-
STAR Protocols Jul 2024Constructing metagenome-assembled genomes (MAGs) from complex metagenomic samples involves a series of bioinformatics operations, each requiring deep bioinformatics...
Constructing metagenome-assembled genomes (MAGs) from complex metagenomic samples involves a series of bioinformatics operations, each requiring deep bioinformatics knowledge. Here, we present a protocol for constructing MAGs and conducting functional profiling to address biological questions. We describe steps for system configuration, data downloads, read processing, removal of human DNA contamination, metagenomic assembly, and statistical quality assessment of the final assembly. Additionally, we detail procedures for the construction and refinement of MAGs, as well as the functional profiling of MAGs.
PubMed: 38954516
DOI: 10.1016/j.xpro.2024.103167 -
JCI Insight Jul 2024Rheumatoid arthritis (RA) management lean toward achieving remission or low-disease activity. In this study, we conducted single-cell RNA sequencing (scRNAseq) of...
Rheumatoid arthritis (RA) management lean toward achieving remission or low-disease activity. In this study, we conducted single-cell RNA sequencing (scRNAseq) of peripheral blood mononuclear cells (PBMCs) from 36 individuals (18 RA patients and 18 matched controls, accounting for age, sex, race, and ethnicity), to identify disease-relevant cell subsets and cell type-specific signatures associated with disease activity. Our analysis revealed 18 distinct PBMC subsets, including an IFITM3 overexpressing Interferon-activated (IFN-activated) monocyte subset. We observed an increase in CD4+ T effector memory cells in patients with moderate to high disease activity (DAS28-CRP ≥ 3.2), and a decrease in non-classical monocytes in patients with low disease activity or remission (DAS28-CRP < 3.2). Pseudobulk analysis by cell type identified 168 differentially expressed genes between RA and matched controls, with a downregulation of pro-inflammatory genes in the gamma-delta T cells subset, alteration of genes associated with RA predisposition in the IFN-activated subset, and non-classical monocytes. Additionally, we identified a gene signature associated with moderate-high disease activity, characterized by upregulation of pro-inflammatory genes such as TNF, JUN, EGR1, IFIT2, MAFB, G0S2, and downregulation of genes including HLA-DQB1, HLA-DRB5, TNFSF13B. Notably, cell-cell communication analysis revealed an upregulation of signaling pathways, including VISTA, in both moderate-high and remission-low disease activity contexts. Our findings provide valuable insights into the systemic cellular and molecular mechanisms underlying RA disease activity.
PubMed: 38954480
DOI: 10.1172/jci.insight.178499 -
Journal of Medical Internet Research Jul 2024In the era of the internet, individuals have increasingly accustomed themselves to gathering necessary information and expressing their opinions on public web-based...
BACKGROUND
In the era of the internet, individuals have increasingly accustomed themselves to gathering necessary information and expressing their opinions on public web-based platforms. The health care sector is no exception, as these comments, to a certain extent, influence people's health care decisions. During the onset of the COVID-19 pandemic, how the medical experience of Chinese patients and their evaluations of hospitals have changed remains to be studied. Therefore, we plan to collect patient medical visit data from the internet to reflect the current status of medical relationships under specific circumstances.
OBJECTIVE
This study aims to explore the differences in patient comments across various stages (during, before, and after) of the COVID-19 pandemic, as well as among different types of hospitals (children's hospitals, maternity hospitals, and tumor hospitals). Additionally, by leveraging ChatGPT (OpenAI), the study categorizes the elements of negative hospital evaluations. An analysis is conducted on the acquired data, and potential solutions that could improve patient satisfaction are proposed. This study is intended to assist hospital managers in providing a better experience for patients who are seeking care amid an emergent public health crisis.
METHODS
Selecting the top 50 comprehensive hospitals nationwide and the top specialized hospitals (children's hospitals, tumor hospitals, and maternity hospitals), we collected patient reviews from these hospitals on the Dianping website. Using ChatGPT, we classified the content of negative reviews. Additionally, we conducted statistical analysis using SPSS (IBM Corp) to examine the scoring and composition of negative evaluations.
