bluuebunny/crossref_metadata_2025_split huggingface dataset:
Responses of Escherichia coli and Listeria monocytogenes to ozone treatment on non-host tomato: Efficacy of intervention and evidence of induced acclimation
Authors: Shu Xiaomei , Singh Manavi , Karampudi Naga Bhushana Rao , Bridges David F. , Kitazumi Ai , Wu Vivian C. H. , De los Reyes Benildo G. 
Published: August 2021

AbstractBecause of the continuous rise of foodborne illnesses caused by the consumption of raw fruits and vegetables, effective post-harvest anti-microbial strategies are needed. This study evaluated the dose × time effects on the anti-microbial action of ozone (O3) gas against the Gram-negative Escherichia coli O157:H7 and Gram-positive Listeria monocytogenes, which are common contaminants in fresh produce. The study on non-host tomato environment correlated the dose × time aspects of xenobiosis by examining the correlation between bacterial survival in terms of log-reduction and defense responses at the level of gene expression. In E. coli, low (1 μg O3/g of fruit) and moderate (2 μg O3/g of fruit) doses caused insignificant reduction in survival, while high dose (3 μg/g of fruit) caused significant reduction in survival in a time-dependent manner. In L. monocytogenes, moderate dose caused significant reduction even with short-duration exposure. Distinct responses to O3 xenobiosis between E. coli and L. monocytogenes are likely related to differences in membrane and cytoplasmic structure and components.Transcriptome profiling by RNA-Seq showed that primary defenses in E. coli were attenuated after exposure to a low dose, while the responses at moderate dose were characterized by massive upregulation of pathogenesis and stress-related genes, which implied the activation of defense responses. More genes were downregulated during the first hour at high dose, with a large number of such genes getting significantly upregulated after 2 hr and 3 hr. This trend suggests that prolonged exposure led to potential adaptation. In contrast, massive downregulation of genes was observed in L. monocytogenes regardless of dose and exposure duration, implying a mechanism of defense distinct from that of E. coli. The nature of bacterial responses revealed by this study should guide the selection of xenobiotic agents for eliminating bacterial contamination on fresh produce without overlooking the potential risks of adaptation.
FLARIM v2.0, an improved method to quantify transcript-ribosome interactions in vivo in the adult Drosophila brain
Authors: Richer Petra , Speese Sean D. , Logan Mary A. 
Published: August 2021

AbstractNeural injury triggers striking immune reactions from glial cells, including significant transcriptional and morphological changes, but it is unclear how these events are coordinated to mount an effective immune response. Here, we present a new variant of the Fluorescence assay to detect ribosome interactions with mRNA (FLARIM), which we term FLARIM v2.0, to visualize single immune gene transcripts and association with ribosomes in glia responding to neurodegeneration. Specifically, using an in vivo axotomy assay in Drosophila, we show that matrix metalloproteinase-1 (Mmp-1) mRNAs and associated ribosomes are detected in distal processes of reactive glia where they are actively engulfing degenerating axonal material, suggesting that local translation is an important component of the glial immune response to axotomy. This work also validates our enhanced FLARIM assay as a promising tool to investigate mechanisms of mRNA transport and translation in a wide range of in vitro and in vivo paradigms.
Partial endothelial-to-mesenchymal transition (EndMT) contributes to lumen re-organization after carotid artery ligation
Authors: Yamashiro Yoshito , Ramirez Karina , Nagayama Kazuaki , Tomita Shuhei , Kubota Yoshiaki , Yanagisawa Hiromi 
Published: August 2021

AbstractEndothelial-to-mesenchymal transition (EndMT) is a fundamental process in vascular remodeling. Carotid artery ligation is commonly used for induction of neointima formation and vessel stenosis; however, the precise regulatory mechanism of vascular remodeling is not entirely understood. In this study, we showed that resident endothelial cells (ECs) are the origin of neointima cells and ECs transiently expressed CD45 in the early stage of neointima formation accompanied by increased expression of EndMT markers. In vitro, CD45-positive EndMT was induced by stabilization of HIF-1α with cobalt chloride or VHL inhibitor in human primary ECs, which mimicked the hypoxic condition of ligated artery, and promoted the formation of integrin α11-SHARPIN complex. Notably, a CD45 phosphatase inhibitor disrupted this complex, thereby destabilizing cell-cell junctions. These results suggest that the CD45 activity is required for the retention of an EC phenotype and cell-cell junctions during EndMT (termed “partial EndMT”). We thus propose a novel mechanism of partial EndMT that contributes to lumen re-organization during vascular injury.
Cortical hyperexcitability drives dying forward ALS symptoms and pathology in mice
Authors: Haidar Mouna , Viden Aida , Cuic Brittany , Wang Taide , Rosier Marius , Tomas Doris , Mills Samuel A. , Govier-Cole Alistair , Djouma Elvan , Luikinga Sophia , Rytova Valeria , Barton Samantha K. , Gonsalvez David G. , Palmer Lucy M. , McLean Catriona , Kiernan Matthew C. , Vucic Steve , Turner Bradley J. 
Published: August 2021

