Tag: nevin manimala

BioData Min. 2023 Jun 10;16(1):17. doi: 10.1186/s13040-023-00333-1.

ABSTRACT

Single-cell RNA-sequencing (scRNA-seq) data can serve as a good indicator of cell-to-cell heterogeneity and can aid in the study of cell growth by identifying cell types. Recently, advances in Variational Autoencoder (VAE) have demonstrated their ability to learn robust feature representations for scRNA-seq. However, it has been observed that VAEs tend to ignore the latent variables when combined with a decoding distribution that is too flexible. In this paper, we introduce ScInfoVAE, a dimensional reduction method based on the mutual information variational autoencoder (InfoVAE), which can more effectively identify various cell types in scRNA-seq data of complex tissues. A joint InfoVAE deep model and zero-inflated negative binomial distributed model design based on ScInfoVAE reconstructs the objective function to noise scRNA-seq data and learn an efficient low-dimensional representation of it. We use ScInfoVAE to analyze the clustering performance of 15 real scRNA-seq datasets and demonstrate that our method provides high clustering performance. In addition, we use simulated data to investigate the interpretability of feature extraction, and visualization results show that the low-dimensional representation learned by ScInfoVAE retains local and global neighborhood structure data well. In addition, our model can significantly improve the quality of the variational posterior.

PMID:37301826 | DOI:10.1186/s13040-023-00333-1

Environ Sci Pollut Res Int. 2023 Jun 10. doi: 10.1007/s11356-023-27883-5. Online ahead of print.

ABSTRACT

Taxis pose a higher threat to global climate change and human health through air emissions. However, the evidence on this topic is scarce, especially, in developing countries. Therefore, this study conducted estimation of fuel consumption (FC) and emission inventories on Tabriz taxi fleet (TTF), Iran. A structured questionnaire to obtain operational data of TTF, municipality organizations, and literature review were used as data sources. Then modeling was used to estimate fuel consumption ratio (FCR), emission factors (EFs), annual FC, and emissions of TTF using uncertainty analysis. Also, the impact of COVID-19 pandemic period was considered on the studied parameters. The results showed that TTF have high FCRs of 18.68 L/100 km (95% CI=17.67-19.69 L/100 km), which are not affected by age or mileage of taxis, significantly. The estimated EFs for TTF are higher than Euro standards, but the differences are not significant. However, it is critical as can be an indication of inefficiency of periodic regulatory technical inspection tests for TTF. COVID-19 pandemic caused significant decrease in annual total FC and emissions (9.03-15.6%), but significant increase in EFs of per-passenger-kilometer traveled (47.9-57.3%). Annual vehicle-kilometer-traveled by TTF and the estimated EFs for gasoline-compressed natural gas bi-fueled TTF are the main influential parameters in the variability of annual FC and emission levels. More studies on sustainable FC and emissions mitigation strategies are needed for TTF.

PMID:37301810 | DOI:10.1007/s11356-023-27883-5

Clin Transl Oncol. 2023 Jun 10. doi: 10.1007/s12094-023-03233-2. Online ahead of print.

ABSTRACT

PURPOSE: The CoVID-TE model was developed with the aim of predicting venous thrombotic events (VTE) in cancer patients with Sars-Cov-2 infection. Moreover, it was capable of predicting hemorrhage and mortality 30 days following infection diagnosis. The model is pending validation.

METHODS/PATIENTS: Multicenter retrospective study (10 centers). Adult patients with active oncologic disease/ antineoplastic therapy with Sars-Cov-2 infection hospitalized between March 1, 2020 and March 1. 2022 were recruited. The primary endpoint was to study the association between the risk categories of the CoVID-TE model and the occurrence of thrombosis using the Chi-Square test. Secondary endpoints were to demonstrate the association between these categories and the occurrence of post-diagnostic Sars-Cov-2 bleeding/ death events. The Kaplan-Meier method was also used to compare mortality by stratification.

RESULTS: 263 patients were enrolled. 59.3% were men with a median age of 67 years. 73.8% had stage IV disease and lung cancer was the most prevalent tumor (24%). A total of 86.7% had an ECOG 0-2 and 77.9% were receiving active antineoplastic therapy. After a median follow-up of 6.83 months, the incidence of VTE, bleeding, and death 90 days after Sars-Cov-2 diagnosis in the low-risk group was 3.9% (95% CI 1.9-7.9), 4.5% (95% CI 2.3-8.6), and 52.5% (95% CI 45.2-59.7), respectively. For the high-risk group it was 6% (95% CI 2.6-13.2), 9.6% (95% CI 5.0-17.9), and 58.0% (95% CI 45.3-66.1). The Chi-square test for trends detected no statistically significant association between these variables (p > 0.05). Median survival in the low-risk group was 10.15 months (95% CI 3.84-16.46), while in the high-risk group it was 3.68 months (95% CI 0.0-7.79). The differences detected were not statistically significant (p = 0.375).

