Tag: nevin manimala

Genome Med. 2023 Mar 6;15(1):15. doi: 10.1186/s13073-023-01162-x.

ABSTRACT

BACKGROUND: There has been a growing appreciation recently that mutagenic processes can be studied through the lenses of mutational signatures, which represent characteristic mutation patterns attributed to individual mutagens. However, the causal links between mutagens and observed mutation patterns as well as other types of interactions between mutagenic processes and molecular pathways are not fully understood, limiting the utility of mutational signatures.

METHODS: To gain insights into these relationships, we developed a network-based method, named GENESIGNET that constructs an influence network among genes and mutational signatures. The approach leverages sparse partial correlation among other statistical techniques to uncover dominant influence relations between the activities of network nodes.

RESULTS: Applying GENESIGNET to cancer data sets, we uncovered important relations between mutational signatures and several cellular processes that can shed light on cancer-related processes. Our results are consistent with previous findings, such as the impact of homologous recombination deficiency on clustered APOBEC mutations in breast cancer. The network identified by GENESIGNET also suggest an interaction between APOBEC hypermutation and activation of regulatory T Cells (Tregs), as well as a relation between APOBEC mutations and changes in DNA conformation. GENESIGNET also exposed a possible link between the SBS8 signature of unknown etiology and the Nucleotide Excision Repair (NER) pathway.

CONCLUSIONS: GENESIGNET provides a new and powerful method to reveal the relation between mutational signatures and gene expression. The GENESIGNET method was implemented in python, and installable package, source codes and the data sets used for and generated during this study are available at the Github site https://github.com/ncbi/GeneSigNet.

PMID:36879282 | DOI:10.1186/s13073-023-01162-x

BMC Nurs. 2023 Mar 7;22(1):62. doi: 10.1186/s12912-023-01204-0.

ABSTRACT

BACKGROUND: With today’s complex needs of the population and high demands in quality of care, there will be a continuing need for expanding role of nurses to assume more responsibilities in healthcare. Newly graduated nurses, who possess the competence to function as Registered Nurses, will soon recognize that lecture-based, passive delivery of content is not sufficient to deal with the complex healthcare environment.

AIM: This study aimed to compare the effects of a blended video watching and peer learning program and the usual lecture-based program on the levels of satisfaction and self-confidence in learning, perceptions of peer learning, and academic performance of students enrolled in a master’s nursing program.

METHODS: A quasi-experimental study was conducted. The program was offered to Master of Science in Nursing students during Spring 2021 (intervention group, n = 46), while the usual face-to-face lectures and tutorial classes were provided to students enrolled during Fall 2020 (control group, n = 46).

RESULTS: There was a statistically significant increase in satisfaction, self-confidence in learning, and academic performance in the intervention group after learning in a blended video-watching and peer learning mode.

CONCLUSION: This study fills a knowledge gap to meet the learning needs of time-conscious, part-time students working full time in hospitals.

PMID:36879268 | DOI:10.1186/s12912-023-01204-0

BMC Cancer. 2023 Mar 6;23(1):212. doi: 10.1186/s12885-023-10643-6.

ABSTRACT

BACKGROUND: Literature review have shown that sarcopenia substantially alters the postoperative outcomes after liver resection for malignant tumors. However, these retrospective studies do not distinguish cirrhotic and non-cirrhotic liver cancer patients, nor combine the assessment of muscle strength in addition to muscle mass. The purpose of this study is to study the relationship between sarcopenia and short-term outcomes after hepatectomy in patients with non-cirrhotic liver cancer.

METHODS: From December 2020 to October 2021, 431 consecutive inpatients were prospectively enrolled in this study. Muscle strength and mass were assessed by handgrip strength and the skeletal muscle index (SMI) on preoperative computed tomographic scans, respectively. Based on the SMI and the handgrip strength, patients were divided into four groups: group A (low muscle mass and strength), group B (low muscle mass and normal muscle strength), group C (low muscle strength and normal muscle mass), and group D (normal muscle mass and strength). The main outcome was major complications and the secondary outcome was 90-d Readmission rate.

