Determining an Appropriate Sample Size for Qualitative Interviews to Achieve True and Near Code Saturation: Secondary Analysis of Data.

BACKGROUND: In-depth interviews are a common method of qualitative data collection, providing rich data on individuals' perceptions and behaviors that would be challenging to collect with quantitative methods. Researchers typically need to decide on sample size a priori. Although studies have assessed when saturation has been achieved, there is no agreement on the minimum number of interviews needed to achieve saturation. To date, most research on saturation has been based on in-person data collection. During the COVID-19 pandemic, web-based data collection became increasingly common, as traditional in-person data collection was possible. Researchers continue to use web-based data collection methods post the COVID-19 emergency, making it important to assess whether findings around saturation differ for in-person versus web-based interviews. OBJECTIVE: We aimed to identify the number of web-based interviews needed to achieve true code saturation or near code saturation. METHODS: The analyses for this study were based on data from 5 Food and Drug Administration-funded studies conducted through web-based platforms with patients with underlying medical conditions or with health care providers who provide primary or specialty care to patients. We extracted code- and interview-specific data and examined the data summaries to determine when true saturation or near saturation was reached. RESULTS: The sample size used in the 5 studies ranged from 30 to 70 interviews. True saturation was reached after 91% to 100% (n=30-67) of planned interviews, whereas near saturation was reached after 33% to 60% (n=15-23) of planned interviews. Studies that relied heavily on deductive coding and studies that had a more structured interview guide reached both true saturation and near saturation sooner. We also examined the types of codes applied after near saturation had been reached. In 4 of the 5 studies, most of these codes represented previously established core concepts or themes. Codes representing newly identified concepts, other or miscellaneous responses (eg, "in general"), uncertainty or confusion (eg, "don't know"), or categorization for analysis (eg, correct as compared with incorrect) were less commonly applied after near saturation had been reached. CONCLUSIONS: This study provides support that near saturation may be a sufficient measure to target and that conducting additional interviews after that point may result in diminishing returns. Factors to consider in determining how many interviews to conduct include the structure and type of questions included in the interview guide, the coding structure, and the population under study. Studies with less structured interview guides, studies that rely heavily on inductive coding and analytic techniques, and studies that include populations that may be less knowledgeable about the topics discussed may require a larger sample size to reach an acceptable level of saturation. Our findings also build on previous studies looking at saturation for in-person data collection conducted at a small number of sites.

Capturing the Effects of Single Atom Substitutions on the Inhibition Efficiency of Glycogen Synthase Kinase-3ß Inhibitors via Markov State Modeling and Experiments.

Small modifications in the chemical structure of ligands are known to dramatically change their ability to inhibit the activity of a protein. Unraveling the mechanisms that govern these dramatic changes requires scrutinizing the dynamics of protein-ligand binding and unbinding at the atomic level. As an exemplary case, we have studied Glycogen Synthase Kinase-3ß (GSK-3ß), a multifunctional kinase that has been implicated in a host of pathological processes. As such, there is a keen interest in identifying ligands that inhibit GSK-3ß activity. One family of compounds that are highly selective and potent inhibitors of GSK-3ß is exemplified by a molecule termed COB-187. COB-187 consists of a five-member heterocyclic ring with a thione at C2, a pyridine substituted methyl at N3, and a hydroxyl and phenyl at C4. We have studied the inhibition of GSK-3ß by COB-187-related ligands that differ in a single heavy atom from each other (either in the location of nitrogen in their pyridine ring, or with the pyridine ring replaced by a phenyl ring), or in the length of the alkyl group joining the pyridine and the N3. The inhibition experiments show a large range of half-maximal inhibitory concentration (IC50) values from 10 nM to 10 µM, implying that these ligands exhibit vastly different propensities to inhibit GSK-3ß. To explain these differences, we perform Markov State Modeling (MSM) using fully atomistic simulations. Our MSM results are in excellent agreement with the experiments in that they accurately capture differences in the binding propensities of the ligands. The simulations show that the binding propensities are related to the ligands' ability to attain a compact conformation where their two aromatic rings are spatially close. We rationalize this result by sampling numerous binding and unbinding events via funnel metadynamics simulations, which show that indeed while approaching the bound state, the ligands prefer to be in their compact conformation. We find that the presence of nitrogen in the aromatic ring increases the probability of attaining the compact conformation. Protein-ligand binding is understood to be dictated by the energetics of interactions and entropic factors, like the release of bound water from the binding pockets. This work shows that changes in the conformational distribution of ligands due to atom-level modifications in the structure play an important role in protein-ligand binding.

