Tag: pubmed

J Proteome Res. 2025 Mar 7. doi: 10.1021/acs.jproteome.4c01068. Online ahead of print.

ABSTRACT

Computational toolkits for data exploration and visualization from widely used omics platforms often lack flexibility and customization. While many tools generate standardized output, advanced programming skills are necessary to create high-quality visualizations. Therefore, user-friendly tools that simplify this crucial, yet time-consuming, step are essential. We developed EasyPubPlot (Easy Publishable Plotting), a straightforward, easy-to-use, no-coding, user experience-oriented, open-source, and shiny web application along with its associated R package to streamline data exploration and visualization for functional omics-empowered research. EasyPubPlot generates publishable scores plots, volcano plots, heatmaps, box plots, dot plots, and bubble plots with minimal necessary steps. The tool was designed to guide new users to accurate and efficient navigation. Step-by-step tutorials for each type of plot are also provided. Herein, we demonstrated EasyPubPlot’s competent functionality and versatility by showcasing metabolomics, proteomics, and transcriptomics data. Collectively, EasyPubPlot reduces the gap between data analysis and stunning visualization, thereby diminishing friction and focusing on science. The app can be downloaded and installed locally (https://github.com/Pharmaco-OmicsLab/EasyPubPlot) or used through a web application (https://pharmaco-omicslab.shinyapps.io/EasyPubPlot).

PMID:40053871 | DOI:10.1021/acs.jproteome.4c01068

Adv Neonatal Care. 2025 Mar 7. doi: 10.1097/ANC.0000000000001233. Online ahead of print.

ABSTRACT

BACKGROUND: Sex-specific differences exist in morbidity and growth yet little is known about other nutritional outcomes in preterm very low birth-weight (VLBW) infants. This is important because providing optimal nutrition is essential to promote growth and reduce neurodevelopmental impairment.

PURPOSE: To determine the effect of sex on days to full enteral feedings and other nutritional outcomes.

METHODS: This was a longitudinal 2-group cohort study using secondary analysis of existing data of 313 infants born ≤32 weeks gestation and weighing ≤1500 g. Information regarding nutritional outcomes was obtained from the infant’s electronic medical records.

RESULTS: While not statistically significant, male infants reached full feeds nearly 3 days later (18.1 vs 15.2; P = .89), required parenteral nutrition for nearly an additional 4 days (18.3 vs 14.1; P = .37), and had a central line for 3 days longer (19.6 vs 15.7; P = .65) than female infants. Males had higher direct bilirubin levels (P = .02), more emesis (P = .003), and more late-onset sepsis (P = .03). Birth weight for males was higher at birth but not at 6 weeks and while the slope of weight increase over the 6 weeks was higher in males (P = .04), growth velocity was similar between sexes yet tended to be higher in females.

IMPLICATIONS FOR PRACTICE AND RESEARCH: Nurses are essential in ensuring preterm infants in the neonatal intensive care unit receive optimal nutrition. This study supports nurses should consider sex-specific differences in nutritional outcomes among VLBW infants in precision based nutritional support.

PMID:40053867 | DOI:10.1097/ANC.0000000000001233

J Extra Corpor Technol. 2025 Mar;57(1):14-17. doi: 10.1051/ject/2024041. Epub 2025 Mar 7.

ABSTRACT

BACKGROUND: Patients receiving mechanical circulatory support (MCS) frequently require renal replacement therapy (RRT). Examining risk factors for requiring RRT in patients receiving MCS may allow improved understanding of these comorbidities and enhance patient outcomes.

METHODS: Following IRB approval, patient characteristics, comorbidities, and the need for RRT were studied in 129 patients who received MCS from January 2017 to October 2023. The clinical variables underwent machine learning to examine their relationships to the outcome of interest, the need for RRT.

