Tag: pubmed

Genome Res. 2024 Apr 16. doi: 10.1101/gr.278268.123. Online ahead of print.

ABSTRACT

Reference-free genome phasing is vital for understanding allele inheritance and the impact of single-molecule DNA variation on phenotypes. To achieve thorough phasing across homozygous or repetitive regions of the genome, long-read sequencing technologies are often used to perform phased de novo assembly. As a step toward reducing the cost and complexity of this type of analysis, we describe new methods for accurately phasing Oxford Nanopore Technologies (ONT) sequence data with the Shasta genome assembler and a modular tool for extending phasing to the chromosome scale called GFAse. We test using new variants of ONT PromethION sequencing, including those using proximity ligation, and show that newer, higher accuracy ONT reads substantially improve assembly quality.

PMID:38627094 | DOI:10.1101/gr.278268.123

Clin Psychopharmacol Neurosci. 2024 May 31;22(2):364-369. doi: 10.9758/cpn.24.1183.

ABSTRACT

OBJECTIVE: This study determined the threshold for recurrent depressive episodes that predicted conversion from major depressive disorder (MDD) to bipolar disorder (BD).

METHODS: We retrospectively reviewed the medical records of 296 patients diagnosed with MDD for a minimum of 5 years in two university hospitals. We examined their the Diagnostic and Statistical Manual of Mental Disorders, 5th edition diagnoses and detailed clinical information at the initial admission and yearly assessments after discharge to establish the threshold for recurrent depressive episodes indicating a risk of diagnostic conversion from MDD to BD. Optimal cut-offs were derived using receiver operating characteristic (ROC) curves.

RESULTS: ROC curve analysis revealed that more than four recurrent depressive episodes was indicative of potential diagnostic conversion from MDD to BD (area under the curve, 0.604; sensitivity, 0.353; specificity, 0.855; positive predictive value, 0.421; negative predictive value, 0.816).

CONCLUSION: These findings suggest that the best predictor of conversion from MDD to BD is more than four recurrent depressive episodes. Our findings have the potential to enhance diagnostic accuracy and treatment efficiency. To validate our results, longitudinal prospective studies are necessary.

PMID:38627083 | DOI:10.9758/cpn.24.1183

Clin Psychopharmacol Neurosci. 2024 May 31;22(2):285-294. doi: 10.9758/cpn.23.1091. Epub 2023 Jul 17.

ABSTRACT

OBJECTIVE: Many psychiatric disorders are linked to low grade systemic inflammation as measured by systemic cytokine levels. Exploration of cytokines and immune activity and their role in psychiatric symptoms may inform pathobiology and treatment opportunities. The aim of this study is to explore if there are associations between cytokines and psychiatric symptom clusters. Comparison between patients regularly using and those not using psychotropic medication is also conducted.

METHODS: This was a cross sectional naturalistic study with 132 participants from a general open inpatient psychiatric ward at the Nordland Hospital Trust, Norway. Serum levels of 28 different cytokines were assessed. Psychiatric symptoms the last week were assessed by a self-rating scale (Symptom check list, SCL-90-R) and grouped in defined clusters. Multiple linear regression model was used for statistical analyses of associations between levels of cytokines and symptoms, adjusting for possible confounding factors.

RESULTS: We found a positive association (p = 0.009) between the chemokine interferon-gamma inducible protein 10 (CXCL 10; IP-10) and the anger hostility cluster. No associations were found between the other symptom clusters and cytokines. IP-10 and the anger hostility cluster were positively associated (p = 0.002) in the subgroup of patients using psychotropic medication, not in the subgroup not using psychotropic medication.

CONCLUSION: Our analyses revealed a significant positive association between the symptom cluster anger hostility in SCL-90-R and the chemokine IP-10 in the subgroup of patients using psychotropic medications.

PMID:38627075 | DOI:10.9758/cpn.23.1091

BMJ Paediatr Open. 2024 Apr 16;8(1):e002502. doi: 10.1136/bmjpo-2024-002502.

ABSTRACT

BACKGROUND: With the increasing survival rate of smaller newborns and twins, previous growth curves may not accurately assess the growth of extremely preterm infants (EPIs). Our study aimed to establish birth weight percentile curves for singletons and twins in EPIs from China and the USA and compare the differences between them.

