Category: Nevin Manimala

Bioinformatics. 2024 Feb 20:btae098. doi: 10.1093/bioinformatics/btae098. Online ahead of print.

ABSTRACT

MOTIVATION: Missing values are commonly observed in metabolomics data from mass spectrometry (MS). Imputing them is crucial because it assures data completeness, increases the statistical power of analyses, prevents inaccurate results, and improves the quality of exploratory analysis, statistical modeling, and machine learning. Numerous Missing Value Imputation Algorithms (MVIAs) employ heuristics or statistical models to replace missing information with estimates. In the context of metabolomics data, we identified 52 MVIAs implemented across 70 R functions. Nevertheless, the usage of those 52 established methods poses challenges due to package dependency issues, lack of documentation and their instability.

RESULTS: Our R package, imputomics, provides a convenient wrapper around 41 (plus random imputation as a baseline model) out of 52 MVIAs in the form of a command-line tool and a web application. In addition, we propose a novel functionality for selecting MVIAs recommended for metabolomics data with the best performance or execution time.

AVAILABILITY: imputomics is freely available as an R package (github.com/BioGenies/imputomics) and a Shiny web application (biogenies.info/imputomics-ws). The documentation is available at biogenies.info/imputomics.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:38377398 | DOI:10.1093/bioinformatics/btae098

Aesthet Surg J. 2024 Feb 20:sjae039. doi: 10.1093/asj/sjae039. Online ahead of print.

ABSTRACT

BACKGROUND: The infraorbital hollow (IOH) is a concavity that interrupts the smooth transition between the lower eyelid and the cheek, resulting in a fatigued and aged appearance. Injectable fillers may be used to correct volume deficit in the under-eye area, restoring a more youthful appearance.

OBJECTIVES: To demonstrate the effectiveness and safety of a Cohesive Polydensified Matrix® (CPM) hyaluronic acid (HA) filler with lidocaine (Belotero Balance® (+)) for correcting volume deficit in the IOH.

METHODS: Eligible patients with a moderate or severe rating on the Merz Infraorbital Hollow Assessment Scale (MIHAS) were randomized 2:1 to treatment or control. Controls remained untreated until Week 8 and were then treated. Touch-up injections were allowed; retreatment was offered only in the treatment group. Effectiveness was evaluated by the MIHAS. Adverse events were recorded over a 76-week period.

RESULTS: The estimated average response rate (≥ 1 point MIHAS improvement) was 80.6% [95% confidence interval (CI): 71.4%, 87.4%] in treated patients and 1.9% [95% CI: 0.3%, 10.2%] in controls at Week 8. The difference in estimated response rates was 78.7% [95% CI: 66.3%, 85.6%], demonstrating a statistically significant, superior response rate in treated patients compared to untreated controls. A total of 88/97 (90.7%) patients who responded to treatment at Week 8 retained improvement 48 weeks after treatment. Use of Belotero Balance (+) in the IOH had a favorable safety profile, with no unexpected adverse events reported.

CONCLUSIONS: Belotero Balance (+) is a safe and effective treatment for correcting volume deficit in the IOH.

PMID:38377391 | DOI:10.1093/asj/sjae039

Aesthet Surg J. 2024 Feb 20:sjae035. doi: 10.1093/asj/sjae035. Online ahead of print.

ABSTRACT

BACKGROUND: Since the early 2000s, Acellular Dermal Matrix has been a popular adjunct to prepectoral breast reconstruction to enhance outcomes.

OBJECTIVES: This study investigated the differences in the postoperative course of two standard acellular dermal matrix companies, AlloDerm SELECT Ready To Use and DermACELL.

METHODS: A prospective, patient-blind study of patients undergoing bilateral nipple and/or skin-sparing mastectomies to either tissue expander or silicone implant insertion between 2019 to 2022 were selected for this study. The study design used patients as their own controls between two products randomly assigned to the left or right breast. Outcomes between the brands included average time for drain removal, infection rate, seroma rate, and incorporation rates.

RESULTS: Prospective clinical data of 55 patients (110 breasts) was recorded for 90 days. There were no significant differences between drain removal time, average drain output, or seroma aspiration amount. There was a higher percentage of seromas recorded in the breasts with AlloDerm (30.91%) compared to breasts containing DermACELL (14.55%, p < 0.05), and a statistically significant difference between incorporation rates of AlloDerm (93.4%) and DermACELL (99.8%, p < 0.05) was observed.

