Category: Nevin Manimala

BMC Bioinformatics. 2022 May 16;23(1):179. doi: 10.1186/s12859-022-04659-1.

ABSTRACT

When analyzing large datasets from high-throughput technologies, researchers often encounter missing quantitative measurements, which are particularly frequent in metabolomics datasets. Metabolomics, the comprehensive profiling of metabolite abundances, are typically measured using mass spectrometry technologies that often introduce missingness via multiple mechanisms: (1) the metabolite signal may be smaller than the instrument limit of detection; (2) the conditions under which the data are collected and processed may lead to missing values; (3) missing values can be introduced randomly. Missingness resulting from mechanism (1) would be classified as Missing Not At Random (MNAR), that from mechanism (2) would be Missing At Random (MAR), and that from mechanism (3) would be classified as Missing Completely At Random (MCAR). Two common approaches for handling missing data are the following: (1) omit missing data from the analysis; (2) impute the missing values. Both approaches may introduce bias and reduce statistical power in downstream analyses such as testing metabolite associations with clinical variables. Further, standard imputation methods in metabolomics often ignore the mechanisms causing missingness and inaccurately estimate missing values within a data set. We propose a mechanism-aware imputation algorithm that leverages a two-step approach in imputing missing values. First, we use a random forest classifier to classify the missing mechanism for each missing value in the data set. Second, we impute each missing value using imputation algorithms that are specific to the predicted missingness mechanism (i.e., MAR/MCAR or MNAR). Using complete data, we conducted simulations, where we imposed different missingness patterns within the data and tested the performance of combinations of imputation algorithms. Our proposed algorithm provided imputations closer to the original data than those using only one imputation algorithm for all the missing values. Consequently, our two-step approach was able to reduce bias for improved downstream analyses.

PMID:35578165 | DOI:10.1186/s12859-022-04659-1

J Cardiovasc Electrophysiol. 2022 May 16. doi: 10.1111/jce.15546. Online ahead of print.

ABSTRACT

Catheter ablation in children has evolved to become a highly effective and safe therapy. Each iterative improvement in ablation technology provides another opportunity to investigate how much incremental benefit can be made without sacrificing safety. Contact force sensing catheters represent an example of such technology that has become commonplace in adult ablation. Its capability in predicting lesion size and collateral damage to critical structures has not been meticulously explored. Backhoff and colleagues describe an animal ablation model where they quantitate lesion characteristics at the atrium, atrioventricular groove, and ventricle using low and high contact force targets, with a specific focus on assessing for coronary arterial injury. In this controlled experiment, chronic lesion characteristics were widely variable (~0-8 mm diameter) yet there was a statistically significant (albeit small) increase in lesion diameter for high (vs low) contact force lesions delivered to the atrioventricular groove. The risk of chronic sub-clinical coronary artery injury was 1-2%. The remarkably weak association between contact force and lesion size suggests that delivery of clinical lesions needs to have both principles of As much as effectively needed (AMEN) and as low as reasonably achievable (ALARA), mirroring radiation exposure This article is protected by copyright. All rights reserved.

PMID:35578108 | DOI:10.1111/jce.15546

Int J Behav Med. 2022 May 16. doi: 10.1007/s12529-022-10087-5. Online ahead of print.

ABSTRACT

BACKGROUND: Migrant domestic workers are vulnerable to physical and mental health problems given the many challenges they experience while working abroad. Using network analysis, this study examined the structure of depression, cardiometabolic health indicators (BMI, waist-hip ratio (WHR), blood pressure, and heart rate), bone mass, and perceived health status in this population. The network model allowed for an examination of central symptoms or symptoms with the most direct connections with other symptoms; bridge symptoms, or symptoms that link two or more communities; and edges, or relationships among symptoms.

METHOD: Cross-sectional data were gathered from 1375 Filipino domestic workers in Macao (SAR), China. Data from a subsample of 510 participants who met a cutoff indicating depression were analyzed. Anthropometric measurements and surveys were used to collect data, which was analyzed using R statistical software.