Maximizing the effectiveness of 1.5 mg levonorgestrel for emergency contraception: The case for precoital use.

Objectives: U.S. and World Health Organization Selected Practice Recommendations for Contraceptive Use state people may have an advanced supply of emergency contraception (EC) to minimize treatment delays. We sought to characterize the potential improvement in effectiveness of 1.5 mg levonorgestrel (LNG-EC) if it were taken up to a few hours before unprotected sex. Study design: We expanded on an existing mathematical model for the maximum attainable effectiveness of LNG-EC, assuming it exclusively works to disrupt ovulation, and compared results with point estimates from nine studies when it was taken up to 72 hours after sex. We then modelled how effectiveness might have improved if subjects had taken LNG-EC up to 3 hours before sex. Results: Taking LNG-EC immediately after sex could potentially reduce the risk of unintended pregnancy by 91%. However, population-average maximum attainable effectiveness levels ranged from just 49% to 67% when accounting for the distributions of postcoital treatment delays in the example studies. If half the subjects had taken it 3 hours before sex, then maximum effectiveness levels would have ranged from 70% to 81%. Conclusions: At the individual level, taking LNG-EC a few hours before sex is a logical extension of Selected Practice Recommendations regarding an advanced supply of EC and, based on our modeling, should be advocated for people who can reasonably anticipate an unprotected sex act. In the absence of more clinical data, however, people should not routinely rely on precoital use of LNG-EC to prevent pregnancy unless modern, effective contraceptives are inaccessible to them. Implications: Based on mathematical modeling, individuals who anticipate needing to take LNG-EC for an impending unprotected act of sex could further reduce their chance of an undesired pregnancy by taking it a few hours in advance.

Avenues for prevention using the epidemiology of sport-related concussion from a large high school surveillance study.

OBJECTIVE: Epidemiology provides fundamental opportunities to protect student-athlete health. The goal of this study was to describe the epidemiology of sport-related concussion (SRC) across 8 years (2015/2016-2022/2023) and compare boys' and girls' sports for SRC incidence and SRC mechanisms. METHODS: This was a retrospective cohort study performed using a statewide high school head injury surveillance system of high school student-athletes (n = 2,182,128; boys, n = 1,267,389; girls, n = 914,739). Exposures of interest included study year and boys and girls in comparable sports. Clinical incidence was calculated by dividing SRC counts in each sport by the number of participants per 100 player-seasons and presented with 95% CIs. The 2019/2020 and 2020/2021 data were included in the analysis, however caution is warranted due to the COVID-19 pandemic. Clinical incidence ratios (CIRs) were estimated for sex-comparable sports, and significance was determined if 95% CIs excluded 1.00. The authors compared mechanism of injury in boys' and girls' comparable sports with chi-square analyses (p < 0.05). RESULTS: Among 25,482 total SRCs, the overall clinical incidence of SRC for all boys and girls was 1.17 (95% CI 1.15-1.18) per 100 player-seasons across all years. Across all years, the overall clinical incidence in boys' sports was 1.34 (95% CI 1.32-1.36) per 100 player-seasons, and 0.93 (95% CI 0.91-0.95) per 100 player-seasons in girls' sports. Boys' sports with the highest clinical incidence included football, ice hockey, and wrestling. Girls' sports with the highest clinical incidence included basketball, soccer, lacrosse, competitive cheer, and gymnastics. Girls consistently had higher SRC rates relative to boys for baseball/softball, basketball, and soccer (CIR range 1.65 [95% CI 1.41-1.93] to 3.32 [95% CI 2.67-4.16]). Girls had lower SRC in lacrosse in 2015/2016 (CIR 0.63, 95% CI 0.40-0.97); no difference in 2016/2017-2020/2021, but had higher clinical incidence in 2021/2022 (CIR 1.69, 95% CI 1.18-2.44) relative to boys. In boys the most common mechanism of SRC occurred from person-to-person contact (n = 8752, 62.8%), whereas girls commonly sustained SRC from person-to-object contact (n = 2369, 33.4%) and from person-to-person contact (n = 2368, 33.4%). There were significant associations between boys' versus girls' sports and mechanism of injury within baseball/softball (χ2 = 12.71, p = 0.005); basketball (χ2 = 36.47, p < 0.001); lacrosse (χ2 = 185.15, p < 0.001); and soccer (χ2 = 122.70, p < 0.001). CONCLUSIONS: These findings can help understand the potential impact of interventions aimed at preventing or reducing SRC. Including girls' sports within this study extends research for a largely underrepresented group.