CONCLUSIONS: Irrespective of patient demographic disparities, both products had a 94.55% success rate for reconstruction outcomes. AlloDerm was determined to have a higher incidence of seromas as a postoperative complication and a trend to lower incorporation.

PMID:38377366 | DOI:10.1093/asj/sjae035

J Exp Psychol Hum Percept Perform. 2024 Feb;50(2):152-162. doi: 10.1037/xhp0001174.

ABSTRACT

Statistical learning, the process of extracting regularities from the environment, is one of the most fundamental abilities playing an essential role in almost all aspects of human cognition. Previous studies have shown that attentional selection is biased toward locations that are likely to contain a target and away from locations that are likely to contain a distractor. The current study investigated whether participants can also learn to extract that a specific motor response is more likely when the target is presented at specific locations within the visual field. To that end, the additional singleton paradigm was adapted such that when the singleton target was presented at one specific location, one response (e.g., right index finger) was more likely than the other (e.g., right middle finger) and the reverse was true for another location. The results show that participants learned to extract that a particular motor response is more likely when the singleton target (which was unrelated to the response) was presented at a specific location within the visual field. The results also suggest that it is the location of the target and not its shape that is associated with the biased response. This learning cannot be considered as being top-down or conscious as participants showed little, if any, awareness of the response biases present. The results are discussed in terms of the event coding theory. The study increases the scope of statistical learning and shows how individuals adapt automatically, without much awareness, to the regularities present in the environment. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

PMID:38376933 | DOI:10.1037/xhp0001174

Clin Cancer Res. 2024 Feb 20. doi: 10.1158/1078-0432.CCR-23-1977. Online ahead of print.

ABSTRACT

PURPOSE: BCI (H/I) has been shown to predict extended endocrine therapy (EET) benefit. We examined BCI (H/I) for EET benefit prediction in NSABP B-42, which evaluated extended letrozole therapy (ELT) in hormone receptor-positive breast cancer patients after 5 years of ET.

METHODS: Stratified Cox model was used to analyze RFI as primary endpoint, with DR, BCFI, and DFS, as secondary endpoints. Due to a non-proportional effect of ELT on DR, time-dependent analyses were performed.

RESULTS: The translational cohort included 2,178 patients (45% BCI (H/I)-High, 55% BCI (H/I)-Low). ELT showed an absolute 10-year RFI benefit of 1.6% (P=0.10), resulting in an underpowered primary analysis (50% power). ELT benefit and BCI (H/I) did not show a significant interaction for RFI (BCI [(H/I])-Low: 10y absolute benefit 1.1% [HR=0.70, 0.43-1.12, P=0.13]; BCI [(H/I])-High: 2.4% [HR=0.83, 0.55-1.26, p=0.38]; Pinteraction=0.56). Time-dependent DR analysis showed that after 4y, BCI (H/I)-High patients had significant ELT benefit (HR=0.29, 0.12-0.69, P<0.01), whereas BCI (H/I)-Low patients were less likely to benefit (HR=0.68, 0.33-1.39, P=0.29) (Pinteraction=0.14). Prediction of ELT benefit by BCI (H/I) was more apparent in the HER2- subset after 4y (ELT-by-BCI (H/I) Pinteraction=0.04).

CONCLUSIONS: BCI(H/I)-High vs -Low did not show a statistically significant difference in ELT benefit for the primary endpoint (RFI). However, in time-dependent DR analysis, BCI (H/I)-High patients experienced statistically significant benefit from ELT after 4y, whereas (H/I)-Low patients did not. Because BCI (H/I) has been validated as a predictive marker of EET benefit in other trials, additional follow-up may enable further characterization of BCI’s predictive ability.

PMID:38376912 | DOI:10.1158/1078-0432.CCR-23-1977

J Med Internet Res. 2024 Feb 20;26:e47040. doi: 10.2196/47040.

ABSTRACT

BACKGROUND: Tobacco consumption is a leading cause of death and disease, killing >8 million people each year. Smoking cessation significantly reduces the risk of developing smoking-related diseases. Although combined treatment for addiction is promising, evidence of its effectiveness is still emerging. Currently, there is no published research comparing the effectiveness of blended smoking cessation treatments (BSCTs) with face-to-face (F2F) treatments, where web-based components replace 50% of the F2F components in blended treatment.

OBJECTIVE: The primary objective of this 2-arm noninferiority randomized controlled trial was to determine whether a BSCT is noninferior to an F2F treatment with identical ingredients in achieving abstinence rates.

