Tag: statistics

BMC Bioinformatics. 2023 Dec 17;24(1):484. doi: 10.1186/s12859-023-05618-0.

ABSTRACT

BACKGROUND: In the field of computational personalized medicine, drug response prediction (DRP) is a critical issue. However, existing studies often characterize drugs as strings, a representation that does not align with the natural description of molecules. Additionally, they ignore gene pathway-specific combinatorial implication.

RESULTS: In this study, we propose drug Graph and gene Pathway based Drug response prediction method (GPDRP), a new multimodal deep learning model for predicting drug responses based on drug molecular graphs and gene pathway activity. In GPDRP, drugs are represented by molecular graphs, while cell lines are described by gene pathway activity scores. The model separately learns these two types of data using Graph Neural Networks (GNN) with Graph Transformers and deep neural networks. Predictions are subsequently made through fully connected layers.

CONCLUSIONS: Our results indicate that Graph Transformer-based model delivers superior performance. We apply GPDRP on hundreds of cancer cell lines’ bulk RNA-sequencing data, and it outperforms some recently published models. Furthermore, the generalizability and applicability of GPDRP are demonstrated through its predictions on unknown drug-cell line pairs and xenografts. This underscores the interpretability achieved by incorporating gene pathways.

PMID:38105227 | DOI:10.1186/s12859-023-05618-0

Inquiry. 2023 Jan-Dec;60:469580231212126. doi: 10.1177/00469580231212126.

ABSTRACT

Low anterior resection for rectal cancer often includes a diverting loop-ileostomy to avoid the severe consequences of anastomotic leakage. Reversal of the stoma is often delayed, which can incur health-care costs on different levels. The aim is to, on population basis, determine stoma-related costs, and to investigate habitual and socioeconomic factors associated to the level of cost. Multi-register design with data from the Swedish Rectal Cancer Registry, the National Prescribed Drug Register, Statistics Sweden and cost-administrative data from the National Board of Health and Welfare. Data was gathered for 3564 patients with rectal cancer surgery 2007 to 2013, for 3 years following the surgery. Factors influencing the cost of inpatient care and stoma-related consumables were assessed with linear regression analyses. All monthly costs were higher for females (consumables P < .001 and in-patient care P = .031). Post-secondary education (P = .003) and younger age (P = .020) was associated with a higher cost for consumables while suffering a surgical complication was associated with increased cost for inpatient care (P < .001). Patients who had their stoma longer had lower monthly costs (consumables P < .001 and in-patient care P < .001). Female gender, longer duration of stoma, young age, and higher education are associated with higher costs for the care of a diverting stoma after rectal cancer surgery. This study does not allow for analyses of causality but the results together with deepened analyses of underlying reasons form a proper basis for decisions in health care planning and allocation of resources. These findings may have implications on the debate of equal care for all.

PMID:38105185 | DOI:10.1177/00469580231212126

Cleft Palate Craniofac J. 2023 Dec 17:10556656231221654. doi: 10.1177/10556656231221654. Online ahead of print.

ABSTRACT

OBJECTIVE: This study aimed to investigate the prevalence of obstructive sleep apnoea (OSA) in patients with craniofacial microsomia (CFM) through polysomnography (PSG) and the relationship with the severity of CFM.

METHODS: This study reviewed patients of CFM with pre-operative PSG data between January 2005 and September 2023. Patients were grouped according to the Pruzansky-Kaban classification. OSA was diagnosed and severity was assessed by the obstructive apnea-hypopnea index. The Pediatric Sleep Questionnaire was used to investigate OSA-related signs and symptoms. The χ 2 test and Fisher’s exact test were used to compare between groups. Univariate logistic regression was used to identify risk factors associated with OSA. A p-value less than 0.05 was considered statistically significant.

RESULTS: A total of 121 patients with CFM were included in the study with 3 bilateral and 118 unilateral patients. In total, 86 patients (71.07%) were diagnosed with OSA. The prevalence of OSA in type IIa, type IIb and type III was 72.97%, 78.33%, and 47.62%. There was no statistically significant difference in the prevalence of OSA between type IIa and type IIb (p > .05). The difference in the prevalence of OSA between type III and type II was statistically significant (p < .05). Snoring was the most common symptom among the patients of CFM with OSA.

CONCLUSIONS: Patients with CFM have a higher incidence of OSA based on PSG in type II and type III patients. The incidence of OSA did not correlate positively with the severity of CFM, with type III patients having certain particularities.