Machine learning without a processor: Emergent learning in a nonlinear analog network.

Standard deep learning algorithms require differentiating large nonlinear networks, a process that is slow and power-hungry. Electronic contrastive local learning networks (CLLNs) offer potentially fast, efficient, and fault-tolerant hardware for analog machine learning, but existing implementations are linear, severely limiting their capabilities. These systems differ significantly from artificial neural networks as well as the brain, so the feasibility and utility of incorporating nonlinear elements have not been explored. Here, we introduce a nonlinear CLLN-an analog electronic network made of self-adjusting nonlinear resistive elements based on transistors. We demonstrate that the system learns tasks unachievable in linear systems, including XOR (exclusive or) and nonlinear regression, without a computer. We find our decentralized system reduces modes of training error in order (mean, slope, curvature), similar to spectral bias in artificial neural networks. The circuitry is robust to damage, retrainable in seconds, and performs learned tasks in microseconds while dissipating only picojoules of energy across each transistor. This suggests enormous potential for fast, low-power computing in edge systems like sensors, robotic controllers, and medical devices, as well as manufacturability at scale for performing and studying emergent learning.

Utility of Body Weight, Urine Color, and Thirst Perception (WUT) in Determining Hydration in Young Adults.

OBJECTIVE: The primary aim of this study was to assess the efficacy of the weight, urine, thirst (WUT) framework in predicting dehydration after a body water manipulation protocol, while concurrently determining the individual and interactive contributions of the model components. METHODS: The total study sample was 93 participants (female, n = 47), recruited from two institutions. Phase 1 involved collecting daily hydration measures from free-living participants (Study 1, 58 participants for 3 days; Study 2, 35 participants for 7 days). Phase 2 entailed a two-hour passive heating protocol, where participants from Study 2 were randomly assigned to one of three groups that manipulated total body water over 24-hours using passive heating and fluid restriction. During each Phase, participants provided urine samples, underwent body mass measurements, and completed questionnaires pertaining to thirst perception. Morning and 24-hour urine samples were assessed for color, osmolality, and specific gravity. Differences between intervention groups, based on the probability of hydration status, were examined (ANOVA) and ridge regression analysis assessed the relative importance of variables within the WUT model. RESULTS: The study revealed significant differences among the intervention groups for predicted probability of dehydration, as determined by changes in body mass (p = 0.001), urine color (p = 0.044), and thirst perception (p < 0.001). Binomial ridge regression indicated that change in body mass (58%) and thirst perception (26%) were the most influential predictors of dehydration. CONCLUSIONS: These data support use of an enhanced version of the WUT model, underscoring the significance of changes in body mass and thirst perception in the assessment of hydration status.

Expression and Functional Characterization of Oryzacystatin II Protein from Oryza sativa L. Indica Rice and Its Potential Role as a Bioinsecticide Against Major Insects of Rice.

Rice (Oryza sativaL.) is a crucial staple food crop globally, facing significant challenges from various pests that affect crop productivity and quality. Conventional pesticide usage has limitations, necessitating the development of sustainable pest management strategies. This study focuses on the expression, purification, and functional characterization of Oryzacystatin II (OC-II), a protein derived from O. sativaL. Indica rice, with the intent to evaluate its potential as a bioinsecticide against rice pests. The OC-II gene was expressed and purified, and purification confirmed its molecular weight (∼12 kDa) and protein sequence through LC-MS/MS analysis and Western blotting. The IC50 value of OC-II was calculated as 0.06 µM, and the inhibition was identified as a competitive inhibition. The protein exhibited efficient control of both pests at the nymph and adult stages, with lower probing marks observed on treated plants. The inhibition of cathepsin B enzyme activity in insects further confirmed the bioactivity of the OC-II protein. Molecular docking and molecular dynamics simulations provided insights into the interaction between the OC-II protein and cathepsin enzymes reported in BPH and WBPH. Further investigations can focus on optimizing production methods and exploring the specificity and efficacy of the OC-II protein against other crop pests to enhance its practical applications.