METHODS: In China, EPIs were from 31 provinces, from 2010 to 2021. The collected information was sex, gestational age, birth weight, singletons and twins. We used the generalised additive models for location scale and shape method to construct the birth weight percentile curves by gestational age and sex for EPIs. The National Vital Statistics System database from 2016 to 2021 was also analysed. We compared the differences between the 50th birth weight percentile curves of the two databases.

RESULTS: We identified 8768 neonates in China (5536 singletons and 3232 twins) and 121 933 neonates in the USA (97 329 singletons and 24 604 twins). We established the 3rd, 10th, 25th, 50th, 75th, 90th and 97th birth weight reference curves for China and the USA. The results showed that males had higher birth weights than females. In China, for the same gestational age and sex, birth weights in singletons and twins were found to be similar, though singleton males born in China had slightly higher birth weights than male twins. In the USA, birth weights were also similar for females and males, with the same gestational age in singletons and twins.

CONCLUSION: We established birth weight reference percentile curves by gestational age and sex for singletons and twins among EPIs in China and the USA.

PMID:38627060 | DOI:10.1136/bmjpo-2024-002502

Int J Gynecol Cancer. 2024 Apr 16:ijgc-2023-005162. doi: 10.1136/ijgc-2023-005162. Online ahead of print.

ABSTRACT

OBJECTIVE: To determine if reviewer experience impacts the ability to discriminate between human-written and ChatGPT-written abstracts.

METHODS: Thirty reviewers (10 seniors, 10 juniors, and 10 residents) were asked to differentiate between 10 ChatGPT-written and 10 human-written (fabricated) abstracts. For the study, 10 gynecologic oncology abstracts were fabricated by the authors. For each human-written abstract we generated a ChatGPT matching abstract by using the same title and the fabricated results of each of the human generated abstracts. A web-based questionnaire was used to gather demographic data and to record the reviewers’ evaluation of the 20 abstracts. Comparative statistics and multivariable regression were used to identify factors associated with a higher correct identification rate.

RESULTS: The 30 reviewers discriminated 20 abstracts, giving a total of 600 abstract evaluations. The reviewers were able to correctly identify 300/600 (50%) of the abstracts: 139/300 (46.3%) of the ChatGPT-generated abstracts and 161/300 (53.7%) of the human-written abstracts (p=0.07). Human-written abstracts had a higher rate of correct identification (median (IQR) 56.7% (49.2-64.1%) vs 45.0% (43.2-48.3%), p=0.023). Senior reviewers had a higher correct identification rate (60%) than junior reviewers and residents (45% each; p=0.043 and p=0.002, respectively). In a linear regression model including the experience level of the reviewers, familiarity with artificial intelligence (AI) and the country in which the majority of medical training was achieved (English speaking vs non-English speaking), the experience of the reviewer (β=10.2 (95% CI 1.8 to 18.7)) and familiarity with AI (β=7.78 (95% CI 0.6 to 15.0)) were independently associated with the correct identification rate (p=0.019 and p=0.035, respectively). In a correlation analysis the number of publications by the reviewer was positively correlated with the correct identification rate (r28)=0.61, p<0.001.

CONCLUSION: A total of 46.3% of abstracts written by ChatGPT were detected by reviewers. The correct identification rate increased with reviewer and publication experience.

PMID:38627032 | DOI:10.1136/ijgc-2023-005162

Arch Dis Child. 2024 Apr 16:archdischild-2023-326331. doi: 10.1136/archdischild-2023-326331. Online ahead of print.

ABSTRACT

BACKGROUND: Internet use has increased and sleep and physical activity (PA) have decreased in recent years among adolescents. Besides sleep and PA, another determinant of future health for adolescents is education. Our aim was to evaluate the associations of excessive internet use (EIU), short sleep duration and low PA with both unexcused absences and medical absences during lower secondary school.

METHODS: The School Health Promotion study is a national survey of adolescents conducted biennially in Finland. We used data collected in 2019, when EIU was assessed for the first time. Cumulative odds ratio analysis was conducted with unexcused absences and medical absences as outcome variables. Besides EIU, sleep duration and PA, the associations of maternal education and parental relations were assessed.

