Cereb Cortex. 2023 Jul 21:bhad291. doi: 10.1093/cercor/bhad291. Online ahead of print.
NO ABSTRACT
PMID:37478404 | DOI:10.1093/cercor/bhad291
Tag: pubmed
Brief Bioinform. 2023 Jul 21:bbad253. doi: 10.1093/bib/bbad253. Online ahead of print.
ABSTRACT
Factor analysis, ranging from principal component analysis to nonnegative matrix factorization, represents a foremost approach in analyzing multi-dimensional data to extract valuable patterns, and is increasingly being applied in the context of multi-dimensional omics datasets represented in tensor form. However, traditional analytical methods are heavily dependent on the format and structure of the data itself, and if these change even slightly, the analyst must change their data analysis strategy and techniques and spend a considerable amount of time on data preprocessing. Additionally, many traditional methods cannot be applied as-is in the presence of missing values in the data. We present a new statistical framework, unified nonnegative matrix factorization (UNMF), for finding informative patterns in messy biological data sets. UNMF is designed for tidy data format and structure, making data analysis easier and simplifying the development of data analysis tools. UNMF can handle a wide range of data structures and formats, and works seamlessly with tensor data including missing observations and repeated measurements. The usefulness of UNMF is demonstrated through its application to several multi-dimensional omics data, offering user-friendly and unified features for analysis and integration. Its application holds great potential for the life science community. UNMF is implemented with R and is available from GitHub (https://github.com/abikoushi/moltenNMF).
PMID:37478378 | DOI:10.1093/bib/bbad253
Brief Bioinform. 2023 Jul 21:bbad236. doi: 10.1093/bib/bbad236. Online ahead of print.
ABSTRACT
Artificial intelligence (AI) systems utilizing deep neural networks and machine learning (ML) algorithms are widely used for solving critical problems in bioinformatics, biomedical informatics and precision medicine. However, complex ML models that are often perceived as opaque and black-box methods make it difficult to understand the reasoning behind their decisions. This lack of transparency can be a challenge for both end-users and decision-makers, as well as AI developers. In sensitive areas such as healthcare, explainability and accountability are not only desirable properties but also legally required for AI systems that can have a significant impact on human lives. Fairness is another growing concern, as algorithmic decisions should not show bias or discrimination towards certain groups or individuals based on sensitive attributes. Explainable AI (XAI) aims to overcome the opaqueness of black-box models and to provide transparency in how AI systems make decisions. Interpretable ML models can explain how they make predictions and identify factors that influence their outcomes. However, the majority of the state-of-the-art interpretable ML methods are domain-agnostic and have evolved from fields such as computer vision, automated reasoning or statistics, making direct application to bioinformatics problems challenging without customization and domain adaptation. In this paper, we discuss the importance of explainability and algorithmic transparency in the context of bioinformatics. We provide an overview of model-specific and model-agnostic interpretable ML methods and tools and outline their potential limitations. We discuss how existing interpretable ML methods can be customized and fit to bioinformatics research problems. Further, through case studies in bioimaging, cancer genomics and text mining, we demonstrate how XAI methods can improve transparency and decision fairness. Our review aims at providing valuable insights and serving as a starting point for researchers wanting to enhance explainability and decision transparency while solving bioinformatics problems. GitHub: https://github.com/rezacsedu/XAI-for-bioinformatics.
PMID:37478371 | DOI:10.1093/bib/bbad236
J Phys Chem B. 2023 Jul 21. doi: 10.1021/acs.jpcb.3c02505. Online ahead of print.
ABSTRACT
A mean field theory model describing the interaction of ion hydration layers with the network of hydrogen bonds of both water and the nonionic polymer poly(ethylene oxide) (PEO) is presented. The predictions of the model for types and statistics of hydrogen bonds, the number of water molecules bound to PEO, or their dependence on temperature are successfully verified from all-atom simulations at different NaCl and PEO concentrations. Furthermore, our simulations show that the binding of cations to PEO increases monotonically with salt concentration, in agreement with recent experimental results, through a mechanism in which the sum of the number of bound water and cations is independent of salt concentration. The model introduced is general and can describe any salt or hydrogen-bond-forming polymer.