Indigo production identifies hotspots in cytochrome P450 BM3 for diversifying aromatic hydroxylation.

Evolution of P450 BM3 is a topic of extensive research, but screening the various substrate/reaction combinations remains a time-consuming process. Indigo production has the potential to serve as a simple high-throughput method for reaction screening, as bacterial colonies expressing indigo (+) variants can be visually identified via their blue phenotype. Indigo (+) single variants, indigo (-) single variants and a combinatorial library, containing mutations that enable the blue phenotype, were screened for their ability to hydroxylate a panel of 12 aromatic compounds using the 4-aminoantipyrine colorimetric assay. Recombination of indigo (+) single variants to create a multiple-variant library is a particularly useful strategy, as all top performing P450 BM3 variants with high hydroxylation activity were either indigo (+) single variants or contained multiple substitutions. Furthermore, active variants, as determined using the 4-AAP assay, were further characterized and several variants were identified that gave more than 90% conversion with 1,3-dichlorobenzene and predominantly formed 2,6-dichlorophenol; other variants showed significant substrate selectivity. This supports the hypothesis that substitution at positions that enable the indigo (+) phenotype, or hotspot residues, is a general mechanism for increasing aromatic hydroxylation activity. Overall, this research demonstrates that indigo (+) single variants, identified via colorimetric colony-based screening, may be recombined to generate a multiply-substituted variant library containing many variants with high aromatic hydroxylation activity. The combination of colony-based screening and other screening assays greatly accelerates enzyme engineering, as readily-identified indigo (+) single variants can be recombined to create a library of active multiple variants without extensive screening of single variants.

Feedback and Financial Incentives for Reducing Cell Phone Use While Driving: A Randomized Clinical Trial.

Importance: Handheld phone use while driving is a major factor in vehicle crashes. Scalable interventions are needed to encourage drivers not to use their phones. Objective: To test whether interventions involving social comparison feedback and/or financial incentives can reduce drivers' handheld phone use. Design, Setting, and Participants: In a randomized clinical trial, interventions were administered nationwide in the US via a mobile application in the context of a usage-based insurance program (Snapshot Mobile application). Customers were eligible to be invited to participate in the study if enrolled in the usage-based insurance program for 30 to 70 days. The study was conducted from May 13 to June 30, 2019. Analysis was completed December 22, 2023. Interventions: Participants were randomly assigned to 1 of 6 trial arms for a 7-week intervention period: (1) control; (2) feedback, with weekly push notification about their handheld phone use compared with that of similar others; (3) standard incentive, with a maximum $50 award at the end of the intervention based on how their handheld phone use compared with similar others; (4) standard incentive plus feedback, combining interventions of arms 2 and 3; (5) reframed incentive plus feedback, with a maximum $7.15 award each week, framed as participant's to lose; and (6) doubled reframed incentive plus feedback, a maximum $14.29 weekly loss-framed award. Main Outcome and Measure: Proportion of drive time engaged in handheld phone use in seconds per hour (s/h) of driving. Analyses were conducted with the intention-to-treat approach. Results: Of 17 663 customers invited by email to participate, 2109 opted in and were randomized. A total of 2020 drivers finished the intervention period (68.0% female; median age, 30 [IQR, 25-39] years). Median baseline handheld phone use was 216 (IQR, 72-480) s/h. Relative to control, feedback and standard incentive participants did not reduce their handheld phone use. Standard incentive plus feedback participants reduced their use by -38 (95% CI, -69 to -8) s/h (P = .045); reframed incentive plus feedback participants reduced their use by -56 (95% CI, -87 to -26) s/h (P < .001); and doubled reframed incentive plus feedback participants reduced their use by -42 s/h (95% CI, -72 to -13 s/h; P = .007). The 5 active treatment arms did not differ significantly from each other. Conclusions and Relevance: In this randomized clinical trial, providing social comparison feedback plus incentives reduced handheld phone use while individuals were driving. Trial Registration: ClinicalTrials.gov Identifier: NCT03833219.

