Miracle-dz/UniFAR-FTUs huggingface dataset:
Improving Timeliness of Antibiotic Administration Using a Provider and Pharmacist Facing Sepsis Early Warning System in the Emergency Department Setting: A Randomized Controlled Quality Improvement Initiative*

OBJECTIVES: Results of pre-post intervention studies of sepsis early warning systems have been mixed, and randomized clinical trials showing efficacy in the emergency department setting are lacking. Additionally, early warning systems can be resource-intensive and may cause unintended consequences such as antibiotic or IV fluid overuse. We assessed the impact of a pharmacist and provider facing sepsis early warning systems on timeliness of antibiotic administration and sepsis-related clinical outcomes in our setting. DESIGN: A randomized, controlled quality improvement initiative. SETTING: The main emergency department of an academic, safety-net healthcare system from August to December 2019. PATIENTS: Adults presenting to the emergency department. INTERVENTION: Patients were randomized to standard sepsis care or standard care augmented by the display of a sepsis early warning system–triggered flag in the electronic health record combined with electronic health record–based emergency department pharmacist notification. MEASUREMENTS AND MAIN RESULTS: The primary process measure was time to antibiotic administration from arrival. A total of 598 patients were included in the study over a 5-month period (285 in the intervention group and 313 in the standard care group). Time to antibiotic administration from emergency department arrival was shorter in the augmented care group than that in the standard care group (median, 2.3 hr [interquartile range, 1.4–4.7 hr] vs 3.0 hr [interquartile range, 1.6–5.5 hr]; p = 0.039). The hierarchical composite clinical outcome measure of days alive and out of hospital at 28 days was greater in the augmented care group than that in the standard care group (median, 24.1 vs 22.5 d; p = 0.011). Rates of fluid resuscitation and antibiotic utilization did not differ. CONCLUSIONS: In this single-center randomized quality improvement initiative, the display of an electronic health record–based sepsis early warning system–triggered flag combined with electronic health record–based pharmacist notification was associated with shorter time to antibiotic administration without an increase in undesirable or potentially harmful clinical interventions.
mTOR Signaling Regulates Metabolic Function in Oligodendrocyte Precursor Cells and Promotes Efficient Brain Remyelination in the Cuprizone Model

In demyelinating diseases, such as multiple sclerosis, primary loss of myelin and subsequent neuronal degeneration throughout the CNS impair patient functionality. While the importance of mechanistic target of rapamycin (mTOR) signaling during developmental myelination is known, no studies have yet directly examined the function of mTOR signaling specifically in the oligodendrocyte (OL) lineage during remyelination. Here, we conditionally deleted Mtor from adult oligodendrocyte precursor cells (OPCs) using Ng2-CreERT in male adult mice to test its function in new OLs responsible for remyelination. During early remyelination after cuprizone-induced demyelination, mice lacking mTOR in adult OPCs had unchanged OL numbers but thinner myelin. Myelin thickness recovered by late-stage repair, suggesting a delay in myelin production when Mtor is deleted from adult OPCs. Surprisingly, loss of mTOR in OPCs had no effect on efficiency of remyelination after lysophosphatidylcholine lesions in either the spinal cord or corpus callosum, suggesting that mTOR signaling functions specifically in a pathway dysregulated by cuprizone to promote remyelination efficiency. We further determined that cuprizone and inhibition of mTOR cooperatively compromise metabolic function in primary rat OLs undergoing differentiation. Together, our results support the conclusion that mTOR signaling in OPCs is required to overcome the metabolic dysfunction in the cuprizone-demyelinated adult brain. SIGNIFICANCE STATEMENT Impaired remyelination by oligodendrocytes contributes to the progressive pathology in multiple sclerosis, so it is critical to identify mechanisms of improving remyelination. The goal of this study was to examine mechanistic target of rapamycin (mTOR) signaling in remyelination. Here, we provide evidence that mTOR signaling promotes efficient remyelination of the brain after cuprizone-mediated demyelination but has no effect on remyelination after lysophosphatidylcholine demyelination in the spinal cord or brain. We also present novel data revealing that mTOR inhibition and cuprizone treatment additively affect the metabolic profile of differentiating oligodendrocytes, supporting a mechanism for the observed remyelination delay. These data suggest that altered metabolic function may underlie failure of remyelination in multiple sclerosis lesions and that mTOR signaling may be of therapeutic potential for promoting remyelination.
A Two‐Stage Flow Cytometry Strategy to Distinguish Single Cells from Doublets in Heterogeneous Cell Mixtures and Improve Cell Cluster Identification: Application to Human Monocyte Subpopulations