PMID:37478338 | DOI:10.1021/acs.jpcb.3c02505
Medicine (Baltimore). 2023 Jul 21;102(29):e34340. doi: 10.1097/MD.0000000000034340.
ABSTRACT
To evaluate the effectiveness of orthodontics in combination with porcelain laminate veneers (PLV) in the aesthetic restoration and flora regulation of anterior teeth. A retrospective analysis of 336 patients who underwent aesthetic restoration of anterior teeth in our hospital from April 2019 to September 2022 was performed and divided into a control group (n = 168) and an observation group (n = 168) according to the restorative modality. The restorative modality in the control group was conventional restorative remediation, while the restorative modality in the observation group was orthodontic combined with PLV treatment. To evaluate the excellent rate of aesthetic restoration of anterior teeth in the 2 groups, and compare the color, shape, degree of translucency, edge aesthetic score, complications and satisfaction rate of restoration of anterior teeth in the 2 groups before and after restoration. The observation group had a significantly higher rate of excellent aesthetic restorations (95.23%) compared to the control group (80.95%) (P < .001). The scores of anterior tooth color, morphology, degree of translucency and marginal aesthetics were improved in both groups after restoration compared to before restoration, and the scores were significantly higher in the observation group (P < .05). After restoration, the subgingival Digestive streptococcus, Campylobacter and Propionibacterium increased in both groups, but the number of bacterial strains was significantly less in the observation group (P < .05). Compared with the total complication rate in the control group (16.66%), the total complication rate in the observation group (2.38%) was significantly lower (P < .001). Compared with the control group (85.71%), the observation group had a significantly higher restoration satisfaction rate of 97.61%, with a statistically significant difference (P < .001). The application of orthodontics combined with PLV in the aesthetic restoration of anterior teeth has a significant clinical effect, which is conducive to improving the aesthetic restoration and satisfaction rate of anterior teeth, reducing the subgingival microbial imbalance and decreasing the incidence of complications.
PMID:37478279 | DOI:10.1097/MD.0000000000034340
Medicine (Baltimore). 2023 Jul 21;102(29):e34308. doi: 10.1097/MD.0000000000034308.
ABSTRACT
Evidence-based nursing practice was used to formulate the enhanced recovery surgery bundle nursing strategy and apply it to patients with gastric cancer, to explore its safety, effectiveness and feasibility in perioperative gastrointestinal function protection in patients with gastric cancer. Selected the clinical medical records of 100 gastric cancer patients treated in our hospital from June 2019 to June 2021 as the research objects, and divided them into the control group and the observation group with 50 cases in each group according to the random number table. Among them, the control group was given routine nursing measures for nursing intervention, and the observation group was given gastrointestinal enhanced recovery surgery cluster nursing on the basis of the control group. The differences in stress response, gastrointestinal function protection, negative emotions and pain scores of gastric cancer patients before and after nursing were compared between the 2 groups. The postoperative bowel sounds recovery time, first anal exhaust, and first defecation time in the observation group were lower than those in the control group, and the differences were statistically significant (P < .05). Before nursing, there was no significant difference in the scores of stress response changes between the 2 groups (P > .05). After nursing, heart rate (HR), mean arterial pressure (MAP), norepinephrine (NE), and epinephrine (E2) in the observation group were lower than those in the control group, and the difference was statistically significant (P < .05). The pain scores of the 2 groups were significantly improved at different time points, and the observation group was significantly less than the control group, and the difference was statistically significant (P < .05). Gastrointestinal enhanced recovery surgery bundle nursing can effectively improve the gastrointestinal function of patients with gastric cancer, improve the emotional response and stress response of patients, and has certain reference value for the nursing of patients with gastric cancer.
