Tag: pubmed

BMC Bioinformatics. 2023 Dec 7;24(1):459. doi: 10.1186/s12859-023-05578-5.

ABSTRACT

BACKGROUND: Variability in datasets is not only the product of biological processes: they are also the product of technical biases. ComBat and ComBat-Seq are among the most widely used tools for correcting those technical biases, called batch effects, in, respectively, microarray and RNA-Seq expression data.

RESULTS: In this technical note, we present a new Python implementation of ComBat and ComBat-Seq. While the mathematical framework is strictly the same, we show here that our implementations: (i) have similar results in terms of batch effects correction; (ii) are as fast or faster than the original implementations in R and; (iii) offer new tools for the bioinformatics community to participate in its development. pyComBat is implemented in the Python language and is distributed under GPL-3.0 ( https://www.gnu.org/licenses/gpl-3.0.en.html ) license as a module of the inmoose package. Source code is available at https://github.com/epigenelabs/inmoose and Python package at https://pypi.org/project/inmoose .

CONCLUSIONS: We present a new Python implementation of state-of-the-art tools ComBat and ComBat-Seq for the correction of batch effects in microarray and RNA-Seq data. This new implementation, based on the same mathematical frameworks as ComBat and ComBat-Seq, offers similar power for batch effect correction, at reduced computational cost.

PMID:38057718 | DOI:10.1186/s12859-023-05578-5

BMC Infect Dis. 2023 Dec 6;23(1):858. doi: 10.1186/s12879-023-08682-2.

ABSTRACT

BACKGROUND: To ensure emergency infection prevention and control (IPC) can be fully supervised and monitored in coronavirus disease (COVID-19) epidemic period, a three-level inspector mechanism called “Internal self-check, Departmental cross-check, and Verification of outstanding key and difficult issues” was established in southwest China. The present study aimed to explore the effectiveness of inspector mechanism for the emergency IPC.

METHODS: A self-control real-world study was conducted during COVID-19 epidemic period from 2020 to 2022. An innovative designed mobile phone application was used to realize paperless information transmission and data management. Data were compared between inspection levels using SPSS 19.0 software.

RESULTS: A total of 2,800,132 supervision records were collected, including 149,137 comprehensive epidemic IPC projects, 1,410,093 personal protective equipment (PPE) use, 1,223,595 wearing and removing process of PPE and 17,307 ultraviolet light-detectable fluorescent (UV/F) surface marker. During the study period, the inspectors and subjects explored many optimized IPC measures. The compliance rate of check items has exceeded 98%, and internal self-check has a statistically significant higher rate than departmental cross-check (99.95% versus 98.74%, χ² = 26111.479, P < 0.001). Compare with the failure rate in internal self check, the failure rate of PPE usage and wearing/removing process was statistically higher in departmental cross-check (χ² = 1957.987, P < 0.001, χ² = 465.610, P < 0.001, respectively). The overall clearance rate of UV/F surface markers is 87.88%, but there is no statistically significant difference over the three years of the present study (F = 2.902, P = 0.071).

CONCLUSIONS: Inspector mechanism for the emergency IPC completed an incredible inspection workload and offered creative assistance to combat the COVID-19 outbreak. These methods and accumulated experiences should be helpful for us to strengthen IPC for future epidemic.

PMID:38057717 | DOI:10.1186/s12879-023-08682-2

Accid Anal Prev. 2023 Dec 4;195:107407. doi: 10.1016/j.aap.2023.107407. Online ahead of print.

ABSTRACT

Driven by advancements in data-driven methods, recent developments in proactive crash prediction models have primarily focused on implementing machine learning and artificial intelligence. However, from a causal perspective, statistical models are preferred for their ability to estimate effect sizes using variable coefficients and elasticity effects. Most statistical framework-based crash prediction models adopt a case-control approach, matching crashes to non-crash events. However, accurately defining the crash-to-non-crash ratio and incorporating crash severities pose challenges. Few studies have ventured beyond the case-control approach to develop proactive crash prediction models, such as the duration-based framework. This study extends the duration-based modeling framework to create a novel framework for predicting crashes and their severity. Addressing the increased computational complexity resulting from incorporating crash severities, we explore a tradeoff between model performance and estimation time. Results indicate that a 15 % sample drawn at the epoch level achieves a balanced approach, reducing data size while maintaining reasonable predictive accuracy. Furthermore, stability analysis of predictor variables across different samples reveals that variables such as Time of day (Early afternoon), Weather condition (Clear), Lighting condition (Daytime), Illumination (Illuminated), and Volume require larger samples for more accurate coefficient estimation. Conversely, Daytime (Early morning, Late morning, Late afternoon), Lighting condition (Dark lighted), Terrain (Flat), Land use (Commercial, Rural), Number of lanes, and Speed converge towards true estimates with small incremental increases in sample size. The validation reveals that the model performs better in highway segments experiencing more frequent crashes (segments where the duration between crashes is less than 100 h, or approximately 4 days).

