Category: Nevin Manimala

J Chem Inf Model. 2023 Nov 22. doi: 10.1021/acs.jcim.3c01293. Online ahead of print.

ABSTRACT

Identifying the interactions between T-cell receptor (TCRs) and human antigens is a crucial step in developing new vaccines, diagnostics, and immunotherapy. Current methods primarily focus on learning binding patterns from known TCR binding repertoires by using sequence information alone without considering the binding specificity of new antigens or exogenous peptides that have not appeared in the training set. Furthermore, the spatial structure of antigens plays a critical role in immune studies and immunotherapy, which should be addressed properly in the identification of interacting TCR-antigen pairs. In this study, we introduced a novel deep learning framework based on generative graph structures, GGNpTCR, for predicting interactions between TCR and peptides from sequence information. Results of real data analysis indicate that our model achieved excellent prediction for new antigens unseen in the training data set, making significant improvements compared to existing methods. We also applied the model to a large COVID-19 data set with no antigens in the training data set, and the improvement was also significant. Furthermore, through incorporation of additional supervised mechanisms, GGNpTCR demonstrated the ability to precisely forecast the locations of peptide-TCR interactions within 3D configurations. This enhancement substantially improved the model’s interpretability. In summary, based on the performance on multiple data sets, GGNpTCR has made significant progress in terms of performance, universality, and interpretability.

PMID:37990917 | DOI:10.1021/acs.jcim.3c01293

Infect Control Hosp Epidemiol. 2023 Nov;44(11):1834-1839. doi: 10.1017/ice.2023.51. Epub 2023 Apr 4.

ABSTRACT

OBJECTIVE: Quantify the frequency and drivers of unreported coronavirus disease 2019 (COVID-19) symptoms among nursing home (NH) staff.

DESIGN: Confidential telephone survey.

SETTING: The study was conducted in 70 NHs in Orange County, California, December 2020-February 2022.

PARTICIPANTS: The study included 120 NH staff with COVID-19.

METHODS: We designed a 40-item telephone survey of NH staff to assess COVID-19 symptom reporting behavior and types of barriers [monetary, logistic, and emotional (fear or stigma)] and facilitators of symptom reporting using 5-point Likert scales. Summary statistics, reliability of survey constructs, and construct and discriminant validity were assessed.

RESULTS: Overall, 49% of surveys were completed during the 2020-2021 COVID-19 winter wave and 51% were completed during severe acute respiratory coronavirus virus 2 (SARS-CoV-2) δ (delta)/ (omicron) waves, with a relatively even distribution of certified nursing assistants, licensed vocational or registered nurses, and nonfrontline staff. Most COVID-19 cases (71%) were detected during mandated weekly NH surveillance testing and most staff (67%) had ≥1 symptom prior to their test. Only 34% of those with symptoms disclosed their symptom to a supervisor. Responses were consistent across 8 discrete survey constructs with Cronbach α > 0.70. In the first wave of the pandemic, fear and lack of knowledge were drivers of symptom reporting. In later waves, adequate staffing and sick days were drivers of symptom reporting. COVID-19 help lines and encouragement from supervisors facilitated symptom reporting and testing.

CONCLUSIONS: Mandatory COVID-19 testing for NH staff is key to identifying staff COVID-19 cases due to reluctance to speak up about existing symptoms. Active encouragement from supervisors to report symptoms and stay home when ill was a major driver of symptom reporting and resultant infection prevention and worker safety measures.

PMID:37990904 | DOI:10.1017/ice.2023.51

Curr HIV Res. 2023 Nov 16. doi: 10.2174/011570162X266922231107094649. Online ahead of print.

ABSTRACT

INTRODUCTION: Comorbidities are increasing in people living with HIV (PLHIV), and different treatment options have advantages and disadvantages. It is important to compare information from real-life treated cases. The aim of this study was to retrospectively evaluate the data on efficacy and clinical and laboratory findings during different antiretroviral therapies.

METHODS: Retrospective file data of 47 PLHIV using Dolutegravir and Lamivudine (3TC/DTG), Tenofovir Alafenamide Emtricitabine and Elvitegravir Cobicistat (EVG/c/TAF/FTC) and Tenofovir Disoproxil Fumarate and Emtricitabine and Efavirenz (EFV/FTC/TDF) were analyzed. Data of the patients at baseline and 12 months after antiretroviral therapy (ART) were compared.