The transcriptional co-repressor Runx1t1 is essential for MYCN-driven neuroblastoma tumorigenesis.

MYCN oncogene amplification is frequently observed in aggressive childhood neuroblastoma. Using an unbiased large-scale mutagenesis screen in neuroblastoma-prone transgenic mice, we identify a single germline point mutation in the transcriptional corepressor Runx1t1, which abolishes MYCN-driven tumorigenesis. This loss-of-function mutation disrupts a highly conserved zinc finger domain within Runx1t1. Deletion of one Runx1t1 allele in an independent Runx1t1 knockout mouse model is also sufficient to prevent MYCN-driven neuroblastoma development, and reverse ganglia hyperplasia, a known pre-requisite for tumorigenesis. Silencing RUNX1T1 in human neuroblastoma cells decreases colony formation in vitro, and inhibits tumor growth in vivo. Moreover, RUNX1T1 knockdown inhibits the viability of PAX3-FOXO1 fusion-driven rhabdomyosarcoma and MYC-driven small cell lung cancer cells. Despite the role of Runx1t1 in MYCN-driven tumorigenesis neither gene directly regulates the other. We show RUNX1T1 forms part of a transcriptional LSD1-CoREST3-HDAC repressive complex recruited by HAND2 to enhancer regions to regulate chromatin accessibility and cell-fate pathway genes.

Primary Practice Patterns For The Initial Management of Open Angle Glaucoma.

PRCIS: About 1/4th of survey respondents from an ASCRS database initiate treatment for primary open-angle glaucoma (POAG) with laser trabeculoplasty. Factors impacting physicians' choice of laser versus topical treatment for POAG were explored. PURPOSE: To characterize primary treatment preferences (topical medication vs. laser trabeculoplasty or intracameral sustained release implants) in primary open-angle glaucoma (POAG) patients and determine factors related to primary intervention selection. METHODS: A 33-question survey was distributed to an American Society of Cataract and Refractive Surgery database on treatment choices made by ophthalmologists for POAG. Data collected included country of practice, years of practice, completion of glaucoma fellowship training, type of practice, and preference for first line of treatment of POAG. Multiple logit regression was used to compare the effect of covariates on physicians' choice of either topical medication or laser trabeculoplasty for POAG. RESULTS: A total of 252/19,246 (1.3%) of surveys were returned. Almost three-quarters of respondents utilized topical medication as first line of treatment for POAG (73.6%) while 26.4% preferred to start with laser treatment. Significant variables associated with the selection of laser (vs. drops) are practicing in the U.S. (odds ratio [OR] 2.85, 95% confidence interval [CI] 1.33-6.10), more recent completion of ophthalmology residency (OR 1.95, 95% CI 1.00-3.77), greater volume of minimally invasive glaucoma surgeries (MIGS) (OR 1.68, 95% CI 1.18-2.40), and a glaucoma patient base greater than 25% (OR 2.21, 95% CI 1.09-4.48). CONCLUSIONS: For the first line treatment of POAG, laser trabeculoplasty is more likely to be preferred, over topical drops, by U.S. physicians who are relatively new in practice, who have a larger glaucoma patient base and who perform more MIGS.

Toxicology findings from drivers suspected of drug-impaired driving in Ontario (2008-2019).

OBJECTIVE: This study examines the results of toxicological tests performed on blood and urine samples collected from suspected drug-impaired drivers in Ontario from 2008 to 2019. The report examines the results of toxicological analysis of the samples submitted, the characteristics of those drivers from whom samples were collected, and the temporal and situational circumstances that led to police investigations and sample collection to better understand drug-impaired driving behavior and to assist in the development and implementation of countermeasure strategies and programs. METHODS: Blood and urine samples were sent to the Center of Forensic Sciences where they were analyzed using standardized comprehensive toxicological analysis to test for a wide variety of potentially impairing drugs. Demographic and temporal information for each case from which a sample was collected were also examined to describe the circumstances and characteristics of these driving incidents. RESULTS: During the 12-year period examined, 5,388 samples collected from suspected drug-impaired drivers were analyzed. The number of samples collected increased substantially following the implementation of the Drug Evaluation and Classification Program (DECP) in July 2008, the enactment of legislation facilitating the collection of blood samples from suspects, and the legalization of cannabis for nonmedical purposes in 2018. The number of samples submitted shows temporal correlation with the number of police officers certified as Drug Recognition Experts (DRE) in the province. Over the 12-year period of this study, cannabis was the most frequently detected substance in drivers (52.8% of cases), followed by cocaine (44.3%) and methamphetamine (24.8%). In 80% of cases, more than one substance was detected. CONCLUSIONS: Examining the characteristics of suspected drug-impaired drivers, the temporal circumstances, and the drug findings throughout the large geographic area of Ontario and over the extended period of this study enhances our understanding of drug-impaired driving behavior. These characteristics can assist in the development and/or evaluation of enforcement strategies and enhanced countermeasure activities.