PMID:38105178 | DOI:10.1177/10556656231221654

J Ethnobiol Ethnomed. 2023 Dec 17;19(1):62. doi: 10.1186/s13002-023-00634-z.

ABSTRACT

BACKGROUND: In multicultural societies, traditional knowledge among minorities faces several challenges. Minority groups often face difficult situations living in specific peripheral geographies and striving to retain their biocultural heritage, including medicinal plant knowledge and practices. Folk medicinal plant knowledge is a dynamic eco-cultural complex influenced by various environmental, socio-cultural, and political factors. Examining medicinal plant knowledge among minorities has been an increasingly popular topic in cross-cultural ethnobiology. It also helps understand the dynamics of local/traditional ecological knowledge (LEK/TEK) change within a given community. The current study was designed to investigate the status of medicinal plant knowledge among two linguistic groups, i.e. Ormurs and Pathans, living in a remote valley of West Pakistan.

METHODS: We recruited 70 male study participants from the studied groups for semi-structured interviews to record the medicinal plant use of their communities. Data were compared among the two studied communities using the stacked charts employing the presence or absence of data with Past 4.03 and Venn diagrams. Use reports (URs) were counted for each recorded taxon.

RESULTS AND DISCUSSION: A total of seventy-four medicinal plants were quoted as used as ethnomedicines by the researched communities. Most of the reported plants were used to treat digestive and liver problems. The cross-cultural comparison revealed a considerable homogeneity of medicinal plant knowledge (the two groups commonly used more than seventy plants); however, comparing uses recorded for the widely utilised medicinal plants showed numerous idiosyncratic uses among Ormurs but very few among Pathans. Ormurs reported a higher number of cultivated, wild, and imported plant uses than did Pathans. These results indicate that, compared to Pathans, the Ormur linguistic minority retain more folk medicinal plant knowledge, which may be explained by the fact that they have incorporated different folk remedies: their “own knowledge” plus that of Pathans, with whom they have lived together for centuries. Moreover, the local plant nomenclature among Ormurs was highly affected by the plant nomenclature of Pathans.

CONCLUSION: The current study revealed that living together for a few centuries has not implied sharing plant knowledge (as the Pathans do not seem to have learnt from the Ormurs) or, in other words, that plant knowledge exchanges have been unidirectional. The findings show that the Pashto dominant culture may have possibly put pressure on the minority groups and affected local plant-centred cultural practices, as we see in the case of local plant nomenclature hybridisation among Omuri speakers. Hence, it is imperative to employ diverse educational strategies to revitalise the decline of medicinal plant knowledge in the studied communities, especially among Ormurs, who need more attention as they face more challenges than the other group. Locally based strategies should be devised to restore the fading connection with nature, which will be advantageous for revitalising plant knowledge.

PMID:38105177 | DOI:10.1186/s13002-023-00634-z

Clin Ther. 2023 Dec 16:S0149-2918(23)00431-9. doi: 10.1016/j.clinthera.2023.11.001. Online ahead of print.

ABSTRACT

PURPOSE: Major adverse drug reactions (ADRs) are the leading causes of poor adherence, switching of drugs, morbidity, and mortality. A limited studies was conducted to investigate major ADR in developing countries including Ethiopia, and the purpose of this study was to assess the incidence and predictors of major ADRs among HIV-infected children receiving antiretroviral therapy (ART) in West Amhara Comprehensive Specialized Hospitals, Northwest Ethiopia.

METHODS: An institutional-based retrospective follow-up study was conducted among 460 children receiving ART from January 1, 2014 to December 31, 2021. A simple random sampling technique was employed, and data were collected using Kobo Toolbox software and then deployed to STATA 14 for analysis. The Kaplan-Meier survival curve and the log-rank test were used to estimate and compare survival times. Both bivariable and multivariable Weibull regression models were fitted to identify predictors. Finally, an adjusted hazards ratio (AHR) with a 95% CI was computed, and variables with P < 0.05 were considered statistically significant predictors of major ADR.

FINDINGS: The overall incidence rate of major ADRs was 5.8 (95% CI, 4.6-7.3) per 1000 child months. Being female (AHR, 2.71; 95% CI, 1.52-4.84), tuberculosis (TB)-HIV co-infection (AHR, 2.49; 95% CI, 1.32-4.68), World Health Organization stage (III and IV) (AHR, 2.52; 95% CI, 1.39-4.56), zidovudine-based (AHR, 2.84; 95% CI, 1.11-7.31), and stavudine-based (AHR, 5.96; 95% CI, 1.63-21.84) regimens were found to be significant predictors of major ADRs.