AbstractAmyotrophic lateral sclerosis (ALS) is a progressive fatal disorder caused by degeneration of motor neurons in the cortex and spinal cord. The origin of ALS in the central nervous system is unclear, however cortical hyperexcitability appears as an early and intrinsic feature of ALS and has been linked to degeneration of spinal motor neurons via a dying-forward mechanism. Here, we implement chemogenetics to validate the dying forward hypothesis of ALS in mice. We show that chronic hyperexcitability of corticomotoneurons induced by excitatory chemogenetics results in motor symptoms and core neuropathological hallmarks of ALS, including corticomotoneuron loss, corticospinal tract degeneration and reactive gliosis. Importantly, corticomotoneuron loss was sufficient to drive degeneration of spinal motor neurons and neuromuscular junctions (NMJs), associated with cytoplasmic TAR DNA binding protein 43 (TDP-43) pathology. These findings establish a cortical origin of ALS mediated by neuronal hyperexcitability, consistent with a dying forward mechanism of neurodegeneration.
Machine-learning-guided library design cycle for directed evolution of enzymes: the effects of training data composition on sequence space exploration
Authors: Saito Yutaka , Oikawa Misaki , Sato Takumi , Nakazawa Hikaru , Ito Tomoyuki , Kameda Tomoshi , Tsuda Koji , Umetsu Mitsuo 
Published: August 2021

AbstractMachine learning (ML) is becoming an attractive tool in mutagenesis-based protein engineering because of its ability to design a variant library containing proteins with a desired function. However, it remains unclear how ML guides directed evolution in sequence space depending on the composition of training data. Here, we present a ML-guided directed evolution study of an enzyme to investigate the effects of a known “highly positive” variant (i.e., variant known to have high enzyme activity) in training data. We performed two separate series of ML-guided directed evolution of Sortase A with and without a known highly positive variant called 5M in training data. In each series, two rounds of ML were conducted: variants predicted by the first round were experimentally evaluated, and used as additional training data for the second-round prediction. The improvements in enzyme activity were comparable between the two series, both achieving enzyme activity 2.2–2.5 times higher than 5M. Intriguingly, the sequences of the improved variants were largely different between the two series, indicating that ML guided the directed evolution to the distinct regions of sequence space depending on the presence/absence of the highly positive variant in the training data. This suggests that the sequence diversity of improved variants can be expanded not only by conventional ML using the whole training data, but also by ML using a subset of the training data even when it lacks highly positive variants. In summary, this study demonstrates the importance of regulating the composition of training data in ML-guided directed evolution.
NLRP1B and NLRP3 control the host response following colonization with the commensal protist Tritrichomonas musculis
Authors: Chiaranunt Pailin , Burrows Kyle , Ngai Louis , Cao Eric Y. , Liang Helen , Streutker Catherine J. , Girardin Stephen E. , Mortha Arthur 
Published: August 2021

