Nevin Manimala

Bioinformatics. 2021 Feb 26:btab134. doi: 10.1093/bioinformatics/btab134. Online ahead of print.

ABSTRACT

SUMMARY: Heterogeneity is a hallmark of many complex human diseases, and unsupervised heterogeneity analysis has been extensively conducted using high-throughput molecular measurements and histopathological imaging features. “Classic” heterogeneity analysis has been based on simple statistics such as mean, variance, and correlation. Network-based analysis takes interconnections as well as individual variable properties into consideration and can be more informative. Several Gaussian graphical model (GGM)-based heterogeneity analysis techniques have been developed, but friendly and portable software is still lacking. To facilitate more extensive usage, we develop the R package HeteroGGM, which conducts GGM-based heterogeneity analysis using the advanced penaliztaion techniques, can provide informative summary and graphical presentation, and is efficient and friendly.

AVAILABILITY: The package is available at https://CRAN.R-project.org/package=HeteroGGM.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:33638346 | DOI:10.1093/bioinformatics/btab134

J Am Med Inform Assoc. 2021 Feb 26:ocaa347. doi: 10.1093/jamia/ocaa347. Online ahead of print.

ABSTRACT

OBJECTIVE: We aimed to develop a model for accurate prediction of general care inpatient deterioration.

MATERIALS AND METHODS: Training and internal validation datasets were built using 2-year data from a quaternary hospital in the Midwest. Model training used gradient boosting and feature engineering (clinically relevant interactions, time-series information) to predict general care inpatient deterioration (resuscitation call, intensive care unit transfer, or rapid response team call) in 24 hours. Data from a tertiary care hospital in the Southwest were used for external validation. C-statistic, sensitivity, positive predictive value, and alert rate were calculated for different cutoffs and compared with the National Early Warning Score. Sensitivity analysis evaluated prediction of intensive care unit transfer or resuscitation call.

RESULTS: Training, internal validation, and external validation datasets included 24 500, 25 784 and 53 956 hospitalizations, respectively. The Mayo Clinic Early Warning Score (MC-EWS) demonstrated excellent discrimination in both the internal and external validation datasets (C-statistic = 0.913, 0.937, respectively), and results were consistent in the sensitivity analysis (C-statistic = 0.932 in external validation). At a sensitivity of 73%, MC-EWS would generate 0.7 alerts per day per 10 patients, 45% less than the National Early Warning Score.

DISCUSSION: Low alert rates are important for implementation of an alert system. Other early warning scores developed for the general care ward have achieved lower discrimination overall compared with MC-EWS, likely because MC-EWS includes both nursing assessments and extensive feature engineering.

CONCLUSIONS: MC-EWS achieved superior prediction of general care inpatient deterioration using sophisticated feature engineering and a machine learning approach, reducing alert rate.

PMID:33638343 | DOI:10.1093/jamia/ocaa347

Chirurgia (Bucur). 2021 Jan-Feb;116(1):51-59. doi: 10.21614/chirurgia.116.1.51.

ABSTRACT

Background: Compliance to adjuvant chemotherapy (AC) for patients undergoing rectal surgery ranges from 43% to 73.6%. Reasons reported for not initiating or completing AC include onset of postoperative complications, drug toxicity, disease progression and/or patient preferences. Little is known regarding the impact of obesity on the compliance to AC in this setting. Methods: This multicenter, retrospective study analyzed compliance to AC and treatment-related morbidity in 511 patients having undergone surgery with curative intent for rectal cancer in six Italian colorectal centers between January 2013 and December 2017. Results: 70 patients were obese (BMI 30 kg/m2). The proportion of open procedures (22.9% vs. 13.4%) and conversions (14.3% vs. 4.8%) was greater in obese compared to non-obese patients (p 0.001). Median hospital stay was one day longer for obese patients (9 days vs. 10 days, p=0.038) while there was no statistically significant difference in the complication rate, whether overall (58.6% in obese vs. 52.3% in non-obese) or with a Clavien-Dindo score 3 (17.1% vs 10.9%). AC was offered to 49/70 (70%) patients in the obese group and 306/441 (69.4%) in the non-obese group (p=0.43). There was no statistically significant difference in AC compliance: 18.4% and 22.9% did not start AC, while 36.7% and 34.6%, started AC but did not complete the scheduled treatment (p=0.79) in the obese and non-obese group, respectively. Overall, 55% of patients who started AC successfully completed their adjuvant treatment. Conclusions: Obesity did not impact compliance to AC for locally advanced rectal cancer: compliance was poor in obese and non-obese patients with no statistically significant difference between the two groups. Major complication rate was not statistically significantly affected by increased BMI.