RESULTS: After strictly exclusion, 171 non-cirrhosis patients (median age, 59.00 [IQR, 50.00-67.00] years; 72 females [42.1%]) were selected in the final analysis. Patients in group A had a statistically significantly higher incidence of major postoperative complications (Clavien-Dindo classification ≥ III) (26.1%, p = 0.032), blood transfusion rate (65.2%, p < 0.001), 90-day readmission rate (21.7%, p = 0.037) and hospitalization expenses (60,842.00 [IQR, 35,563.10-87,575.30], p < 0.001) than other groups. Sarcopenia (hazard ratio, 4.21; 95% CI, 1.44-9.48; p = 0.025) and open approach (hazard ratio, 2.56; 95% CI, 1.01-6.49; p = 0.004) were independent risk factors associated with major postoperative complications.

CONCLUSIONS: Sarcopenia is closely related to poor short-term postoperative outcomes in non-cirrhosis liver cancer patients and the assessment that combines muscle strength and muscle mass can simply and comprehensively identify it.

TRIAL REGISTRATION: ClinicalTrials.gov identifiers NCT04637048 . (19/11/2020).

PMID:36879265 | DOI:10.1186/s12885-023-10643-6

Hum Genomics. 2023 Mar 6;17(1):18. doi: 10.1186/s40246-023-00465-9.

ABSTRACT

BACKGROUND: The metabolome is the best representation of cancer phenotypes. Gene expression can be considered a confounding covariate affecting metabolite levels. Data integration across metabolomics and genomics to establish the biological relevance of cancer metabolism is challenging. This study aimed to eliminate the confounding effect of metabolic gene expression to reflect actual metabolite levels in microsatellite instability (MSI) cancers.

METHODS: In this study, we propose a new strategy using covariate-adjusted tensor classification in high dimensions (CATCH) models to integrate metabolite and metabolic gene expression data to classify MSI and microsatellite stability (MSS) cancers. We used datasets from the Cancer Cell Line Encyclopedia (CCLE) phase II project and treated metabolomic data as tensor predictors and data on gene expression of metabolic enzymes as confounding covariates.

RESULTS: The CATCH model performed well, with high accuracy (0.82), sensitivity (0.66), specificity (0.88), precision (0.65), and F1 score (0.65). Seven metabolite features adjusted for metabolic gene expression, namely, 3-phosphoglycerate, 6-phosphogluconate, cholesterol ester, lysophosphatidylethanolamine (LPE), phosphatidylcholine, reduced glutathione, and sarcosine, were found in MSI cancers. Only one metabolite, Hippurate, was present in MSS cancers. The gene expression of phosphofructokinase 1 (PFKP), which is involved in the glycolytic pathway, was related to 3-phosphoglycerate. ALDH4A1 and GPT2 were associated with sarcosine. LPE was associated with the expression of CHPT1, which is involved in lipid metabolism. The glycolysis, nucleotide, glutamate, and lipid metabolic pathways were enriched in MSI cancers.

CONCLUSIONS: We propose an effective CATCH model for predicting MSI cancer status. By controlling the confounding effect of metabolic gene expression, we identified cancer metabolic biomarkers and therapeutic targets. In addition, we provided the possible biology and genetics of MSI cancer metabolism.

PMID:36879264 | DOI:10.1186/s40246-023-00465-9

J Orthop Surg Res. 2023 Mar 6;18(1):172. doi: 10.1186/s13018-023-03627-6.

ABSTRACT

BACKGROUND: The effect of percutaneous kyphoplasty (PKP) or rather polymethylmethacrylate (PMMA) on adjacent intervertebral discs is still controversial. The evidence from experimental study to clinical study presents bipolar conclusions. In this study, we investigated the effect of PKP on adjacent intervertebral disc degeneration (IDD).

METHODS: The experimental group included adjacent intervertebral discs of vertebrae treated with the PKP procedure, and the control group included adjacent intervertebral discs of non-traumatized vertebrae. All measurements were taken by magnetic resonance imaging or X-ray. The intervertebral disc height, the modified Pfirrmann grading system (MPGS), and its differences with Klezl Z and Patel S (ZK and SP) classifications were compared.

RESULTS: A total of 264 intervertebral discs from 66 individuals were selected for the study. The comparison of intervertebral disc height between the two groups pre and post-operatively resulted in a p-value of > 0.05. No significant change was observed in the adjacent discs in the control groups post-operatively. Post-operatively, the mean Ridit increased significantly from 0.413 to 0.587 in the upper disc and from 0.404 to 0.595 in the lower disc in the experimental group. The comparison of MPGS differences showed that the predominant value was 0 in the Low-grade leaks group and 1 in the Medium and high-grade leaks group.