AbstractCommensal intestinal protozoa, unlike their pathogenic relatives, are neglected members of the mammalian microbiome. These microbes have a significant impact on the host’s intestinal immune homeostasis, typically by elevating anti-microbial host defense. Tritrichomonas musculis (T. mu), a protozoan gut commensal, strengthens the intestinal host defense against enteric Salmonella infections through Asc- and Il1r1-dependent Th1 and Th17 cell activation. However, the underlying inflammasomes mediating this effect remain unknown. Here, we report that colonization with T. mu results in an increase in luminal extracellular ATP, elevated levels of IL-1β, and increased numbers of IL-18 receptor-expressing Th1 and Th17 cells in the colon. Mice deficient in either Nlrp1b or Nlrp3 failed to display these protozoan-driven immune changes and lost resistance to enteric Salmonella infections even in the presence of T. mu. These findings demonstrate that T. mu-mediated host protection requires sensors of extra and intracellular ATP to confer resistance to enteric Salmonella infections.KEY POINTSIntestinal colonization with the commensal Tritrichomonas musculis elevates luminal ATP levelsNLRP1B and NLRP3 activation is required for Tritrichomonas musculis-driven Th cell response.
Cardiomyocyte BRAF and type 1 RAF inhibitors promote cardiomyocyte and cardiac hypertrophy in mice in vivo
Authors: Clerk A , Meijles DN , Hardyman MA , Fuller SJ , Chothani SP , Cull JJ , Cooper STE , Alharbi HO , Vanezis K , Felkin LE , Markou T , Leonard SJ , Shaw SW , Rackham OJL , Cook SA , Glennon PE , Sheppard MN , Sembrat JC , Rojas M , McTiernan CF , Barton PJ , Sugden PH 
Published: August 2021

AbstractThe extracellular signal-regulated kinase 1/2 (ERK1/2) cascade promotes cardiomyocyte hypertrophy and is cardioprotective, with the three RAF kinases forming a node for signal integration. Our aims were to determine if BRAF is relevant for human heart failure, if BRAF promotes cardiomyocyte hypertrophy, and if Type 1 RAF inhibitors developed for cancer (that paradoxically activate ERK1/2 at low concentrations: the “RAF paradox”) may have the same effect. BRAF was upregulated in heart samples from patients with heart failure compared with normal controls. We assessed the effects of activated BRAF in the heart using mice with tamoxifen-activated Cre for cardiomyocyte-specific knock-in of the activating V600E mutation into the endogenous gene. We used echocardiography to measure cardiac dimensions/function. Cardiomyocyte BRAFV600E induced cardiac hypertrophy within 10 d, resulting in increased ejection fraction and fractional shortening over 6 weeks. This was associated with increased cardiomyocyte size without significant fibrosis, consistent with compensated hypertrophy. The experimental Type 1 RAF inhibitor, SB590885, and/or encorafenib (a RAF inhibitor used clinically) increased ERK1/2 phosphorylation in cardiomyocytes, and promoted hypertrophy, consistent with a “RAF paradox” effect. Both promoted cardiac hypertrophy in mouse hearts in vivo, with increased cardiomyocyte size and no overt fibrosis. In conclusion, BRAF potentially plays an important role in human failing hearts, activation of BRAF is sufficient to induce hypertrophy, and Type 1 RAF inhibitors promote hypertrophy via the “RAF paradox”. Cardiac hypertrophy resulting from these interventions was not associated with pathological features, suggesting that Type 1 RAF inhibitors may be useful to boost cardiomyocyte function.
Cannabinoids differentially modulate behavioral and developmental responses to ethanol in Drosophila
Authors: He Jianzheng , Ng Si Yun , Tan Alice Mei Xien , Yong Wei Lin , Yu Fengwei 
Published: August 2021

AbstractProlonged prenatal or adult exposure to ethanol is detrimental to mental and physical well-being, resulting in developmental abnormalities, progressive addiction and ultimate death. A growing number of studies have shown the therapeutic potential of cannabinoids in ethanol-related behaviors in mammals. However, the potential pharmacological actions of cannabinoids in ethanol responses have not been examined in the model organism Drosophila melanogaster. Here, we systematically investigated the effects of various cannabinoids on ethanol preference, ethanol sensitivity and tolerance, and ethanol-induced developmental defect in Drosophila. We showed that treatment with the phytocannabinoid cannabidiol (CBD) displayed a significant decrease in preference for consuming ethanol in adult flies. Interestingly, cannabinoids exhibited differential roles in short- and long-term ethanol tolerance in flies. Although cannabinoids had no detectable effects on short-term ethanol tolerance, CBD and the endocannabinoid anandamide (AEA) suppressed long-term tolerance to ethanol. Moreover, ethanol exposure delayed larval-to-pupal development and increased larval/pupal size. Unexpectedly, treatment with CBD or endocannabinoids did not attenuate ethanol-induced developmental delay, instead, exacerbated its detrimental effect. Thus, our systematical study reveals, for the first time, a differential role of the cannabinoids in the modulation of ethanol-related responses in Drosophila.
Household transmission of SARS-CoV-2; a prospective longitudinal study showing higher viral load and transmissibility of the Alpha variant compared to previous strains
Authors: Julin Cathinka Halle , Robertson Anna Hayman , Hungnes Olav , Tunheim Gro , Bekkevold Terese , Laake Ida , Aune Idunn Forland , Rykkvin Rikard , Dorenberg Dagny Haug , Stene-Johansen Kathrine , Berg Einar Sverre , Bodin Johanna Eva , Oftung Fredrik , Steens Anneke , Næss Lisbeth Meyer 
Published: August 2021