PMID:33638326 | DOI:10.21614/chirurgia.116.1.51

Cancer Med. 2021 Feb 26. doi: 10.1002/cam4.3735. Online ahead of print.

ABSTRACT

BACKGROUND: Although elevated serum gamma-glutamyltransferase (GGT) is a known indicator of increased risk of several cancers, the clinical value of repeated measurements of GGT has not been determined. Therefore, we aimed to investigate whether repeatedly elevated serum GGT levels are associated with the risk of respiratory cancer incidence.

METHODS: We included participants who had undergone the Korean Health screening four times during 2009-2012 and had previously undergone four consecutive examinations. Those who were diagnosed with respiratory cancer before the date of examination were excluded. The participants obtained one GGT point if their GGT levels were in the highest quartile (the quartile 4 group). We analyzed the association between GGT points and respiratory cancer incidence by Cox proportional hazard models.

RESULTS: During mean follow-up of 6.39 ± 1.2 years, 3,559,109 participants were enrolled. Of them, 8,944 (0.34%) men and 1,484 (0.14%) women were newly diagnosed with respiratory cancer. In multivariate analysis adjusted for confounding factors, male participants with 4 GGT points had a significantly higher hazards of developing respiratory cancer than those with 0 GGT points (hazard ratio [HR]: 1.39; 95% confidence interval [CI]: 1.31-1.48). Among female, participants with the highest points of GGT also had sixfold increased risk of developing laryngeal cancer. However, no significant association was observed between GGT points and lung cancer incidence among women (HR: 0.95; 95% CI: 0.81-1.11).

CONCLUSION: Repeatedly elevated serum levels of GGT were associated with a higher risk of respiratory cancer incidence, especially in men. This finding suggests that physicians can identify a person with a higher risk of respiratory cancer through a simple repeated measurement of GGT.

PMID:33638317 | DOI:10.1002/cam4.3735

Cancer Med. 2021 Feb 26. doi: 10.1002/cam4.3747. Online ahead of print.

ABSTRACT

OBJECTIVE: Papillary thyroid microcarcinoma (PTMC) has a good prognosis and a long survival time, surgery is the common treatment including total thyroidectomy (TT) and unilateral lobectomy (LT), but recent studies showed that TT does not show an advantage over LT for PTMC in preventing cancer recurrence and reducing mortality. Given this, the health-related quality of life (HRQoL) has become one of the important factors that physicians must consider when making treatment decisions. The aim of this study was to compare the HRQoL of patients between undergoing TT and LT.

METHODS: From October 2019 to December 2019, 69 PTMC patients were enrolled in our study, including 34 in the LT group and 35 in the TT group, respectively. We used three questionnaires which included the 36-item short-form health survey (SF-36), thyroid cancer-specific quality of life (THYCA-QOL), and Fear of Progression Questionnaire-Short Form (FoP-Q-SF) for each patient to evaluate their scores of HRQoL.

RESULTS: According to the SF-36, the scores of the domain for the role limitation due to physical problems, emotional problems, and social function (RP, RE, and SF) as well as Physical Component Summary (PCS) and Mental Component Summary (MCS) showed a significant negative linear association between the LT group and TT group: RP (coefficient [coef]: -33.953 [confidence interval (CI) -51.187 to -16.720], p < 0.001, RE (coef: -21.633 [CI -39.500 to -3.766], p = 0.018), SF (coef: -10.169 [CI -19.586 to -0.752], p = 0.035)and PCS (coef: -10.571 [CI -17.768 to -3.373], p = 0.005), MCS (coef: -10.694 [CI -19.465 to -1.923], p = 0.018). The THYCA-QOL showed that the scores of the TT group were higher than that of the LT group in the problem of scar (coef: 16.245 [CI 1.697 to 30.794], p = 0.029 according to the multivariate analysis), suggesting a higher level of complaint in the TT group. There was no statistically significant difference in the scores of FoP-Q-SF between the two groups.

CONCLUSIONS: In patients with PTMC, LT offers an advantage over TT in terms of HRQoL, which supports the role of LT as an alternative strategy to TT.