CONCLUSIONS: The data from our series does not validate of the CoVID-TE as a model to predict thrombosis, hemorrhage, or mortality in cancer patients with Sars-Cov-2 infection.

PMID:37301805 | DOI:10.1007/s12094-023-03233-2

Rheumatol Int. 2023 Jun 10. doi: 10.1007/s00296-023-05358-7. Online ahead of print.

ABSTRACT

This systematic review is aimed to evaluate the effects of balneotherapy with thermal mineral water for managing the symptoms and signs of osteoarthritis located at any anatomical site. The systematic review was conducted according to the PRISMA Statement. The following databases were consulted: PubMed, Scopus, Web of Science, Cochrane Library, DOAJ and PEDro. We included clinical trials evaluating the effects of balneotherapy as a treatment for patients with osteoarthritis, published in English and Italian language, led on human subjects. The protocol was registered in PROSPERO. Overall, 17 studies have been included in the review. All of these studies were performed on adults or elderly patients suffering from osteoarthritis localized to knees, hips, hands or lumbar spine. The treatment assessed was always the balneotherapy with thermal mineral water. The outcomes evaluated were pain, palpation/pressure sensibility, articular tenderness, functional ability, quality of life, mobility, deambulation, ability to climb stairs, medical objective and patients’ subjective evaluation, superoxide dismutase enzyme activity, serum levels of interleukin-2 receptors. The results of all the included studies agree and demonstrated an improvement of all the symptoms and signs investigated. In particular, pain and quality of life were the main symptoms evaluated and both improved after the treatment with thermal water in all the studies included in the review. These effects can be attributed to physical and chemical-physical properties of thermal mineral water used. However, the quality of many studies resulted not so high due and, consequently, it is necessary to perform new clinical trial in this field using more correct methods for conducting the study and for processing statistical data.

PMID:37301799 | DOI:10.1007/s00296-023-05358-7

J Math Biol. 2023 Jun 11;87(1):5. doi: 10.1007/s00285-023-01944-2.

ABSTRACT

Dengue is the most rapidly spreading mosquito-borne disease that poses great threats to public health. We propose a compartmental model with primary and secondary infection and targeted vaccination to assess the impact of serostatus-dependent immunization on mitigating the spread of dengue virus. We derive the basic reproduction number and investigate the stability and bifurcations of the disease-free equilibrium and endemic equilibria. The existence of a backward bifurcation is proved and is used to explain the threshold dynamics of the transmission. We also carry out numerical simulations and present bifurcation diagrams to reveal rich dynamics of the model such as bi-stability of the equilibria, limit cycles, and chaos. We prove the uniform persistence and global stability of the model. Sensitivity analysis suggests that mosquito control and protection from mosquito bites are still the key measures of controlling the spread of dengue virus, though serostatus-dependent immunization is implemented. Our findings provide insightful information for public health in mitigating dengue epidemics through vaccination.

PMID:37301798 | DOI:10.1007/s00285-023-01944-2

Glob Chang Biol. 2023 Jun 10. doi: 10.1111/gcb.16801. Online ahead of print.