RESULTS: The mean age of the 86 270 participants was 15.3 years. Girls scored higher than boys on EIU. In all, 34.7% of participants slept less than 8 hours per night during the school week, and 34.3% reported low PA (ie, less than 3 days per week with minimum 1 hour of PA per day). EIU, short sleep and low PA were associated with both unexcused absences and medical absences from school. Longer sleep during weekends showed no association with absences, but good parental relations had the strongest protective association with both unexcused and medical absences.

CONCLUSIONS: EIU, short sleep duration and low PA were associated with both unexcused and medical absences from school. This has important implications for both the promotion of general health and the support offered to students with alarming school absences.

PMID:38627028 | DOI:10.1136/archdischild-2023-326331

J Nucl Med Technol. 2024 Apr 16:jnmt.123.267156. doi: 10.2967/jnmt.123.267156. Online ahead of print.

ABSTRACT

Fibroblast activation protein is a promising target for oncologic molecular imaging with radiolabeled fibroblast activation protein inhibitors (FAPI) in a large variety of cancers. However, there are yet no published recommendations on how to set up an optimal imaging protocol for FAPI PET/CT. It is important to optimize the acquisition duration and strive toward an acquisition that is sufficiently short while simultaneously providing sufficient image quality to ensure a reliable diagnosis. The aim of this study was to evaluate the feasibility of reducing the acquisition duration of [⁶⁸Ga]FAPI-46 imaging while maintaining satisfactory image quality, with certainty that the radiologist’s ability to make a clinical diagnosis would not be affected. Methods: [⁶⁸Ga]FAPI-46 PET/CT imaging was performed on 10 patients scheduled for surgical resection of suspected pancreatic cancer, 60 min after administration of 3.6 ± 0.2 MBq/kg. The acquisition time was 4 min/bed position, and the raw PET data were statistically truncated and reconstructed to represent images with an acquisition duration of 1, 2, and 3 min/bed position, additional to the reference images of 4 min/bed position. Four image quality criteria that focused on the ability to distinguish specific anatomic details, as well as perceived image noise and overall image quality, were scored on a 4-point Likert scale and analyzed with mixed-effects ordinal logistic regression. Results: A trend toward increasing image quality scores with increasing acquisition duration was observed for all criteria. For the overall image quality, there was no significant difference between 3 and 4 min/bed position, whereas 1 and 2 min/bed position were rated significantly (P < 0.05) lower than 4 min/bed position. For the other criteria, all images with a reduced acquisition duration were rated significantly inferior to images obtained at 4 min/bed position. Conclusion: The acquisition duration can be reduced from 4 to 3 min/bed position while maintaining satisfactory image quality. Reducing the acquisition duration to 2 min/bed position or lower is not recommended since it results in inferior-quality images so noisy that clinical interpretation is significantly disrupted.

PMID:38627014 | DOI:10.2967/jnmt.123.267156

J Nucl Med Technol. 2024 Apr 16:jnmt.123.267113. doi: 10.2967/jnmt.123.267113. Online ahead of print.

ABSTRACT

The Alzheimer disease (AD) continuum is a neurodegenerative disorder with cognitive decline and pathologic changes. Tau PET imaging can detect tau pathology, and ¹⁸F-flortaucipir PET imaging is expected to visualize progression through the stages of AD, for which quantitative assessment is essential. Two measurement methods, statistically defined multiblock barycentric discriminant analysis (MUBADA)/parametric estimation of reference signal intensity (PERSI) and anatomically defined tau meta-volume of interest (VOI)/cerebellar gray matter (CGM) for SUV ratio (SUVR), were compared in this study to assess their relationship to AD clinical stage using 2 open multicenter PET databases. Methods: Data were selected for 106 cases from 2 databases, AMED Preclinical AD study (AMED-PRE) (n = 15) and Alzheimer Disease Neuroimaging Initiative 3 (n = 91). The data of the participants were categorized into 4 groups based on the clinical criteria. Tau PET imaging was conducted using ¹⁸F-flortaucipir, and the 2 SUVR measurement methods, MUBADA/PERSI and tau meta-VOI/CGM, were compared among different clinical categories: amyloid-negative cognitively normal, preclinical AD, amyloid-negative mild cognitive impairment (MCI), and amyloid-positive MCI. Results: Significant differences were found between cognitively normal and preclinical AD, as well as between cognitively normal and amyloid-positive MCI and between amyloid-negative MCI and -positive MCI in SUVR derived by MUBADA/PERSI, whereas SUVR by tau meta-VOI/CGM did not provide significant differences between any pair. The tau meta-VOI/CGM method consistently provided higher SUVRs and larger individual variations than MUBADA/PERSI, with a mean SUVR difference of 0.136 for the studied databases. Conclusion: MUBADA/PERSI provided the SUVR of ¹⁸F-flortaucipir uptake with better association with the clinical severity of the AD continuum and with smaller variability. The results support the usefulness of MUBADA/PERSI as a quantitative measure of ¹⁸F-flortaucipir uptake in multicenter studies using different PET systems and scanning methods. However, limitations of the study include the small sample size and the unbalanced distribution among clinical categories in the AMED Preclinical AD study database.

