bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Opioid Sparing Anesthesia Protocol for Pediatric Open Inguinal Hernia Repair: A Quality Improvement Project
Authors: Chiem Jennifer L. , Franz Amber , Bishop Nicholas , Liston David , Low Daniel K. 
Published: March 2022

Introduction:
Using plan-do-study-act (PDSA) cycles, this quality improvement (QI) project aimed to standardize an anesthetic protocol to optimize multimodal pain management for pediatric open inguinal hernia repair (OIHR).

Methods:
PDSA cycle 1: in December 2017, we standardized the intraoperative OIHR anesthesia protocol by replacing transversus abdominis plane (TAP) or ilioinguinal-iliohypogastric (II) blocks and fentanyl with exclusively II blocks and fentanyl. PDSA cycle 2: in January 2019, we used an opioid sparing strategy, replacing II blocks and fentanyl with II blocks and dexmedetomidine. We used statistical process control (SPC) charts to analyze data from the medical record. Outcome measures included the percent of patients requiring rescue morphine in the postanesthesia care unit (PACU), maximum PACU pain score, PACU length of stay (LOS), and anesthesia preparation duration.

Results:
The team performed a total of 641 pediatric OIHRs between July 2015 and June 2021. The three groups included 203 patients in our baseline group, 127 patients in the PDSA cycle 1 group, and 311 patients in the PDSA cycle 2 group. Special cause variation (SCV) occurred for the percent of patients requiring rescue morphine, anesthesia preparation duration, and PACU LOS. The percent of patients requiring rescue morphine showed improvement. Anesthesia preparation duration improved compared to baseline. There was no SCV detected in the SPC chart for maximum PACU pain score.

Conclusion:
We implemented an opioid sparing anesthetic protocol for pediatric OIHR utilizing II blocks and dexmedetomidine without adversely affecting postoperative pain score or morphine rescue rate over 6 years.
Transcriptomic profiling implicates PAF1 in both active and repressive immune regulatory networks
Authors: Kenaston Matthew W. , Pham Oanh H. , Petit Marine J. , Shah Priya S. 
Published: March 2022

AbstractBackgroundSitting at the interface of gene expression and host-pathogen interaction, polymerase associated factor 1 complex (PAF1C) is a rising player in the innate immune response. The complex localizes to the nucleus and associates with chromatin to modulate RNA polymerase II (RNAPII) elongation of gene transcripts. Performing this function at both proximal and distal regulatory elements, PAF1C interacts with many host factors across such sites, along with several microbial proteins during infection. Therefore, translating the ubiquity of PAF1C into specific impacts on immune gene expression remains especially relevant.ResultsAdvancing past work, we treat PAF1 knockout cells with a slate of immune stimuli to identify key trends in PAF1-dependent gene expression with broad analytical depth. From our transcriptomic data, we confirm PAF1 is an activator of traditional immune response pathways as well as other cellular pathways correlated with pathogen defense. With this model, we employ computational approaches to refine how PAF1 may contribute to both gene activation and suppression. Specifically focusing on transcriptional motifs, we predict gene regulatory elements strongly associated with PAF1, including those implicated in an immune response. Overall, our results suggest PAF1 is potentially involved in innate immunity at several distinct axes of regulation.ConclusionsBy identifying PAF1-dependent gene expression across several pathogenic contexts, we confirm PAF1C to be a key mediator of innate immunity. Combining these transcriptomic profiles with potential regulatory networks corroborates the previously identified functions of PAF1C. With this, we foster new avenues for its study as a regulator of innate immunity, and our results will serve as a basis for targeted study of PAF1C in future validation studies.
Cell-free prototyping enables implementation of optimized reverse β-oxidation pathways in heterotrophic and autotrophic bacteria
Authors: Vögeli Bastian , Schulz Luca , Garg Shivani , Tarasava Katia , Clomburg James M. , Lee Seung Hwan , Gonnot Aislinn , Moully Elamar Hakim , Kimmel Blaise R. , Tran Loan , Zeleznik Hunter , Brown Steven D. , Simpson Séan D. , Mrksich Milan , Karim Ashty S. , Gonzalez Ramon , Köpke Michael , Jewett Michael C. 
Published: March 2022