RESULTS
A total of 30,317 pieces of effective comment information were collected from January 1, 2018, to August 15, 2023, including 7696 pieces of negative comment information. Manual inspection results indicated that ChatGPT had an accuracy rate of 92.05%. The F1-score was 0.914. The analysis of this data revealed a significant correlation between the comments and ratings received by hospitals during the pandemic. Overall, there was a significant increase in average comment scores during the outbreak (P<.001). Furthermore, there were notable differences in the composition of negative comments among different types of hospitals (P<.001). Children's hospitals received sensitive feedback regarding waiting times and treatment effectiveness, while patients at maternity hospitals showed a greater concern for the attitude of health care providers. Patients at tumor hospitals expressed a desire for timely examinations and treatments, especially during the pandemic period.
CONCLUSIONS
The COVID-19 pandemic had some association with patient comment scores. There were variations in the scores and content of comments among different types of specialized hospitals. Using ChatGPT to analyze patient comment content represents an innovative approach for statistically assessing factors contributing to patient dissatisfaction. The findings of this study could provide valuable insights for hospital administrators to foster more harmonious physician-patient relationships and enhance hospital performance during public health emergencies.
Topics: COVID-19; Humans; China; Internet; Pandemics; Hospitals; Patient Satisfaction; SARS-CoV-2; Empirical Research
PubMed: 38954461
DOI: 10.2196/52992 -
Journal of Medical Internet Research Jul 2024The patient-centered approach is essential for quality health care and patient safety. Understanding the service user's perspective on the factors maintaining the health...
Issues Related to the Use of Visual Social Networks and Perceived Usefulness of Social Media Literacy During the Recovery Phase: Qualitative Research Among Girls With Eating Disorders.
BACKGROUND
The patient-centered approach is essential for quality health care and patient safety. Understanding the service user's perspective on the factors maintaining the health problem is crucial for successful treatment, especially for patients who do not recognize their condition as clinically relevant or concerning. Despite the association between intensive use of visual social media and body dissatisfaction and eating disorders, little is known about the meanings users assign to posting or searching for edited photos and the strategies they use to protect themselves from digital risks.
OBJECTIVE
This study aims to examine how young women recovering from eating disorders in Northern Italy perceive the health risks and potential benefits associated with visual social networks (ie, Instagram and Snapchat). The literature has found these platforms to be detrimental to online body comparisons. It also explores the perceived usefulness, willingness, and personal interest in coconstructing social media literacy programs with girls recovering from eating disorders.
METHODS
A total of 30 semistructured interviews were conducted with adolescent girls aged 14-17 years at the end of their treatment for eating disorders. The following areas of research were addressed: (1) the meanings associated with the use of Instagram and Snapchat; (2) the investment in the photographic dimension and feedback; (3) the impact of visual social networks on body experiences; (4) the potential and risks perceived in their use; (5) the importance of supporting girls undergoing treatment for eating disorders in using social networks; and (6) the usefulness and willingness to co-design social network literacy programs. Content analysis was applied.
RESULTS
A total of 7 main contents emerged: active or passive role in using social networks, the impact of online interactions on body image, investment in the photographic dimension, effects on self-representation, perceived risks, self-protective strategies, and potential benefits. The findings highlight a strong awareness of the processes that trigger body comparisons in the virtual context, creating insecurity and worsening the relationship with oneself. The self-protective behaviors identified are the development of critical thinking, the avoidance of sensitive content, increased control over social networking site use, and a certain skepticism toward developing antagonistic ideologies. All these topics were considered fundamental.
CONCLUSIONS
The findings provide important insights for health professionals working with youth in preparing media literacy programs. These programs aim to reduce potential risks and amplify the positive effects of online resources. They underscore the importance of addressing this issue during hospitalization to develop skills and critical thinking aimed at changing small habits that perpetuate the problem in everyday life. The inherent limitations in current service practices, which may not adequately address individual needs or impact posttreatment life, must also be considered.