RESULTS: In this study, the incidence of RRT was 36% with a 95% confidence interval ranging from 29% to 44%. Following machine learning, patients with a history of immunologic therapy or having a pacemaker or internal cardiac defibrillator (ICD) were associated with the need for RRT (χ² = 44, P = 0.0003). The c-index statistic for this model was 0.81. The anticoagulation therapy administered in these two groups was also analyzed. Patients in these two groups receiving unfractionated heparin were observed to have a higher incidence (44%) in the need for RRT.

CONCLUSION: The incidence of RRT was high in this patient population. The novel associations in patients requiring MCS who have received prior immunologic therapy or have pre-existing pacemaker/ICDs suggest that an increased systemic inflammatory state exists that escalates the need for RRT. Unfractionated heparin appears to provide minimal protection from the need for RRT in patients requiring MCS. These findings suggest that other options for systemic anticoagulation in patients requiring MCS should be considered. Further investigation into how these background inflammatory conditions contribute to the need for RRT in patients requiring MCS is warranted.

PMID:40053853 | DOI:10.1051/ject/2024041

Proc Natl Acad Sci U S A. 2025 Mar 11;122(10):e2413443122. doi: 10.1073/pnas.2413443122. Epub 2025 Mar 7.

ABSTRACT

Large language models can now generate political messages as persuasive as those written by humans, raising concerns about how far this persuasiveness may continue to increase with model size. Here, we generate 720 persuasive messages on 10 US political issues from 24 language models spanning several orders of magnitude in size. We then deploy these messages in a large-scale randomized survey experiment (N = 25,982) to estimate the persuasive capability of each model. Our findings are twofold. First, we find evidence that model persuasiveness is characterized by sharply diminishing returns, such that current frontier models are only slightly more persuasive than models smaller in size by an order of magnitude or more. Second, we find that the association between language model size and persuasiveness shrinks toward zero and is no longer statistically significant once we adjust for mere task completion (coherence, staying on topic), a pattern that highlights task completion as a potential mediator of larger models’ persuasive advantage. Given that current frontier models are already at ceiling on this task completion metric in our setting, taken together, our results suggest that further scaling model size may not much increase the persuasiveness of static LLM-generated political messages.

PMID:40053360 | DOI:10.1073/pnas.2413443122

JAMA Netw Open. 2025 Mar 3;8(3):e250185. doi: 10.1001/jamanetworkopen.2025.0185.

ABSTRACT

IMPORTANCE: Best practices for improving access to assessment of hereditary cancer risk in primary care are lacking.

OBJECTIVE: To compare 2 population-based engagement strategies for identifying primary care patients with a family or personal history of cancer and offering eligible individuals genetic testing for cancer susceptibility.

DESIGN, SETTING, AND PARTICIPANTS: The EDGE (Early Detection of Genetic Risk) clinical trial cluster-randomized 12 clinics from 2 health care systems in Montana, Wyoming, and Washington state to 1 of 2 engagement approaches for assessment of hereditary cancer risk in primary care. The study population included 95 623 English-speaking patients at least 25 years old with a primary care visit during the recruitment window between April 1, 2021, and March 31, 2022.

INTERVENTION: The intervention comprised 2 risk assessment engagement approaches: (1) point of care (POC), conducted by staff immediately preceding clinical appointments, and (2) direct patient engagement (DPE), where letter and email outreach facilitated at-home completion. Patients who completed risk assessment and met prespecified criteria were offered genetic testing via a home-delivered saliva testing kit at no cost.

MAIN OUTCOMES AND MEASURES: Primary outcomes were the proportion of patients with a visit who (1) completed the risk assessment and (2) completed genetic testing. Logistic regression models were used to compare the POC and DPE approaches, allowing for overdispersion and including clinic as a design factor. An intention-to-treat analysis was used to evaluate primary outcomes.