The fate of anti-HLA antibodies following liver transplantation.

Introduction: Liver transplant recipients may have pre-formed anti-HLA antibodies directed to mismatched HLA of the liver donor (donor specific antibodies, DSA) or not directed to the liver donor (non-donor specific, non-DSA). We observed the fate of these antibodies (DSA and non-DSA) at 12 months after transplant. Methods: Patients transplanted between 4/2015 and 12/2018 (N = 216) who had anti-HLA antibody measurements at both transplant and 12 months posttransplant (N = 124) and with DSAs at transplant (N = 31) were considered informative for a paired analysis of the natural history of DSA and non-DSA following liver transplantation. Results: Class I DSAs and non-DSAs decreased between transplant and 12 months; however, Class I DSAs essentially disappeared by 12 months while Class I non-DSAs did not. Anti-HLA Class II DSAs performed differently. While there was a significant drop in values between transplant and 12 months, these antibodies mostly persisted at a low level. Discussion: Our study demonstrated a significant difference in the kinetics of DSA compared to non-DSA following liver transplantation, most profoundly for anti-HLA Class I antibodies. Class I DSAs were mostly absent at 12 months while Class II DSAs persisted, although at lower levels. The mechanisms of reduction in anti-HLA antibodies following liver transplantation are not completely understood and were not pursued as a part of this study. This detailed analysis of Class I and Class II DSAs and non-DSAs represents and important study to explore the change in antibodies at one year from liver transplantation.

Shortened food chain length in a fished versus unfished coral reef.

Direct exploitation through fishing is driving dramatic declines of wildlife populations in ocean environments, particularly for predatory and large-bodied taxa. Despite wide recognition of this pattern and well-established consequences of such trophic downgrading on ecosystem function, there have been few empirical studies examining the effects of fishing on whole system trophic architecture. Understanding these kinds of structural impacts is especially important in coral reef ecosystems-often heavily fished and facing multiple stressors. Given the often high dietary flexibility and numerous functional redundancies in diverse ecosystems such as coral reefs, it is important to establish whether web architecture is strongly impacted by fishing pressure or whether it might be resilient, at least to moderate-intensity pressure. To examine this question, we used a combination of bulk and compound-specific stable isotope analyses measured across a range of predatory and low-trophic-level consumers between two coral reef ecosystems that differed with respect to fishing pressure but otherwise remained largely similar. We found that even in a high-diversity system with relatively modest fishing pressure, there were strong reductions in the trophic position (TP) of the three highest TP consumers examined in the fished system but no effects on the TP of lower-level consumers. We saw no evidence that this shortening of the affected food webs was being driven by changes in basal resource consumption, for example, through changes in the spatial location of foraging by consumers. Instead, this likely reflected internal changes in food web architecture, suggesting that even in diverse systems and with relatively modest pressure, human harvest causes significant compressions in food chain length. This observed shortening of these food webs may have many important emergent ecological consequences for the functioning of ecosystems impacted by fishing or hunting. Such important structural shifts may be widespread but unnoticed by traditional surveys. This insight may also be useful for applied ecosystem managers grappling with choices about the relative importance of protection for remote and pristine areas and the value of strict no-take areas to protect not just the raw constituents of systems affected by fishing and hunting but also the health and functionality of whole systems.

Entire expressed peripheral blood transcriptome in pediatric severe malarial anemia.