Flow cytometry is a powerful method, widely used to identify cell types present in tissues, to describe their phenotypes, and to purify cells for functional analyses. As a single cell technique, flow cytometry relies on identifying and excluding cell doublets and aggregates present in samples in the initial gating steps. This identification is based on detection of events generating electrical pulses falling outside of linear variations of pulse height, width, and area in a singlet population with increasing cell sizes. In heterogeneous cell mixtures, however, with cell types varying extensively in size and granularity, exclusion of doublets has the risk of removing single cells that co‐localize with doublets of another cell type. This is particularly the case when doublets of a smaller cell type overlap with large cells of a distinct, larger cell type. Here, we describe a gating method to reduce this risk. In this protocol, initial gating steps aim to segregate cells according to physical characteristics (such as size and granularity) and gene expression properties in order to obtain more homogeneous cell clusters. Doublet exclusion is then performed separately in each cluster, minimizing the risk of confusion between single cells and doublets. To illustrate this protocol, human blood monocytes are separated and analyzed. By implementing this protocol, we were able to reveal the existence of a population of large monocytes previously unrecognized using conventional gating strategies. In subsequent functional assays, we have shown that this novel population exhibits unique inflammatory responses, highlighting the need and pertinence of this approach to identify and characterize infrequent—yet functionally relevant—cell populations present in complex cell mixtures. © 2021 Wiley Periodicals LLC.
Codon usage and protein length-dependent feedback from translation elongation regulates translation initiation and elongation speed

Abstract Essential cellular functions require efficient production of many large proteins but synthesis of large proteins encounters many obstacles in cells. Translational control is mostly known to be regulated at the initiation step. Whether translation elongation process can feedback to regulate initiation efficiency is unclear. Codon usage bias, a universal feature of all genomes, plays an important role in determining gene expression levels. Here, we discovered that there is a conserved but codon usage-dependent genome-wide negative correlation between protein abundance and CDS length. The codon usage effects on protein expression and ribosome flux on mRNAs are influenced by CDS length; optimal codon usage preferentially promotes production of large proteins. Translation of mRNAs with long CDS and non-optimal codon usage preferentially induces phosphorylation of initiation factor eIF2α, which inhibits translation initiation efficiency. Deletion of the eIF2α kinase CPC-3 (GCN2 homolog) in Neurospora preferentially up-regulates large proteins encoded by non-optimal codons. Surprisingly, CPC-3 also inhibits translation elongation rate in a codon usage and CDS length-dependent manner, resulting in slow elongation rates for long CDS mRNAs. Together, these results revealed a codon usage and CDS length-dependent feedback mechanism from translation elongation to regulate both translation initiation and elongation kinetics.
“Nobody Knows How You’re Supposed to Interpret it:” End-user Perspectives on Prescription Drug Monitoring Program in Massachusetts

Objectives America’s overdose crisis spurred rapid expansion in the number and scope of prescription drug monitoring programs (PDMPs). As their public health impact remains contested, little is known about PDMP user experiences and perspectives. We explore perspectives of PDMP end-users in Massachusetts. Methods Between 2016 and 2017, we conducted semi-structured qualitative interviews on overdose crisis dynamics and PDMP experiences with a purposive sample of 18 stakeholders (prescribers, pharmacists, law enforcement, and public health regulators). Recordings were transcribed and double-coded using a grounded hermeneutic approach. Results Perspectives on prescription monitoring as an element of overdose crisis response differed across sectors, but narratives often critiqued PDMPs as poorly conceived to serve end-user needs. Respondents indicated that PDMP: (1) lacked clear orientation towards health promotion; (2) was not optimally configured or designed as a decision support tool, resulting in confusion over interpreting data to guide health care or law enforcement actions; and, (3) problematized communication and relationships between prescribers, pharmacists, and patients. Conclusions User insights must inform design, programmatic, and policy reform to maximize PDMP benefits while minimizing harm.
Ozone kinetics in low-pressure discharges

A combined experimental and modeling investigation of the ozone kinetics in the afterglow of pulsed direct current discharges in oxygen is carried out. The discharge is generated in a cylindrical silica tube of radius 1 cm, with short pulse durations between 0.5 and 2 ms, pressures in the range 1–5 Torr and discharge currents ∼40–120 mA. Time-resolved absolute concentrations of ground-state atoms and ozone molecules were measured simultaneously in situ, by two-photon absorption laser-induced fluorescence and ultraviolet absorption, respectively. The experiments were complemented by a self-consistent model developed to interpret the results and, in particular, to evaluate the roles of vibrationally excited ozone and of ozone formation on surfaces. It is found that vibrationally excited ozone, O3, plays an important role in the ozone kinetics, leading to a decrease in the ozone concentration and an increase in its formation time. In turn, the kinetics of O3 is strongly coupled with those of atomic oxygen and O2(a 1 g) metastables. Ozone formation at the wall does not contribute significantly to the total ozone production under the present conditions. Upper limits for the effective heterogeneous recombination probability of O atoms into ozone are established. (Some figures may appear in colour only in the online journal)
Structure of Usutu virus SAAR-1776 displays fusion loop asymmetry