PMID:37478274 | DOI:10.1097/MD.0000000000034308
Medicine (Baltimore). 2023 Jul 21;102(29):e34381. doi: 10.1097/MD.0000000000034381.
ABSTRACT
OBJECTIVE: To evaluate the efficacy and safety of perioperative cryotherapy combined with intra-articular injection of tranexamic acid (TXA) in total knee arthroplasty (TKA) and explore a new strategy of enhanced recovery after TKA.
METHODS: We randomly divided 200 patients into 4 groups: normal saline (10 mL) by drainage (Group A, placebo); intra-articular injection of TXA (1 g, 10 mL, Group B); normal saline (10 mL) and continuous cryotherapy postoperatively (Group C) and intra-articular injection of TXA (1 g, 10 mL) and continuous cryotherapy postoperatively (Group D). Primary outcomes were blood loss volume, postoperative pain and circumference variation. We also recorded consumption of analgesics, postoperative length of stay (p-LOS), range of motion (ROM), function score (Hospital for Special Surgery) and severe complications.
RESULTS: There were statistically significant differences in postoperative drainage volume, total blood loss, hidden blood loss, and visual analogue scale at rest and walking on postoperative day 1 (POD1), POD2, POD3, ROM (POD3, 7, discharge, postoperative month), circumference variation (POD3, 7), p-LOS, Hospital for Special Surgery score (discharge) and drop of hemoglobin on POD3 (P < .05) among 4 groups, but there were no significant differences in intraoperative blood loss, postoperative prothrombin, activated partial thromboplastin time, overall number of patients or total consumption of oxycodone and perioperative complications (e.g., incidence of surgical site infection, deep venous thrombosis, and cold injury) among them (P > .05).
CONCLUSION: Continuous cryotherapy combined with intra-articular injection of TXA provides short-term advantages in reducing blood loss, pain, postoperative swelling, p-LOS and increasing ROM and joint function in the early postoperative period after TKA without increasing any severe complications.
PMID:37478271 | DOI:10.1097/MD.0000000000034381
Medicine (Baltimore). 2023 Jul 21;102(29):e34210. doi: 10.1097/MD.0000000000034210.
ABSTRACT
To investigate the potential effect of repeated intravitreal injection of anti-vascular endothelial growth factor (anti-VEGF) drugs on corneal nerves. A total of 64 patients were treated with intravitreal injection of anti-VEGF drugs. There were 19 cases of neovascular age-related macular degeneration (AMD), 20 cases of diabetic macular edema (DME) and 25 cases of retinal vein occlusion (RVO). Twenty-nine cases were treated with aflibercept (2 mg/0.05 mL) whereas 35 cases were managed with ranibizumab (0.5 mg/0.05 mL). A corneal confocal microscope was used to collect images of corneal subbasal nerve plexus, and Image J was used for image analysis. The changes in corneal nerve were compared between 1 month after each injection and before injection. There were no significant differences in the density and length of corneal nerve at specific time after the surgery in comparison with baseline in patients who were given 3 intravitreal injections. There was no significant correlation between the numbers of injections and the changes of the corneal nerves. After 3rd injection, the nerve length of the DME group was markedly lower than that of AMD and RVO groups, the difference was statistically significant (P < .05). The nerve density of the DME group was not significantly different from that of AMD and RVO groups, whereas the nerve length and nerve density of the AMD and RVO groups were not statistically significant between each other also. The corneal nerve length after the 2nd and 3rd injections of Aflibercept were lower than that before surgery, the difference was statistically significant. There were no significant differences in nerve density and nerve length at each time point after Ranibizumab injection. The length and density of the corneal nerve after multiple injections in contralateral eye displayed no significant changes compared with the baseline. Repeated intravitreal anti-VEGF drug can reduce the length of corneal nerves. For patients who need repeated intravitreal injections of anti-VEGF drugs, especially in DM, attention should be paid on the changes affecting the corneal nerves. It is also needed to strengthen the local anti-inflammatory therapy to avoid infection and to use artificial tears to protect the microenvironment of the ocular surface after the surgery.