PMID:33638269 | DOI:10.1002/cam4.3747

Hum Brain Mapp. 2021 Feb 27. doi: 10.1002/hbm.25391. Online ahead of print.

ABSTRACT

Previous neuroimaging studies have revealed abnormal functional connectivity of brain networks in patients with major depressive disorder (MDD), but findings have been inconsistent. A recent big-data study found abnormal intrinsic functional connectivity within the default mode network in patients with recurrent MDD but not in first-episode drug-naïve patients with MDD. This study also provided evidence for reduced default mode network functional connectivity in medicated MDD patients, raising the question of whether previously observed abnormalities may be attributable to antidepressant effects. The present study (ClinicalTrials.gov identifier: NCT03294525) aimed to disentangle the effects of antidepressant treatment from the pathophysiology of MDD and test the medication normalization hypothesis. Forty-one first-episode drug-naïve MDD patients were administrated antidepressant medication (escitalopram or duloxetine) for 8 weeks, with resting-state functional connectivity compared between posttreatment and baseline. To assess the replicability of the big-data finding, we also conducted a cross-sectional comparison of resting-state functional connectivity between the MDD patients and 92 matched healthy controls. Both Network-Based Statistic analyses and large-scale network analyses revealed intrinsic functional connectivity decreases in extensive brain networks after treatment, indicating considerable antidepressant effects. Neither Network-Based Statistic analyses nor large-scale network analyses detected significant functional connectivity differences between treatment-naïve patients and healthy controls. In short, antidepressant effects are widespread across most brain networks and need to be accounted for when considering functional connectivity abnormalities in MDD.

PMID:33638263 | DOI:10.1002/hbm.25391

Trop Med Int Health. 2021 Feb 26. doi: 10.1111/tmi.13566. Online ahead of print.

ABSTRACT

OBJECTIVE: To assess adherence to COVID-19 preventive measures and its associated factors among pregnant women in Ghana METHODS: This was a cross-sectional study conducted in the Nabdam district, Ghana. Data were collected from 527 pregnant women randomly selected from antenatal care clinics from 16 healthcare facilities. Descriptive statistics were used to assess the prevalence of adherence to COVID-19 preventive measures. Multivariable logistic regression was used to estimate the factors associated with COVID-19 preventive measures, whilst adjusting for potential confounders.

RESULTS: The prevalence of wearing a face mask 18.0% (95% CI: 14.73%, 21.32%); of handwashing/hand sanitizing 31.7% (95% CI: 27.70%, 35.67%), and of social distancing, 22.0% (95% CI:18.46%, 25.56%). Multivariable logistic regression analysis revealed that knowledge of COVID-19 symptoms [Adjusted odds ratios (aOR): 2.86, 95% CI: 1.03,7.89], and knowledge of COVID-19 transmission via contaminated surfaces/objects (aOR: 4.60, 95% CI:1.23,17.18) were associated with wearing a face mask. Pregnant women who knew that avoiding the touching of eyes, nose and mouth can prevent COVID-19 (aOR:2.71, 95% CI:1.01,7.28), and knowledge of the virus being transmitted via contaminated objects/surfaces (aOR: 4.08, 95% CI:1.42,11.76), were associated with handwashing/hand sanitizing. Knowledge of COVID-19 transmission via contaminated surfaces/objects (aOR:15.27, 95% CI:1.87,124.43), was also associated with social distancing.

CONCLUSION: The findings of our study suggest that knowledge of COVID-19 symptoms, transmission and preventive measures may play an important role in the practice of preventive measures against COVID-19 among pregnant women.

PMID:33638230 | DOI:10.1111/tmi.13566

Clin Oral Implants Res. 2021 Feb 26. doi: 10.1111/clr.13733. Online ahead of print.

ABSTRACT

OBJECTIVES: To compare the one-year aesthetic results of flapless single implants, placed in fresh extraction sockets with bone replacement and immediate provisional restoration with or without a connective tissue graft (CGT).

MATERIAL AND METHODS: The present study proposes a partially blinded multicenter parallel randomized controlled trial, where computer-generated tables were used for central randomization to allocate treatments. 59 out of the 60 patients screened by eight private practices in Northern Italy fulfilled the inclusion criteria. Immediate implants was placed in a fresh extraction socket with a non-functional immediate provisional restoration with (Test group) or without (Control group) a CGT. The primary outcome variable was the implant Crown Aesthetic Index (ICAI) at the 1-year follow-up.