RESULTS: Results showed four community clusters: three communities consisted of at least two depression symptoms each and the fourth community included physical health indicators. Strong edges were formed between BMI-bone mass, psychomotor-concentration, BMI-WHR, and sad mood-anhedonia. The node with the highest expected influence was BMI. There were three bridges: worthlessness, psychomotor difficulties, and concentration difficulties.

CONCLUSION: The link between depression, cardiometabolic indicators, bone mass, and poor perceived health reinforces the need to address multimorbidity within migrant populations. Health promotion interventions that address mental and physical health may improve the health of this population.

PMID:35578098 | DOI:10.1007/s12529-022-10087-5

Oral Radiol. 2022 May 16. doi: 10.1007/s11282-022-00619-w. Online ahead of print.

ABSTRACT

OBJECTIVES: This study was conducted to evaluate the accuracy of navigation process according to the type of tracking methods and registration markers. The target registration errors (TREs) were measured at seven anatomical landmarks of the mandible.

METHODS: Four different experiments were performed to obtain the TREs using two tracking methods, the optical tracker (Polaris) and the electromagnetic (EM) tracker (Aurora), and two types of registration markers, invasive and noninvasive markers. All comparisons of TREs were statistically analyzed using SPSS and Python-based statistical package.

RESULTS: The average TRE values obtained from the four experiments were as follows: (1) 0.85 mm (± 0.07) using invasive marker and Aurora, (2) 1.06 mm (± 0.12) using invasive marker and Polaris, (3) 1.43 mm (± 0.15) using noninvasive marker and Aurora, and (4) 1.57 mm (± 0.23) using noninvasive marker and Polaris. Comparisons between all the experimental results revealed statistically significant differences except for the type of tracking system. Although the comparison between the modality of the tracking system showed no significant differences, the EM-based approach consistently demonstrated better performances than the optical type in all comparisons.

CONCLUSIONS: This study demonstrates that irrespective of the tracking modality, using invasive marker is a better choice in terms of accuracy. When using noninvasive marker, it is important to consider the increased TREs. In this study, the noninvasive marker caused a maximum increment of TREs of 0.81 mm compared with the invasive marker. Furthermore, using an EM-based tracker with invasive marker may result in the best accuracy for navigation.

PMID:35578091 | DOI:10.1007/s11282-022-00619-w

J Relig Health. 2022 May 17. doi: 10.1007/s10943-022-01580-y. Online ahead of print.

ABSTRACT

To analyze which pandemic related changes of attitudes and behaviors were perceived by Seventh-day Adventists (SDA) and how these relate to wellbeing, a cross-sectional survey with standardized questionnaires was performed. Participants (n = 1,494) stated changes for Relationships, Digital media usage and Nature/Silence/Contemplation, but not for Spirituality or Reflection of life. Best predictors of psychological wellbeing (WHO-5) were Spiritual wellbeing, perceived Restrictions and Awe/Gratitude (R² = .32). Mediation analyses (R² = 0.51) revealed a mediation effect of Awe/Gratitude between spiritual to psychological wellbeing (β = 0.11, p < 0.0001). Perceived changes were less relevant to buffer the negative effects of the pandemic; instead, they were related to fears of future. More relevant to stabilize SDAs´ wellbeing was their spirituality.

PMID:35578058 | DOI:10.1007/s10943-022-01580-y

Surg Endosc. 2022 May 16. doi: 10.1007/s00464-022-09320-9. Online ahead of print.

ABSTRACT

INTRODUCTION: Robotic inguinal hernia repair is growing in popularity among general surgeons despite little high-quality evidence supporting short- or long-term advantages over traditional laparoscopic inguinal hernia repair. The original RIVAL trial showed increased operative time, cost, and surgeon frustration for the robotic approach without advantages over laparoscopy. Here we report the 1- and 2-year outcomes of the trial.

METHODS: This is a multi-center, patient-blinded, randomized clinical study conducted at six sites from 2016 to 2019, comparing laparoscopic versus robotic transabdominal preperitoneal (TAPP) inguinal hernia repair with follow-up at 1 and 2 years. Outcomes include pain (visual analog scale), neuropathic pain (Leeds assessment of neuropathic symptoms and signs pain scale), wound morbidity, composite hernia recurrence (patient-reported and clinical exam), health-related quality of life (36-item short-form health survey), and physical activity (physical activity assessment tool).