CONCLUSIONS: The PKP procedure can accelerate adjacent IDD, but it does not cause disc height changes in the early stage. The quantity of cement leaking into the disc space positively correlated with the rate of disc degeneration progression.

PMID:36879260 | DOI:10.1186/s13018-023-03627-6

BMC Health Serv Res. 2023 Mar 6;23(1):213. doi: 10.1186/s12913-023-09193-1.

ABSTRACT

PURPOSE: The purpose of this study was to analyze and compare the clinical characteristics of patients with 30-day planned and unplanned readmissions and to identify patients at high risk for unplanned readmissions. This will facilitate a better understanding of these readmissions and improve and optimize resource utilization for this patient population.

METHODS: A retrospective cohort descriptive study was conducted at the West China Hospital (WCH), Sichuan University from January 1, 2015, to December 31, 2020. Discharged patients (≥ 18 years old) were divided into unplanned readmission and planned readmission groups according to 30-day readmission status. Demographic and related information was collected for each patient. Logistic regression analysis was used to assess the association between unplanned patient characteristics and the risk of readmission.

RESULTS: We identified 1,118,437 patients from 1,242,496 discharged patients, including 74,494 (6.7%) 30-day planned readmissions and 9,895 (0.9%) unplanned readmissions. The most common diseases of planned readmissions were antineoplastic chemotherapy (62,756/177,749; 35.3%), radiotherapy sessions for malignancy (919/8,229; 11.2%), and systemic lupus erythematosus (607/4,620; 13.1%). The most common diseases of unplanned readmissions were antineoplastic chemotherapy (2038/177,747; 1.1%), age-related cataract (1061/21,255; 5.0%), and unspecified disorder of refraction (544/5,134; 10.6%). There were statistically significant differences between planned and unplanned readmissions in terms of patient sex, marital status, age, length of initial stay, the time between discharge, ICU stay, surgery, and health insurance.

CONCLUSION: Accurate information on 30-day planned and unplanned readmissions facilitates effective planning of healthcare resource allocation. Identifying risk factors for 30-day unplanned readmissions can help develop interventions to reduce readmission rates.

PMID:36879245 | DOI:10.1186/s12913-023-09193-1

BMC Psychiatry. 2023 Mar 6;23(1):138. doi: 10.1186/s12888-023-04647-6.

ABSTRACT

BACKGROUND: Children with autism spectrum disorders (ASD) usually experience difficulty regarding symbolic play. However, studies on whether symbolic play test (SPT) can differentiate between ASD and other developmental disorders are inconsistent, and evaluating the application value of the SPT in the identification of ASD without global developmental delay (GDD) and developmental language disorder (DLD) is necessary.

METHODS: A total of 200 children were selected as the research participants. There were 100 cases of ASD without GDD and 100 cases of DLD. All children were tested by SPT and Children Neuropsychological and Behavioral Scale-Revision (CNBS-R2016). Binomial logistic regression was used for multivariate analysis. The receiver operating characteristic (ROC) curve was used to evaluate the value of SPT in identifying ASD without GDD and DLD.

RESULTS: SPT equivalent age was lower than chronological age in the two groups, the difference between the ASD without GDD group was greater than that in the DLD group, and the proportion of SPT equivalent age retardation was higher than that in the DLD group; the differences were statistically significant. Logistic regression analysis showed that there was a difference in SPT equivalent age between DLD and ASD without GDD. When the cut-off value of the SPT was 8.5, the largest area under the ROC curve was 0.723, and the sensitivity and specificity for the diagnosis of ASD without GDD were 0.720 and 0.620 respectively.

CONCLUSIONS: Symbolic play ability in ASD children is worse than that of DLD children at comparable development levels. SPT may be helpful to distinguish ASD without GDD from children with DLD.

PMID:36879230 | DOI:10.1186/s12888-023-04647-6

BMC Ophthalmol. 2023 Mar 6;23(1):88. doi: 10.1186/s12886-023-02828-1.

ABSTRACT

PURPOSE: To report the time trends in basic patient characteristics and the number of specimens received at a national referral center for ophthalmic pathology.

METHODS: Data on patient sex, age at surgical resection and geographical location of the referring unit were obtained for all specimens received at the St. Erik Ophthalmic Pathology laboratory, Stockholm, Sweden, between January 1^st, 1959, and December 31^st, 2021.