Topics: Humans; Female; Social Media; Adolescent; Feeding and Eating Disorders; Qualitative Research; Italy
PubMed: 38954459
DOI: 10.2196/53334 -
JMIR Research Protocols Jul 2024Obesity prevalence in youth with spina bifida is higher than in their typically developing peers. Obesity is associated with lifelong medical, psychological, and...
BACKGROUND
Obesity prevalence in youth with spina bifida is higher than in their typically developing peers. Obesity is associated with lifelong medical, psychological, and economic burdens. Successful prevention or treatment of obesity in individuals with spina bifida is compromised by (1) the lack of valid and reliable methods to identify body fat in a clinical setting and (2) limited data on energy expenditure that are necessary to provide daily caloric recommendations.
OBJECTIVE
The objectives of this study will be to develop 2 algorithms for use in youth with spina bifida in a clinical setting, one to model body fat and one to predict total daily energy expenditure. In addition, physical activity and dietary intake will be described for the sample.
METHODS
This multisite, prospective, national clinical study will enroll 232 youth with myelomeningocele aged 5 to 18 years (stratified by age and mobility). Participants will be enrolled for 1 week. Data obtained include 4 measures of body composition, up to 5 height measures, a ramped activity protocol, and a nutrition and physical activity screener. Participants will wear an accelerometer for the week. On the final study day, 2 samples of urine or saliva, which complete the doubly labeled water protocol, will be obtained. The analysis will include descriptive statistics, Bland-Altman plots, concordance correlation, and regression analysis.
RESULTS
The study received extramural federal funding in July 2019. Data collection was initiated in March 2020. As of April 2024, a total of 143 (female participants: n=76, 53.1%; male participants: n=67, 46.9%) out of 232 participants have been enrolled. Data collection is expected to continue throughout 2024. A no-cost extension until November 2025 will be requested for data analysis and dissemination of findings.
CONCLUSIONS
This study furthers previous pilot work that confirmed the acceptability and feasibility of obtaining alternate height, body composition, and energy expenditure measures. The findings from this study will enhance screening, prevention, and treatment of abnormal weight status by facilitating the accurate identification of youths' weight status category and recommendations of daily caloric needs for this population that is at higher risk of obesity. Furthermore, the findings have the potential to impact outcomes for youth diagnosed with disabilities other than spina bifida who experience similar challenges related to alterations in body composition or fat distribution or measurement challenges secondary to mobility issues or musculoskeletal problems.
INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)
DERR1-10.2196/52779.
Topics: Humans; Adolescent; Child; Spinal Dysraphism; Energy Metabolism; Cross-Sectional Studies; Body Composition; Female; Male; Child, Preschool; Prospective Studies; Exercise
PubMed: 38954458
DOI: 10.2196/52779 -
ELife Jul 2024
PubMed: 38954437
DOI: 10.7554/eLife.100778 -
JMIR Research Protocols Jul 2024Starting in 2010, the epidermal growth factor receptor (EGFR) kinase inhibitors erlotinib and gefitinib were introduced into routine use in Aotearoa New Zealand (NZ) for...
Erlotinib or Gefitinib for Treating Advanced Epidermal Growth Factor Receptor Mutation-Positive Lung Cancer in Aotearoa New Zealand: Protocol for a National Whole-of-Patient-Population Retrospective Cohort Study and Results of a Validation Substudy.
BACKGROUND
Starting in 2010, the epidermal growth factor receptor (EGFR) kinase inhibitors erlotinib and gefitinib were introduced into routine use in Aotearoa New Zealand (NZ) for treating advanced lung cancer, but their impact in this setting is unknown.
OBJECTIVE
The study described in this protocol aims to understand the effectiveness and safety of these new personalized lung cancer treatments and the contributions made by concomitant medicines and other factors to adverse outcomes in the general NZ patient population. A substudy aimed to validate national electronic health databases as the data source and the methods for determining patient eligibility and identifying outcomes and variables.