PMID:38056024 | DOI:10.1016/j.aap.2023.107407

Ann Med. 2023;55(2):2286638. doi: 10.1080/07853890.2023.2286638. Epub 2023 Dec 6.

ABSTRACT

BACKGROUND: The clinical manifestations of maintenance haemodialysis (MHD) outpatients diagnosed with coronavirus disease 2019 (COVID-19) are highly heterogeneous. They are prone to progress to severe conditions, and they often require hospitalization. To better guide the management of MHD outpatients, this retrospective observational study assessed risk factors for hospitalization of MHD patients after a diagnosis of COVID-19.

METHODS: The demographic data, comorbidities, laboratory indicators and imaging data of 128 MHD outpatients at our haemodialysis centre with confirmed COVID-19 infection from December 2022 to January 2023 were collected. The relationships between these factors and hospitalization of patients were analyzed.

RESULTS: Among the 128 patients, 25 (19.53%) were hospitalized. One of the 25 inpatients was mechanically ventilated, and two of them died. Multivariate logistic regression analysis showed that the hospitalization rate was correlated with age, comorbid diabetes and peripheral blood lymphocyte count.

CONCLUSION: Older age, comorbid diabetes and lower lymphocyte count are important risk factors for hospitalization of MHD outpatients after a diagnosis of COVID-19. Focusing on these factors may help in early identification of patients who may need to be admitted due to potential disease progression.

PMID:38056005 | DOI:10.1080/07853890.2023.2286638

Int J Biol Markers. 2023 Dec 6:3936155231217268. doi: 10.1177/03936155231217268. Online ahead of print.

ABSTRACT

BACKGROUND: Gastric cancer is a common cancer developed in a carcinogenesis process from precancerous lesions including chronic gastritis, intestinal metaplasia, and dysplasia. Survivin, an inhibitor-of-apoptosis protein, is associated with the initiation and progression of gastric cancer. The present study aimed to evaluate the immunohistochemical expression patterns of survivin and its relationship with early diagnosis of gastric cancer in Iranian patients.

METHODS: In this retrospective case-control study, immunoexpression of survivin was investigated on sections obtained from formalin-fixed paraffin-embedded tissue blocks of 38 chronic gastritis, 32 intestinal metaplasia, 20 dysplasia, 28 gastric adenocarcinoma, and 22 controls.

RESULTS: Survivin immunoexpression in chronic gastritis was higher than controls, but this difference was not statistically significant (P > 0.05). However, survivin immunoexpression had a steady significant increase from control and chronic gastritis to intestinal metaplasia to dysplasia to gastric adenocarcinoma (P < 0.05). Sensitivity, specificity, and area under the curve of survivin immunohistochemical test for the diagnosis of gastric cancer were 87.5%, 74.4%, and 0.85, respectively. Males had a significantly higher survivin expression than females (P < 0.001). Also, survivin expression was significantly higher in older patients than in younger ones (P < 0.001).

CONCLUSION: It seems that the steady increase in survivin expression from different precancerous lesions to gastric adenocarcinoma suggests that survivin can be used as a potential biomarker for the prevention and early diagnosis of gastric cancer.

PMID:38055975 | DOI:10.1177/03936155231217268

J Insect Sci. 2023 Nov 1;23(6):21. doi: 10.1093/jisesa/iead094.

ABSTRACT

European foulbrood (EFB) is a severe disease of honey bee (Apis mellifera) larvae caused by the bacterium Linnaeus [Hymenoptera: Apidae]) Melissococcus plutonius (ex White) Bailey and Collins (Lactobacillales: Enterococcaceae). Many beekeepers in North America report severe EFB following blueberry pollination, but it is not clear what factors during pollination are related to clinical disease. Additionally, the impact that other factors such as viral load and hygienic behavior have on EFB has not been studied. In Spring of 2020 we enrolled 60 commercial honey bee colonies in a prospective cohort study. Colonies were inspected 3 times over the season with hive metrics and samples taken for viral testing. Each colony was tested for hygienic behavior twice and the score was averaged. Viral loads were determined by qPCR for deformed wing virus (DWV) A and B. We found no statistical difference in the EFB prevalence or severity between the 2 yards at any timepoint; 50% (n = 16) of the colonies in the holding yard and 63% (n = 17) in blueberry developed moderate to severe EFB over the study period. When colonies from both yards were pooled, we found no relationship between viral load or hygienic behavior and development of EFB. These results suggest that other factors may be responsible for driving EFB virulence and hygienic behavior is not likely helpful in managing this disease.

