Nevin Manimala

Brief Bioinform. 2023 Nov 22;25(1):bbad456. doi: 10.1093/bib/bbad456.

ABSTRACT

Molecular dynamics (MD) is the primary computational method by which modern structural biology explores macromolecule structure and function. Boltzmann generators have been proposed as an alternative to MD, by replacing the integration of molecular systems over time with the training of generative neural networks. This neural network approach to MD enables convergence to thermodynamic equilibrium faster than traditional MD; however, critical gaps in the theory and computational feasibility of Boltzmann generators significantly reduce their usability. Here, we develop a mathematical foundation to overcome these barriers; we demonstrate that the Boltzmann generator approach is sufficiently rapid to replace traditional MD for complex macromolecules, such as proteins in specific applications, and we provide a comprehensive toolkit for the exploration of molecular energy landscapes with neural networks.

PMID:38095857 | DOI:10.1093/bib/bbad456

Clin Drug Investig. 2023 Dec 14. doi: 10.1007/s40261-023-01331-1. Online ahead of print.

ABSTRACT

The approval of lecanemab by the US Food and Drug Administration has been touted as a defining moment in the treatment of Alzheimer’s disease. Lecanemab, an anti-amyloid beta monoclonal antibody, is the first Alzheimer’s disease drug targeting amyloid beta that has shown statistically significant cognitive benefits in phase III trials. However, there have been many questions raised over the clinical relevance of the otherwise minimal cognitive improvements. Furthermore, its rapid approval has been mired in controversy, in addition to the reports of adverse events such as amyloid-related imaging abnormalities and several deaths of participants in the lecanemab trials. Here, we analyze the evidence supporting lecanemab as an amyloid beta therapy and also discuss the concerns raised about its efficacy and safety.

PMID:38095822 | DOI:10.1007/s40261-023-01331-1

Breast Cancer Res Treat. 2023 Dec 14. doi: 10.1007/s10549-023-07174-w. Online ahead of print.

ABSTRACT

PURPOSE: There are differences in the distributions of breast cancer incidence and risk factors by race and ethnicity. Given the strong association between breast density and breast cancer, it is of interest describe racial and ethnic variation in the determinants of breast density.

METHODS: We characterized racial and ethnic variation in reproductive history and several measures of breast density for Hispanic (n = 286), non-Hispanic Black (n = 255), and non-Hispanic White (n = 1694) women imaged at a single hospital. We quantified associations between reproductive factors and percent volumetric density (PVD), dense volume (DV), non-dense volume (NDV), and a novel measure of pixel intensity variation (V) using multivariable-adjusted linear regression, and tested for statistical heterogeneity by race and ethnicity.

RESULTS: Reproductive factors most strongly associated with breast density were age at menarche, parity, and oral contraceptive use. Variation by race and ethnicity was most evident for the associations between reproductive factors and NDV (minimum p-heterogeneity:0.008) and V (minimum p-heterogeneity:0.004) and least evident for PVD (minimum p-heterogeneity:0.042) and DV (minimum p-heterogeneity:0.041).

CONCLUSION: Reproductive choices, particularly those related to childbearing and oral contraceptive use, may contribute to racial and ethnic variation in breast density.

PMID:38095811 | DOI:10.1007/s10549-023-07174-w

J Gastrointest Cancer. 2023 Dec 14. doi: 10.1007/s12029-023-00999-0. Online ahead of print.

ABSTRACT

INTRODUCTION: Hepatocellular carcinoma is a lethal disease and there has been a debate regarding the first-line treatment of its advanced and unresectable form. Observational studies have explored atezolizumab plus bevacizumab versus lenvatinib, yielding mixed results. This systematic review and meta-analysis aim to compare efficacy and safety of both treatment arms.

METHODS: A systematic literature review was conducted in accordance with PRISMA guidelines. Randomized control trials, cohort studies, or case-control that included patients above age 60 with unresectable hepatocellular carcinoma confirmed by radiological imaging were included. At least one of the outcomes: overall survival (OS), progression-free survival (PFS), objective response rate (ORR), duration of response, or adverse events was included in the selected studies.

RESULTS: Ten cohorts were included in the analysis with a total of 6493 patients. Nine of the included studies had patients with advanced HCC (BCLC-C) or intermediate HCC (BCLC-B) and 1 study included patients with all three stages (BCLC-A, BCLC-B, and BCLC-C). Of these patients, 2524 patients received atezolizumab plus bevacizumab (A + B) combination while 3969 received lenvatinib. The overall survival was better statistically in the A + B group then the lenvatinib group (MD: – 5.06; 95% CI: – 7.79 to – 2.33; p = 0.0003, I² = 0%). The progression-free survival was significantly improved in A + B arm as well group (MD: – 4.96; 95% CI: – 7.67 to – 2.26; I² = 0%, p = 0. 0003). There was no significant difference in objective response rate, disease control rate, and frequency of adverse events in either of the group.