RESULTS: Over a 12-month window, 95 623 patients had a primary care visit across the 12 clinics. Those who completed the risk assessment (n = 13 705) were predominately female (64.7%) and aged between 65 and 84 years (39.6%). The POC approach resulted in a higher proportion of patients completing risk assessment than the DPE approach (19.1% vs 8.7%; adjusted odds ratio [AOR], 2.68; 95% CI, 1.72-4.17; P < .001) but a similar proportion completing testing (1.5% vs 1.6%; AOR, 0.96; 95% CI, 0.64-1.46; P = .86). Among those eligible for testing, POC test completion was approximately half of that for the DPE approach (24.7% vs 44.7%; AOR, 0.49; 95% CI, 0.37-0.64; P < .001). The proportion of tested patients identified with an actionable pathogenic variant was significantly lower for the POC approach than the DPE approach (3.8% vs 6.6%; AOR, 0.61; 95% CI, 0.44-0.85; P = .003).

CONCLUSIONS AND RELEVANCE: In this cluster randomized clinical trial of risk assessment delivery, POC engagement resulted in a higher rate of assessment of hereditary cancer risk than the DPE approach but a similar rate of genetic testing completion. Using a combination of engagement strategies may be the optimal approach for greater reach and impact.

TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT04746794.

PMID:40053353 | DOI:10.1001/jamanetworkopen.2025.0185

JAMA Netw Open. 2025 Mar 3;8(3):e250274. doi: 10.1001/jamanetworkopen.2025.0274.

ABSTRACT

IMPORTANCE: Benefits of breastfeeding are extensive, but racial and ethnic disparities persist. Mama Sana (Spanish for healthy mother) is a bilingual, culturally tailored program that aims to reduce breastfeeding inequities.

OBJECTIVE: To examine differences in lactation support and breastfeeding outcomes among Spanish-speaking Hispanic birthing parents who participated in Mama Sana compared with a historical control (pre-Mama Sana) group.

DESIGN, SETTING, AND PARTICIPANTS: In this cohort study, patients who participated in the Mama Sana program during their delivery hospitalization from January 2022 to September 2023 were compared with a historical control group who delivered prior to the implementation of the program (July 2019 to December 2021). The study took place at an academic medical center in Boston with a high-risk obstetric service. Data were analyzed from January to September 2024.

EXPOSURE: Beginning in January 2022, a bilingual native Spanish-speaker licensed as a registered dietitian and certified lactation counselor provided lactation support to participants during their delivery hospitalization with follow-up phone calls after discharge (until 6 months post partum).

MAIN OUTCOMES AND MEASURES: The primary outcome was exclusive breastfeeding at discharge. Secondary outcomes included any breastfeeding at discharge, any breastfeeding and exclusive breastfeeding at 6 weeks post partum, and change in maternal body mass index (BMI). Process measures included inpatient lactation consult placement and receipt of any and language-concordant lactation support. The χ2 test was used to analyze outcomes, process measures, and balancing measures.

RESULTS: In this study, 417 patients were included (Mama Sana group, 175 patients; mean [SD] age, 28.9 [6.1] years; pre-Mama Sana group: 242 patients; mean [SD] age, 29.8 [6.1] years). Sociodemographic characteristics including age and BMI were similar between groups. Mama Sana participants were less likely to be multiparous or to have diabetes compared with the pre-Mama Sana group. At hospital discharge, 36 of 175 Mama Sana participants (20.6%) were exclusively breastfeeding compared with 39 of 242 pre-Mama Sana (16.1%) (adjusted risk difference [aRD], 2.5%; 95% CI, -1.2 to 6.4). Significantly more Mama Sana participants engaged in any breastfeeding prior to hospital discharge (172 of 175 [98.3%] vs 222 of 242 [91.7%]; aRD, 7.1%; 95% CI, 2.8% to 11.5%) and at the 6 week postpartum visit (81 of 102 [79.4%] vs 109 of 170 [64.1%]; aRD, 15.6%; 95% CI, 4.8% to 26.4%) compared with the pre-Mama Sana group. More Mama Sana participants had a lactation consult placed (109 of 175 [62.3%] vs 108 of 242 [44.6%]; P < .001) and received lactation support in Spanish (175 of 175 [100%] vs 49 of 242 [20.3%]; P < .001) than those in the pre-Mama Sana group.