AbstractCarbon-negative synthesis of biochemical products has the potential to mitigate global CO2 emissions. An attractive route to do this is the reverse β-oxidation (r-BOX) pathway coupled to the Wood-Ljungdahl pathway. Here, we optimized and implemented r-BOX for the synthesis of C4-C6 acids and alcohols. With a high-throughput in vitro prototyping workflow, we screened 762 unique pathway combinations using cell-free extracts tailored for r-BOX to identify enzyme sets for enhanced product selectivity. Implementation of these pathways into Escherichia coli generated designer strains for the selective production of butanoic acid (4.9 ±0.1 gL-1), hexanoic acid (3.06 ± 0.03 gL-1) and 1-hexanol (1.0 ± 0.1 gL-1) at the best performance reported to date in this bacterium. We also generated Clostridium autoethanogenum strains able to produce 1-hexanol from syngas, achieving a titer of 0.26 gL-1 in a 1.5-L continuous fermentation. Our strategy enables optimization of rBOX derived products for biomanufacturing and industrial biotechnology.
Paclitaxel-loaded Cationic Fluid Lipid Nanodiscs and Liposomes with Brush-Conformation PEG Chains Penetrate Breast Tumors and Trigger Caspase-3 Activation
Authors: Simón-Gracia Lorena , Scodeller Pablo , Fisher William S. , Sidorenko Valeria , Steffes Victoria M. , Ewert Kai K. , Safinya Cyrus R. , Teesalu Tambet 
Published: March 2022

AbstractNovel approaches are required to address the urgent need to develop lipid-based carriers of paclitaxel (PTX) and other hydrophobic drugs for cancer chemotherapy. Carriers based on cationic liposomes (CLs) with fluid (i.e., chain-melted) membranes (e.g., EndoTAG-1®) have shown promise in preclinical and late-stage clinical studies. Recent work found that the addition of a cone-shaped poly(ethylene glycol)-lipid (PEG-lipid) to PTX-loaded CLs (CLsPTX) promotes a transition to sterically stabilized, higher-curvature (smaller) nanoparticles consisting of a mixture of PEGylated CLsPTXand PTX-containing fluid lipid nanodiscs (nanodiscsPTX). These CLsPTXand nanodiscsPTXshow significantly improved uptake and cytotoxicity in cultured human cancer cells at PEG coverage in the brush regime (10 mol% PEG-lipid).Here, we studied the PTX loading,in vivocirculation half-life, and biodistribution of systemically administered CLsPTXand nanodiscsPTXand assessed their ability to induce apoptosis in triple-negative breast cancer-bearing immunocompetent mice. We focused onfluidrather thansolidlipid nanodiscs because of the significantly higher solubility of PTX in fluid membranes. At 5 and 10 mol% of a PEG-lipid (PEG5K-lipid, molecular weight of PEG 5000 g/mol), the mixture of PEGylated CLsPTXand nanodiscsPTXwas able to incorporate up to 2.5 mol% PTX without crystallization for at least 20 h. Remarkably, compared to preparations containing 2 and 5 mol% PEG5K-lipid (with the PEG chains in the mushroom regime), the particles at 10 mol% (with PEG chains in the brush regime) showed significantly higher blood half-life, tumor penetration and proapoptotic activity. Our study suggests that increasing the PEG coverage of CL-based drug nanoformulations can improve their pharmacokinetics and therapeutic efficacy.
Effect of TSS on anti-CVB3 through TLR3 pathway
Authors: Zheng Xiao-han , Yuan Ming-ming , Wang Yuan , Zhou Jing , Zhang Lei 
Published: March 2022