CONCLUSION: Our study concluded that combination therapy with atezolizumab plus bevacizumab could increase the survival duration without affecting the disease course. Moreover, while the severity of adverse events was greater in the A + B group, their frequency was comparable to the lenvatinib group.

PMID:38095799 | DOI:10.1007/s12029-023-00999-0

Environ Sci Pollut Res Int. 2023 Dec 14. doi: 10.1007/s11356-023-31362-2. Online ahead of print.

ABSTRACT

In this study, a new hybrid bench-scale electrocoagulation-sand filtration (FECF) reactor was developed for purifying nitrate-contaminated samples. Before and after electrochemical treatment, two sand filters were included in this continuous system to facilitate the purification procedure, and the contaminated water flows horizontally through the entire system according to a specific hydraulic gradient within the reactor, resulting in water purification. Significant improvement in treatment performance was observed due to the presence of metal hydroxides in the second filter media that were not fully involved in the electrocoagulation treatment. Energy dispersive X-ray (EDX) analysis was performed to detect metal hydroxide species in the sand media, and the need for filter regeneration was evaluated by monitoring changes in the system flow rate. Moreover, an evaluation of the effects of different factors including operating time, current intensity, initial pH, type of anode and cathode, initial nitrate concentration, hydraulic head level inside the reactor, number of electrodes, and NaCl electrolyte concentration on the performance of nitrate removal was conducted through the Taguchi design. Further, ANOVA analysis verified the accuracy of the predicted model, and the variables were classified based on their relative importance in the FECF process. According to the regression model, 97% of nitrates were removed with Al electrodes as anode and Fe as cathode, 70 min purification time, current intensity of 3 A, 100 mg/l initial nitrate concentration, pH 8, electrolyte concentration of 1 g/l, electrode number of 6, and 1.5 cm head level.

PMID:38095796 | DOI:10.1007/s11356-023-31362-2

Environ Sci Pollut Res Int. 2023 Dec 14. doi: 10.1007/s11356-023-30478-9. Online ahead of print.

ABSTRACT

This research explores the theory that cultural factors shape how people feel about the environment. Both theoretical and empirical approaches are used in our investigation of this problem. In the theoretical part of the study, we provide a model for transferring cultural practices from one generation to the next. To provide empirical evidence for the existence of this cultural factor in environmental views, we analyze survey data from the European Values Research. Using a comparative method, we use differences caused by migration patterns in Europe and America. According to our research, cultural influences on migrants’ ecological beliefs are long-lasting and statistically significant. Variations in migrants’ environmental views may be traced back to societal norms that endure in their home countries. We also demonstrate that ecological views are robust in the face of incentives originating from the external environment, demonstrating that migrants’ choices in the host nation are not much influenced by the environmental circumstances they were exposed to in their home countries. We uncover fascinating variations in the cultural transfer procedure, and our results hold up under various hypotheses. These findings suggest that, in light of the prevalence of ecological problems requiring community action, it is crucial to formulate policies that consider the factors that led to the development of ecological cultures.

PMID:38095793 | DOI:10.1007/s11356-023-30478-9

Curr Pain Headache Rep. 2023 Dec 14. doi: 10.1007/s11916-023-01196-1. Online ahead of print.

ABSTRACT

PURPOSE OF REVIEW: Neuropathic pain (NP) remains a challenge to treat, with 50% of patients experiencing limited efficacy from current treatments. Medicinal cannabis, which contains tetrahydrocannabinol (THC), cannabidiol (CBD) and other minor cannabinoids, is garnering attention as an alternative treatment for NP. This paper reviews the clinical evidence for phytocannabinoid treatment of NP.

RECENT FINDINGS: Seventeen randomised controlled trials (RCT) were identified for inclusion in this review. Of these, ten studies using phytocannabinoid preparations containing THC alone had the most evidence for pain relief. Four studies investigating THC/CBD combinations showed some reductions in pain scores, although not all findings were statistically significant, whereas studies investigating CBD (two studies) or cannabidivarin (one study) showed no analgesic effect over placebo. However, CBD studies were of small sample size when compared to other studies in the review and short duration. Results for treatment of diabetic peripheral neuropathy patients with THC showed better improvements over those for NP induced by chemotherapy and multiple sclerosis, with these trials using vaporised whole plant cannabis. This formulation may have trace amounts of other minor cannabinoids, compared with synthetic cannabinoids such as dronabinol or nabilone that were investigated in other studies. This review provides an overview of RCTs that have investigated phytocannabinoid use for the treatment of NP. There appears to be evidence to necessitate further high quality RCTs into novel formulations of phytocannabinoids for the treatment of NP.

PMID:38095748 | DOI:10.1007/s11916-023-01196-1

Intern Emerg Med. 2023 Dec 14. doi: 10.1007/s11739-023-03490-7. Online ahead of print.