IMPLICATIONS: The major ADR incidence rate was high. Health professionals should employ early screening and close follow-up for children with advanced World Health Organization clinical staging, females, those with TB-HIV co-infection, and those receiving stavudine- and zidovudine-based initial regimens to reduce the incidence of major ADRs.

PMID:38105175 | DOI:10.1016/j.clinthera.2023.11.001

Cont Lens Anterior Eye. 2023 Dec 16:102106. doi: 10.1016/j.clae.2023.102106. Online ahead of print.

ABSTRACT

PURPOSE: RigidCare is an electrolysis-based device that recently obtained approval from the US’s FDA to sterilise microorganisms and remove proteins for orthokeratology (O-K) lenses. The study was conducted to investigate the device’s performance in varied clinical circumstances.

METHODS: Trial lenses and private lenses were employed by O-K lens wearers from five hospitals for an evaluation of disinfection and sterilisation and an assessment of protein removal, respectively. Menicon multipurpose solution and protein remover were selected for use with the control group. Following the instructions, pre-cleaning lens samples, post-cleaning lens samples and residual solution samples of trial lenses of the experimental and control groups were collected for microorganism examinations by an experienced third-party testing organisation. The levels of protein deposition for these two approaches were rated by senior O-K experts. Categorical variables were analysed using statistical tests, such as the chi-squared test and Fisher’s exact test.

RESULTS: The microbial positive rate detected from the pre-cleaning and post-cleaning lens samples and the residual solution of the trial lenses for the experimental and control group was 4/76 vs 1/74 (P = 0.37), 1/76 vs 0/74 (P = 1.00) and 0/76 vs 8/74 (P = 0.006), respectively. Following protein removal, the experimental group exhibited a significantly higher overall proportion of lenses rated as ‘clean’ or with a ‘mild deposit’ (96.4 %, 79/82) compared to the control group (85.7 %, 66/77), with a significant difference (P < 0.05).

CONCLUSION: This multi-center study demonstrated that RigidCare exhibited superior efficacy in disinfection, sterilisation and protein removal as compared to Menicon multipurpose solution and protein remover.

PMID:38105172 | DOI:10.1016/j.clae.2023.102106

Surgeon. 2023 Dec 16:S1479-666X(23)00142-7. doi: 10.1016/j.surge.2023.11.008. Online ahead of print.

ABSTRACT

BACKGROUND: There is a trend for specialist care in breast surgery resulting in fewer primary operative cases for general surgery trainees; and subsequently that trainees performing advanced oncoplastic techniques in breast surgery may negatively impact patient morbidity. We have reviewed the complication rates between Australian general surgery trainees and Breast Consultants.

METHODS: A retrospective analysis was performed over a 5-year period (January 2016-December 2021). The key endpoints measured were relative complication rates for consultants compared to trainees, subdivided by surgery type. Surgeries were categorised as either benign, primary breast cancer surgery or re-excision.

RESULTS: A total of 2646 operative cases were performed with the primary operator rate for consultants 58.35 % (n = 1544) and for trainees 41.65 %% (n = 1102). The overall complication rate was 2.83 % (n = 75); the overall rate for the consultants was 2.65 % and 3.08 % for the trainees. The complication rates were not statistically significant (p = 0.59) between the two groups. The mastectomy only complication rate was higher in the consultant group with a result of 7.3 % compared to 2.8 % for the trainees however was not statistically significant (p = 0.18). The most common complication was haematoma formation for both groups.

CONCLUSIONS: This study has demonstrated that trainees can safely perform advanced oncoplastic techniques without statistically elevated morbidity. In an era where breast surgery caseloads are increasing, but the exposure to breast surgery during training are decreasing, it is necessary to implement a practice where trainees can perform breast operations under supervision at a specialized unit.

PMID:38105134 | DOI:10.1016/j.surge.2023.11.008

J Cardiothorac Vasc Anesth. 2023 Nov 19:S1053-0770(23)00931-X. doi: 10.1053/j.jvca.2023.11.024. Online ahead of print.

ABSTRACT

OBJECTIVES: It is unknown whether there is a difference in pulmonary outcome in different intraoperative ventilation modes for cardiac surgery with cardiopulmonary bypass (CPB). The aim of this trial was to determine whether patients undergoing cardiac surgery with CPB could benefit from intraoperative optimal ventilation mode.

DESIGN: This was a single-center, prospective, randomized controlled trial.

