Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics.

Single-cell and single-nucleus RNA-sequencing technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these technologies are gaining traction in plant molecular and developmental biology for elucidating the transcriptional changes across cell types in a specific tissue or organ, upon treatments, in response to biotic and abiotic stresses, or between genotypes. Despite the rapidly accelerating use of these technologies, collective and standardized experimental and analytical procedures to support the acquisition of high-quality data sets are still missing. In this commentary, we discuss common challenges associated with the use of single-cell transcriptomics in plants and propose general guidelines to improve reproducibility, quality, comparability, and interpretation and to make the data readily available to the community in this fast-developing field of research.

Factors Shaping the Implementation of Strategies to Prevent Acute Kidney Injury: A Qualitative Study.

Reducing the prevalence of acute kidney injury (AKI) is an important patient safety objective set forth by the National Quality Forum. Despite international guidelines to prevent AKI, there continues to be an inconsistent uptake of these interventions by cardiac teams across practice settings. The IMPROVE-AKI study was designed to test the effectiveness and implementation of AKI preventive strategies delivered through team-based coaching activities. Qualitative methods were used to identify factors that shaped sites' implementation of AKI prevention strategies. Semi-structured interviews were conducted with staff in a range of roles within the cardiac catheterization laboratories, including nurses, laboratory managers, and interventional cardiologists (N = 50) at multiple time points over the course of the study. Interview transcripts were qualitatively coded, and aggregated code reports were reviewed to construct main themes through memoing. In this paper, we report insights from semi-structured interviews regarding workflow, organizational culture, and leadership factors that impacted implementation of AKI prevention strategies.

Application of the threshold of toxicological concern (TTC) in the evaluation of drinking water contact chemicals.

The Threshold of Toxicological Concern (TTC) is an approach for assessing the safety of chemicals with low levels of exposure for which limited toxicology data are available. The original TTC criteria were derived for oral exposures from a distributional analysis of a dataset of 613 chemicals that identified 5th percentile no observed effect level (NOEL) values grouped within three tiers of compounds having specific structural functional groups and/or toxic potencies known as Cramer I, II and III classifications. Subsequent assessments of the TTC approach have established current thresholds to be scientifically robust. While the TTC has gained acknowledgment and acceptance by many regulatory agencies and organizations, use of the TTC approach in evaluating drinking water chemicals has been limited. To apply the TTC concept to drinking water chemicals, an exposure-based approach that incorporates the current weight of evidence for the target chemical is presented. Such an approach provides a comparative point of departure to the 5th percentile TTC NOEL using existing data, while conserving the allocation of toxicological resources for quantitative risk assessment to chemicals with greater exposure or toxicity. This approach will be considered for incorporation into NSF/ANSI/CAN 600, a health effects standard used in the safety evaluation of chemicals present in drinking water from drinking water contact additives and materials certified to NSF/ANSI/CAN 60 and 61, respectively.

Team-Based Coaching Intervention to Improve Contrast-Associated Acute Kidney Injury: A Cluster-Randomized Trial.

BACKGROUND: Up to 14% of patients in the United States undergoing cardiac catheterization each year experience AKI. Consistent use of risk minimization preventive strategies may improve outcomes. We hypothesized that team-based coaching in a Virtual Learning Collaborative (Collaborative) would reduce postprocedural AKI compared with Technical Assistance (Assistance), both with and without Automated Surveillance Reporting (Surveillance). METHODS: The IMPROVE AKI trial was a 2×2 factorial cluster-randomized trial across 20 Veterans Affairs medical centers (VAMCs). Participating VAMCs received Assistance, Assistance with Surveillance, Collaborative, or Collaborative with Surveillance for 18 months to implement AKI prevention strategies. The Assistance and Collaborative approaches promoted hydration and limited NPO and contrast dye dosing. We fit logistic regression models for AKI with site-level random effects accounting for the clustering of patients within medical centers with a prespecified interest in exploring differences across the four intervention arms. RESULTS: Among VAMCs' 4517 patients, 510 experienced AKI (235 AKI events among 1314 patients with preexisting CKD). AKI events in each intervention cluster were 110 (13%) in Assistance, 122 (11%) in Assistance with Surveillance, 190 (13%) in Collaborative, and 88 (8%) in Collaborative with Surveillance. Compared with sites receiving Assistance alone, case-mix-adjusted differences in AKI event proportions were -3% (95% confidence interval [CI], -4 to -3) for Assistance with Surveillance, -3% (95% CI, -3 to -2) for Collaborative, and -5% (95% CI, -6 to -5) for Collaborative with Surveillance. The Collaborative with Surveillance intervention cluster had a substantial 46% reduction in AKI compared with Assistance alone (adjusted odds ratio=0.54; 0.40-0.74). CONCLUSIONS: This implementation trial estimates that the combination of Collaborative with Surveillance reduced the odds of AKI by 46% at VAMCs and is suggestive of a reduction among patients with CKD. CLINICAL TRIAL REGISTRY NAME AND REGISTRATION NUMBER: IMPROVE AKI Cluster-Randomized Trial (IMPROVE-AKI), NCT03556293.

