A Case Demonstration of the Open Health Natural Language Processing Toolkit From the National COVID-19 Cohort Collaborative and the Researching COVID to Enhance Recovery Programs for a Natural Language Processing System for COVID-19 or Postacute Sequelae of SARS CoV-2 Infection: Algorithm Development and Validation.

BACKGROUND: A wealth of clinically relevant information is only obtainable within unstructured clinical narratives, leading to great interest in clinical natural language processing (NLP). While a multitude of approaches to NLP exist, current algorithm development approaches have limitations that can slow the development process. These limitations are exacerbated when the task is emergent, as is the case currently for NLP extraction of signs and symptoms of COVID-19 and postacute sequelae of SARS-CoV-2 infection (PASC). OBJECTIVE: This study aims to highlight the current limitations of existing NLP algorithm development approaches that are exacerbated by NLP tasks surrounding emergent clinical concepts and to illustrate our approach to addressing these issues through the use case of developing an NLP system for the signs and symptoms of COVID-19 and PASC. METHODS: We used 2 preexisting studies on PASC as a baseline to determine a set of concepts that should be extracted by NLP. This concept list was then used in conjunction with the Unified Medical Language System to autonomously generate an expanded lexicon to weakly annotate a training set, which was then reviewed by a human expert to generate a fine-tuned NLP algorithm. The annotations from a fully human-annotated test set were then compared with NLP results from the fine-tuned algorithm. The NLP algorithm was then deployed to 10 additional sites that were also running our NLP infrastructure. Of these 10 sites, 5 were used to conduct a federated evaluation of the NLP algorithm. RESULTS: An NLP algorithm consisting of 12,234 unique normalized text strings corresponding to 2366 unique concepts was developed to extract COVID-19 or PASC signs and symptoms. An unweighted mean dictionary coverage of 77.8% was found for the 5 sites. CONCLUSIONS: The evolutionary and time-critical nature of the PASC NLP task significantly complicates existing approaches to NLP algorithm development. In this work, we present a hybrid approach using the Open Health Natural Language Processing Toolkit aimed at addressing these needs with a dictionary-based weak labeling step that minimizes the need for additional expert annotation while still preserving the fine-tuning capabilities of expert involvement.

Evaluation of the survival of bacterial contaminants in an inhalable insulin powder.

Survival and growth of three model test bacterial species (Pseudomonas fluorescens, Staphylococcus epidermidis and Bacillus subtilis), present in the air and/or in the human respiratory tract, were tested in inhalable insulin-lactose powder under optimal relative humidity and temperature conditions (RH = 96% and optimal growth temperature for each bacterium of 26-37 degrees C) as well as representative indoor conditions (RH = 43% and T = 20 degrees C). The bacteria survived from 12 h to 7 days depending on the bacterial species and the test condition. P. fluorescens vegetative cells had the lowest and B. subtilis spores the highest survival rate. It was found that insulin-lactose powder does not support bacterial growth and that higher bacterial survival rate was found under representative indoor conditions. Selected experiments were performed with B. subtilis by adding sterile saliva into insulin-lactose powder to represent a typical condition for inhaler use. Furthermore, two other powders were tested with B. subtilis: one representing an inert powder without any nutrients (glass beads) and the other representing a powder with optimal nutrients (tryptic soy broth powder). The data indicate that the survival rate of B. subtilis did not change after the saliva was added and that the survival in insulin-lactose powder was similar to that in inert powder but lower than in powder with optimal nutrients. These results suggest that bacterial growth on residual powder in the inhaler under patient use conditions is unlikely and therefore the concern for patient safety is remote.

Unique pattern of renal κ light chain amyloid deposition with histiocytic transdifferentiation of tubular epithelial cells.

Monoclonal gammopathies can cause renal tubular epithelial damage through multiple mechanisms, the most common manifestation being myeloma cast nephropathy. Amyloid light chain amyloidosis rarely affects the renal tubular epithelium directly and usually causes glomerular injury. Amyloid deposition can also be seen within vessel walls and in the renal tubulointerstitium. Herein, we describe a unique pattern of κ light chain amyloid deposition involving the proximal tubule epithelium in a patient with multiple myeloma, characterized by intracellular amyloid globule formation with concomitant phenotypic changes suggestive of histiocytic differentiation of tubular epithelial cells. Amyloid pathogenesis is thought to be closely associated with the reticuloendothelial system, more specifically macrophages, and histiocytic differentiation of mesangial cells seems to be an integral step in glomerulopathic amyloid production. Our report proposes a similar mechanism of amyloidogenesis in the renal tubular epithelium.

Calcineurin-NFATc signaling pathway regulates AQP2 expression in response to calcium signals and osmotic stress.

The aquaporin (AQP)2 channel mediates the reabsorption of water in renal collecting ducts in response to arginine vasopressin (AVP) and hypertonicity. Here we show that AQP2 expression is induced not only by the tonicity-responsive enhancer binding protein (TonEBP)/nuclear factor of activated T cells (NFAT)5-mediated hypertonic stress response but also by the calcium-dependent calcineurin-NFATc pathway. The induction of AQP2 expression by the calcineurin-NFATc pathway can occur in the absence of TonEBP/NFAT5. Mutational and chromatin immunoprecipitation analyses revealed the existence of functional NFAT binding sites within the proximal AQP2 promoter responsible for regulation of AQP2 by NFATc proteins and TonEBP/NFAT5. Contrary to the notion that TonEBP/NFAT5 is the only Rel/NFAT family member regulated by tonicity, we found that hypertonicity promotes the nuclear translocation of NFATc proteins for the subsequent induction of AQP2 expression. Calcineurin activity was also found to be involved in the induction of TonEBP/NFAT5 expression by hypertonicity, thus further defining the signaling mechanisms that underlie the TonEBP/NFAT5 osmotic stress response pathway. The coordinate regulation of AQP2 expression by both osmotic stress and calcium signaling appears to provide a means to integrate diverse extracellular signals into optimal cellular responses.

Congenital progressive hydronephrosis (cph) is caused by an S256L mutation in aquaporin-2 that affects its phosphorylation and apical membrane accumulation.

Congenital progressive hydronephrosis (cph) is a spontaneous recessive mutation that causes severe hydronephrosis and obstructive nephropathy in affected mice. The mutation has been mapped to the distal end of mouse chromosome 15, but the mutated gene has not been found. Here, we describe the identification of a single base pair change in aquaporin-2 (Aqp2) in cph mutants through genetic linkage mapping. The C-T change led to the substitution of a Ser (S256) by a Leu in the cytoplasmic tail of the Aqp2 protein, preventing its phosphorylation at S256 and the subsequent accumulation of Aqp2 on the apical membrane of the collecting duct principal cells. The interference with normal trafficking of Aqp2 by this mutation resulted in a severe urine concentration defect. cph homozygotes demonstrated polydipsia and produced a copious amount of hypotonic urine. The urine concentration defect could not be corrected by [deamino-Cys1,D-Arg8]-vasopressin (DDAVP, a vasopressin analog), characteristic of nephrogenic diabetes insipidus. The nephrogenic diabetes insipidus symptoms and the absence of developmental defects in the pyeloureteral peristaltic machinery in the mutants before the onset of hydronephrosis suggest that the congenital obstructive nephropathy is most likely a result of the polyuria. This study has revealed the genetic basis for the classical cph mutation and has provided direct genetic evidence that S256 in Aqp2 is indispensable for the apical accumulation, but not the general glycosylation or membrane association, of Aqp2.