RESULTS: About 47 PLHIV were included in the study. Of the patients, 22 (46.8%) were in the 3TC/DTG group, 19 (40.4%) in the EVG/c/TAF/FTC, and 6 (12.8%) in the EFV/FTC/TDF group. After 12 months of treatment, BMI, HIV-RNA, CD4, WBC, hemoglobin, MCV, PDW, RDW, platelet count, creatinine, eGFR, HDL, AST, glucose values of the 3TC/DTG group were significantly different (p<0.05). After 12 months of treatment, BMI, HIV-RNA, CD4 count, MCV, creatinine, eGFR, HDL, LDL, TG, TC, AST, and HOMA-IR values of the EVG/c/TAF/FTC treatment group were significantly different (p<0.05). After 12 months of treatment, HIV RNA, total bilirubin, and LDL values in the EFV/FTC/TDF treatment group were statistically different (p<0.05).

CONCLUSION: All treatment groups showed a decrease in HIV-RNA and an increase in CD4 at the end of one year. While CD4 elevation is lower in EFV recipients than in integrase inhibitor (INSTI) recipients, weight gain is higher in INSTI recipients. While the lipid profile was more positively affected in the 3TC/DTG group, lipid profiles were more negatively affected in the EVG/c/TAF/FTC group, although liver and kidney functions were preserved.

PMID:37990894 | DOI:10.2174/011570162X266922231107094649

Expert Rev Vaccines. 2023 Nov 22. doi: 10.1080/14760584.2023.2287135. Online ahead of print.

ABSTRACT

OBJECTIVES: Despite their use, differences in human papillomavirus (HPV) vaccine efficacies remain uncertain. This study assesses efficacy differences among bivalent, quadrivalent, and nine-valent HPV (2vHPV, 4vHPV, and 9vHPV) vaccines.

METHODS: PubMed, Web of Science, Embase, and the Cochrane Library were searched for randomized controlled trials comparing HPV vaccine efficacy against persistent infection (≥6 months) and cervical intraepithelial neoplasia grade 2 or worse (CIN2+). Network meta-analysis yielded direct and indirect comparisons. Risk ratios (RRs) and 95% confidence intervals (95% CIs) were reported, and robustness was evaluated via sensitivity analysis.

RESULTS: In 11 randomized controlled trials with 58,881 healthy women, for persistent infection with HPV 16, 9vHPV was most effective at 97% (RR = 0.03, 95% CI: 0.01-0.08); for HPV 18, 2vHPV (Cecolin) was most effective at 98% (RR = 0.02, 95% CI: 0.00-0.29); for CIN2+ associated with HPV 16 and 18, 4vHPV was most effective at 99% (RR = 0.01, 95% CI: 0.00-0.10) and 97% (RR = 0.03, 95% CI: 0.00-0.45), respectively; for persistent infection with HPV 31, 33, 45, 52, and 58, 9vHPV was ≥ 95% effective; both 2vHPV vaccines were cross-effective against HPV 31, 33, and 45; and 4vHPV was cross-effective against HPV 31.

CONCLUSIONS: HPV vaccine efficacies differ for different HPV types. Additional data are needed to determine the cross-efficacy of 2vHPV (Cecolin).

PMID:37990881 | DOI:10.1080/14760584.2023.2287135

Hypertension. 2023 Nov 22. doi: 10.1161/HYPERTENSIONAHA.123.21304. Online ahead of print.

ABSTRACT

BACKGROUND: Diabetes is an important risk factor for heart failure (HF) and is associated with left ventricular (LV) diastolic dysfunction. However, diabetic comorbid conditions, such as nocturnal hypertension, as predictors of diastolic dysfunction are not known in the absence of an HF period. The present study was conducted as the longitudinal examination of the predictive value of nocturnal hypertension profiles on the progression of LV diastolic dysfunction in patients with and without diabetes without HF.