This study on severe malarial anemia (SMA: Hb < 6.0 g/dL), a leading global cause of childhood morbidity and mortality, compares the entire expressed whole blood host transcriptome between Kenyan children (3-48 mos.) with non-SMA (Hb ≥ 6.0 g/dL, n = 39) and SMA (n = 18). Differential expression analyses reveal 1403 up-regulated and 279 down-regulated transcripts in SMA, signifying impairments in host inflammasome activation, cell death, and innate immune and cellular stress responses. Immune cell profiling shows decreased memory responses, antigen presentation, and immediate pathogen clearance, suggesting an immature/improperly regulated immune response in SMA. Module repertoire analysis of blood-specific gene signatures identifies up-regulation of erythroid genes, enhanced neutrophil activation, and impaired inflammatory responses in SMA. Enrichment analyses converge on disruptions in cellular homeostasis and regulatory pathways for the ubiquitin-proteasome system, autophagy, and heme metabolism. Pathway analyses highlight activation in response to hypoxic conditions [Hypoxia Inducible Factor (HIF)-1 target and Reactive Oxygen Species (ROS) signaling] as a central theme in SMA. These signaling pathways are also top-ranking in protein abundance measures and a Ugandan SMA cohort with available transcriptomic data. Targeted RNA-Seq validation shows strong concordance with our entire expressed transcriptome data. These findings identify key molecular themes in SMA pathogenesis, offering potential targets for new malaria therapies.

Molecular Characterization of High and Low Virulent Escherichia coli Clinical Strains Isolated from Patients with Urinary Tract Infections with or without Bacteremia in Southern Taiwan.

Objective: The most common extraintestinal pathogen and infection site is uropathogenic Escherichia coli (UPEC), which causes urinary tract infections (UTIs). UPEC is also a common pathogen in bloodstream infections; in severe cases, it can lead to death. Although host and bacterial virulence factors have been demonstrated to be associated with UTI pathogenesis, the role of the related contributing factors in UTI and urinary source bacteremia is not yet fully understood. This study aimed to compare and analyze the factors contributing to urinary bacteremia in patients with UTI. Methods: A total of 171 E. coli strains collected from patients with UTI and urinary source bacteremia at Chiayi Christian Hospital were used. Phylogenetic groups and virulence factors were determined using PCR. Drug resistance patterns were determined using the disk diffusion assay. Results: Previous studies have demonstrated that fimbriae and papGII may be associated with first-step infections and severe UTIs, respectively. As expected, highly virulent E. coli strains (belonging to the phylogenetic B2 and D groups) were dominant in the bacteremic UTI (90%) and UTI (86.27%) groups. However, our results showed that the UTI group had a significantly higher prevalence of sfa/focDE (belonging to the S and FIC fimbriae) than the bacteremic UTI group (29.4% vs 12.5%; p=0.008). In the bacteremic group, we found that sfa/focDE was only detected in highly virulent strains. The bacteremic UTI group had a significantly higher prevalence of papGII (belonging to P fimbriae) than the UTI group (55.8% vs 37.3%; p=0.026). In addition, the P fimbriae gene cluster, including papC, papEF, and papGII, was predominant in highly virulent strains. Notably, our results show that multidrug-resistant (MDR) strains were significantly less virulent than non MDR strains. Conclusion: Taken together, our results provide insights into the contributing factors in patients with UTI and urinary bacteremia.

Bellybutton: accessible and customizable deep-learning image segmentation.

The conversion of raw images into quantifiable data can be a major hurdle and time-sink in experimental research, and typically involves identifying region(s) of interest, a process known as segmentation. Machine learning tools for image segmentation are often specific to a set of tasks, such as tracking cells, or require substantial compute or coding knowledge to train and use. Here we introduce an easy-to-use (no coding required), image segmentation method, using a 15-layer convolutional neural network that can be trained on a laptop: Bellybutton. The algorithm trains on user-provided segmentation of example images, but, as we show, just one or even a sub-selection of one training image can be sufficient in some cases. We detail the machine learning method and give three use cases where Bellybutton correctly segments images despite substantial lighting, shape, size, focus, and/or structure variation across the regions(s) of interest. Instructions for easy download and use, with further details and the datasets used in this paper are available at pypi.org/project/Bellybuttonseg .

Using mobile health to expedite access to specialty care for youth presenting to the emergency department with concussion at highest risk of developing persisting symptoms: a protocol paper for a non-randomised hybrid implementation-effectiveness trial.