SETTING: The study was conducted at a single-center tertiary-care hospital.

PARTICIPANTS: A total of 1,364 adults undergoing cardiac surgery with CPB participated in this trial.

INTERVENTIONS: Patients were assigned randomly (1:1:1) to receive 1 of 3 ventilation modes: volume-controlled ventilation (VCV), pressure-controlled ventilation (PCV), and pressure-controlled ventilation-volume guaranteed (PCV-VG). All arms of the study received the lung-protective ventilation strategy.

MEASUREMENTS AND MAIN RESULTS: The primary outcome was a composite of postoperative pulmonary complications (PPCs) within the first 7 postoperative days. Pulmonary complications occurred in 168 of 455 patients (36.9%) in the PCV-VG group, 171 (37.6%) in the PCV group, and 182 (40.1%) in the VCV group, respectively. There was no statistical difference in the risk of overall pulmonary complications among groups (p = 0.585). There were no significant differences in the severity grade of PPCs within 7 days, postoperative ventilation duration, intensive care unit stay, postoperative hospital stay, or 30-day postoperative mortality.

CONCLUSIONS: Among patients scheduled for cardiac surgery with CPB, intraoperative ventilation mode type did not affect the risk of postoperative pulmonary complications.

PMID:38105126 | DOI:10.1053/j.jvca.2023.11.024

Int J Occup Saf Ergon. 2023 Dec 17:1-33. doi: 10.1080/10803548.2023.2294627. Online ahead of print.

ABSTRACT

ABSTRACTThis systematic review and meta-analysis study aimed to explore the global prevalence of MSDs among firefighters. A systematical search was performed in three international academic databases (Scopus, PubMed, and Web of Science). Overall, 31 articles were included in this review. The pooled prevalence of total MSDs in firefighters was identified as 41% (95% CI (33, 50)). The prevalence of MSDs in neck, shoulders, upper back, lower back, upper extremity, and lower extremity was 9% (95% CI (7, 10)), 11% (95% CI (8, 15)), 8% (95% CI (5, 12)), 31% (95% CI (27, 34)), 13% (95% CI (9, 17)), and 16% (95% CI (14, 18)), respectively. No statistically significant relationship was observed between prevalence of MSDs and year of study, mean of age, size of sample, duration of prevalence, region, or income level. The demographic, occupational, and medical condition factors were identified that can create these disorders among firefighters.

PMID:38105113 | DOI:10.1080/10803548.2023.2294627

Am J Emerg Med. 2023 Dec 10;77:72-76. doi: 10.1016/j.ajem.2023.12.003. Online ahead of print.

ABSTRACT

OBJECTIVE: To determine the rates of clinically significant tachyarrhythmias and mortality in the management of post-resuscitative shock after return of spontaneous circulation (ROSC) in patients with out-of-hospital cardiac arrest (OHCA) who receive a continuous epinephrine versus norepinephrine infusion.

DESIGN: Retrospective cohort study.

SETTING: A large multi-site health system with hospitals across the United States.

PATIENTS: Adult patients admitted for OHCA with post-resuscitative shock managed with either epinephrine or norepinephrine infusions within 6 h of ROSC.

INTERVENTIONS: None.

MEASUREMENTS AND MAIN RESULTS: Between May 5^th, 2018, to January 31^st, 2022, there were 221 patients admitted for OHCA who received post-resuscitative epinephrine or norepinephrine infusions. There was no difference in the rate of tachyarrhythmias between epinephrine and norepinephrine infusion in univariate (47.1% vs 41.7%, OR 1.24, 95% CI 0.71-2.20) or multivariable analysis (OR 1.34, 95% CI 0.68-2.62). Patients treated with epinephrine were more likely to die during hospitalization than those treated with norepinephrine (90.0% vs 54.3%, OR 6.21, 95% CI 2.37-16.25, p < 0.001). Epinephrine treated patients were more likely to have re-arrest during hospital admission (55.7% vs 14.6%, OR 5.77, 95% CI 2.74-12.18, p < 0.001).

CONCLUSION: There was no statistically significant difference in clinically significant cardiac tachyarrhythmias in post-OHCA patients treated with epinephrine versus norepinephrine infusions after ROSC. Re-arrest rates and in-hospital mortality were higher in patients who received epinephrine infusions in the first 6 h post-ROSC. Results of this study add to the literature suggesting norepinephrine may be the vasopressor of choice in post-OHCA patients with post-resuscitative shock after ROSC.

PMID:38104386 | DOI:10.1016/j.ajem.2023.12.003