RESULTS: Early trial participation included 102 patients; 83 (81%) completed 1-year follow-up (45 laparoscopic vs. 38 robotic) and 77 (75%) completed 2-year follow-up (43 laparoscopic vs. 34 robotic). At 1 and 2 years, pain was similar for both groups. No patients in either treatment arm experienced neuropathic pain. Health-related quality of life and physical activity were similar for both groups at 1 and 2 years. No long-term wound morbidity was seen for either repair type. At 2 years, there was no difference in hernia recurrence (1 laparoscopic vs. 1 robotic; P = 1.0).

CONCLUSIONS: Laparoscopic and robotic inguinal hernia repairs have similar long-term outcomes when performed by surgeons with experience in minimally invasive inguinal hernia repairs.

PMID:35578051 | DOI:10.1007/s00464-022-09320-9

J Mol Model. 2022 May 17;28(6):154. doi: 10.1007/s00894-022-05146-3.

ABSTRACT

Cancer affects a major part of the worldwide population, and, to minimize deaths, the diagnosis in the early stages of the disease is fundamental. Thus, to improve diagnosis and treatment new potential spectroscopic probes are crucial. Benzothiazole derivates present antitumor properties and are highly selective and interact strongly with the enzyme phosphoinositide 3-kinase (PI3K), which was associated with cell proliferation and breast cancer cells. In this paper, the rhenium shielding tensors (¹⁸⁷Re(σ)) and hydrogen and carbon chemical shifts (¹H(δ) and ¹³C(δ)) of the Re(CO)₃(NNO) complex conjugated with 2-(4′-aminophenyl)benzothiazole (ReABT) were evaluated. A statistical HCA model was used to analyze the best DFT protocol to compute σ and δ values and to evaluate the relativistic effects, both in the basis set and Hamiltonian as well as the functionals M06L or PBE0. The best protocol was applied to obtain ¹⁸⁷Re(σ) of the ReABT complex in different environments (gas phase, solution, and in the active site of the PI3K enzyme). The results point out that ¹⁸⁷Re(σ) values of the ReABT complex change significantly when the complex is docked in the PI3K enzyme.

PMID:35578053 | DOI:10.1007/s00894-022-05146-3

Surg Endosc. 2022 May 16. doi: 10.1007/s00464-022-09300-z. Online ahead of print.

ABSTRACT

OBJECTIVE: To investigate the effect of intraoperative lymph node (LN) dissection and postoperative adjuvant chemotherapy on the overall survival (OS) of gastric cancer (GC) patients and their reciprocity.

METHODS: LN noncompliance was defined as the absence of more than one LN station, as described in the protocol for D2 lymphadenectomy in the Japanese Gastric Cancer Association. The definition of adjuvant chemotherapy (AC) noncompliance was that the chemotherapy planned dose does not meet the requirements.

RESULTS: Kaplan-Meier survival curves showed that the OS of patients with major LN noncompliance was significantly lower than that of patients with nonmajor LN noncompliance, and the OS of AC noncompliance patients was significantly lower than that of AC compliance patients. If there was nonmajor LN noncompliance during surgery, the OS of patients with AC compliance was significantly higher than that of patients with AC noncompliance (P = 0.035). In the case of major LN noncompliance during surgery, there was no statistically significant difference in OS between those with AC compliance and those with AC noncompliance (P = 0.682). Multivariate Cox regression analysis including AC noncompliance indicated that major LN noncompliance was an independent prognostic factor for poor OS (P = 0.012), while AC noncompliance was not an independent prognostic factor for OS (P = 0.609).

CONCLUSION: Adequate lymph node dissection and adjuvant chemotherapy are both key steps to improve the awful prognosis of GC patients. Adjuvant chemotherapy may fail to remedy the poor prognosis caused by major LN noncompliance.

PMID:35578049 | DOI:10.1007/s00464-022-09300-z

JBRA Assist Reprod. 2022 May 16. doi: 10.5935/1518-0557.20220008. Online ahead of print.