METHODS
This study will include all NZ patients with advanced EGFR mutation-positive lung cancer who were first dispensed erlotinib or gefitinib before October 1, 2020, and followed until death or for at least 1 year. Routinely collected health administrative and clinical data will be collated from national electronic cancer registration, hospital discharge, mortality registration, and pharmaceutical dispensing databases by deterministic data linkage using National Health Index numbers. The primary effectiveness and safety outcomes will be time to treatment discontinuation and serious adverse events, respectively. The primary variable will be high-risk concomitant medicines use with erlotinib or gefitinib. For the validation substudy (n=100), data from clinical records were compared to those from national electronic health databases and analyzed by agreement analysis for categorical data and by paired 2-tailed t tests for numerical data.
RESULTS
In the validation substudy, national electronic health databases and clinical records agreed in determining patient eligibility and for identifying serious adverse events, high-risk concomitant medicines use, and other categorical data with overall agreement and κ statistic of >90% and >0.8000, respectively; for example, for the determination of patient eligibility, the comparison of proxy and standard eligibility criteria applied to national electronic health databases and clinical records, respectively, showed overall agreement and κ statistic of 96% and 0.8936, respectively. Dates for estimating time to treatment discontinuation and other numerical variables and outcomes showed small differences, mostly with nonsignificant P values and 95% CIs overlapping with zero difference; for example, for the dates of the first dispensing of erlotinib or gefitinib, national electronic health databases and clinical records differed on average by approximately 4 days with a nonsignificant P value of .33 and 95% CIs overlapping with zero difference. As of May 2024, the main study is ongoing.
CONCLUSIONS
A protocol is presented for a national whole-of-patient-population retrospective cohort study designed to describe the safety and effectiveness of erlotinib and gefitinib during their first decade of routine use in NZ for treating EGFR mutation-positive lung cancer. The validation substudy demonstrated the feasibility and validity of using national electronic health databases and the methods for determining patient eligibility and identifying the study outcomes and variables proposed in the study protocol.
TRIAL REGISTRATION
Australian New Zealand Clinical Trials Registry ACTRN12615000998549; https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=368928.
INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)
DERR1-10.2196/51381.
Topics: Humans; Erlotinib Hydrochloride; Gefitinib; Lung Neoplasms; ErbB Receptors; Retrospective Studies; New Zealand; Mutation; Female; Male; Protein Kinase Inhibitors; Antineoplastic Agents; Cohort Studies; Middle Aged; Aged
PubMed: 38954434
DOI: 10.2196/51381 -
JAMA Network Open Jul 2024Current evidence is conflicting for associations of extended-infusion β-lactam (EI-BL) therapy with clinical outcomes.
IMPORTANCE
Current evidence is conflicting for associations of extended-infusion β-lactam (EI-BL) therapy with clinical outcomes.
OBJECTIVE
To investigate the association of EI-BL therapy with survival, adverse events, and emergence of antibiotic resistance in adults with gram-negative bloodstream infections (GN-BSI).
DESIGN, SETTING, AND PARTICIPANTS
This cohort study of consecutive adults with GN-BSI admitted to 24 United States hospitals between January 1, 2019, and December 31, 2019, receiving EI-BL were compared with adults with GN-BSI receiving the same agents as intermittent infusion β-lactam (II-BL; ≤1-hour infusions). Statistical analysis was performed from January to October 2023.
EXPOSURES
EI-BL (ie, ≥3-hour infusion).
MAIN OUTCOMES AND MEASURES
EI-BL and II-BL groups underwent 1:3 nearest-neighbor propensity score matching (PSM) without replacement. Multivariable regression was applied to the PSM cohort to investigate outcomes, all censored at day 90. The primary outcome was mortality; secondary outcomes included antibiotic adverse events and emergence of resistance (≥4-fold increase in the minimum inhibitory concentration of the β-lactam used to treat the index GN-BSI).