PMID:38627012 | DOI:10.2967/jnmt.123.267113

Can Fam Physician. 2024 Apr;70(4):e52-e60. doi: 10.46747/cfp.7004e52.

ABSTRACT

OBJECTIVE: To explore barriers and facilitators for family physicians in Saskatchewan prescribing opioid agonist therapy (OAT).

DESIGN: Self-administered postal survey.

SETTING: Family medicine practices in Saskatchewan.

PARTICIPANTS: A total of 218 Saskatchewan family physicians who were not authorized to prescribe OAT as of June 2022.

MAIN OUTCOME MEASURES: Descriptive and inferential statistics of physicians’ self-reported barriers to and facilitators of prescribing OAT for opioid use disorder (OUD).

RESULTS: Most respondents (84.8%) had some comfort with diagnosing OUD. However, more than half (58.3%) did not feel confident or knowledgeable about prescribing OAT. Barriers to OAT prescribing included lack of time, incomplete training requirements, lack of interest, insufficient funding or support, feeling overwhelmed, and perceiving that OAT does not work and thus is not necessary. Physicians working in core neighbourhoods and those receiving fee-for-service compensation reported the least available time to prescribe OAT. Conversely, physicians working in interdisciplinary team settings had increased time for OAT prescribing compared with physicians in other settings. Having a close personal relationship with someone with OUD was correlated with increased comfort in diagnosing OUD as well as with knowledge about and confidence in prescribing OAT. Themes identified as facilitators to increasing OAT prescribing included the addition of resources and supports, increased training, more awareness about OUD and OAT, enhanced compensation, and altered prescribing regulations.

CONCLUSION: Despite the presence of several real and perceived barriers limiting OAT prescribing by Saskatchewan family physicians, there are family physicians interested in providing this therapy. Increased clinical resources and support, including increased interdisciplinary practice, are actionable steps that should be considered by policy decision makers to address this issue. Additionally, increased OUD and OAT education, which includes the perspectives of those with lived experience of OUD, would help address physician confidence, knowledge, and awareness in this area.

PMID:38626996 | DOI:10.46747/cfp.7004e52

BMJ Open. 2024 Apr 15;14(4):e082654. doi: 10.1136/bmjopen-2023-082654.

ABSTRACT

BACKGROUND: Globally, cardiovascular disease (CVD) remains the leading cause of death, warranting effective management and prevention measures. Risk prediction tools are indispensable for directing primary and secondary prevention strategies for CVD and are critical for estimating CVD risk. Machine learning (ML) methodologies have experienced significant advancements across numerous practical domains in recent years. Several ML and statistical models predicting CVD time-to-event outcomes have been developed. However, it is not known as to which of the two model types-ML and statistical models-have higher discrimination and calibration in this regard. Hence, this planned work aims to systematically review studies that compare ML with statistical methods in terms of their predictive abilities in the case of time-to-event data with censoring.

METHODS: Original research articles published as prognostic prediction studies, which involved the development and/or validation of a prognostic model, within a peer-reviewed journal, using cohort or experimental design with at least a 12-month follow-up period will be systematically reviewed. The review process will adhere to the Critical Appraisal and Data Extraction for Systematic Reviews of Prediction Modelling Studies checklist.

ETHICS AND DISSEMINATION: Ethical approval is not required for this review, as it will exclusively use data from published studies. The findings of this study will be published in an open-access journal and disseminated at scientific conferences.

PROSPERO REGISTRATION NUMBER: CRD42023484178.

PMID:38626976 | DOI:10.1136/bmjopen-2023-082654