested the hypothesis that terazosin protects against cognitive symptoms associated with PD. We report two main results. First, in rodents with ventral tegmental area (VTA) dopamine depletion modeling aspects of PD-related cognitive dysfunction, we found that terazosin preserved cognitive function and produced a non-statistically significant trend towards protected VTA tyrosine hydroxylase levels. Second, we found that after matching for demographics, comorbidities, and disease duration, PD patients newly started on terazosin, alfuzosin, or doxazosin had a lower hazard of being diagnosed with dementia compared to tamsulosin, an α1-adrenergic receptor antagonist that does not enhance glycolysis. Together, these findings suggest that in addition to slowing motor symptom progression, glycolysis-enhancing drugs protect against cognitive symptoms of PD.
Pre-existing population immunity and SARS-CoV-2 variant establishment and dominance dynamics in the United States: An ecological study
Authors: Ankomah Pierre O. , Siedner Mark J. , Bhattacharyya Roby P. 
Published: July 2022

AbstractWe conducted an ecological analysis of the dynamics of Delta and Omicron establishment and dominance in U.S. states. Omicron became the dominant circulating variant later in states with higher population-level immunity. By contrast, population immunity did not impact the rates of transition from prior variants to either Delta or Omicron.
DIFFERENTIAL SARS-COV-2 ANTIGEN SPECIFICITY OF THE HUMORAL RESPONSE IN INACTIVATED VIRUS-VACCINATED, CONVALESCENT, AND BREAKTHROUGH SUBJECTS
Authors: Duarte Luisa F. , Vázquez Yaneisi , Diethelm-Varela Benjamín , Pavez Valentina , Berríos-Rojas Roslye , White Jessica A. , Kalergis Alexis M. , Bueno Susan M. , González Pablo A. 
Published: July 2022

ABSTRACTAnalytical methods for the differential determination between natural infection with SARS- CoV-2 vs. immunity elicited by vaccination or infection after immunization (breakthrough cases) represent attractive new research venues in the context of the ongoing COVID-19 pandemic caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2). Herein, we set out to compare humoral responses against several SARS-CoV-2 structural and non-structural proteins in infected unvaccinated (convalescent), vaccinated, as well as vaccinated and infected (breakthrough) individuals. Our results indicate that immunization with an inactivated SARS-CoV-2 vaccine (CoronaVac) induces significantly higher levels of IgG antibodies against the membrane (M) protein of SARS-CoV-2 as compared to convalescent subjects both, after the primary vaccination schedule and after a booster dose. Moreover, we found that CoronaVac-immunized individuals, after receiving a third vaccine shot, display equivalent levels of N-specific IgG antibodies as convalescents subjects. Regarding non-structural viral proteins, for the two viral proteins ORF3a and NSP8, IgG antibodies were produced in more than 50% of the convalescent subjects. Finally, a logistic regression model and a receiver operating characteristic (ROC) analysis show that combined detection of M and N proteins may be useful as a biomarker to differentiate breakthrough cases from vaccinated and convalescent individuals that did not receive prior vaccination. Taken together, these results suggest that multiple SARS-CoV-2 antigens may be used as differential biomarkers for distinguishing natural infection from vaccination.
Speech-In-Noise Comprehension is Improved When Viewing a Deep-Neural-Network-Generated Talking Face
Authors: Shan Tong , Xu Chenliang , Duan Zhiyao , Maddox Ross K. 
Published: July 2022

AbstractListening in a noisy environment is challenging, but many previous studies have demonstrated that comprehension of speech can be substantially improved by looking at the talker’s face. We recently developed a deep neural network (DNN) based system that generates movies of a talking face from speech audio and a single face image. In this study, we aimed to quantify the benefits that such a system can bring to speech comprehension, especially in noise. The target speech audio was masked with signal to noise ratios of −9, −6, −3, and 0 dB and was presented to subjects in three audio-visual (AV) stimulus conditions: 1) synthesized AV: audio with the synthesized talking face movie; 2) natural AV: audio with the original movie from the corpus; and 3) audio-only: audio with a static image of the talker. Subjects were asked to type the sentences they heard in each trial and keyword recognition was quantified for each condition. Overall, performance in the synthesized AV condition fell approximately halfway between the other two conditions, showing a marked improvement over the audio-only control but still falling short of the natural AV condition. Every subject showed some benefit from the synthetic AV stimulus. The results of this study support the idea that a DNN-based model that generates a talking face from speech audio can meaningfully enhance comprehension in noisy environments, and has the potential to be used as a “visual hearing aid.”
Clonal breeding strategies to harness heterosis: insights from stochastic simulation
Authors: Labroo Marlee R. , Endelman Jeffrey B. , Gemenet Dorcus C. , Werner Christian R. , Gaynor R. Chris , Covarrubias-Pazaran Giovanny E. 
Published: July 2022