ABSTRACT

Biodiversity offsetting is a globally influential policy mechanism for reconciling trade-offs between development and biodiversity loss. However, there is little robust evidence of its effectiveness. We evaluated the outcomes of a jurisdictional offsetting policy (Victoria, Australia). Offsets under Victoria’s Native Vegetation Framework (2002-2013) aimed to prevent loss and degradation of remnant vegetation, and generate gains in vegetation extent and quality. We categorised offsets into those with near-complete baseline woody vegetation cover (“avoided loss”, 2702 ha) and with incomplete cover (“regeneration”, 501 ha), and evaluated impacts on woody vegetation extent from 2008 to 2018. We used two approaches to estimate the counterfactual. First, we used statistical matching on biophysical covariates: a common approach in conservation impact evaluation, but which risks ignoring potentially important psychosocial confounders. Second, we compared changes in offsets with changes in sites that were not offsets for the study duration but were later enrolled as offsets, to partially account for self-selection bias (where landholders enrolling land may have shared characteristics affecting how they manage land). Matching on biophysical covariates, we estimated that regeneration offsets increased woody vegetation extent by 1.9%-3.6%/year more than non-offset sites (138-180 ha from 2008 to 2018) but this effect weakened with the second approach (0.3%-1.9%/year more than non-offset sites; 19-97 ha from 2008 to 2018) and disappeared when a single outlier land parcel was removed. Neither approach detected any impact of avoided loss offsets. We cannot conclusively demonstrate whether the policy goal of ‘net gain’ (NG) was achieved because of data limitations. However, given our evidence that the majority of increases in woody vegetation extent were not additional (would have happened without the scheme), a NG outcome seems unlikely. The results highlight the importance of considering self-selection bias in the design and evaluation of regulatory biodiversity offsetting policy, and the challenges of conducting robust impact evaluations of jurisdictional biodiversity offsetting policies.

PMID:37300408 | DOI:10.1111/gcb.16801

Muscle Nerve. 2023 Jun 10. doi: 10.1002/mus.27916. Online ahead of print.

ABSTRACT

INTRODUCTION/AIMS: Switching between different types of electrodes during motor and sensory nerve conduction studies adds time to a study. We investigated the use of disposable disc electrodes (DDE) used for motor nerve conduction studies to record the antidromic sensory nerve action potential (SNAP) in median, ulnar and radial sensory nerve conduction studies.

METHODS: The SNAP was recorded using four different electrode types: reusable ring, reusable bar, disposable ring, and DDE in a random rotating order. Studies were performed in healthy subjects. Other than being an adult with no history of neuromuscular disease, there were no exclusion criteria.

RESULTS: We studied 20 subjects (11 females, 9 males; age 41.1 ± 15.7 y). The SNAP waveforms recorded by all four electrode types were similar. There was no statistically significant difference in the onset latency, peak latency (PL), negative peak amplitude (NPA), peak to peak amplitude, or conduction velocity. In individual nerve recordings, the absolute PL difference between reusable ring electrodes (our current standard) and DDE was less than 0.2 ms in 58 of 60 (97%) nerves. The mean absolute NPA difference was 3.1 μV (standard deviation = 2.85 μV). Recordings with NPA difference >5 μV also had high NPA and/or had large artifacts.

DISCUSSION: DDE may be used for performing motor and sensory nerve conduction studies. This can reduce the time required for electrodiagnostic testing.

PMID:37300406 | DOI:10.1002/mus.27916

J Endovasc Ther. 2023 Jun 10:15266028231179425. doi: 10.1177/15266028231179425. Online ahead of print.

ABSTRACT

PURPOSE: To determine whether the STOP-Bang questionnaire, which is a tool for evaluating obstructive sleep apnea, is associated with aortic remodeling after thoracic endovascular aortic repair (TEVAR) in patients with type B aortic dissection (TBAD).

METHODS: Patients with TBAD who underwent standard TEVAR at our center from January 2015 to December 2020 were enrolled. For the included patients, we recorded baseline characteristics, comorbidities, preoperative computed tomographic angiography findings, procedure details, and complications. The STOP-Bang questionnaire was administered to each patient. Total scores comprised points for 4 yes/no questions and 4 clinical measurements. STOP-Bang ≥5 and STOP-Bang <5 groups were then created using the STOP-Bang total scores. We evaluated aortic remodeling 1 year after discharge and the reintervention rate, as well as false lumen complete thrombosis (FLCT) and non-FLCT length.

RESULTS: Fifty-five patients were enrolled in the study; STOP-Bang <5, n=36, and STOP-Bang ≥5, n=19. Compared with the STOP-Bang ≥5 group, the STOP-Bang <5 group achieved statistically significantly higher descending aorta positive aortic remodeling (PAR) rates in zones 3 to 5 (zone 3: p=0.002; zone 4: p=0.039; zone 5: p=0.023), higher total descending aorta-PAR rate (66.7% vs 36.8%, respectively; p=0.004), and lower reintervention rate (8.1% vs 38.9%, respectively; p=0.005). In the logistic regression analysis, STOP-Bang ≥5 had an odds ratio of 0.12 (95% confidence interval: 0.03-0.58; p=0.008). There was no significant difference in overall survival between the groups.

CONCLUSION: STOP-Bang questionnaire scores were associated with aortic remodeling after TEVAR in patients with TBAD. Increasing the frequency of surveillance after TEVAR might be beneficial in these patients.