RESULTS: A total of 33 057 specimens had been received, of which 14 560 (44%) came from men and 18 477 (56%) from women (for 20 patients, the sex was not specified). The average annual percent change (AAPC) in the number specimens received was + 10.5%, whereas the Swedish population increased with 0.5% per year. Patients became older throughout the period, with an average yearly increase of patient age at surgery of 0.3 years (AAPC 0.2%). Overall, women were three years older than men at surgery (59.4 versus 56.4 years, P < 0.0001) The number of specimens increased with patient age from the first to the 8^th decade, after which it decreased to zero in the 11^th decade. The largest portion of patients had undergone their surgery in one of the hospitals or clinics in the capital region, with four of the five largest sources corresponding to the most populous counties in the country.

CONCLUSIONS: During six decades, the growth in number of specimens sent to our national referral center for ophthalmic pathology has greatly outpaced the growth of the population, indicating an increasing demand for subspecialized services. Throughout the period, patients have become older, and a higher number of specimens have been submitted from female patients.

PMID:36879224 | DOI:10.1186/s12886-023-02828-1

Chin Med J (Engl). 2023 Jan 5;136(1):45-52. doi: 10.1097/CM9.0000000000002259.

ABSTRACT

BACKGROUND: Managing acute postoperative pain is challenging for anesthesiologists, surgeons, and patients, leading to adverse events despite making significant progress. Patient-controlled intravenous analgesia (PCIA) is a recommended solution, where oxycodone has depicted unique advantages in recent years. However, controversy still exists in clinical practice and this study aimed to compare two drugs in PCIA.

METHODS: We performed a literature search in PubMed, Embase, the Cochrane Central Register of Controlled Trials, Web of Science, Chinese National Knowledge Infrastructure, Wanfang, and VIP databases up to December 2020 to select specific randomized controlled trials (RCTs) comparing the efficacy of oxycodone with sufentanil in PCIA. The analgesic effect was the primary outcome and the secondary outcome included PCIA consumption, the Ramsay sedation scale, patients’ satisfaction and side effects.

RESULTS: Fifteen RCTs were included in the meta-analysis. Compared with sufentanil, oxycodone showed lower Numerical Rating Scale scores (mean difference [MD] = -0.71, 95% confidence interval [CI]: -1.01 to -0.41; P < 0.001; I2 = 93%), demonstrated better relief from visceral pain (MD = -1.22, 95% CI: -1.58 to -0.85; P < 0.001; I2 = 90%), promoted a deeper sedative level as confirmed by the Ramsay Score (MD = 0.77, 95% CI: 0.35-1.19; P < 0.001; I2 = 97%), and resulted in fewer side effects (odds ratio [OR] = 0.46, 95% CI: 0.35-0.60; P < 0.001; I2 = 11%). There was no statistical difference in the degree of patients’ satisfaction (OR = 1.13, 95% CI: 0.88-1.44; P = 0.33; I2 = 72%) and drug consumption (MD = -5.55, 95% CI: -14.18 to 3.08; P = 0.21; I2 = 93%).

CONCLUSION: Oxycodone improves postoperative analgesia and causes fewer adverse effects, and could be recommended for PCIA, especially after abdominal surgeries.

REGISTRATION: PROSPERO; https://www.crd.york.ac.uk/PROSPERO/; CRD42021229973.

PMID:36878002 | DOI:10.1097/CM9.0000000000002259

Nurse Educ. 2023 Mar 3. doi: 10.1097/NNE.0000000000001386. Online ahead of print.

ABSTRACT

BACKGROUND: The COVID-19 pandemic has been a defining event for the next generation of the nursing workforce. Complex pandemic practice environments have raised concerns for the preparation and support of novice nurses, even as a multitude of nurses leave the profession.

PURPOSE: Researchers sought to examine nursing students’ and new graduate nurses’ impressions of the nursing profession in contrasting regions of New York State during the first wave of the COVID-19 pandemic.

METHODS: Inductive content analysis was performed on narrative text responses (n = 295) drawn from a larger multisite mixed-methods survey.

RESULTS: Five subconcepts were abstracted, leading to the main concept of shocked moral distress.

CONCLUSION: Nursing students and new graduate nurses have experienced high levels of moral distress but remain committed to the profession. Building moral resilience, fostering ethical decision making, and implementing protective policies can reduce the incidence of moral distress.

PMID:36877986 | DOI:10.1097/NNE.0000000000001386