PMID:38055945 | DOI:10.1093/jisesa/iead094

Ocul Immunol Inflamm. 2023 Dec 6:1-7. doi: 10.1080/09273948.2023.2280709. Online ahead of print.

ABSTRACT

BACKGROUND: Immunoglobulin G4-related ophthalmic disease (IgG4-ROD) poses clinical challenges due to its heterogeneous ocular and systemic manifestations. We aim to report the systemic involvement and the clinical, serological and radiological associations of a cohort of Chinese patients.

METHODS: A territory-wide, biopsy-proven, Chinese cohort. A retrospective, masked chart review of medical records, orbital images, and histopathology reports.

RESULTS: A total of 122 (65 male) patients with a follow-up of 81 ± 49 (24 to 84) months were reviewed. Ninety (74%) patients presented bilaterally. Subacute upper eyelid swelling was the commonest presentation (82/122, 67%). During follow-up, 91/122 patients (75%) underwent extra-orbital imaging including computer tomography (692 films), ultrasonography (182 films), magnetic resonance imaging (76 films) and whole body FDG-PET scan (33 films). Eighty-six (95%) of these 91 patients had extra-orbital involvement radiologically (2.7 ± 1.6 regions, range: 0 to 9). Lymph node was the most prevalent (N = 60,66%), followed by salivary gland (N = 51,56%), lung (N = 49,54%), kidney (N = 22, 24%), hepatobiliary tree (N = 18, 20%) and pancreas (N = 17, 19%). Other organs include thyroid, aorta, meninges/brain and skin. Twenty-eight (23%) patients had allergic diseases (19 asthma, 16 allergic rhinitis, and 6 eczemas). Fifty-seven (48%) patients had paranasal sinusitis. Serum eosinophilia was associated with a higher number (3.24 versus 2.52, P = 0.0304) of organ involvement. Patients with deep organ involvement was associated with a higher age of IgG4-ROD onset (70 ± 12 versus 56 ± 13, P < 0.0001).

CONCLUSIONS: 95% of the patients who underwent systemic imaging in our cohort had systemic organ involvement. An early physicians’ assessment and radiological imaging are recommended after the diagnosis of IgG4-ROD.

PMID:38055933 | DOI:10.1080/09273948.2023.2280709

Aesthet Surg J. 2023 Dec 6:sjad362. doi: 10.1093/asj/sjad362. Online ahead of print.

ABSTRACT

BACKGROUND: As the prevalence of neck lift surgeries increases, the field is continually enriched by evolving techniques for enhancing neck aesthetics. While many recent publications focus on deep neck procedures, it is essential not to overlook the significance of platysmal contouring as an integral aspect of neck rejuvenation surgery. Accordingly, we would like to elucidate our unique approach to contouring the platysma.

OBJECTIVES: This study was designed to assess the efficacy of the progressive contouring concept, a technique wherein the neck is reshaped using barbed sutures synergistically with other treatment strategies.

METHODS: Our study encompassed 337 patients who received neck rejuvenation treatment using the progressive contouring concept from 2014 to 2021. We conducted a retrospective review to evaluate the change in cervicomental angle (CMA) using Mirror software during the preoperative and postoperative stages.

RESULTS: The study sample predominantly comprised females (304 out of 337), with a median age of 61 years (24-88). Most patients (95%) underwent deep cervicoplasty, with a surgical net used in all cases for skin adaptation. After a median follow-up of 14 months, significant improvements were observed in CMA values (reducing from 149.8° to 106.7°). This demonstrated statistically significant differences when comparing preoperative and postoperative outcomes.

CONCLUSIONS: Progressive shaping of the neck with barbed sutures is an effective technique in neck rejuvenation. It utilizes multipoint and multi-vector plication, particularly when integrated with other adjunctive surgical maneuvers.

PMID:38055921 | DOI:10.1093/asj/sjad362

J Clin Oncol. 2023 Dec 6:JCO2301053. doi: 10.1200/JCO.23.01053. Online ahead of print.

ABSTRACT

PURPOSE: Primary mediastinal large B-cell lymphoma (PMBCL) is a rare aggressive lymphoma predominantly affecting young female patients. Large-scale genomic investigations and genetic markers for risk stratification are lacking.