AbstractTo produce genetic gain, hybrid crop breeding can change the additive as well as dominance genetic value of populations, which can lead to utilization of heterosis. A common hybrid breeding strategy is reciprocal recurrent selection (RRS), in which parents of hybrids are typically recycled within pools based on general combining ability (GCA). However, the relative performance of RRS and other possible breeding strategies have not been thoroughly compared. RRS can have relatively increased costs and longer cycle lengths which reduce genetic gain, but these are sometimes outweighed by its ability to harness heterosis due to dominance and increase genetic gain. Here, we used stochastic simulation to compare gain per unit cost of various clonal breeding strategies with different amounts of population inbreeding depression and heterosis due to dominance, relative cycle lengths, time horizons, estimation methods, selection intensities, and ploidy levels. In diploids with phenotypic selection at high intensity, whether RRS was the optimal breeding strategy depended on the initial population heterosis. However, in diploids with rapid cycling genomic selection at high intensity, RRS was the optimal breeding strategy after 50 years over almost all amounts of initial population heterosis under the study assumptions. RRS required more population heterosis to outperform other strategies as its relative cycle length increased and as selection intensity decreased. Use of diploid fully inbred parents vs. outbred parents with RRS typically did not affect genetic gain. In autopolyploids, RRS typically was not beneficial regardless of the amount of population inbreeding depression.Key MessageReciprocal recurrent selection sometimes increases genetic gain per unit cost in clonal diploids with heterosis due to dominance, but it typically does not benefit autopolyploids.
Longitudinal, multi-platform metagenomics yields a high-quality genomic catalog and guides an in vitro model for cheese communities
Authors: Saak Christina C. , Pierce Emily C. , Dinh Cong B. , Portik Daniel , Hall Richard , Ashby Meredith , Dutton Rachel J. 
Published: July 2022

AbstractMicrobiomes are intricately intertwined with human health, geochemical cycles and food production. While many microbiomes of interest are highly complex and experimentally intractable, cheese rind microbiomes have proven powerful model systems for the study of microbial interactions. To provide a more comprehensive view of the genomic potential and temporal dynamics of cheese rind communities, we combine longitudinal, multi-platform metagenomics of three ripening washed-rind cheeses with whole genome sequencing of community isolates. Sequencing-based approaches revealed a highly reproducible microbial succession in each cheese, co-existence of closely related Psychrobacter species, and enabled the prediction of plasmid and phage diversity and their host associations. Combined with culture-based approaches, we established a genomic catalog and a paired 16-member in vitro washed rind cheese system. The combination of multi-platform metagenomic time-series data and an in vitro model provides a rich resource for further investigation of cheese rind microbiomes both computationally and experimentally.ImportanceMetagenome sequencing can provide great insights into microbiome composition and function and help researchers develop testable hypotheses. Model microbiomes, such as those composed of cheese rind bacteria and fungi, then allow the testing of these hypotheses in a controlled manner. Here, we first generate an extensive longitudinal metagenomic dataset. This dataset reveals successional dynamics, yields a phyla-spanning bacterial genomic catalog, associates mobile genetic elements with their hosts and provides insights into functional enrichment of Psychrobacter in the cheese environment. Next, we show that members of the washed-rind cheese microbiome lend themselves to in vitro community reconstruction. This paired metagenomic data and in vitro system can thus be used as a platform for generating and testing hypotheses related to the dynamics within, and functions associated with, cheese rind microbiomes.
Identification of a Broadly Fibrogenic Macrophage Subset Induced by Type 3 Inflammation in Human and Murine Liver and Lung Fibrosis
Authors: Fabre Thomas , Barron Alexander M. S. , Christensen Stephen M. , Asano Shoh , Wadsworth Marc H. , Chen Xiao , Wang Ju , McMahon James , Schlerman Frank , White Alexis , Kravarik Kellie , Fisher Andrew J. , Borthwick Lee A. , Hart Kevin M. , Henderson Neil C. , Wynn Thomas A. , Dower Ken 
Published: July 2022