METHODS: 422 subjects (154 diabetes and 268 nondiabetes) in the absence of HF were followed for 36.8±18.2 months. The relationships among the patterns of nocturnal hypertension and the outcome of LV diastolic dysfunction, defined as an increase in E/e’>14, were investigated in the patients with and without diabetes.

RESULTS: The interaction effect of the diabetes status and the patterns of nocturnal hypertension on the hazard rate of the occurrence of E/e’>14 was statistically significant (P=0.017). Kaplan-Meier analysis results revealed that patients with diabetes with nondipper (P=0.021 versus dipper) and riser (P=0.006 versus dipper) had a greater risk for a diastolic dysfunction event. Furthermore, multivariable Cox proportional hazards analysis revealed that nondipper (hazard ratio, 4.56 [95% CI, 1.49-13.96]; P=0.007) and riser (hazard ratio, 3.89 [95% CI, 1.31-11.57]; P=0.014) patterns were associated with elevated risk of the outcome of LV diastolic dysfunction. In contrast, no similar significant associations were found in patients without diabetes.

CONCLUSIONS: During the absence of HF periods, nocturnal hypertension is an important predictor for the progression of LV diastolic dysfunction in patients with diabetes.

PMID:37990873 | DOI:10.1161/HYPERTENSIONAHA.123.21304

Sports Biomech. 2023 Nov 22:1-12. doi: 10.1080/14763141.2023.2278154. Online ahead of print.

ABSTRACT

We assessed lower limb muscle activity during the execution of first and second tennis serves, exploring whether the extent of these differences is influenced by the chosen method for normalising surface electromyography (EMG) data. Ten male competitive tennis players first completed three rounds of maximal isometric voluntary contractions (MVC) of knee extensors and plantar flexors for the left (front) and right (back) leg separately, and three squat jumps. Afterward, they executed ten first and ten-second serves. Surface EMG activity of four lower limb muscles (vastus lateralis, rectus femoris, gastrocnemius lateralis, and soleus muscles) on each leg was recorded and normalised in three different ways: to MVC; to peak/maximal activity measured during squat jump; and to the actual serve. For the rectus femoris and soleus muscles of the left leg, and the gastrocnemius lateralis and soleus muscles of the right leg, EMG amplitude differed significantly between normalisation techniques (P ≤ 0.012). All muscles showed greater activity during the first serve, although this difference was only statistically significant for the right vastus lateralis muscle (P = 0.014). In conclusion, the EMG normalisation method selected may offer similar information when comparing first and second serve, at least for leg muscles studied here.

PMID:37990861 | DOI:10.1080/14763141.2023.2278154

J Surg Oncol. 2023 Nov 22. doi: 10.1002/jso.27533. Online ahead of print.

ABSTRACT

BACKGROUND: Using real working examples, we provide strategies and address challenges in linear and logistic regression to demonstrate best practice guidelines and pitfalls of regression modeling in surgical oncology research.

METHODS: To demonstrate our best practices, we reviewed patients who underwent tissue expander breast reconstruction between 2019 and 2021. We assessed predictive factors that affect BREAST-Q Physical Well-Being of the Chest (PWB-C) scores at 2 weeks with linear regression modeling and overall complications and malrotation with logistic regression modeling. Model fit and performance were assessed.

RESULTS: The 1986 patients were included in the analysis. In linear regression, age [β = 0.18 (95% CI: 0.09, 0.28); p < 0.001], single marital status [β = 2.6 (0.31, 5.0); p = 0.026], and prepectoral pocket dissection [β = 4.6 (2.7, 6.5); p < 0.001] were significantly associated with PWB-C at 2 weeks. For logistic regression, BMI [OR = 1.06 (95% CI: 1.04, 1.08); p < 0.001], age [OR = 1.02 (1.01, 1.03); p = 0.002], bilateral reconstruction [OR = 1.39 (1.09, 1.79); p = 0.009], and prepectoral dissection [OR = 1.53 (1.21, 1.94); p < 0.001] were associated with increased likelihood of a complication.

CONCLUSION: We provide focused directives for successful application of regression techniques in surgical oncology research. We encourage researchers to select variables with clinical judgment, confirm appropriate model fitting, and consider clinical plausibility for interpretation when utilizing regression models in their research.