PATIENTS AND METHODS: To elucidate the full spectrum of genomic alterations, samples from 340 patients with previously untreated PMBCL were investigated by whole-genome (n = 20), whole-exome (n = 78), and targeted (n = 308) sequencing. Statistically significant prognostic variables were identified using a multivariable Cox regression model and confirmed by L1/L2 regularized regressions.

RESULTS: Whole-genome sequencing revealed a commonly disrupted p53 pathway with nonredundant somatic structural variations (SVs) in TP53-related genes (TP63, TP73, and WWOX) and identified novel SVs facilitating immune evasion (DOCK8 and CD83). Integration of mutation and copy-number data expanded the repertoire of known PMBCL alterations (eg, ARID1A, P2RY8, and PLXNC1) with a previously unrecognized role for epigenetic/chromatin modifiers. Multivariable analysis identified six genetic lesions with significant prognostic impact. CD58 mutations (31%) showed the strongest association with worse PFS (hazard ratio [HR], 2.52 [95% CI, 1.50 to 4.21]; P < .001) and overall survival (HR, 2.33 [95% CI, 1.14 to 4.76]; P = .02). IPI high-risk patients with mutated CD58 demonstrated a particularly poor prognosis, with 5-year PFS and OS rates of 41% and 58%, respectively. The adverse prognostic significance of the CD58 mutation status was predominantly observed in patients treated with nonintensified regimens, indicating that dose intensification may, to some extent, mitigate the impact of this high-risk marker. By contrast, DUSP2-mutated patients (24%) displayed durable responses (PFS: HR, 0.2 [95% CI, 0.07 to 0.55]; P = .002) and prolonged OS (HR, 0.11 [95% CI, 0.01 to 0.78]; P = .028). Upon CHOP-like treatment, these patients had very favorable outcome, with 5-year PFS and OS rates of 93% and 98%, respectively.

CONCLUSION: This large-scale genomic characterization of PMBCL identified novel treatment targets and genetic lesions for refined risk stratification. DUSP2 and CD58 mutation analyses may guide treatment decisions between rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone and dose-adjusted etoposide, prednisone, vincristine, cyclophosphamide, doxorubicin, and rituximab.

PMID:38055913 | DOI:10.1200/JCO.23.01053

Br J Surg. 2023 Dec 6:znad375. doi: 10.1093/bjs/znad375. Online ahead of print.

ABSTRACT

BACKGROUND: There is a clinical need for treatments that can slow or prevent the growth of an abdominal aortic aneurysm, not only to reduce the need for surgery, but to provide a means to treat those who cannot undergo surgery.

METHODS: Analysis of the UK Aneurysm Growth Study (UKAGS) prospective cohort was conducted to test for an association between cardiometabolic medications and the growth of an abdominal aortic aneurysm above 30 mm in diameter, using linear mixed-effect models.

RESULTS: A total of 3670 male participants with data available on abdominal aortic aneurysm growth, smoking status, co-morbidities, and medication history were included. The mean age at recruitment was 69.5 years, the median number of surveillance scans was 6, and the mean(s.e.) unadjusted abdominal aortic aneurysm growth rate was 1.75(0.03) mm/year. In a multivariate linear mixed-effect model, smoking (mean(s.e.) +0.305(0.07) mm/year, P = 0.00003) and antiplatelet use (mean(s.e.) +0.235(0.06) mm/year, P = 0.00018) were found to be associated with more rapid abdominal aortic aneurysm growth, whilst metformin was strongly associated with slower abdominal aortic aneurysm growth (mean(s.e.) -0.38(0.1) mm/year, P = 0.00019), as were angiotensin-converting enzyme inhibitors (mean(s.e.) -0.243(0.07) mm/year, P = 0.0004), angiotensin II receptor antagonists (mean(s.e.) -0.253(0.08) mm/year, P = 0.00255), and thiazides/related diuretics (mean(s.e.) -0.307(0.09) mm/year, P = 0.00078).

CONCLUSION: The strong association of metformin with slower abdominal aortic aneurysm growth highlights the importance of the ongoing clinical trials assessing the effectiveness of metformin with regard to the prevention of abdominal aortic aneurysm growth and/or rupture. The association of angiotensin-converting enzyme inhibitors, angiotensin II receptor antagonists, and diuretics with slower abdominal aortic aneurysm growth points to the possibility that optimization of cardiovascular risk management as part of abdominal aortic aneurysm surveillance may have the secondary benefit of also reducing abdominal aortic aneurysm growth rates.

PMID:38055889 | DOI:10.1093/bjs/znad375