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It is difficult to capture the large numbers of steps and details that often characterize research in the biomedical sciences. We present an approach that is based on commercial spreadsheet software so it is easily adaptable by the experimentalist. The approach is designed to be compatible with an experimentalist’s workflow and allows the capture in real time of detailed information associated, in this use case, with laboratory actions involved in the process of editing, enriching and isolating clonal gene-edited pluripotent stem cell (PSC) lines. Intuitive features and flexibility allow an experimentalist without extensive programming knowledge to modify spreadsheets in response to changes in protocols and to perform simple queries. The experimental details are collated in a table format from which they can be exported in open standard formats (e.g., Extensible Markup Language (XML) or Comma Separated Values (CSV) for ingestion into a data repository supporting interoperability with other applications. We demonstrate a sample- and file-naming convention that enables the automated creation of file directory folders with human readable semantic titles within a local file system. These operations facilitate the local organization of documentation and data for each cell line derived from each transfection in designated folder/file locations. This approach is generalizable to experimental applications beyond this use case.

Erwin Gelfand, Andrew Snow, Joshua Milner and colleagues identify heterozygous CARD11 mutations associated with severe atopic disease in eight individuals from four families. They further show that the mutant CARD11 proteins exhibit both loss-of-function and dominant-interfering activity and that the cellular defects in patient T cells can be partially rescued by supplementing with glutamine. Few monogenic causes for severe manifestations of common allergic diseases have been identified. Through next-generation sequencing on a cohort of patients with severe atopic dermatitis with and without comorbid infections, we found eight individuals, from four families, with novel heterozygous mutations in CARD11 , which encodes a scaffolding protein involved in lymphocyte receptor signaling. Disease improved over time in most patients. Transfection of mutant CARD11 expression constructs into T cell lines demonstrated both loss-of-function and dominant-interfering activity upon antigen receptor–induced activation of nuclear factor-κB and mammalian target of rapamycin complex 1 (mTORC1). Patient T cells had similar defects, as well as low production of the cytokine interferon-γ (IFN-γ). The mTORC1 and IFN-γ production defects were partially rescued by supplementation with glutamine, which requires CARD11 for import into T cells. Our findings indicate that a single hypomorphic mutation in CARD11 can cause potentially correctable cellular defects that lead to atopic dermatitis.

Purpose Activating germline mutations in CARD11 have recently been linked to a rare genetic disorder associated with congenital B cell lymphocytosis. We describe a patient with a similar clinical phenotype who had a de novo germline G123D CARD11 mutation. Methods Whole exome sequencing was performed on DNA from the patient and his biological parents. Laboratory studies examined characteristics of the patient’s B and T lymphocytes. A CARD11 cDNA containing the mutation was transfected into a lymphocyte cell line to gain an understanding of its function. RNA sequencing was performed on samples from the patient and from patients with alternate germline CARD11 mutations and differential gene expression analysis was performed. Results The patient had a decade-long history of severe polyclonal B lymphocytosis in the 20,000–90,000 lymphocytes/mm 3 range, which was markedly exacerbated by EBV infection and splenectomy at different times. He had a heterozygous germline CARD11 mutation causing a G123D amino acid substitution, which was demonstrated to induce NF-κB activation in unstimulated lymphocytes. In contrast to previous patients with CARD11 mutations, this patient’s B cells exhibited higher expression of several cell cycle progression genes, as well as enhanced proliferation and improved survival following B cell receptor stimulation. Conclusions This is the third reported germline and first de novo CARD11 mutation shown to cause congenital B cell lymphocytosis. The mutation was associated with a dramatically greater lymphocytosis than in previously described cases, disproportionate to the level of constitutive NF-κB activation. However, comparative review of the patient’s clinical history, combined with additional genomic and functional analyses, underscore other important variables that may affect pathophysiology or regulate mutant CARD11 function in B cell proliferation and disease. We now refer to these patients as having BENTA disease ( B cell E xpansion with N F-κB and T cell A nergy).

Recombinant cDNA libraries to poly(A)RNA isolated from mature pollen of Zea mays and Tradescantia paludosa have been constructed. Northern blot analyses indicate that several of the clones are unique to pollen and are not expressed in vegetative tissues. The majority, however, are expressed both in pollen and vegetative tissues. Southern hybridizations show that the pollen specific sequences in corn are present in one or a very few copies in the genome. By using several of the clones as probes, it was found that there are at least two different groups of mRNAs with respect to their synthesis. The mRNAs of the first group represented by the pollen specific clones are synthesized after microspore mitosis and increase in concentration up to maturity. The second group, exemplified by actin mRNA, begins to accumulate soon after meiosis, reaches its maximum by late pollen interphase, and decreases thereafter. Although the actin mRNA and the pollen specific mRNAs studied show very different patterns of initiation of synthesis and accumulation during pollen development, the rates of decline of these mRNAs during the first 60 minutes of germination and pollen tube growth in Tradescantia are similar and reflect the previously observed declines in rates of protein synthesis during this period.

Nat. Genet.; 10.1038/ng.3898; corrected online 14 July 2017 In the version of this article initially published online, the name of author Neil Romberg appeared incorrectly as Neil D Romberg, and the affiliation of author Nina Jones was incorrect and should have appeared as Clinical Research Directorate/Clinical Monitoring Research Program, Leidos Biomedical Research, Inc.