CLINICAL IMPACT: We analysed aortic remodelling 1 year after thoracic endovascular aortic repair (TEVAR) in acute type B aortic dissection (TBAD) patients with STOP-Bang < 5 and STOP-Bang ≥ 5. Aortic remodelling was better, and the reintervention rate was higher in patients with STOP-Bang < 5 compared with patients with STOP-Bang ≥ 5. In patients with STOP-Bang ≥ 5, aortic remodelling was worse in zones 3-5 compared with zones 6-9. This study suggests that the STOP-Bang questionnaire results is associated with aortic remodelling after TEVAR in patients with TBAD.

PMID:37300399 | DOI:10.1177/15266028231179425

Clin Oral Implants Res. 2023 Jun 10. doi: 10.1111/clr.14108. Online ahead of print.

ABSTRACT

OBJECTIVE: The aims of this clinical trial were to evaluate the radiographic dimensional changes in alveolar ridge and patient-reported outcomes following tooth extraction and alveolar ridge preservation (ARP) using either deproteinized bovine bone mineral (DBBM) with EMD or DBBM alone.

METHODS: Participants requiring at least one posterior tooth extraction and ARP were randomly allocated into two treatment groups: ARP using either DBBM with EMD or DBBM alone. Cone-beam computed tomography (CBCT) images were recorded immediately prior to extraction and at 6 months. Changes in alveolar ridge height (ARH) and alveolar ridge width (ARW) at 1, 3, and 5 mm were recorded.

RESULTS: A total of 18 participants with 25 preserved sites were evaluated. ARH and ARW changed significantly from baseline to 6 months for both treatment groups but the difference between the groups was not statistically significant over the 6-month follow-up period (ARH: DBBM/EMD 1.26 ± 1.53 mm vs. DBBM 2.26 ± 1.60 mm; ARW-1 DBBM/EMD 1.98 ± 1.80 mm vs. DBBM 2.34 ± 1.89 mm). A significant difference, favoring DBBM with EMD group, was observed in percentage of sites that had less than 1 mm loss in ARH (54.5% sites in DBBM/EMD group vs. 14.3% sites in DBBM alone group). The participants’ perception of bruising, bleeding, and pain in the first two postoperative days was significantly in favor of DBBM alone group.

CONCLUSIONS: There were no significant differences in radiographic mean measurements of ARH and ARW following ARB with DBBM and EMD or DBBM alone.

PMID:37300378 | DOI:10.1111/clr.14108

United European Gastroenterol J. 2023 Jun 10. doi: 10.1002/ueg2.12403. Online ahead of print.

ABSTRACT

BACKGROUND: The role of radiological staging and surveillance imaging is under debate for T1 colorectal cancer (CRC) as the risk of distant metastases is low and imaging may lead to the detection of incidental findings.

OBJECTIVE: The aim of this study was to evaluate the yield of radiological staging and surveillance imaging for T1 CRC.

METHODS: In this retrospective multicenter cohort study, all patients of 10 Dutch hospitals with histologically proven T1 CRC who underwent radiological staging in the period 2000-2014 were included. Clinical characteristics, pathological, endoscopic, surgical and imaging reports at baseline and during follow-up were recorded and analyzed. Patients were classified as high-risk T1 CRC if at least one of the histological risk factors (lymphovascular invasion, poor tumor differentiation, deep submucosal invasion or positive resection margins) was present and as low-risk when all risk factors were absent.

RESULTS: Of the 628 included patients, 3 (0.5%) had synchronous distant metastases, 13 (2.1%) malignant incidental findings and 129 (20.5%) benign incidental findings at baseline staging. Radiological surveillance was performed among 336 (53.5%) patients. The 5-year cumulative incidence of distant recurrence, malignant and benign incidental findings were 2.4% (95% confidence interval (CI): 1.1%-5.4%), 2.5% (95% CI: 0.6%-10.4%) and 18.3% (95% CI: 13.4%-24.7%), respectively. No distant metastatic events occurred among low-risk T1 CRC patients.

CONCLUSION: The risk of synchronous distant metastases and distant recurrence in T1 CRC is low, while there is a substantial risk of detecting incidental findings. Radiological staging seems unnecessary prior to local excision of suspected T1 CRC and after local excision of low-risk T1 CRC. Radiological surveillance should not be performed in patients with low-risk T1 CRC.

PMID:37300377 | DOI:10.1002/ueg2.12403