PMID:37990858 | DOI:10.1002/jso.27533

Mater Horiz. 2023 Nov 22. doi: 10.1039/d3mh01500a. Online ahead of print.

ABSTRACT

Point defects often appear in two-dimensional (2D) materials and are mostly correlated with physical phenomena. The direct visualisation of point defects, followed by statistical inspection, is the most promising way to harness structure-modulated 2D materials. Here, we introduce a deep learning-based platform to identify the point defects in 2H-MoTe₂: synergy of unit cell detection and defect classification. These processes demonstrate that segmenting the detected hexagonal cell into two unit cells elaborately cropped the unit cells: further separating a unit cell input into the Te₂/Mo column part remarkably increased the defect classification accuracies. The concentrations of identified point defects were 7.16 × 10²⁰ cm² of Te monovacancies, 4.38 × 10¹⁹ cm² of Te divacancies and 1.46 × 10¹⁹ cm² of Mo monovacancies generated during an exfoliation process for TEM sample-preparation. These revealed defects correspond to the n-type character mainly originating from Te monovacancies, statistically. Our deep learning-oriented platform combined with atomic structural imaging provides the most intuitive and precise way to analyse point defects and, consequently, insight into the defect-property correlation based on deep learning in 2D materials.

PMID:37990857 | DOI:10.1039/d3mh01500a

Urol J. 2023 Nov 22. doi: 10.22037/uj.v20i.7768. Online ahead of print.

ABSTRACT

PURPOSE: To investigate the effect of pyeloplasty in pediatric patients with poor function kidneys٫ focusing on the split renal function (SRF) and anteroposterior diameter (APD) of the renal pelvis.

MATERIALS AND METHODS: A retrospective study included 47 pediatric patients with ureteropelvic junction obstruction (UPJO) who underwent open pyeloplasty with SRF< 20%. All patients were recruited from the Labbafinejad University Hospital center from April 2014 to October 2020. The results of preoperative ultrasonography and Diethylenetriamine pentaacetate (DTPA) scan compared with the results of the ultrasonography and DTPA scan 6 months and one year after surgery. Finally, Wilcoxon signed-rank test was used to test differences by SPSS (version 25) software statistical computer package.

RESULTS: The mean age of participants was 1.5 years. There were 34 cases with SRF between 10% and 20%, and 13 cases with SRF <10%. The findings showed that pyeloplasty for UPJO leads to a significant improvement in renal function in poorly functioning renal units with 10% ≤SRF<20%. Although improvement in renal function occurred in the group with SRF of less than 10%, it was not statistically significant. The APD in both groups was statistically significantly improved. No correlation between genders and outcomes was found.

CONCLUSION: Poorly functioning renal unit (SRF < 20%) can show functional improvement after the pyeloplasty.

PMID:37990849 | DOI:10.22037/uj.v20i.7768

Urol J. 2023 Nov 22. doi: 10.22037/uj.v20i.7738. Online ahead of print.

ABSTRACT

PURPOSE: The choice between using the internal or external iliac arteries to supply a transplanted kidney poses is a dilemma during renal transplantation. As the internal iliac artery branches to the genital tract, cutting it could potentially result in sexual dysfunction. The purpose of this study was to compare the effects of these two surgical methods on sexual function.

MATERIALS AND METHODS: 122 sexually active male patients under the age of sixty were randomly divided into two groups: the internal iliac anastomosis group and the external iliac artery anastomosis group. Before surgery and one year after the procedure, patients completed the International Index of Erectile Function-15 questionnaire (IIEF-15), and the difference in scores of each domain was measured.

RESULTS: Statistically, kidney transplantation improved all domains of IIEF in both groups, except for the erectile function in for patients who underwent internal iliac artery anastomosis group. Additionally, Also, there were significant differences between the two groups in the domains of erectile function (p-value=0.04) and overall satisfaction (p-value= 0.002), while other domains such as orgasmic function, sexual desire, and intercourse satisfaction did not show any statistically significant differences.

CONCLUSION: In conclusion, the choice between using the internal or external iliac artery for arterial anastomosis during kidney transplantation does not significantly impact graft function. However, it may negatively affect erectile function in patients who undergo internal iliac artery anastomosis.

PMID:37990848 | DOI:10.22037/uj.v20i.7738