Tag: nevin manimala

Methods Mol Biol. 2023;2595:225-237. doi: 10.1007/978-1-0716-2823-2_16.

ABSTRACT

The bioinformatics analysis of miRNA is a complicated task with multiple operations and steps involved from processing of raw sequence data to finally identifying accurate microRNAs associated with the phenotypes of interest. A complete analysis process demands a high level of technical expertise in programming, statistics, and data management. The goal of this chapter is to reduce the burden of technical expertise and provide readers the opportunity to understand crucial steps involved in the analysis of miRNA sequencing data.In this chapter, we describe methods and tools employed in processing of miRNA reads, quality control, alignment, quantification, and differential expression analysis.

PMID:36441466 | DOI:10.1007/978-1-0716-2823-2_16

Mol Divers. 2022 Nov 28. doi: 10.1007/s11030-022-10574-7. Online ahead of print.

ABSTRACT

Cytochrome P450-1B1 is a majorly overexpressed drug-metabolizing enzyme in tumors and is responsible for inactivation and subsequent resistance to a variety of anti-cancer drugs, i.e., docetaxel, tamoxifen, and cisplatin. In the present study, a 3D quantitative structure-activity relationship (3D-QSAR) model has been constructed for the identification, design, and optimization of novel CYP1B1 inhibitors. The model has been built using a set of 148 selective CYP1B1 inhibitors. The developed model was evaluated based on certain statistical parameters including q² and r² which showed the acceptable predictive and descriptive capability of the generated model. The developed 3D-QSAR model assisted in understanding the key molecular fields which were firmly related to the selective CYP1B1 inhibition. A theoretic approach for the generation of new lead compounds with optimized CYP1B1 receptor affinity has been performed utilizing bioisosteric replacement analysis. These generated molecules were subjected to a developed 3D-QSAR model to predict the inhibitory activity potentials. Furthermore, these compounds were scrutinized through the activity atlas model, molecular docking, electrostatic complementarity, molecular dynamics, and waterswap analysis. The final hits might act as selective CYP1B1 inhibitors which could address the issue of resistance. This 3D-QSAR includes several chemically diverse selective CYP1B1 receptor ligands and well accounts for the individual ligand’s inhibition affinities. These features of the developed 3D-QSAR model will ensure future prospective applications of the model to speed up the identification of new potent and selective CYP1B1 receptor ligands.

PMID:36441444 | DOI:10.1007/s11030-022-10574-7

Oral Radiol. 2022 Nov 28. doi: 10.1007/s11282-022-00665-4. Online ahead of print.

ABSTRACT

OBJECTIVES: To investigate the possible risk factors for mastoid cellulitis after treatment in patients with oral cancer.

METHODS: Patients with oral cancer who underwent preoperative and postoperative contrast-enhanced computed tomography (CECT) between January 2017 and March 2020 were retrospectively evaluated. Using an image reporting system, cases with reports containing the keyword “mastoid cellulitis” were registered in the mastoid cellulitis group. Fifty patients with oral cancer who did not develop mastoid cellulitis were randomly selected as the control group. Information concerning age, sex, location, and histopathological type of the primary tumor, presence or absence of cervical lymph node metastasis, and treatment methods were obtained from the hospital’s electronic medical records to investigate the association between these factors and the occurrence of mastoid cellulitis.

RESULTS: Statistically significant differences were observed in the following factors: age (p = 0.004), primary tumor site (p < 0.001), histopathological type (p = 0.032), radiotherapy (p < 0.001), and chemotherapy (p < 0.001). Logistic regression analysis revealed that maxillary tumors (p < 0.001), histopathological type (p = 0.047), and radiotherapy (p = 0.0301) were significantly associated with the occurrence of mastoid cellulitis.

CONCLUSIONS: In oral cancer, the risk of postoperative mastoid cellulitis was higher in patients with a maxillary tumor, histopathology other than squamous cell carcinoma, and history of radiotherapy.

PMID:36441420 | DOI:10.1007/s11282-022-00665-4

Oral Radiol. 2022 Nov 28. doi: 10.1007/s11282-022-00666-3. Online ahead of print.