SUMMARYObjectivesWe studied the secondary attack rate (SAR), risk factors, and precautionary practices of household transmission in a prospective, longitudinal study. We further compared transmission between the Alpha (B.1.1.7) variant and non-Variant of Concern (non-VOC) viruses.MethodsWe recruited households of 70 confirmed COVID-19 cases with 146 household contacts from May 2020 to May 2021. Participants donated biological samples 8 times over 6 weeks and answered questionnaires. Whole genome sequencing and droplet digital PCR were used to establish the SARS-CoV-2 variant and viral load.ResultsSARS-CoV-2 transmission occurred in 60% of the households, and the overall SAR for household contacts was 50%. The SAR was significantly higher for the Alpha variant (78%) compared with non-VOC viruses (43%) and was associated with a higher viral load. SAR was higher in household contacts aged ≥40 years (69%) than in younger contacts (40-47%), and for contacts of cases with loss of taste/smell. Children had lower viral loads and were more often asymptomatic than adults. Sleeping separately from the primary case reduced the risk of transmission.ConclusionsWe found substantial household transmission, particularly for the Alpha variant. Precautionary practices seem to reduce SAR, but preventing household transmission may become difficult with more contagious variants.
Seasonal betacoronavirus antibodies expansion post BNT161b2 vaccination associates with reduced SARS-CoV-2 VoCs neutralization
Authors: Dispinseri Stefania , Marzinotto Ilaria , Brigatti Cristina , Pirillo Maria Franca , Tolazzi Monica , Bazzigaluppi Elena , Canitano Andrea , Borghi Martina , Gallinaro Alessandra , Caccia Roberta , Vercesi Riccardo , McKay Paul F , Ciceri Fabio , Piemonti Lorenzo , Negri Donatella , Cinque Paola , Cara Andrea , Lampasona Vito , Scarlatti Gabriella 
Published: August 2021

AbstractSARS-CoV-2 vaccination is known to induce antibodies that recognize also variants of concerns (VoCs) of the virus. However, epidemiological and laboratory evidences indicate that these antibodies have a reduce neutralization ability against VoCs. We studied binding and neutralizing antibodies against the Spike RBD and S2 domains of the Wuhan-Hu-1 virus and its alpha and beta VoCs and of seasonal betacoronaviruses (HKU1 and OC43) in a cohort of 31 health care workers vaccinated with BNT162b2-Comirnaty and prospectively followed post-vaccination. The study of sequential samples collected up to 64 days post-vaccination showed that serological assays measuring IgG against Wuhan-Hu-1 antigens were a poor proxy for VoCs neutralization. In addition, in subjects who had asymptomatic or mild COVID-19 prior to vaccination the loss of nAbs following disease can be rapid and protection from re-infection post-vaccination is often no better than in naïve subjects. Interestingly, in health care workers naïve for SARS-CoV-2 infection, vaccination induced a rapid and transient reactivation of pre-existing seasonal coronaviruses IgG responses that was associated with a subsequent reduced ability to neutralize some VoCs.
Time needed to perform intermittent catheterization in adults with spinal cord injury: A pilot randomized controlled cross-over study
Authors: Gopalakrishnan Karthik , Nielsen Nick Fabrin , Ramirez Andrea L. , Sørensen Jeppe , Walter Matthias , Krassioukov Andrei V. 
Published: August 2021