AbstractMacrophages are central orchestrators of the tissue response to injury, with distinct macrophage activation states playing key roles in the progression and resolution of fibrosis. Identifying the unique fibrogenic macrophages that are found in human fibrotic tissues could lead to new and more effective treatments for fibrosis. Here we used human liver and lung single cell RNA sequencing datasets to identify a unique subset of CD9+ TREM2+ macrophages expressing SPP1, GPNMB, FABP5, and CD63 with strong pro-fibrotic activity. This population was validated across orthogonal techniques, species and tissues. These macrophages were enriched at the outside edges of scarring adjacent to activated mesenchymal cells, and in the fibrotic niche across species and organs. Neutrophils producing the type 3 cytokines GM-CSF and IL-17A, and expressing MMP9, which participates in the activation of TGF-β1, clustered with these scar-associated macrophages. Using in vitro primary human cell assays, we determined that GM-CSF, IL-17A and TGF-β1 drive the differentiation of these scar-associated macrophages, and that co-culture of monocyte-derived macrophages with hepatic stellate cells and TGF-β1 augmented type 1 collagen deposition. In vivo blockade of GM-CSF, IL-17A or TGF-β1 with small or large molecules reduced scar-associated macrophage expansion and fibrosis in multiple models of hepatic and pulmonary fibrosis. Our work demonstrates that a specific scar-associated macrophage population is linked with fibrosis across species and tissues. It further provides a strategy for unbiased discovery, triage and preclinical validation of therapeutic targets within this fibrogenic macrophage population.
Imaging Giant Vesicle Membrane Domains with a Luminescent Europium Tetracycline Complex
Authors: Cawley Jennie L. , Berger Brett A. , Odudimu Adeyemi T. , Singh Aarshi N. , Santa Dane E. , McDarby Ariana I. , Honerkamp-Smith Aurelia R. , Wittenberg Nathan J. 
Published: July 2022

ABSTRACTMicrodomains in lipid bilayer membranes are routinely imaged using organic fluorophores that preferentially partition into one of the lipid phases, resulting in fluorescence contrast. Here we show that membrane microdomains in giant unilamellar vesicles (GUVs) can be visualized with europium luminescence using a complex of europium (III) and tetracycline (EuTc). EuTc is unlike typical organic lipid probes in that it is a coordination complex with a unique excitation/emission wavelength combination (396/617 nm), a very large Stokes shift (221 nm), and a very narrow emission bandwidth (8 nm). The probe preferentially interacts with liquid disordered domains in GUVs, which results in intensity contrast across the surface of phase-separated GUVs. Interestingly, EuTc also alters GM1 ganglioside partitioning. GM1 typically partitions into liquid ordered domains, but after labeling phase-separated GUVs with EuTc, cholera toxin B-subunit (CTxB), which binds GM1, labels liquid disordered domains. We also demonstrate that EuTc, but not free Eu3+or Tc, significantly reduces lipid diffusion coefficients. Finally, we show that EuTc can be used to label cellular membranes similar to a traditional membrane probe. EuTc may find utility as a membrane imaging probe where its large Stokes shift and sharp emission band would enable multicolor imaging.
Helping can be driven by non-affective cues in rat
Authors: Sugano Y. Vieira , Shan H.Z. , Molasky N.M.R. , Mason P. 
Published: July 2022