ABSTRACT

OBJECTIVES: To evaluate the relationship between proximity of the root apices of healthy maxillary posterior teeth to the maxillary sinus floor (MSF) and mucosal thickening (MT) of the MSF using cone beam computed tomography (CBCT).

METHODS: Eighty-four CBCT images obtained from the patients, aged between 20 and 70 years with healthy and fully dentate maxillary posterior sextants, were included. The anatomical relationship between root apices of maxillary posterior teeth and MSF, was evaluated: (Type 1: no contact, Type 2: at least one root apex in contact, Type 3: at least one root apex protruding into MSF). Besides, MT of the MSF was measured from the thickest region. The patients were categorized into two groups based on the absence (≤ 2 mm) or the presence (2 < mm) of MT. Statistical significance was accepted at p < 0.05.

RESULTS: Intraexaminer consistency demonstrated an excellent agreement (p < 0.05). The prevalence of Type 1, 2, and 3 proximity were found as 26 (15.5%), 61 (36.3%), and 81 (48.2%); respectively. Overall, 62 (36.9%) maxillary sinuses demonstrated MT (2 < mm, mean: 8.6 ± 7.5 mm). The prevalence and mean values of MT (2 < mm) were not found to be statistically significantly different in terms of sex and proximity types (p > 0.05). Logistic regression analysis results were not found to be statistically significant (p > 0.05).

CONCLUSION: The proximity of healthy maxillary posterior teeth to the MSF was not found to be a contributing factor for the MT of the MSF. Further studies with larger samples, taking the other factors causing MT into consideration, are needed.

PMID:36441419 | DOI:10.1007/s11282-022-00666-3

J Robot Surg. 2022 Nov 28. doi: 10.1007/s11701-022-01495-6. Online ahead of print.

ABSTRACT

As the growing popularity of robotic-assisted laparoscopic procedures for the treatment of renal cancer increases, there exists a variation in surgical technique among institutions and surgeons alike. One variation that exists in robotics is the anatomical placement of the camera port (medial versus lateral camera port placement). The purpose of this study is to evaluate surgical complications and outcomes in comparison to site of camera port placement during nephron-sparing surgery in an academic setting. Over a three-year period, outcomes for all robotic surgeries for renal cancer were examined. A total of 229 cases were discovered. Patient demographics and comorbidities were analyzed along with perioperative surgical data including location of camera port, surgery length, warm ischemia time, blood loss, pathological tumor margins, tumor size, length of stay and laboratory data. 134 patients had surgery performed with lateral camera port placement versus 95 patients with medial camera port placement. Operative time was significantly lower with an average operative time of 165.8 min for the lateral group versus 209.1 min in the medial group (p < 0. 0001). Warm ischemia time was also less in the lateral group with an average of 11 min versus 15.5 min for the medial group (p < 0. 0001). Blood loss was less in the lateral camera port group with an average of 158.2 mL (± 196.5 mL) versus 248.6 mL in the medial group (± 252.6) (p = 0.0040). Drain use, positive surgical margin rate, transfusion rate, conversion to radical nephrectomy, change in pre-operative versus postoperative creatinine and glomerular filtration rate and length of hospital stay did not statistically differ. Lateral camera port placement is associated with decreased operative time and warm ischemia time in this series. There may be certain laparoscopic advantages through a better visualization of surgical anatomy, thus allowing for faster extirpation of renal lesions and decrease in surgical time. These advantages may result in better long-term renal function and decreased clinical sequela from chronic kidney disease.

PMID:36441417 | DOI:10.1007/s11701-022-01495-6

Metabolomics. 2022 Nov 28;18(12):99. doi: 10.1007/s11306-022-01959-8.

ABSTRACT

INTRODUCTION: Previous studies have explored prediction value of serum metabolites in neoadjuvant chemoradiation therapy (NCRT) response for rectal cancer. To date, limited literature is available for serum metabolome changes dynamically through NCRT.

OBJECTIVES: This study aimed to explore temporal change pattern of serum metabolites during NCRT, and potential metabolic biomarkers to predict the pathological response to NCRT in locally advanced rectal cancer (LARC) patients.