ABSTRACTBackgroundIntermittent catheterization (IC), considered the gold standard for bladder management for individuals with spinal cord injury (SCI) with sufficient dexterity, is usually performed using hydrophilic (HPC) or non-hydrophilic (non-HPC) catheters. Currently, there is no evidence on the temporal burden associated with IC with either catheter.ObjectiveTo compare both catheters regarding their time requirement for IC and participant satisfaction.Design, setting and participantsTwenty individuals with chronic (>1-year) SCI at any spinal segment were randomized to undergo two cross-over assessments within 10 days (i.e., either starting with HPC or non-HPC). We measured time taken to perform IC using a 13 step pre-determined IC protocol (e.g., enter bathroom, wash hands, transfer to toilet, etc.). Furthermore, we assessed user satisfaction of both catheters using a Likert scale (i.e., strongly agree=5, strongly disagree=1).Outcome measures and statistical analysisTime (i.e., for each step and in total) to perform IC and participant satisfaction were compared between catheters using non-parametric statistics, i.e., Wilcoxon rank sign tests. Results are presented as median with interquartile range.Results and limitationsParticipants using HPCs spent less time to prepare a catheter [15 s (10-20) vs. 41 (20-69), p=0.002] and overall to perform IC [283 s (242-352) vs. 373 (249-441), p=0.01] compared to non-HPCs. Moreover, participants rated the preparation of HPCs to be easier [5 (4-5) vs. 4 (2-4), p=0.047] compared to non-HPCs. The key limitation of this pilot study was the sample size.ConclusionsPreparation and usage of HPCs for IC is easier and faster compared to non-HPCs. IC can be a significant temporal burden for SCI individuals.Patient summaryWe compared coated and uncoated catheters on time needed for intermittent catheterization and user satisfaction in individuals with spinal cord injury. Participants can manually empty their bladder quicker and easier with coated compared to uncoated catheters.
Peripheral Artery Disease and COVID-19 Outcomes: Insights from the Yale DOM-CovX Registry
Authors: Smolderen Kim G. , Lee Megan , Arora Tanima , Simonov Michael , Mena-Hurtado Carlos 
Published: August 2021

AbstractBackgroundBoth COVID-19 infection and peripheral arterial disease (PAD) cause hypercoagulability in patients, and it remains unknown whether PAD predisposes patients to experience worse outcomes when infected with SARS-CoV-2.MethodsThe Yale DOM-CovX Registry consecutively enrolled inpatients for SARS-CoV-2 between March 1, 2020, and November 10, 2020. Adjusted logistic regression models examined associations between PAD and mortality, stroke, myocardial infarction (MI), and major adverse cardiovascular events (MACE, all endpoints combined).ResultsOf the 3,830 patients were admitted with SARS-CoV-2, 50.5% were female, mean age was 63.1 ±18.4 years, 50.7% were minority race, and 18.3% (n = 693) had PAD. PAD was independently associated with increased mortality (OR=1.45, 95% CI 1.11-1.88) and MACE (OR=1.48, 95% CI 1.16-1.87). PAD was not independently associated with stroke (p=0.06) and MI (p=0.22).ConclusionPatients with PAD have a >40% odds of mortality and MACE when admitted with a SARS-CoV-2, independent of known risk factors.
DeepSARS: simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2
Authors: Yermanos Alexander , Hong Kai-Lin , Agrafiotis Andreas , Han Jiami , Nadeau Sarah , Valenzuela Cecilia , Azizoglu Asli , Ehling Roy , Gao Beichen , Spahr Michael , Neumeier Daniel , Chang Ching-Hsiang , Dounas Andreas , Petrillo Ezequiel , Nissen Ina , Burcklen Elodie , Feldkamp Mirjam , Beisel Christian , Oxenius Annette , Savic Miodrag , Stadler Tanja , Rudolf Fabian , Reddy Sai T. 
Published: August 2021

AbstractThe continued spread of SARS-CoV-2 and emergence of new variants with higher transmission rates and/or partial resistance to vaccines has further highlighted the need for large-scale testing and genomic surveillance. However, current diagnostic testing (e.g., PCR) and genomic surveillance methods (e.g., whole genome sequencing) are performed separately, thus limiting the detection and tracing of SARS-CoV-2 and emerging variants. Here, we developed DeepSARS, a high-throughput platform for simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2 by the integration of molecular barcoding, targeted deep sequencing, and computational phylogenetics. DeepSARS enables highly sensitive viral detection, while also capturing genomic diversity and viral evolution. We show that DeepSARS can be rapidly adapted for identification of emerging variants, such as alpha, beta, gamma, and delta strains, and profile mutational changes at the population level. DeepSARS sets the foundation for quantitative diagnostics that capture viral evolution and diversity.Abstract FigureGraphical abstractDeepSARS uses molecular barcodes (BCs) and multiplexed targeted deep sequencing (NGS) to enable simultaneous diagnostic detection and genomic surveillance of SARS-CoV-2.