AbstractHelping another in distress can be motivated by either affective or cognitive empathy, with the latter commonly believed to be restricted to humans and possibly other apes. Here, we found evidence for rodent helping that occurs in the absence of affective cues. We employed a paradigm in which a free rat can open the door to a restrainer containing a trapped rat. When the trapped rat was treated with the anxiolytic midazolam, the helping behavior exhibited by the free rat was diminished but did not extinguish. Correspondingly, midazolam-treated trapped rats still released themselves when given the opportunity, albeit at longer latencies than controls, evidence that midazolam only partially reduced the distress experienced by trapped rats. To test whether helping could occur for a rat who exhibited no affect, trapped rats were immobilized by general anesthesia or heavy sedation. Surprisingly, rats opened the door to restrainers containing these immobilized rats and pulled the incapacitated rats out of the restrainer, pushing them away from the arena center. The same solicitous behavior was observed when an anesthetized rat was simply placed in the center of the arena, without being confined within a restrainer. We speculate that the cognitive dissonance of immobile rats, at odds with predictive expectations of rat behavior built up over a lifetime, motivated solicitous behavior including helping. To block affective behavioral displays without associated dissonant cues of immobility, metyrapone, a drug that selectively blocks corticosterone synthesis, was administered to trapped rats. Under such circumstances, little helping behavior occurred. In sum, rats may be motivated either by affect or by cognitive dissonance, the latter comprising a rudimentary form of cognitive empathy.
Genome sequencing and comparative analysis of Wolbachia strain wAlbA reveals Wolbachia-associated plasmids are common
Authors: Martinez Julien , Ant Thomas H. , Murdochy Shivan M. , Tong Lily , da Silva Filipe Ana , Sinkins Steven P. 
Published: July 2022

AbstractWolbachia are widespread maternally-transmitted bacteria of arthropods that often spread by manipulating their host’s reproduction through cytoplasmic incompatibility (CI). Their invasive potential is currently being harnessed in field trials aiming to control mosquito-borne diseases. Wolbachia genomes commonly harbour prophage regions encoding the cif genes which confer their ability to induce CI. Recently, a plasmid-like element was discovered in wPip, a Wolbachia strain infecting Culex mosquitoes; however, it is unclear how common such extra-chromosomal elements are in Wolbachia. Here we sequenced the complete genome of wAlbA, a strain of the symbiont found in Aedes albopictus. We show that wAlbA is associated with two new plasmids and identified additional Wolbachia plasmids and related chromosomal islands in over 20% of publicly available Wolbachia genome datasets. These plasmids encode a variety of accessory genes, including several phage-like DNA packaging genes as well as genes potentially contributing to host-symbiont interactions. In particular, we recovered divergent homologues of the cif genes in both Wolbachia- and Rickettsia-associated plasmids. Our results indicate that plasmids are common in Wolbachia and raise fundamental questions around their role in symbiosis. In addition, our comparative analysis provides useful information for the future development of genetic tools to manipulate and study Wolbachia symbionts.
Humanized NBSGW PDX Models of Disseminated Ovarian Cancer Recapitulate Key Aspects of the Tumor Immune Environment within the Peritoneal Cavity
Authors: Steinkamp Mara P. , Lagutina Irina , Brayer Kathryn J. , Schultz Fred , Burke Danielle , Pankratz Vernon S. , Adams Sarah F. , Hudson Laurie G. , Ness Scott A. , Wandinger-Ness Angela 
Published: July 2022

ABSTRACTThe importance of the immune microenvironment in ovarian cancer progression, metastasis, and response to therapies has become increasingly clear, especially with the new emphasis on immunotherapies. In order to leverage the power of patient-derived xenograft (PDX) models within a humanized immune microenvironment, three ovarian cancer PDX were grown in humanized NBSGW mice engrafted with human CD34+ cord blood-derived hematopoietic stem cells. Analysis of cytokine levels in the ascites fluid and infiltrating immune cells in the tumors demonstrated that these humanized PDX (huPDX) established an immune tumor microenvironment similar to what has been reported for ovarian cancer patients. The lack of human myeloid cell differentiation has been a major setback for humanized mouse models, but our analysis shows that PDX engraftment increases the human myeloid population in the peripheral blood. Analysis of cytokines within the ascites fluid of huPDX revealed high levels of human M-CSF, a key myeloid differentiation factor as well as other elevated cytokines that have previously been identified in ovarian cancer patient ascites fluid including those involved in immune cell differentiation and recruitment. Human tumor-associated macrophages and tumor-infiltrating lymphocytes were detected within the tumors of humanized mice, demonstrating immune cell recruitment to tumors. Comparison of the three huPDX revealed certain differences in cytokine signatures and in the extent of immune cell recruitment. Our studies show that huNBSGW PDX models reconstitute important aspects of the ovarian cancer immune tumor microenvironment making this a superior approach for therapeutic trials.