INTRODUCTION: Paediatric concussion is a common injury. Approximately 30% of youth with concussion will experience persisting postconcussion symptoms (PPCS) extending at least 1 month following injury. Recently, studies have shown the benefit of early, active, targeted therapeutic strategies. However, these are primarily prescribed from the specialty setting. Early access to concussion specialty care has been shown to improve recovery times for those at risk for persisting symptoms, but there are disparities in which youth are able to access such care. Mobile health (mHealth) technology has the potential to improve access to concussion specialists. This trial will evaluate the feasibility of a mHealth remote patient monitoring (RPM)-based care handoff model to facilitate access to specialty care, and the effectiveness of the handoff model in reducing the incidence of PPCS. METHODS AND ANALYSIS: This study is a non-randomised type I, hybrid implementation-effectiveness trial. Youth with concussion ages 13-18 will be enrolled from the emergency department of a large paediatric healthcare network. Patients deemed a moderate-to-high risk for PPCS using the predicting and preventing postconcussive problems in paediatrics (5P) stratification tool will be registered for a web-based chat platform that uses RPM to collect information on symptoms and activity. Those patients with escalating or plateauing symptoms will be contacted for a specialty visit using data collected from RPM to guide management. The primary effectiveness outcome will be the incidence of PPCS, defined as at least three concussion-related symptoms above baseline at 28 days following injury. Secondary effectiveness outcomes will include the number of days until return to preinjury symptom score, clearance for full activity and return to school without accommodations. The primary implementation outcome will be fidelity, defined as the per cent of patients meeting specialty care referral criteria who are ultimately seen in concussion specialty care. Secondary implementation outcomes will include patient-defined and clinician-defined appropriateness and acceptability. ETHICS AND DISSEMINATION: This study was approved by the Institutional Review Board of the Children's Hospital of Philadelphia (IRB 22-019755). Study findings will be published in peer-reviewed journals and disseminated at national and international meetings. TRIAL REGISTRATION NUMBER: NCT05741411.

The Role of Routine Pathologic Assessment After Pediatric Osteochondroma Excision.

BACKGROUND: Osteochondromas are benign osseous lesions often excised for pain, growth abnormalities, and aesthetic concerns. While characteristic clinical and radiographic features leave little diagnostic ambiguity in most cases of osteochondroma, pathologic analysis to confirm the diagnosis and screen for malignancy is routinely performed following surgical excision. The purpose of this study was to determine the clinical and economic value of routine pathologic analysis after osteochondroma excision in a pediatric population. METHODS: A retrospective review of clinical records from 2 pediatric orthopaedic hospitals (St. Louis Children's Hospital and Shriner's Hospital for Children, St. Louis) identified 426 osteochondroma lesions surgically resected from 201 patients. Patients with solitary and multiple lesions were included. Clinical, radiographic, and surgical data were recorded for each resection surgery. Pathologic reports were evaluated. Costs incurred for routine pathologic assessment was also noted. RESULTS: Totally, 132 patients were treated with surgical resection of a solitary osteochondroma lesion, while an additional 291 lesions were resected from 69 patients with multiple lesions. Average age at the time of surgical resection was 13.0 years (2.1 to 17.9). The most common anatomic locations of excised lesions included the distal femur (110, 25.8%), proximal tibia/fibula (95, 22.3%), and distal radius/ulna (58, 13.6%). All resected specimens were sent for pathologic analysis. The average size of the resected lesions was 19.9 mm3 (0.02 to 385.0 mm3). In all cases, the histologic diagnosis confirmed benign osteochondroma. The total charges of pathologic analysis including processing and interpretation fees was ∼$755.00 for each lesion assessed, for a total cohort charge of $321,630. CONCLUSION: We propose that in most cases of pediatric osteochondroma excision procedures, postoperative histologic analysis is not strictly indicated as it rarely, if ever, alters diagnosis or management. We suggest using a "gross only" analysis in these cases. However, we do believe that with preoperative diagnostic ambiguity, or if patients present with concerning features such as rapidly expansile lesions or cortical destruction, have axial skeleton or pelvic involvement, or enlarged cartilaginous caps, full histologic evaluation of the excised lesions will continue to be prudent. LEVEL OF EVIDENCE: Level IV-case series.