PMID:37478270 | DOI:10.1097/MD.0000000000034210
Medicine (Baltimore). 2023 Jul 21;102(29):e34094. doi: 10.1097/MD.0000000000034094.
ABSTRACT
Physical workplace violence (WPV) occurs worldwide, causing psychological and physical injuries. However, reports from Saudi Arabia investigating which specialty is the most exposed are scarce. This study aimed to determine the prevalence and circumstances related to physical WPV among all healthcare providers in Saudi Arabia in 12 months, as well as the consequences for both attackers and targets of physical WPV. This cross-sectional study included all healthcare providers registered with the Saudi Commission for Health Specialties who had worked for more than 1 year in the health sector in Saudi Arabia until May 2019. Researchers distributed the questionnaire to the participants via email. Descriptive statistics were used to describe the basic features of the data. Correlations between the categorically measured variables were explored using a chi-square test of independence. Overall, 7398 healthcare workers (HCWs) voluntarily participated in the study, 51.3% being men and 48.7% being women. The mean age was 40 ± 8.62 years), and most participants were of non-Saudi origin. Overall, 9.3% HCWs had encountered physical violence. Male HCWs, pharmacists, nurses, and HCWs of non-Saudi origin were significantly more exposed to physical violence. Furthermore, those with direct physical contact with patients and those working with male patients only were more exposed to physical violence. Physical WPV is an important issue faced by HCWs, particularly those who work night shifts or have direct contact with patients. Results showed that more support, specific strategies and policies to reduce violence occurrence, and protection for healthcare providers are required.
PMID:37478266 | DOI:10.1097/MD.0000000000034094
Medicine (Baltimore). 2023 Jul 21;102(29):e34374. doi: 10.1097/MD.0000000000034374.
ABSTRACT
The aging of the population is becoming an increasingly severe issue. How can we develop caring services for the elderly and promote healthy aging? Investigating care preferences is an essential step in addressing this issue. A self-designed questionnaire was employed to collect data online. The impact of personal circumstances on care preferences was ascertained using the chi-squared test and multivariate logistic regression. An optimal parameters-based geographical detector was introduced to examine the influence of spatially heterogeneous regional factors on care preferences. The online survey produced 1178 valid questionnaires. Home-based elderly care was the preference of 91.9% of respondents, followed by community-based care and medical-nursing care; institutional care was the least preferred alternative. Age, education, living style, and health states of the elderly significantly influenced the preferred care option. When compared to home-based elderly care, older respondents (odds ratio [OR] = 3.776) preferred institutional care, highly educated respondents preferred community-based care (higher education: OR = 5.206; secondary education: OR = 3.049) and medical-nursing care (higher education: OR = 4.484); the elderly living alone (OR = 0.101) excluded institutional care, and the elderly living with their children excluded non-family care method of institutional care (OR = 0.031) and medical-nursing care (OR = 0.391). Regional medical resources and old-age security significantly affect the preferences of the elderly (q-statistic [q] > 0.5); local economic development significantly affects community-based care (q > 0.6); the availability of financial subsidies significantly affects home-based care and medical-nursing care (q > 0.9); and the availability of institutional resources significantly affects the preference for institutional care (q > 0.8). We found that it is necessary to improve the level of medical care given by non-family members and care facilities, vigorously develop new methods of elderly care, promote humanistic care in non-family care settings, and increase available regional medical resources, financial subsidies, and social security. This study integrates economic and social perspectives to examine and analyze retirement willingness, thereby broadening the scope of social surveys and research methodologies, and offering valuable insights with potential directive implications.
PMID:37478262 | DOI:10.1097/MD.0000000000034374