ABSTRACT

OBJECTIVE: To compare the efficacy of two density gradient centrifugation media for retrieving spermatozoa from semen samples by evaluating the total motile sperm count (TMSC) and the percentage recovery.

METHODS: Twenty-two men with different sperm counts participated in the study. The samples were divided into two equal aliquots and processed using the commercial ISolate Sperm Separation Medium (Irvine Scientific, United States) and the GV Gradiente (IngáMed, Brazil). After separation, samples were counted and evaluated for motile sperm recovery.

RESULTS: The mean TMSC in the fresh sample was 19.65±21.08 million/mL. After the ISolate separation the TMSC was 6.71±7.29 million/mL, and for the GV Gradiente it was 6.27±6.82 million/mL. The percentage of motile spermatozoa recovered was 36.47%±21.61 for ISolate and 35.22%±21.24 for the GV Gradiente (p>0.05). The samples from 6 oligospermic patients (27%) were evaluated separately and the TMSC for ISolate was 4.83±2.92 million/mL, and for the GV Gradiente, it was 4.16±3.12 million/mL (p=0.54). When evaluating only normospermic patient samples, the TMSC for ISolate was 9.05±7.29 million/mL, and for the GV Gradiente, it was 8.47±6.79 million/mL (p=0.83).

CONCLUSIONS: There was no statistical difference in retrieving motile sperm using the GV Gradiente and the ISolate Separation Medium.

PMID:35575660 | DOI:10.5935/1518-0557.20220008

J Comput Assist Tomogr. 2022 May-Jun 01;46(3):492-498. doi: 10.1097/RCT.0000000000001285.

ABSTRACT

OBJECTIVE: The aim of the study was to compare a pediatric ultralow-dose pectus excavatum computed tomography (CT) protocol versus standard-dose pediatric thoracic CT in terms of radiation dose, subjective and objective image quality, and its ability to detect incidental nonosseous thoracic pathology compared with imaging and clinical reference.

METHODS: A single institution radiology database identified a total of 104 ultralow-dose pediatric thoracic CT cases with an equal number of age-matched standard-dose chest CT cases also selected for retrospective analysis. Objective image quality (contrast-to-noise and signal-to-noise ratios) and radiation dose were assessed. Qualitative Likert scorings of the bone, lung, and soft tissues were performed by 2 expert radiologists. Electronic health records of the ultralow-dose cohort were reviewed for at least 1 year to evaluate for potentially missed thoracic pathology and symptoms. Variables were compared using parametric and nonparametric tests in R software 4.0.5.

RESULTS: The ultralow-dose protocol group had statistically significant reductions (P < 0.001) in the volume CT dose index (0.31 ± 0.19 vs 2.20 ± 1.64 mGy), effective radiation dose (0.14 ± 0.08 vs 1.07 ± 0.86 mSv), and size-specific dose estimates (0.50 ± 0.30 vs 3.43 ± 2.56 mGy) compared with the standard protocol, yielding an 86.51% and 85.32% reduction, respectively. The signal-to-noise ratio (20.49 ± 6.19 vs 36.48 ± 10.20), contrast-to-noise (21.65 ± 6.57 vs 38.47 ± 10.59), and subjective measures of image quality (lung parenchyma [3.07 ± 0.92 vs 4.42 ± 0.47], bony structures [3.30 ± 0.86 vs 4.52 ± 0.51], and surrounding soft tissues [2.57 ± 0.63 vs 3.89 ± 0.65]) were also significantly lower in the ultralow-dose protocol (P < 0.001). No differences were seen in the number and size of pulmonary nodules between groups. Clinical and imaging follow of all 104 patients undergoing ultralow-dose CT demonstrated no evidence of missed thoracic pathology causing symptoms.

CONCLUSIONS: Ultralow-dose thoracic CT is an acceptable modality for imaging pediatric patients with pectus excavatum and other conditions primarily causing osseous pathology, with effective radiation dose comparable to plain radiographs and a moderate increase in image noise that did not significantly reduce its ability to detect incidental nonosseous thoracic pathology.

PMID:35575655 | DOI:10.1097/RCT.0000000000001285