CONCLUSIONS AND RELEVANCE: In this cohort study, Mama Sana’s language-concordant, culturally tailored lactation program was associated with higher rates of lactation support and some breastfeeding outcomes, which suggests the program may be a useful approach to perinatal care equity.

PMID:40053351 | DOI:10.1001/jamanetworkopen.2025.0274

JAMA Netw Open. 2025 Mar 3;8(3):e250283. doi: 10.1001/jamanetworkopen.2025.0283.

ABSTRACT

INTRODUCTION: Mass shootings, defined as incidents where 4 or more people are shot with a firearm, have become a significant public health concern in the US.

OBJECTIVE: To estimate the prevalence of direct exposure to mass shootings among US adults and identify the sociodemographic groups most affected.

DESIGN, SETTING, AND PARTICIPANTS: A survey was administered in January 2024 to a sample of 10 000 respondents (18 years or older) designed to be representative of US adults using a multistage matched sampling design. In addition to exposure to mass shootings, the survey also collected sociodemographic information, including age, gender, self-reported race and ethnicity, and socioeconomic status.

EXPOSURE: Survey respondents were asked about their lifetime presence at the scene of a mass shooting, any physical injuries sustained (including being shot or trampled or experiencing a related physical injury), and the features of such incidents.

MAIN OUTCOME AND MEASURES: Multivariable logistic regression was used to generate adjusted odds ratios (AORs) of the associations between sociodemographic measures and being present on the scene of and injured in a mass shooting. All analyses undertaken to generate population and relational inferences were weighted to achieve representativeness of US adults.

RESULTS: Of the 10 000 respondents included in the analysis, 51.34% (95% CI, 50.27%-52.40%) were female. In terms of race and ethnicity, 3.04% (95% CI, 2.71%-3.38%) were Asian, 12.46% (95% CI, 11.81%-13.12%) were Black, 16.04% (95% CI, 15.10%-16.98%) were Hispanic, 62.78% (95% CI, 61.73%-63.84%) were White, and 5.67% (95% CI, 5.23%-6.11%) were other race or ethnicity. The findings indicated that 6.95% (95% CI, 6.39%-7.50%) of respondents were present at the scene of a mass shooting, and 2.18% (95% CI, 1.85%-2.50%) sustained physical injuries, such as being shot or trampled, during such incidents. A total of 54.89% of mass shootings to which respondents were exposed occurred in 2015 or more recently, and 76.15% took place in respondents’ local communities. Mass shootings were most likely to occur in neighborhoods. Younger individuals (eg, AOR for Baby Boomer and Silent generations vs Generation Z, 0.12; 95% CI, 0.09-0.18) and males (AOR, 1.55; 95% CI, 1.29-1.85) were more likely to report exposure compared with those from older generations or female individuals, respectively. Black respondents reported higher rates of being present at mass shootings (AOR, 1.87; 95% CI, 1.49-2.34), while Asian respondents reported lower rates (AOR, 0.36; 95% CI, 0.19-0.66), compared with White respondents, but there were no racial and ethnic differences in injuries sustained.

CONCLUSIONS AND RELEVANCE: The findings from this survey study of US adults underscore the extensive and often overlooked regular exposure to mass shootings in this country. The demographic disparities in exposure highlight the need for targeted interventions and support for the most affected groups, particularly younger generations and males. Understanding these patterns is essential for addressing the broader impacts of gun violence on public health and community well-being.

PMID:40053350 | DOI:10.1001/jamanetworkopen.2025.0283

JAMA Netw Open. 2025 Mar 3;8(3):e250295. doi: 10.1001/jamanetworkopen.2025.0295.

ABSTRACT

IMPORTANCE: Surgical cancer treatments may be delayed for patients who smoke over concerns for increased risk of complications. Quantifying risks for people who had recently smoked can inform any trade-offs of delaying surgery.