Significance Usutu virus (USUV) was first identified in Africa in 1959; however, multiple, independent introductions via migratory birds and vector proliferation facilitated by climate change expanded the ecological niche of USUV across Europe. In humans, some African USUV lineages typically cause mild disease; however, the European strains, marked by their generally asymptomatic existence, possess the ability to cause meningoencephalitis and other neurological complications in some individuals. Treatment options for such infections are lacking. Our work provides the structural understanding into USUV biology and provides insight into pathogenesis for the development of therapies. The high-resolution structures highlight unique USUV characteristics as well as provide distinct details for the field of flavivirus biology, each with functional implications in the viral life cycle. Usutu virus (USUV) is an emerging arbovirus in Europe that has been increasingly identified in asymptomatic humans and donated blood samples and is a cause of increased incidents of neuroinvasive human disease. Treatment or prevention options for USUV disease are currently nonexistent, the result of a lack of understanding of the fundamental elements of USUV pathogenesis. Here, we report two structures of the mature USUV virus, determined at a resolution of 2.4 Å, using single-particle cryogenic electron microscopy. Mature USUV is an icosahedral shell of 180 copies of envelope (E) and membrane (M) proteins arranged in the classic herringbone pattern. However, unlike previous reports of flavivirus structures, we observe virus subpopulations and differences in the fusion loop disulfide bond. Presence of a second, unique E glycosylation site could elucidate host interactions, contributing to the broad USUV tissue tropism. The structures provide a basis for exploring USUV interactions with glycosaminoglycans and lectins, the role of the RGD motif as a receptor, and the inability of West Nile virus therapeutic antibody E16 to neutralize the mature USUV strain SAAR-1776. Finally, we identify three lipid binding sites and predict key residues that likely participate in virus stability and flexibility during membrane fusion. Our findings provide a framework for the development of USUV therapeutics and expand the current knowledge base of flavivirus biology.
Microwave-assisted reduction method under nitrogen atmosphere for synthesis and electrical conductivity improvement of reduced graphene oxide (rGO)

A facile method to synthesize rGO using a microwave-assisted method under N2-atmosphere conditions is reported. Two different reducing agents were used in this research, hydrazine hydrate and L-ascorbic acid (L-AA). The reduction of graphene oxide was completed in 3 minutes by the microwave-assisted method under N2-atmosphere conditions. The structures and morphologies of both rGOs prepared by this new method were confirmed by attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectrometry, X-ray diffraction (XRD), Raman spectroscopy, scanning electron microscopy (SEM), transmission electron microscopy (TEM) and energy dispersive X-ray spectrometry (EDX), confirming the formation of rGO. Four-point probe measurements showed an electrical conductivity of 18.10 S cm−1 for the rGO reduced by hydrazine hydrate and 12.02 S cm−1 for the rGO reduced by L-AA. Combining this new method with annealing at 300 °C for 30 min resulted in a higher electrical conductivity: up to 23.26 S cm−1 for the rGO reduced by hydrazine hydrate and up to 16.19 S cm−1 for the rGO reduced by L-AA. This study provides a new perspective on synthesizing rGO with high electrical conductivity using an effective and efficient method.
An in vivo selection-derived d-peptide for engineering erythrocyte-binding antigens that promote immune tolerance

Significance Erythrocyte-bound antigens can drive immune tolerance in an antigen-specific fashion. Exploiting this phenomenon, we developed a general strategy to promote antigen-specific tolerance by engineering peptide and protein antigens to bind erythrocytes. Here, we showed that a fully d-chiral peptide library can be selected in vivo for the de novo discovery of a robust erythrocyte binder, which we attached to peptide and protein antigens. An administration of engineered peptide and protein antigens mitigated antigen-specific inflammatory responses, suggesting the generalizability of this immune tolerance-induction strategy and validating our in vivo ligand selection technique. When displayed on erythrocytes, peptides and proteins can drive antigen-specific immune tolerance. Here, we investigated a straightforward approach based on erythrocyte binding to promote antigen-specific tolerance to both peptides and proteins. We first identified a robust erythrocyte-binding ligand. A pool of one million fully d-chiral peptides was injected into mice, blood cells were isolated, and ligands enriched on these cells were identified using nano-liquid chromatography–tandem mass spectrometry. One round of selection yielded a murine erythrocyte-binding ligand with an 80 nM apparent dissociation constant, Kd. We modified an 83-kDa bacterial protein and a peptide antigen derived from ovalbumin (OVA) with the identified erythrocyte-binding ligand. An administration of the engineered bacterial protein led to decreased protein-specific antibodies in mice. Similarly, mice given the engineered OVA-derived peptide had decreased inflammatory anti-OVA CD8+ T cell responses. These findings suggest that our tolerance-induction strategy is applicable to both peptide and protein antigens and that our in vivo selection strategy can be used for de novo discovery of robust erythrocyte-binding ligands.
Disease-related blood-based differential methylation in cystic fibrosis and its representation in lung cancer revealed a regulatory locus in PKP3 in lung epithelial cells