Intra-cavity frequency-doubled VECSEL system for narrow linewidth Rydberg EIT spectroscopy.

High-power, narrow-linewidth light sources in the visible and UV spectra are in growing demand, particularly as quantum information and sensing research proliferates. Vertical external-cavity surface-emitting lasers (VECSELs) with intra-cavity frequency conversion are emerging as an attractive platform to fill these needs. Using such a device, we demonstrate 3.5 MHz full-width half-maximum Rydberg-state spectroscopy via electromagnetically induced transparency (EIT). The laser's 690 mW of output power at a wavelength of 475 nm enables large Rabi frequencies and strong signal-to-noise ratio in shorter measurement times. In addition, we characterize the frequency stability of the VECSEL using the delayed self-heterodyne technique and direct comparison with a commercial external-cavity diode laser (ECDL). We measure the pre-doubled light's Lorentzian linewidth to be 2π × 5.3(2) kHz, and the total linewidth to be 2π × 23(2) kHz. These measurements provide evidence that intra-cavity frequency-doubled VECSELs can perform precision spectroscopy at and below the MHz level, and are a promising tool for contemporary, and future, quantum technologies.

Automated imaging of duckweed growth and development.

Duckweeds are the smallest angiosperms, possessing a simple body architecture and highest rates of biomass accumulation. They can grow near-exponentially via clonal propagation. Understanding their reproductive biology, growth, and development is essential to unlock their potential for phytoremediation, carbon capture, and nutrition. However, there is a lack of non-laborious and convenient methods for spatially and temporally imaging an array of duckweed plants and growth conditions in the same experiment. We developed an automated microscopy approach to record time-lapse images of duckweed plants growing in 12-well cell culture plates. As a proof-of-concept experiment, we grew duckweed on semi-solid media with and without sucrose and monitored its effect on their growth over 3 days. Using the PlantCV toolkit, we quantified the thallus area of individual plantlets over time, and showed that L. minor grown on sucrose had an average growth rate four times higher than without sucrose. This method will serve as a blueprint to perform automated high-throughput growth assays for studying the development patterns of duckweeds from different species, genotypes, and conditions.

Information Extraction From Electronic Health Records to Predict Readmission Following Acute Myocardial Infarction: Does Natural Language Processing Using Clinical Notes Improve Prediction of Readmission?

Background Social risk factors influence rehospitalization rates yet are challenging to incorporate into prediction models. Integration of social risk factors using natural language processing (NLP) and machine learning could improve risk prediction of 30-day readmission following an acute myocardial infarction. Methods and Results Patients were enrolled into derivation and validation cohorts. The derivation cohort included inpatient discharges from Vanderbilt University Medical Center between January 1, 2007, and December 31, 2016, with a primary diagnosis of acute myocardial infarction, who were discharged alive, and not transferred from another facility. The validation cohort included patients from Dartmouth-Hitchcock Health Center between April 2, 2011, and December 31, 2016, meeting the same eligibility criteria described above. Data from both sites were linked to Centers for Medicare & Medicaid Services administrative data to supplement 30-day hospital readmissions. Clinical notes from each cohort were extracted, and an NLP model was deployed, counting mentions of 7 social risk factors. Five machine learning models were run using clinical and NLP-derived variables. Model discrimination and calibration were assessed, and receiver operating characteristic comparison analyses were performed. The 30-day rehospitalization rates among the derivation (n=6165) and validation (n=4024) cohorts were 15.1% (n=934) and 10.2% (n=412), respectively. The derivation models demonstrated no statistical improvement in model performance with the addition of the selected NLP-derived social risk factors. Conclusions Social risk factors extracted using NLP did not significantly improve 30-day readmission prediction among hospitalized patients with acute myocardial infarction. Alternative methods are needed to capture social risk factors.

Organizing your space: The potential for integrating spatial transcriptomics and 3D imaging data in plants.

Plant cells communicate information for the regulation of development and responses to external stresses. A key form of this communication is transcriptional regulation, accomplished via complex gene networks operating both locally and systemically. To fully understand how genes are regulated across plant tissues and organs, high resolution, multi-dimensional spatial transcriptional data must be acquired and placed within a cellular and organismal context. Spatial transcriptomics (ST) typically provides a two-dimensional spatial analysis of gene expression of tissue sections that can be stacked to render three-dimensional data. For example, X-ray and light-sheet microscopy provide sub-micron scale volumetric imaging of cellular morphology of tissues, organs, or potentially entire organisms. Linking these technologies could substantially advance transcriptomics in plant biology and other fields. Here, we review advances in ST and 3D microscopy approaches and describe how these technologies could be combined to provide high resolution, spatially organized plant tissue transcript mapping.