RESULTS
Among the 4861 patients included, 2547 (52.4%) were male; and the median (IQR) age was 67 (55-77) years. There were 352 patients in the EI-BL 1:3 PSM group, and 1056 patients in the II-BL 1:3 PSM group. Among 1408 PSM patients, 373 (26.5%) died by day 90. The odds of mortality were lower in the EI-BL group (adjusted odds ratio [aOR], 0.71 [95% CI, 0.52-0.97]). In a stratified analysis, a survival benefit was only identified in patients with severe illness or elevated minimum inhibitory concentrations (ie, in the intermediate range for the antibiotic administered). There were increased odds of catheter complications (aOR, 3.14 [95% CI, 1.66-5.96]) and antibiotic discontinuation because of adverse events (eg, acute kidney injury, cytopenias, seizures) in the EI-BL group (aOR, 3.66 [95% CI, 1.68-7.95]). Emergence of resistance was similar in the EI-BL and II-BL groups at 2.9% vs 7.2%, respectively (P = .35).
CONCLUSIONS AND RELEVANCE
In this cohort study of patients with GN-BSI, EI-BL therapy was associated with reduced mortality for patients with severe illness or those infected with nonsusceptible organisms; potential advantages in other groups remain unclear and need to be balanced with potential adverse events. The subsequent emergence of resistance warrants investigation in a larger cohort.
Topics: Humans; Male; Female; Middle Aged; Gram-Negative Bacterial Infections; Anti-Bacterial Agents; beta-Lactams; Aged; Bacteremia; Infusions, Intravenous; Cohort Studies; United States; Adult; Retrospective Studies
PubMed: 38954416
DOI: 10.1001/jamanetworkopen.2024.18234 -
JAMA Network Open Jul 2024Socioeconomically disadvantaged individuals (ie, those with low socioeconomic status [SES]) have difficulty quitting smoking and may benefit from incentive-based... (Randomized Controlled Trial)
Randomized Controlled Trial
IMPORTANCE
Socioeconomically disadvantaged individuals (ie, those with low socioeconomic status [SES]) have difficulty quitting smoking and may benefit from incentive-based cessation interventions.
OBJECTIVES
To evaluate the impact of incentivizing smoking abstinence on smoking cessation among adults with low SES.
DESIGN, SETTING, AND PARTICIPANTS
This study used a 2-group randomized clinical trial design. Data collection occurred between January 30, 2017, and February 7, 2022. Participants included adults with low SES who were willing to undergo smoking cessation treatment. Data were analyzed from April 18, 2023, to April 19, 2024.
INTERVENTIONS
Participants were randomized to usual care (UC) for smoking cessation (counseling plus pharmacotherapy) or UC plus abstinence-contingent financial incentives (UC plus FI).
MAIN OUTCOMES AND MEASURES
The primary outcome was biochemically verified 7-day point prevalence smoking abstinence (PPA) at 26 weeks after the quit date. Secondary outcomes included biochemically verified 7-day PPA at earlier follow-ups, 30-day PPA at 12 and 26 weeks, repeated 7-day PPA, and continuous abstinence. Multiple approaches were employed to handle missing outcomes at follow-up, including categorizing missing data as smoking (primary), complete case analysis, and multiple imputation.
RESULTS
The 320 participants had a mean (SD) age of 48.9 (11.6) and were predominantly female (202 [63.1%]); 82 (25.6%) were Black, 15 (4.7%) were Hispanic, and 200 (62.5%) were White; and 146 (45.6%) participated during the COVID-19 pandemic. Overall, 161 were randomized to UC and 159 were randomized to UC plus FI. After covariate adjustment with missing data treated as smoking, assignment to UC plus FI was associated with a greater likelihood of 7-day PPA at the 4-week (adjusted odds ratio [AOR], 3.11 [95% CI, 1.81-5.34]), 8-week (AOR, 2.93 [95% CI, 1.62-5.31]), and 12-week (AOR, 3.18 [95% CI, 1.70-5.95]) follow-ups, but not at the 26-week follow-up (22 [13.8%] vs 14 [8.7%] abstinent; AOR, 1.79 [95% CI, 0.85-3.80]). However, the association of group assignment with smoking cessation reached statistical significance at all follow-ups, including 26 weeks, with multiple imputation (37.37 [23.5%] in the UC plus FI group vs 19.48 [12.1%] in the UC group were abstinent; AOR, 2.29 [95% CI, 1.14-4.63]). Repeated-measures analyses indicated that participants in the UC plus FI group were significantly more likely to achieve PPA across assessments through 26 weeks with all missing data estimation methods. Other secondary cessation outcomes also showed comparable patterns across estimation methods. Participants earned a mean (SD) of $72 ($90) (of $250 possible) in abstinence-contingent incentives. Participation during the COVID-19 pandemic reduced the likelihood of cessation across assessments.