ABSTRACTToll-like receptors (TLRs) can recognize molecular patterns associated with microorganisms and induce immune responses. TLR3 is responsible for recognizing viruses and making hosts resistant to Coxsackie B3 (CVB3) infection. In this study, we found that Tectorigenin Sodium Sulfonate (TSS) has a TLR3 inhibitory effect and exerts strong anti-CVB3 activity through the TLR3 pathway both in vivo and in vitro. Balb/c mice were infected by ip injection of CVB3 virus, and subcutaneously injected with TSS at 264mg·Kg-1·d-1 for 7 d. The life extension rate of CVB3-infected mice was up to 46.67%, and the mean time to death was prolonged from 6.00 ± 0.47 d to 8.80 ± 2.78 d (P < 0.01). TSS was also able to reduce the level of weight loss in mice, significantly reduce the symptoms of myocarditis caused by CVB3, reduce the virus titer in the heart, improve the spleen and thymus index, and enhance immune function. We further explored the underlying mechanism of TSS in CVB3-infected HT-29 cells and mice: TSS reduced TLR3 expression and downregulated its downstream TRIF, TRAF6, IRF3, NF-κ B. MAPK, AP1 expression, reduced expression of IFN-β、IL-6、TNF-α. TSS has strong anti-CVB3 activity in vitro and in vivo and has the effect of inhibiting the activation of TLR3 pathway.IMPORTANCETSS is expected to be an antiviral drug for the treatment of CVB3 infection. Its regulatory effect on the immune system provides a new approach for antiviral research.
Vomocytosis ofCryptococcus neoformanscells from murine, bone marrow-derived dendritic cells
Authors: Pacifici Noah , Cruz-Acuña Melissa , Diener Agustina , Senthil Neeraj , Han Hyunsoo , Lewis Jamal S. 
Published: March 2022

AbstractCryptococcus neoformans(CN) cells survive within the acidic phagolysosome of macrophages for extended times, then escape without impacting the viability of the host cell via a phenomenon that has been coined ‘vomocytosis’. Through this mechanism, CN disseminate throughout the body, sometimes resulting in a potentially fatal condition - Cryptococcal Meningitis (CM). Justifiably, vomocytosis studies have focused primarily on macrophages, as alveolar macrophages within the lung act as first responders that ultimately expel this fungal pathogen. Herein, we hypothesize that dendritic cells (DCs), an innate immune cell with attributes that include phagocytosis and antigen presentation, can also act as ‘vomocytes’. Presciently, this report shows that vomocytosis of CN indeed occurs from DCs. Primarily through time-lapse microscopy imaging, we show that rates of vomocytosis events from DCs are comparable to those seen from macrophages and further, are independent of the presence of the CN capsule and infection ratios. Moreover, phagosome-altering drugs such as chloroquine and bafilomycin A, as well as the actin-modifying drug, cytochalasin B inhibit this phenomenon from DCs. Although DC immunophenotype does not affect the total number of vomocytic events, we observed differences in the numbers of CN per phagosome and expulsion times. Interestingly, these observations were similar in primary, murine macrophages. Understanding the vomocytic behavior of different phagocytes and their phenotypic subtypes is needed to help elucidate the full picture of the dynamic interplay between CN and the immune system. Critically, deeper insight into vomocytosis could reveal novel approaches to treat CM, as well as other immune-related conditions.
Sleep spindles favor emotion regulation over memory consolidation of stressors in PTSD
Authors: Natraj Nikhilesh , Neylan T.C. , Yack L.M. , Metzler T.J. , Woodward S.H. , Hubachek S.Q. , Dukes C. , Udupa N.S. , Mathalon D.H. , Richards A. 
Published: March 2022

AbstractPosttraumatic stress disorder (PTSD) is a trauma-induced debilitating condition, with symptoms that revolve around a declarative memory of a severe stressor. How does the brain process declarative and emotional information of stressors in PTSD? We evaluated the role of NREM sleep spindles in this process after exposure to laboratory stress, in a cohort of human subjects with different levels of PTSD symptoms. Subjects performed two laboratory visits: 1) a stress visit which involved exposure to negatively-valent images in the morning and 2) a control visit. In both visits subjects had a sleep/nap opportunity in the afternoon monitored via electroencephalography (EEG). In the stress visit, self-reported anxiety confirmed elevated stress immediately after stressor exposure (pre-sleep) that decayed to control levels post-sleep. An image recall session took place in the late afternoon. Overall, NREM2 spindle rates were elevated in the stress visit as compared to the control visit. This increase in NREM2 spindle rates, especially over occipital cortex, was significantly greater in subjects with high vs. low PTSD symptoms. However in high-PTSD subjects, NREM2 spindle rates correlated with poorer recall accuracy of stressor images as compared to lower symptomatic individuals while surprisingly correlating with a greater reduction in anxiety levels across sleep. Thus although NREM2 spindles are known to play a role in declarative memory processes, our findings highlight an important role of NREM sleep in favoring sleep-dependent anxiety regulation over memory consolidation after exposure to stressors in PTSD and shed new light on the function of NREM2 spindles in PTSD.
Single-cell dissection of a collective behaviour in honeybees
Authors: Traniello Ian M. , Bukhari Syed Abbas , Dibaeinia Payam , Serrano Guillermo , Avalos Arian , Ahmed Amy Cash , Sankey Alison L. , Hernaez Mikel , Sinha Saurabh , Zhao Sihai Dave , Catchen Julian , Robinson Gene E. 
Published: March 2022