OBJECTIVE: To investigate the association between smoking status or smoking cessation time and complications after cancer surgery.

DATA SOURCES: Embase, CINAHL, Medline COMPLETE, and Cochrane Library were systematically searched for studies published from January 1, 2000, to August 10, 2023.

STUDY SELECTION: Observational and interventional studies comparing the incidence of complications in patients undergoing cancer surgery who do and do not smoke.

DATA EXTRACTION AND SYNTHESIS: Two reviewers screened results and extracted data according to the Meta-Analyses of Observational Studies in Epidemiology (MOOSE) reporting guidelines. Data were pooled with a random-effects model and adjusted analysis was performed.

MAIN OUTCOMES AND MEASURES: The odds ratio (OR) of postoperative complications (of any type) for people who smoke currently vs in the past (4-week preoperative cutoff), currently smoked vs never smoked, and smoked within shorter (2-week cutoff) and longer (1-year cutoff) time frames.

RESULTS: The meta-analyses across 24 studies with a pooled sample of 39 499 participants indicated that smoking within 4 weeks preoperatively was associated with higher odds of postoperative complications compared with ceasing smoking for at least 4 weeks (OR, 1.31 [95% CI, 1.10-1.55]; n = 14 547 [17 studies]) and having never smoked (OR, 2.83 [95% CI, 2.06-3.88]; n = 9726 [14 studies]). Within the shorter term, there was no statistically significant difference in postoperative complications between people who had smoked within 2 weeks preoperatively and those who had stopped between 2 weeks and 3 months in postoperative complications (OR, 1.19 [95% CI, 0.89-1.59]; n = 5341 [10 studies]), although the odds of complications among people who smoked within a year of surgery were higher compared with those who had quit smoking for at least 1 year (OR, 1.13 [95% CI, 1.00-1.29]; N = 31 238 [13 studies]). The results from adjusted analyses were consistent with the key findings.

CONCLUSIONS AND RELEVANCE: In this systematic review and meta-analysis of smoking cessation and complications after cancer surgery, people with cancer who had stopped smoking for at least 4 weeks before surgery had fewer postoperative complications than those smoking closer to surgery. High quality, intervention-based evidence is needed to identify the optimal cessation period and inform clinicians on the trade-offs of delaying cancer surgery.

PMID:40053349 | DOI:10.1001/jamanetworkopen.2025.0295

JAMA Netw Open. 2025 Mar 3;8(3):e250314. doi: 10.1001/jamanetworkopen.2025.0314.

ABSTRACT

IMPORTANCE: Studies of brain imaging and movements during rapid eye movement sleep indicate basal ganglia involvement in pediatric acute-onset neuropsychiatric syndrome (PANS). Characterizing neurological findings that commonly present among patients with PANS could improve diagnostic accuracy.

OBJECTIVES: To evaluate the prevalence of neurological soft signs (NSSs) that may be associated with basal ganglia dysfunction among youths presenting with PANS and assess whether clinical characteristics of PANS correlate with NSSs that may be associated with basal ganglia dysfunction.

DESIGN, SETTING, AND PARTICIPANTS: This cohort study included 135 new patients who met strict PANS criteria and were evaluated at the Stanford Children’s Immune Behavioral Health Clinic between November 1, 2014, and March 1, 2020. Data on these patients were retrospectively reviewed between December 13, 2020, and September 25, 2023. Sixteen patients were excluded because they had no neurological examination within the first 3 visits and within 3 months of clinical presentation. Statistical analysis was conducted between September 26, 2023, and November 22, 2024.

MAIN OUTCOMES AND MEASURES: The following NSSs that may be associated with basal ganglia dysfunction were recorded from medical record review: (1) glabellar tap reflex, (2) tongue movements, (3) milkmaid’s grip, (4) choreiform movements, (5) spooning, and (6) overflow movements. Data from prospectively collected symptoms and impairment scales (Global Impairment Score [GIS; score range, 1-100, with higher scores indicating greater impairment] and Caregiver Burden Inventory [score range, 0-96, with higher scores indicating greater caregiver burden]) were included.