CONCLUSIONS AND RELEVANCE
In this randomized clinical trial, incentivizing smoking cessation did not increase cessation at 26 weeks when missing data were treated as smoking; however, the UC plus FI group had greater odds of quitting at follow-ups through 12 weeks. Cessation rates were higher for the UC plus FI group at all follow-ups through 26 weeks when multiple imputation was used to estimate missing outcomes.
TRIAL REGISTRATION
ClinicalTrials.gov Identifier: NCT02737566.
Topics: Humans; Smoking Cessation; Female; Male; Motivation; Adult; Middle Aged; Vulnerable Populations; Poverty
PubMed: 38954415
DOI: 10.1001/jamanetworkopen.2024.18821 -
JAMA Network Open Jul 2024Older adults who are hospitalized for COVID-19 are at risk of delirium. Little is known about the association of in-hospital delirium with functional and cognitive...
IMPORTANCE
Older adults who are hospitalized for COVID-19 are at risk of delirium. Little is known about the association of in-hospital delirium with functional and cognitive outcomes among older adults who have survived a COVID-19 hospitalization.
OBJECTIVE
To evaluate the association of delirium with functional disability and cognitive impairment over the 6 months after discharge among older adults hospitalized with COVID-19.
DESIGN, SETTING, AND PARTICIPANTS
This prospective cohort study involved patients aged 60 years or older who were hospitalized with COVID-19 between June 18, 2020, and June 30, 2021, at 5 hospitals in a major tertiary care system in the US. Follow-up occurred through January 11, 2022. Data analysis was performed from December 2022 to February 2024.
EXPOSURE
Delirium during the COVID-19 hospitalization was assessed using the Chart-based Delirium Identification Instrument (CHART-DEL) and CHART-DEL-ICU.
MAIN OUTCOMES AND MEASURES
Primary outcomes were disability in 15 functional activities and the presence of cognitive impairment (defined as Montreal Cognitive Assessment score <22) at 1, 3, and 6 months after hospital discharge. The associations of in-hospital delirium with functional disability and cognitive impairment were evaluated using zero-inflated negative binominal and logistic regression models, respectively, with adjustment for age, month of follow-up, and baseline (before COVID-19) measures of the respective outcome.
RESULTS
The cohort included 311 older adults (mean [SD] age, 71.3 [8.5] years; 163 female [52.4%]) who survived COVID-19 hospitalization. In the functional disability sample of 311 participants, 49 participants (15.8%) experienced in-hospital delirium. In the cognition sample of 271 participants, 31 (11.4%) experienced in-hospital delirium. In-hospital delirium was associated with both increased functional disability (rate ratio, 1.32; 95% CI, 1.05-1.66) and increased cognitive impairment (odds ratio, 2.48; 95% CI, 1.38-4.82) over the 6 months after discharge from the COVID-19 hospitalization.
CONCLUSIONS AND RELEVANCE
In this cohort study of 311 hospitalized older adults with COVID-19, in-hospital delirium was associated with increased functional disability and cognitive impairment over the 6 months following discharge. Older survivors of a COVID-19 hospitalization who experience in-hospital delirium should be assessed for disability and cognitive impairment during postdischarge follow-up.
Topics: Humans; COVID-19; Delirium; Female; Male; Aged; Cognitive Dysfunction; Prospective Studies; Hospitalization; SARS-CoV-2; Aged, 80 and over; Middle Aged
PubMed: 38954414
DOI: 10.1001/jamanetworkopen.2024.19640