ABSTRACT Cystic fibrosis (CF) is a monogenic disease, characterized by massive chronic lung inflammation. The observed variability in clinical phenotypes in monozygotic CF twins is likely associated with the extent of inflammation. This study sought to investigate inflammation-related aberrant DNA methylation in CF twins and to determine to what extent acquired methylation changes may be associated with lung cancer. Blood-based genome-wide DNA methylation analysis was performed to compare the DNA methylomes of monozygotic twins, from the European CF Twin and Sibling Study with various degrees of disease severity. Putatively inflammation-related and differentially methylated positions were selected from a large lung cancer case-control study and investigated in blood by targeted bisulphite next-generation-sequencing. An inflammation-related locus located in the Plakophilin-3 (PKP3) gene was functionally analysed regarding promoter and enhancer activity in presence and absence of methylation using luciferase reporter assays. We confirmed in a unique cohort that monozygotic twins, even if clinically discordant, have only minor differences in global DNA methylation patterns and blood cell composition. Further, we determined the most differentially methylated positions, a high proportion of which are blood cell-type-specific, whereas others may be acquired and thus have potential relevance in the context of inflammation as lung cancer risk factors. We identified a sequence in the gene body of PKP3 which is hypermethylated in blood from CF twins with severe phenotype and highly variably methylated in lung cancer patients and controls, independent of known clinical parameters, and showed that this region exhibits methylation-dependent promoter activity in lung epithelial cells.
Personalization of Medical Treatment Decisions: Simplifying Complex Models while Maintaining Patient Health Outcomes

Background Personalizing medical treatments based on patient-specific risks and preferences can improve patient health. However, models to support personalized treatment decisions are often complex and difficult to interpret, limiting their clinical application. Methods We present a new method, using machine learning to create meta-models, for simplifying complex models for personalizing medical treatment decisions. We consider simple interpretable models, interpretable ensemble models, and noninterpretable ensemble models. We use variable selection with a penalty for patient-specific risks and/or preferences that are difficult, risky, or costly to obtain. We interpret the meta-models to the extent permitted by their model architectures. We illustrate our method by applying it to simplify a previously developed model for personalized selection of antipsychotic drugs for patients with schizophrenia. Results The best simplified interpretable, interpretable ensemble, and noninterpretable ensemble models contained at most half the number of patient-specific risks and preferences compared with the original model. The simplified models achieved 60.5% (95% credible interval [crI]: 55.2–65.4), 60.8% (95% crI: 55.5–65.7), and 83.8% (95% crI: 80.8–86.6), respectively, of the net health benefit of the original model (quality-adjusted life-years gained). Important variables in all models were similar and made intuitive sense. Computation time for the meta-models was orders of magnitude less than for the original model. Limitations The simplified models share the limitations of the original model (e.g., potential biases). Conclusions Our meta-modeling method is disease- and model- agnostic and can be used to simplify complex models for personalization, allowing for variable selection in addition to improved model interpretability and computational performance. Simplified models may be more likely to be adopted in clinical settings and can help improve equity in patient outcomes.
Circular Stapled Technique Versus Modified Collard Technique for Cervical Esophagogastric Anastomosis After Esophagectomy

Objective: This study was performed to investigate the efficacy of the modified Collard (MC) technique for reducing anastomotic stricture after esophagectomy compared with the circular stapled (CS) technique. Summary Background Data: The currently available techniques of anastomosis after esophagectomy are associated with a significant risk of anasto-motic complications. However, the optimal anastomotic technique after esophagectomy has not yet been established. Methods: We randomly allocated patients to either the CS group or the MC group. The primary endpoint was the incidence of anastomotic stricture. The secondary endpoints included the incidence of postoperative complications (including anastomotic leakage) and quality of life (QoL). All anastomoses were performed after indocyanine green evaluation for objective homogeni-zation of blood flow to the gastric conduit between the 2 techniques. Results: Among 100 randomized patients (CS group, n = 50; MC group, n = 50), anastomotic strictures were observed in 18 (42%) patients in the CS group and in no patients in the MC group. There were no significant between-group differences in anastomotic leakage (CS group, 7% vs MC group, 8%; P = 0.94). Quality of life domains of dysphagia and choking when swallowing at 3 months after surgery were significantly better in the MC group than in the CS group. Conclusions: The MC technique reduces the incidence of anastomotic stricture and improves postoperative quality of life. Furthermore, the incidence of anastomotic leakage is comparable between the 2 techniques based on accurate comparison under objective homogenization of the gastric conduit condition.