RESULTS: ICAI for the 59 randomized patients (Test group = 31, Control group = 28) at the 1-year follow-up was 4.69 (95% CI = 3.16 – 6.22) for the Test group and 3.45 (95%CI = 1.83-5.08) for the Control group, without statistically significant difference between the two groups (p=0.086). One implant failure was recorded in each group, resulting in an implant survival rate of 96.8% [95%CI = 83.3 – 99.9] for the Test group and 96.4% [95%CI = 81.7 -99.9] for the Control group. Other secondary outcome variables and complication rates were comparable across the two groups.

CONCLUSIONS: Within the limitations of the present clinical trial, the results suggested that the adjunct use of CTG is not mandatory to achieve successful aesthetic outcomes for a well-planned immediate implant placement with immediate non-functional provisional restoration in a fresh extraction socket.

PMID:33638216 | DOI:10.1111/clr.13733

Dev Med Child Neurol. 2021 Feb 26. doi: 10.1111/dmcn.14844. Online ahead of print.

ABSTRACT

AIM: To examine interrater agreement and validity of the Functional Communication Classification System (FCCS) for young children with cerebral palsy (CP) aged 2 or 3 years.

METHOD: Speech-language pathologist (SLP) and parent FCCS ratings for 31 children with CP (aged 2y, n=16; aged 3y, n=15; 18 males, 13 females) were examined for interrater agreement using a weighted Cohen’s kappa statistic. Relationships between FCCS (SLP) ratings and: (1) concurrent validity with the Language Use Inventory, a standardized pragmatic assessment for children aged 18 to 47 months, (2) gross motor and fine motor function, (3) associated impairments (visual and intellectual), and (4) primary expressive communication mode were examined using Spearman’s correlation coefficients.

RESULTS: Almost perfect interrater agreement between SLP and parent FCCS ratings were found (k_w =0.94). Correlations with FCCS (SLP) were excellent for pragmatic function (r_s =-0.83, p<0.001), intellectual function (r_s =0.89, p<0.001), and primary expressive communication mode (r_s =0.92, p<0.001). Correlations were good for gross motor function (r_s =0.72, p<0.001) and visual impairment (r_s =0.70, p<0.001) and fair for fine motor function (r_s =0.53, p<0.002). Analysis was unwarranted for epilepsy (n=1 out of 31) and hearing-associated impairments (n=0 out of 31).

INTERPRETATION: The FCCS has excellent interrater agreement and validity for communication classification of children with CP aged 2 or 3 years and is highly suitable for surveillance and research purposes.

PMID:33638178 | DOI:10.1111/dmcn.14844

J Environ Qual. 2021 Feb 26. doi: 10.1002/jeq2.20209. Online ahead of print.

ABSTRACT

In August 2015, 11.3 million L of heavy metal contaminated water spilled into the Animas River from the Gold King Mine (GKM). National attention focused on water quality and agricultural production in areas affected by the spill. In response to local concerns, surface soil elemental concentrations were analyzed in three New Mexico, USA agricultural fields to determine potential threats to agronomic production. Irrigated fields in the Animas Watershed were scanned using portable X-ray fluorescence (PXRF) spectrometry to monitor the spatiotemporal variability of Pb, As, Cu, and Cr. Total of 175 locations were scanned using PXRF before and after the growing season for three years. Geostatistical model with the lowest Root Mean Square Error (RMSE) was chosen as the optimal model. The lowest RMSE for the elements ranged from to 0.10 to 0.44 meters (m) for As, 0.50 to 0.98 m for Cr, 0.15 to 0.91 m for Cu and 0.14 to 0.44 m for Pb across the models selected. The spatial dependence between the measured values exhibited strong to moderate autocorrelation for all metals except for As, it was strong to weak. Some areas in each field exceeded the New Mexico Environment Department soil screening limit of 7.07 mg As kg^-1 . All sampling locations were below the screening limit at last sampling time in 2019. Mixed models used for temporal analysis showed significant decrease only in As below the screening value at the end of the study. Results indicate that the agricultural soils were below the soil screening guideline values. This article is protected by copyright. All rights reserved.

PMID:33638153 | DOI:10.1002/jeq2.20209