METHODS: Based on dynamic UHPLC-QTOF-MS untargeted metabolomics design, this study included 106 LARC patients treated with NCRT. Biological samples of the enrolled patients were collected in five consecutive time-points. Untargeted metabolomics was used to profile serum metabolic signatures from LARC patients. Then, we used fuzzy C-means clustering (FCM) to explore temporal change patterns in metabolites cluster and identify monotonously changing metabolites during NCRT. Repeated measure analysis of variance (RM-ANOVA) and multilevel partial least-squares discriminant analysis (ML-PLS-DA) were performed to select metabolic biomarkers. Finally, a panel of dynamic differential metabolites was used to build logistic regression prediction models.

RESULTS: Metabolite profiles showed a clearly tendency of separation between different follow-up panels. We identified two clusters of 155 serum metabolites with monotonously changing patterns during NCRT (74 decreased metabolites and 81 increased metabolites). Using RM-ANOVA and ML-PLS-DA, 8 metabolites (L-Norleucine, Betaine, Hypoxanthine, Acetylcholine, 1-Hexadecanoyl-sn-glycero-3-phosphocholine, Glycerophosphocholine, Alpha-ketoisovaleric acid, N-Acetyl-L-alanine) were further identified as dynamic differential biomarkers for predicting NCRT sensitivity. The area under the ROC curve (AUC) of prediction model combined with the baseline measurement was 0.54 (95%CI = 0.43 ~ 0.65). By incorporating the variability indexes of 8 dynamic differential metabolites, the prediction model showed better discrimination performance than baseline measurement, with AUC = 0.67 (95%CI 0.57 ~ 0.77), 0.64 (0.53 ~ 0.75), 0.60 (0.50 ~ 0.71), and 0.56 (0.45 ~ 0.67) for the variability index of difference, linear slope, ratio, and standard deviation, respectively.

CONCLUSION: This study identified eight metabolites as dynamic differential biomarkers to discriminate NCRT-sensitive and resistant patients. The changes of metabolite level during NCRT show better performance in predicting NCRT sensitivity. These findings highlight the clinical significance of metabolites variabilities in metabolomics analysis.

PMID:36441416 | DOI:10.1007/s11306-022-01959-8

AIDS Behav. 2022 Nov 28. doi: 10.1007/s10461-022-03925-w. Online ahead of print.

ABSTRACT

This study used an intersectional approach to explore the association between enacted and internalized drug use and HIV stigma on HIV care outcomes among HIV-positive women who inject drugs in Ukraine. Surveys were conducted in Kyiv in 2019-2020. Among the 306 respondents, 55% were engaged in HIV care. More than half (52%) of participants not engaged in care reported internalized stigma related to both drug use and HIV status (i.e., intersectional stigma), compared to only 35% of those who were engaged in HIV care. Among those engaged in care, 36% reported intersectional enacted stigma compared to 44% of those not engaged in care; however, this difference was not statistically significant in the univariable analysis (p = 0.06). In the univariable analysis, participants who reported intersectional internalized stigma had 62% lower odds of being engaged in HIV care (OR 0.38, 95% CI 0.22, 0.65, p < 0.001). In the adjusted model, reported intersectional internalized stigma (aOR 0.52, 95% CI 0.30, 0.92, p = 0.026), reported intersectional enacted stigma (aOR 0.47, 95% CI 0.23, 0.95, p = 0.036), and knowing their HIV status for more than 5-years (aOR 2.29, 95% CI 1.35, 3.87, p = 0.002) were significant predictors of HIV care engagement. These findings indicate that interventions to improve HIV care engagement must address women’s experiences of both HIV and drug use stigma and the different mechanisms through which stigma operates.

PMID:36441406 | DOI:10.1007/s10461-022-03925-w

Curr Cardiol Rep. 2022 Nov 28. doi: 10.1007/s11886-022-01790-6. Online ahead of print.

ABSTRACT

PURPOSE OF REVIEW: Prior European Society of Cardiology (ESC) guidelines endorsed the SCORE 10-year cardiovascular disease (CVD) risk calculator to inform the total risk approach to CVD prevention, including the use of preventive interventions like lipid lowering therapies. However, SCORE was released in 2003, did not allow for estimation of fatal and non-fatal CVD events, and was limited to adults aged 40 to 70 years. The ESC’s Cardiovascular Risk Collaboration (CRC) was tasked with updating SCORE (SCORE2) and with extending the upper age range of adults eligible for risk estimation (SCORE2-OP). This review summarises these two deliverables.