METHODS: This study included 344 individuals who smoke (at least 1 cigarette per day) attending an outpatient smoking cessation clinic in the Netherlands. The participants received either a blended 50% F2F and 50% web-based BSCT or only F2F treatment with similar content and intensity. The primary outcome measure was cotinine-validated abstinence rates from all smoking products at 3 and 15 months after treatment initiation. Additional measures included carbon monoxide-validated point prevalence abstinence; self-reported point prevalence abstinence; and self-reported continuous abstinence rates at 3, 6, 9, and 15 months after treatment initiation.

RESULTS: None of the 13 outcomes showed statistically confirmed noninferiority of the BSCT, whereas 4 outcomes showed significantly (P<.001) inferior abstinence rates of the BSCT: cotinine-validated point prevalence abstinence rate at 3 months (difference 12.7, 95% CI 6.2-19.4), self-reported point prevalence abstinence rate at 6 months (difference 19.3, 95% CI 11.5-27.0) and at 15 months (difference 11.7, 95% CI 5.8-17.9), and self-reported continuous abstinence rate at 6 months (difference 13.8, 95% CI 6.8-20.8). The remaining 9 outcomes, including the cotinine-validated point prevalence abstinence rate at 15 months, were inconclusive.

CONCLUSIONS: In this high-intensity outpatient smoking cessation trial, the blended mode was predominantly less effective than the traditional F2F mode. The results contradict the widely assumed potential benefits of blended treatment and suggest that further research is needed to identify the critical factors in the design of blended interventions.

TRIAL REGISTRATION: Netherlands Trial Register 27150; https://onderzoekmetmensen.nl/nl/trial/27150.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR2-doi.org/10.1186/s12889-016-3851-x.

PMID:38376901 | DOI:10.2196/47040

Ocul Immunol Inflamm. 2024 Feb 20:1-7. doi: 10.1080/09273948.2024.2317416. Online ahead of print.

ABSTRACT

PURPOSE: This study aims to evaluate the ocular surface characteristics in children diagnosed with uveitis and explore the association between uveitis and dry eye disease (DED).

METHODS: We included 84 children, 42 with uveitis and 42 healthy children. We performed the OSDI questionnaire and several ocular surface tests, including osmolarity, NITBUT, Schirmer test, and vital staining. We used Fisher’s exact test and Mann-Whitney to compare variables and a binomial logistic regression to determine the factors associated with DED.

RESULTS: The difference in the prevalence of DED between uveitis (54.8%) and healthy (31%) groups was statistically significant (p < 0.05). Most patients with uveitis had mixed DED, and none of the healthy subjects had a severe form of the disease. There were no statistically significant differences in most of the tear film tests. However, all parameters tended to worsen in the uveitis group, and lipid layer thickness was thinner (p < 0.036). The uveitis group exhibited significantly more symptoms (p < 0.05). In the multivariate logistic regression, uveitis was associated with an odds ratio (OR) of 3.0 (95% CI: 1.07-8.42, p < 0.05) for DED.

CONCLUSIONS: Our findings demonstrate a significantly higher prevalence of DED in children with uveitis compared to their healthy counterparts. Furthermore, our analysis indicates that the risk of DED in pediatric patients with uveitis is threefold higher than in healthy children. Therefore, it is crucial for clinicians to vigilantly monitor the development of DED in pediatric patients with uveitis and consider the implementation of preventive treatments.

PMID:38376892 | DOI:10.1080/09273948.2024.2317416

Phys Chem Chem Phys. 2024 Feb 20. doi: 10.1039/d3cp04140a. Online ahead of print.

ABSTRACT

The partition coefficient (log P) is an important physicochemical property that provides information regarding a molecule’s pharmacokinetics, toxicity, and bioavailability. Methods to accurately predict the partition coefficient have the potential to accelerate drug design. In an effort to test current methods and explore new computational techniques, the statistical assessment of the modeling of proteins and ligands (SAMPL) has established a blind prediction challenge. The ninth iteration challenge was to predict the toluene-water partition coefficient (log P_tol/w) of sixteen drug molecules. Herein, three approaches are reported broadly under the categories of quantum mechanics (QM), molecular mechanics (MM), and data-driven machine learning (ML). The three blind submissions yield mean unsigned errors (MUE) ranging from 1.53-2.93 log P_tol/w units. The MUEs were reduced to 1.00 log P_tol/w for the QM methods. While MM and ML methods outperformed DFT approaches for challenge molecules with fewer rotational degrees of freedom, they suffered for the larger molecules in this dataset. Overall, DFT functionals paired with a triple-ζ basis set were the simplest and most effective tool to obtain quantitatively accurate partition coefficients.