AbstractUnderstanding how genotypic variation results in phenotypic variation, a major challenge in biology, is especially difficult for collective behaviour because collective group phenotypes arise from complex interactions between group members1. Honeybees aggressively defend their colony from attacks with highly integrated collective behaviour in which different groups of bees play specific roles, giving rise to distinct colony-level differences in aggression. A previous genome-wide association study of a population of Africanized honeybees (Apis mellifera scutellata) from Puerto Rico that recently evolved decreased aggression identified hundreds of genes with single nucleotide polymorphisms (SNPs) that associated with colony-level variation in aggression2. Many of these SNPs also showed strong signals of selection for decreased aggression2,3, but their influence on brain function was unknown. Using brain single-cell (sc) transcriptomics and sc gene regulatory network analysis, we show here that variants of these genes give rise to genetic differences in transcription factor-target gene relationships. These differences involved the activity of several TFs, some that have been previously associated with aggression, likesingle stranded-binding protein c31A, and some that have been associated with tissue morphogenesis but not behaviour, likeapontic. The activity of these and other TFs was located in specific brain cell populations related to olfaction and vision, the two sensory modalities that bees use in colony defence. They also implicate metabolism of serotonin, a neurochemical already known to influence honeybee aggression, but not from a genetic perspective. Surprisingly, genetic differences were more pronounced in the brains of forager bees than in similarly aged but more aggressive soldier bees, pointing to an evolutionary change in division of labour for colony defence. Our results demonstrate how group genetics can shape a collective phenotype by modulating individual brain gene regulatory network architecture.
Reproducible and sensitive micro-tissue RNA-sequencing from formalin-fixed paraffin-embedded tissue for spatial gene expression analysis
Authors: Matsunaga Hiroko , Arikawa Koji , Yamazaki Miki , Wagatsuma Ryota , Ide Keigo , Zachariah Samuel Ashok , Takamochi Kazuya , Suzuki Kenji , Hayashi Takuo , Hosokawa Masahito , Kambara Hideki , Takeyama Haruko 
Published: March 2022

AbstractSpatial transcriptome analysis of formalin-fixed paraffin-embedded (FFPE) tissues using RNA-sequencing (RNA-seq) provides interactive information on morphology and gene expression, which is useful for clinical applications. However, despite the advantages of long-term storage at room temperature, FFPE tissues may be severely damaged by methylene crosslinking and provide less gene information than fresh-frozen tissues. In this study, we proposed a sensitive FFPE micro-tissue RNA-seq method that combines the punching of tissue sections (diameter: 100 μm) and the direct construction of RNA-seq libraries. We evaluated a method using mouse liver tissues at 2 years after fixation and embedding and detected approximately 7,000 genes in micro-punched tissue-spots (thickness: 10 μm), similar to that detected with purified total RNA (2.5 ng) equivalent to the several dozen cells in the spot. We applied this method to clinical FFPE specimens of lung cancer that had been fixed and embedded 6 years prior, and found that it was possible to determine characteristic gene expression in the microenvironment containing tumor and non-tumor cells of different morphologies. This result indicates that spatial gene expression analysis of the tumor microenvironment is feasible using FFPE tissue sections stored for extensive periods in medical facilities.
DNA methylation in human gastric epithelial cells allows cell type-related plasticity and defines regional identity
Authors: Fritsche Kristin , Boccellato Francesco , Schlaermann Philipp , Koeppel Max , Denecke Christian , Gut Ivo , Meyer Thomas F. , Berger Hilmar 
Published: March 2022