RESULTS: The study included 119 patients; the mean (SD) age at PANS onset was 8.2 (3.6) years, the mean (SD) age at initial presentation was 10.4 (3.6) years, and 66 (55.5%) were boys. At least 1 NSS that may be associated with basal ganglia dysfunction was observed in 95 patients (79.8%); the mean (SD) number of NSSs was 2.1 (1.6). Patients with 4 or more NSSs had higher GISs (mean [SD] score, 56.0 [22.6] vs 40.6 [26.7]; P = .05) and more symptoms (mean [SD] number, 15.1 [4.9] vs 11.5 [4.2]; P = .008) than patients with 0 NSSs. There was no significant difference in age at visit or in Caregiver Burden Inventory score. On Poisson and linear regression, the number of NSSs was associated with global impairment, with 1 more sign increasing the GIS by 2.86 (95% CI, 0.09-5.62; P = .04), and with the number of symptoms, with 1 more sign increasing the number of symptoms by 5% (1.05; 95% CI, 1.02-1.08; P = .002), but not with age or duration of PANS at presentation.

CONCLUSIONS AND RELEVANCE: This cohort study of patients with PANS found a high prevalence of NSSs that may be associated with basal ganglia dysfunction and an association between these NSSs and disease severity that was not associated with younger age. PANS may have a unique profile, suggesting that targeted neurological examinations may support PANS diagnosis.

PMID:40053347 | DOI:10.1001/jamanetworkopen.2025.0314

JAMA Health Forum. 2025 Mar 7;6(3):e250054. doi: 10.1001/jamahealthforum.2025.0054.

ABSTRACT

IMPORTANCE: Parental substance use is a primary driver of child welfare system involvement, and child welfare services primarily seek to address caregiver challenges, including connecting parents to treatment. Although research highlights that formal child welfare services connect children to health care professionals, less is known about how the system affects caregivers’ substance use treatment.

OBJECTIVE: To examine the prevalence of maternal substance use disorder (SUD) in the Pennsylvania child welfare system and the association between formal child welfare system response and mothers’ take-up of SUD treatment.

DESIGN, SETTING, AND PARTICIPANTS: This cohort study used linked Medicaid claims and child welfare system records for mothers enrolled in Medicaid and involved in the Pennsylvania child welfare system between 2015 and 2018, followed by 12 months postsystem contact. The study applied a difference-in-differences framework to estimate associations between child welfare system intervention and maternal SUD treatment utilization. Data were analyzed from January to September 2024.

EXPOSURE: Child welfare system intervention was defined in 3 categories: no formal services, in-home services, and foster care services.

MAIN OUTCOMES AND MEASURES: Maternal SUD was defined by International Classification of Diseases, Ninth Revision or Tenth Revision diagnosis codes. Dependent variables were mothers’ monthly and cumulative use of inpatient and outpatient SUD treatment, defined by procedure and service location codes.

RESULTS: Among 46 484 mothers, the prevalence of maternal SUD was estimated at 62% within the child welfare system population, predominantly involving opioid and polysubstance use. Compared with mothers who did not receive a formal child welfare system response, those who received a formal intervention had a statistically significant higher probability of monthly outpatient (in-home services: 24%; 95% CI, 18%-28%; foster care: 63%; 95% CI, 55%-75%) and inpatient (in-home services: 36%; 95% CI, 23%-48%; foster care: 130%; 95% CI, 103%-156%) SUD treatment in the 12 months after referral.

CONCLUSIONS AND RELEVANCE: This cohort study demonstrates that formal child welfare services can facilitate substance use treatment for caregivers. As states seek to reduce the role of formal child welfare system responses in responding to parental substance use, alternative strategies to engage and retain parents in treatment are needed.

PMID:40053337 | DOI:10.1001/jamahealthforum.2025.0054