Space: the final frontier - achieving single-cell, spatially resolved transcriptomics in plants.

Single-cell RNA-seq is a tool that generates a high resolution of transcriptional data that can be used to understand regulatory networks in biological systems. In plants, several methods have been established for transcriptional analysis in tissue sections, cell types, and/or single cells. These methods typically require cell sorting, transgenic plants, protoplasting, or other damaging or laborious processes. Additionally, the majority of these technologies lose most or all spatial resolution during implementation. Those that offer a high spatial resolution for RNA lack breadth in the number of transcripts characterized. Here, we briefly review the evolution of spatial transcriptomics methods and we highlight recent advances and current challenges in sequencing, imaging, and computational aspects toward achieving 3D spatial transcriptomics of plant tissues with a resolution approaching single cells. We also provide a perspective on the potential opportunities to advance this novel methodology in plants.

Effect of brexpiprazole on control of impulsivity in schizophrenia: A randomized functional magnetic resonance imaging study.

Impulsivity in schizophrenia is a risk factor for suicide, drug abuse, and other risk-taking behaviors. This exploratory, multicenter, randomized, double-blind, functional magnetic resonance imaging (fMRI) study assessed the effects of brexpiprazole on brain regions that control impulsive behavior. Thirty-eight outpatients with stable schizophrenia and impulsivity symptoms were randomized to 6 weeks of brexpiprazole 2 or 4 mg/day. The prespecified outcome measure was blood oxygen-level dependent (BOLD) activation in the right ventrolateral prefrontal cortex (VLPFC) during performance of tasks associated with inhibition/control of impulsivity: the go/no-go task and stop-signal task. Secondary objectives evaluated the efficacy, safety and tolerability of brexpiprazole. Over 6 weeks, patients receiving brexpiprazole had no statistically significant change in right VLPFC BOLD activation during the go/no-go task, but showed a significant decrease in right VLPFC BOLD activation during the stop-signal task. Brexpiprazole was also associated with significantly improved stop-signal reaction time (SSRT). No worsening of psychiatric symptoms, functioning, or impulsivity occurred in these patients. No unexpected safety or tolerability concerns were identified. In conclusion, brexpiprazole treatment among patients with schizophrenia and impulsivity was associated with decreased right VLPFC activation and decreased SSRT, supportive of a benefit of brexpiprazole on inhibition-related brain activation and behavior. ClinicalTrials.gov identifier: NCT02194933.

Cataract surgery in patients with left ventricular assist devices.

PURPOSE: To determine the safety and efficacy of cataract surgery in patients with left ventricular assist devices (LVADs). SETTING: Duke Eye Center, Durham, North Carolina, USA. DESIGN: Retrospective case series. METHODS: Electronic medical records were used to collect patient demographics, preoperative planning, intraoperative details, and postoperative outcomes of patients with LVADs who underwent cataract surgery between March 2012 and August 2019. RESULTS: A total of 53 cataract surgeries were identified involving 31 patients. Most patients were men (n = 27) and white (n = 25) with a mean age of 69.5 years. Preoperative biometry was unchanged from standard protocol. Femtosecond laser, intraoperative aberrometry, and/or a premium IOL was used in 25 cases (47.2%) . Patients were on warfarin, warfarin plus aspirin, and warfarin plus clopidogrel in 51.6% (n = 16), 45.2% (n = 14), and 3.2% (n = 1) of cases, respectively. Patients underwent topical anesthesia with monitored anesthesia care from an experienced LVAD team as planned with no episodes of hemodynamic instability, respiratory compromise, or intraoperative adverse events related to the LVAD. All patients were discharged the same day as surgery. There were no hospitalizations or deaths within 30 days that were attributed to the cataract procedure. At 1 month postoperatively, 61.1% of eyes were ±0.5 diopter of their predicted spherical equivalent (n = 11/18), with a high proportion of patients returning to local providers for postoperative care. CONCLUSIONS: Cataract surgery was safe and feasible in patients with LVADs when performed with additional perioperative considerations and in conjunction of an experienced LVAD team. The presence of LVAD itself was not found to be a contraindication for cataract surgery.

Return of old foes - recurrence of bacterial blight and Fusarium wilt of cotton.

Bacterial blight of cotton, caused by Xanthomonas citri subsp. malvacearum, and Fusarium wilt of cotton, caused by Fusarium oxysporum f. sp. vasinfectum, contribute cotton losses worldwide. Resurgences of these diseases in the United States were reported in recent years. There is a pressing need to understand pathogenicity and host responses to the pathogens and develop effective strategies for disease prevention and management. Here, we discuss the current status of bacterial blight and Fusarium wilt of cotton in the field as well as the knowledge of cotton resistance and susceptibility to these pathogens. In addition, we aim to provide insights into how these diseases are recurring and possible methods to use current technologies for biological control of these pathogens.