AbstractBackgroundEpigenetic modifications in mammalian DNA are commonly manifested by DNA methylation. In the stomach, altered DNA methylation patterns have been observed following chronic Helicobacter pylori infections and in gastric cancer. In the context of epigenetic regulation, the regional nature of the stomach has been rarely considered in detail.ResultsHere, we describe the DNA methylation landscape across the phenotypically different regions of the healthy human stomach (i.e., antrum, corpus, fundus) together with the corresponding transcriptomes. We show that stable regional DNA methylation differences translate to a limited extent into regulation of the transcriptomic phenotype, indicating a largely permissive epigenetic regulation. We identify a small number of transcription factors with novel region-specific activity and likely epigenetic impact in the stomach, including GATA4, IRX5, IRX2, PDX1, and CDX2. Detailed analysis of the Wnt pathway reveals differential regulation along the craniocaudal axis, which involves non-canonical Wnt signaling in determining cell fate in the proximal stomach.ConclusionsBy extending our analysis to pre-neoplastic lesions and gastric cancers, we conclude that epigenetic dysregulation already characterizes intestinal metaplasia as a founding basis for functional changes in gastric cancer. Finally, our study provides a well-defined resource of regional stomach transcription and epigenetics as a starting point for further studies.
Glia-neuron coupling via a bipartite sialylation pathway promotes neural transmission and stress tolerance in Drosophila
Authors: Scott Hilary , Novikov Boris , Ugur Berrak , Allen Brooke , Mertsalov Ilya , Monagas-Valentin Pedro , Koff Melissa , Robinson Sarah Baas , Aoki Kazuhiro , Veizaj Raisa , Lefeber Dirk , Tiemeyer Michael , Bellen Hugo , Panin Vlad 
Published: March 2022

AbstractModification by sialylated glycans can affect protein functions, underlying mechanisms that control animal development and physiology. Sialylation relies on a dedicated pathway involving evolutionarily conserved enzymes, including CMP-sialic acid synthetase (CSAS) and sialyltransferase (SiaT) that mediate the activation of sialic acid and its transfer onto glycan termini, respectively. In Drosophila, CSAS and DSiaT genes function in the nervous system, affecting neural transmission and excitability. We found that these genes function in different cells: the function of CSAS is restricted to glia, while DSiaT functions in neurons. This partition of the sialylation pathway allows for regulation of neural functions via a glia-mediated control of neural sialylation. The sialylation genes were shown to be required for tolerance to heat and oxidative stress and for maintenance of the normal level of voltage-gated sodium channels. Our results uncovered a unique bipartite sialylation pathway that mediates glia-neuron coupling and regulates neural excitability and stress tolerance.Graphical Abstract
Patient-derived recombinant autoantibodies reveal the subcellular neuroglial distribution and heterogeneous interactome of leucine-rich glioma-inactivated 1
Authors: Ramirez-Franco Jorge , Debreux Kévin , Extremet Johanna , Maulet Yves , Belghazi Maya , Villard Claude , Sangiardi Marion , Youssouf Fahamoe , Far Lara El , Lévêque Christian , Debarnot Claire , Marchot Pascale , Paneva Sofija , Debanne Dominique , Russier Michael , Seagar Michael , Irani Sarosh R , Far Oussama El 
Published: March 2022

AbstractAutoantibodies against leucine-rich glioma-inactivated 1 (LGI1) occur in patients with encephalitis who present with frequent focal seizures and a pattern of amnesia consistent with focal hippocampal damage. To investigate whether the cellular and subcellular distribution of LGI1 may explain the localisation of these features, and gain broader insights into LGI1 neurobiology, we analysed the detailed localisation of LGI1, and the diversity of its protein interactome, in mouse brains using recombinant monoclonal LGI1-antibodies derived from encephalitis patients. Combined immunofluorescence and mass spectrometry analyses showed that LGI1 is enriched in excitatory and inhibitory synaptic contact sites, most densely within CA3 regions of the hippocampus. LGI1 is secreted in both neuronal somatodendritic and axonal compartments, and occurs in oligodendrocytic, neuro- oligodendrocytic and astro-microglial protein complexes. Proteomic data support the hypothesis that destabilization of Kv1 / MAGUK complexes by autoantibodies could promote excitability, but did not reveal LGI1 complexes with postsynaptic glutamate receptors. Our results extend our understanding of regional, cellular and subcellular LGI1 expression profiles and reveal novel LGI1-associated complexes, thus providing insights into the complex biology of LGI1 and its relationship to seizures and memory loss.