RECENT FINDINGS: Published in 2021, these updated risk scores allow for estimation of 10 year total (fatal + non-fatal) risks of a first atherosclerotic cardiovascular event in adults (SCORE2) and older persons (SCORE2-OP), calibrated for use in four European risk regions. The models account for competing risk of non-CVD death. These were extensively validated with excellent calibration and C-statistics ranging from 0.67 to 0.81. SCORE2 and SCORE2-OP have informed the 2021 ESC Guidelines on cardiovascular disease prevention in clinical practice. In addition to endorsing these two updated risk calculators, these guidelines have, for the first time, recommended the use of age-related risk categories. This change was motivated to prevent overreliance on age when making CVD prevention decisions.

PMID:36441402 | DOI:10.1007/s11886-022-01790-6

Child Psychiatry Hum Dev. 2022 Nov 28. doi: 10.1007/s10578-022-01468-8. Online ahead of print.

ABSTRACT

In recent years, in addition to its clinical importance, interest in the social-cognitive aspect of internet gaming disorder (IGD) has increased. This study aimed to investigate autistic traits, executive functions, and self-regulation abilities of patients with IGD. Eighty-seven male patients with IGD and eighty-three male healthy controls (HC) were included in the study. All patients were diagnosed with IGD as per the diagnostic criteria of Diagnostic and Statistical Manual of Mental Disorders-5. Healthy controls without any comorbid psychiatric diagnosis were recruited from the community. The Brief Rating Inventory of Executive Function (BRIEF) and the Social Responsiveness Scale (SRS) were implemented to evaluate autistic traits, executive functions, and self-regulation skills. The Beck Depression Inventory (BDI), Screen for Child Anxiety and Related Disorders and Internet Gaming Disorder Scale-Short-Form were used to evaluate psychopathology. The effect size of the impairments in executive functions and self-regulation skills was large (Cohen’s d = 1.0-2.0). IGD groups had higher levels of autistic traits compared to healthy controls (d = 1.0-1.4). The differences in BDI and BRIEF scores remained significant in logistic regression analysis. Age at illness-onset, total severity of anxiety, and autistic traits were found as significant correlates of deficits in executive functions among patients with IGD. The results of this study supported the higher autistic traits and poorer executive function skills of patients with IGD. Deficits in executive functions were associated with autistic traits and younger age-onset of the illness.

PMID:36441375 | DOI:10.1007/s10578-022-01468-8

Wien Med Wochenschr. 2022 Nov 28. doi: 10.1007/s10354-022-00984-5. Online ahead of print.

ABSTRACT

BACKGROUND: Despite the existence of internationally consistent guidelines for the management of pain, efficient regional anesthesia techniques, safe pain medications, and organizational structures, e.g., acute pain services, various studies have shown that pain is still common among both surgical and non-surgical in-patients.

OBJECTIVE: The primary objective of this study was to evaluate, on a multi-center basis, the point pain prevalence of surgical and non-surgical in-patients. We further analyzed pain intensities, in-hospital pain triggers, pain-related impairments, pain assessments, patient information about pain, and patient satisfaction with pain therapy. This benchmark information should lead to better implementation of pain management strategies and thus improve health care quality.

METHODS: We surveyed all adult in-patients in three general hospitals in Austria (general hospital Klagenfurt am Wörthersee, general hospital Villach, general hospital Wolfsberg) on the index day with two standardized questionnaires for both surgical and non-surgical patients.

RESULTS: Overall, a pain prevalence of 40.0%, with no statistically significant difference between surgical and non-surgical patients, was shown. Higher pain prevalence in female patients, high pain prevalence in the age group 18-30 years, and highest pain prevalence in the age group over 90 years old was found. Overall pain intensity was relatively low, but unacceptable maximum pain within the preceding 24 h was shown. Different in-hospital pain triggers like patient’s care and mobilization were found. Our survey has shown that pain has an impact on personal hygiene, mobilization, mood, sleep, and appetite. However, patients were very satisfied with their pain therapy.

CONCLUSION: Medical staff and nurses have to be sensitized to the urgent need to improve pain management strategies.

PMID:36441358 | DOI:10.1007/s10354-022-00984-5