PMID:38376855 | DOI:10.1039/d3cp04140a

JAMA Netw Open. 2024 Feb 5;7(2):e240062. doi: 10.1001/jamanetworkopen.2024.0062.

ABSTRACT

IMPORTANCE: For some low-income people, access to care during pregnancy is not guaranteed through Medicaid, based on their immigration status. While states have the option to extend Emergency Medicaid coverage for prenatal and postpartum care, many states have not expanded coverage.

OBJECTIVE: To determine whether receipt of first prenatal care services and subsequently receipt of postpartum care through extensions of Emergency Medicaid coverage were associated with increases in diagnosis and treatment of perinatal mental health conditions.

DESIGN, SETTING, AND PARTICIPANTS: This cohort study used linked Medicaid claims and birth certificate data from 2010 to 2020 with a difference-in-difference design to compare the rollout of first prenatal care coverage in 2013 and then postpartum services in Oregon in 2018 with a comparison state, South Carolina, which did not cover prenatal or postpartum care as part of Emergency Medicaid and only covered emergent conditions and obstetric hospital admissions. Medicaid claims and birth certificate data were linked by Medicaid identification number prior to receipt by the study team. Participants included recipients of Emergency Medicaid who gave birth in Oregon or South Carolina. Data were analyzed from April 1 to October 15, 2023.

EXPOSURE: Medicaid coverage of prenatal care and Medicaid coverage of postpartum care.

MAIN OUTCOMES AND MEASURES: The main outcome was the diagnosis of a perinatal mental health condition within 60 days postpartum. Secondary outcomes included treatment of a mood disorder with medication or talk therapy.

RESULTS: The study sample included 43 889 births to Emergency Medicaid recipients who were mainly aged 20 to 34 years (32 895 individuals [75.0%]), multiparous (33 887 individuals [77.2%]), and living in metropolitan areas (32 464 individuals [74.0%]). Following Oregon’s policy change to offer prenatal coverage to pregnant individuals through Emergency Medicaid, there was a significant increase in diagnosis frequency (4.1 [95% CI, 1.7-6.5] percentage points) and a significant difference between states in treatment for perinatal mental health conditions (27.3 [95% CI, 13.2-41.4] percentage points). Postpartum Medicaid coverage (in addition to prenatal Medicaid coverage) was associated with an increase of 2.6 (95% CI, 0.6-4.6) percentage points in any mental health condition being diagnosed, but there was no statistically significant difference in receipt of mental health treatment.

CONCLUSIONS AND RELEVANCE: These findings suggest that changing Emergency Medicaid policy to include coverage for prenatal and 60 days of postpartum care for immigrants is foundational to improving maternal mental health. Expanded postpartum coverage length, or culturally competent interventions, may be needed to optimize receipt of postpartum treatment.

PMID:38376840 | DOI:10.1001/jamanetworkopen.2024.0062

Vet Ital. 2023 Jul 31;59(2). doi: 10.12834/VetIt.2710.17457.2.

ABSTRACT

Wild birds have been reported to be reservoirs of viral diseases of poultry, and play an epidemiological role in their maintenance and spread. A serological survey was undertaken to determine the evidence of Newcastle disease virus (NDV) antibodies in wild birds in Zaria Kaduna State, Nigeria. A total of 150 apparently healthy wild birds comprising 30 each laughing dove, speckled pigeons, cattle egrets, village weavers and African silver bills were sampled. Sera collected were analysed for the presence of antibodies against NDV and avian paramyxovirus‑2 (APMV‑2) using the haemagglutination inhibition test. The results showed an overall seroprevalence of 4% (95% CI: 2.05‑10.1) to NDV. African silver bill showed a seroprevalence of 10.0% (95% CI: 2.61‑24.9) NDV antibodies while seroprevalence of 3.3% (95% CI: 0.16‑15.4) was recorded for cattle egrets, village weavers and laughing doves respectively. No statistically significant difference existed for NDV seroprevalence (P>0.05) among the different species of wild birds. All the 150 sera tested negative for APMV‑2 antibodies. The result of this study confirmed the exposure of wild birds to NDV in the study area. Continuous surveillance with isolation and characterization of NDV in the wild birds is therefore recommended for strategic planning for control.

PMID:38376832 | DOI:10.12834/VetIt.2710.17457.2