Genet.; doi:10.1038/ng.3898; corrected online 14 July 2017 In the version of this article initially published online, the name of author Neil Romberg appeared incorrectly as Neil D Romberg, and the affiliation of author Nina Jones was incorrect and should have appeared as Clinical Research Directorate/Clinical Monitoring Research Program, Leidos Biomedical Research, Inc., NCI Campus at Frederick, Frederick, Maryland, USA. The content of this publication does not necessarily reflect the views or policies ofthe Department of Health and Human Services, nor does mention of trade names, commercial products or organizations imply endorsement by the US government.\"

In many forested ecosystems, the architecture and functional ecology of certain tree species define forest structure and their species-specific traits control ecosystem dynamics. Such foundation tree species are declining throughout the world due to introductions and outbreaks of pests and pathogens, selective removal of individual taxa, and over-harvesting. Through a series of case studies, we show that the loss of foundation tree species changes the local environment on which a variety of other species depend; how this disrupts fundamental ecosystem processes, including rates of decomposition, nutrient fluxes, carbon sequestration, and energy flow; and dramatically alters the dynamics of associated aquatic ecosystems. Forests in which dynamics are controlled by one or a few foundation species appear to be dominated by a small number of strong interactions and may be highly susceptible to alternating between stable states following even small perturbations. The ongoing decline of many foundation species provides a set of important, albeit unfortunate, opportunities to develop the research tools, models, and metrics needed to identify foundation species, anticipate the cascade of immediate, short- and long-term changes in ecosystem structure and function that will follow from their loss, and provide options for remedial conservation and management.

To assess the impact of a diagnostic test stewardship intervention focused on tracheal aspirate cultures. Quality improvement intervention. Tertiary care pediatric intensive care unit (PICU). Mechanically ventilated children admitted between 9/2018 and 8/2022. We developed and implemented a consensus guideline for obtaining tracheal aspirate cultures through a series of Plan-Do-Study-Act cycles. Change in culture rates and broad-spectrum antibiotic days of therapy (DOT) per 100 ventilator days were analyzed using statistical process control charts. A secondary analysis comparing the preintervention baseline (9/2018-8/2020) to the postintervention period (9/2020-8/2021) was performed using Poisson regression. The monthly tracheal aspirate culture rate prior to the COVID-19 pandemic (9/2018-3/2020) was 4.6 per 100 ventilator days. A centerline shift to 3.1 cultures per 100 ventilator days occurred in 4/2020, followed by a second shift to 2.0 cultures per 100 ventilator days in 12/2020 after guideline implementation. In our secondary analysis, the monthly tracheal aspirate culture rate decreased from 4.3 cultures preintervention (9/2018-8/2020) to 2.3 cultures per 100 ventilator days postintervention (9/2020-8/2021) (IRR 0.52, 95% CI 0.47-0.59, < 0.01). Decreases in tracheal aspirate culture use were driven by decreases in inappropriate cultures. Treatment of ventilator-associated infections decreased from 1.0 to 0.7 antibiotic courses per 100 ventilator days ( = 0.03). There was no increase in mortality, length of stay, readmissions, or ventilator-associated pneumonia postintervention. A diagnostic test stewardship intervention was both safe and effective in reducing the rate of tracheal aspirate cultures and treatment of ventilator-associated infections in a tertiary PICU.

Adolescence is a period of increased susceptibility to developing obesity-related health issues due to poor eating patterns and increased sedentary behaviors. Recommendations for pediatric obesity management include dietary assessments. However, adolescents often avoid food logging through traditional methods. The use of image-recognition dietary assessment apps in adolescents with obesity is not well studied. Eating for Wellness (E4W) is a mobile app that determines the nutritional content of meals from photos and incorporates nutritional goal setting. Nutritional data can be displayed for health care providers (HCPs) via the Clinician Portal, while the data are presented to the user in a manner that minimizes the focus on calorie counting. This study aims to evaluate the usability and feasibility of E4W, a mobile health app designed to improve dietary intake in adolescents with obesity attending an obesity clinic, using a phased approach. The overall study was conducted in 2 phases to refine and evaluate E4W. In Phase 1, usability was tested through 3 iterative cycles of patient interviews. A total of 14 patient participants, aged 12-18 years with a BMI≥97th percentile, were included. Participants performed standardized scenario-based tasks in E4W and provided feedback on the app. Two iterative cycles were conducted for HCPs (n=4). Refinements were made during each cycle based on issues encountered and feedback provided. In Phase 2, a pilot randomized controlled trial of 32 adolescents (16 adolescents enrolled in the experimental group for 1 month, and 16 controls enrolled for 1 month) was completed. Both groups met with their dietitian at baseline, midstudy, and 1 month following their baseline visit to discuss goals and eating patterns. The control group was instructed to take photos of all intake using their default phone camera, without access to E4W, while those in the experimental group received full access to E4W. The primary outcome was the feasibility of implementation. Secondary outcomes examined overall change in dietary intake and achievement of nutritional goals. Usability testing demonstrated that E4W and the Clinician Portal were easy to use, efficient, and well-liked by patients and HCPs. Feasibility testing revealed high patient acceptability scores. However, significant technical challenges were encountered. Although the use of E4W did not significantly impact patient engagement (control: mean 0.9, SD 0.7; experimental: mean 1.7, SD 1.9; P=.14), there were outliers in the experimental group with very high engagement and improved self-reported efficacy. Overall, there was no improvement in dietary intake, although assessment was hindered by poor adherence to traditional methods of food logging. E4W and the Clinician Portal were well-received by patients and HCPs. Further research is warranted and planned to determine if E4W can improve dietary intake and achievement of nutritional goals in adolescents with obesity. ClinicalTrials.gov NCT05548868; https://clinicaltrials.gov/study/NCT05548868.