ABSTRACT

To develop and internally validate a multivariable logistic regression model (LRM) for the prediction of the probability of 1-year readmission to the emergency department (ED) in patients with acute alcohol intoxication (AAI). We developed and internally validated the LRM on a previously analyzed retrospective cohort of 3304 patients with AAI admitted to the ED of the Sant’Orsola-Malpighi Hospital (Bologna, Italy). The benchmark LRM employed readmission to the same ED for AAI within 1 year as the binary outcome, age as a continuous predictor, and sex, alcohol use disorder, substance use disorder, at least one previous admission for trauma, mental or behavioral disease, and homelessness as the binary predictors. Optimism correction was performed using the bootstrap on 1000 samples without replacement. The benchmark LRM was gradually simplified to get the most parsimonious LRM with similar optimism-corrected overall fit, discrimination and calibration. The 1-year readmission rate was 15.7% (95% CI 14.4-16.9%). A reduced LRM based on sex, age, at least one previous admission for trauma, mental or behavioral disease, and homelessness, performed nearly as well as the benchmark LRM. The reduced LRM had the following optimism-corrected metrics: scaled Brier score 17.0%, C-statistic 0.799 (95% CI 0.778 to 0.821), calibration in the large 0.000 (95% CI – 0.099 to 0.099), calibration slope 0.985 (95% CI 0.893 to 1.088), and an acceptably accurate calibration plot. An LRM based on sex, age, at least one previous admission for trauma, mental or behavioral disease, and homelessness can be used to estimate the probability of 1-year readmission to ED for AAI. To begin proving its clinical utility, this LRM should be validated in external cohorts.

PMID:38095747 | DOI:10.1007/s11739-023-03490-7

Eur Arch Otorhinolaryngol. 2023 Dec 14. doi: 10.1007/s00405-023-08361-7. Online ahead of print.

ABSTRACT

PURPOSE: Idiopathic sudden sensorineural hearing loss (ISSHL) can cause acute damage not only to the auditory function, but also to the vestibular function in addition to damage to the hearing function. The aim of this study was to perform vestibular assessment using caloric test and video head impulse test in patients with idiopathic sudden sensorineural hearing loss. In addition, to evaluate the relationship of dizziness with vestibular tests and post-treatment responses of vestibular tests.

METHODS: This is an observational, longitudinal and prospective study, including patients diagnosed with idiopathic sudden sensorineural hearing. Patients were divided into two groups according to the presence of vestibular complaints at presentation: Group 1: Patients with vestibular complaints, Group 2: Patients without vestibular complaints. All subjects underwent pure tone audiometry (PTA) testing, cold caloric test and video head impulse test (vHIT) during their admission and on the 10th day, 3rd month, and 1st year of their follow-up outpatient clinic controls. A unilateral weakness (UW) in the caloric test response was quantified according to the Jongkees formula.

RESULTS: A positive and significant relationship was found between the degree of hearing loss according to the ASHA criteria pre-treatment and the level of improvement created according to Siegel criteria at the 10th day, 3rd month, 1st year after treatment (respectively p = 0.001, p = 0.001, p < 0.001). When both short-term and long-term results were evaluated after treatment, a positive improvement in the degree of hearing loss was observed. A statistically significant difference was observed between Groups 1 and 2 when the pre-treatment, at 10 days, 3 months and 1 year after treatment the caloric test UW value was compared (respectively p = 0.020, p = 0.004, p = 0.004, p = 0.004). A statistically significant difference was observed between Groups 1 and 2 when the pre-treatment, at 10 days, 3 months and 1 year after treatment vHIT lateral canal VOR value was compared (respectively p = 0.000, p = 0.001, p = 0.000, p = 0.004). When both short-term and long-term results were evaluated after treatment, a positive improvement was observed in both caloric test results and lateral vHIT VOR values. Pre-treatment, post-treatment 10th day, 3rd month, 1st year vHIT anterior and posterior canal VOR values were found to be VOR˃0.8 in all patients. No difference was observed in anterior and posterior canal VOR values.

CONCLUSION: Vertigo in patients with ISSHL “as objectively confirmed through caloric testing and vHIT” can be considered a sign of severe cochlear damage. Our study demonstrated a significantly increased risk of vestibular affect in patients with ISSHL, especially in the presence of vertigo. Thus, we conclude that the focus in ISSHL should not only be on the cochlea but also on the vestibular system.

PMID:38095708 | DOI:10.1007/s00405-023-08361-7

Equine Vet J. 2023 Dec 14. doi: 10.1111/evj.14034. Online ahead of print.

ABSTRACT

BACKGROUND: Determination of horse breeds predisposed to congenital and juvenile cataracts will enable investigations into potential genetic mechanisms for cataracts in horses.

OBJECTIVE: To investigate horse breed predispositions to congenital and juvenile cataracts in two academic referral populations.

STUDY DESIGN: Retrospective case series.

METHODS: Medical record identification of horses diagnosed with congenital or juvenile cataracts at the Cornell University Equine Hospital (2000-2022) and the University of California-Davis (UCD) Large Animal Clinic (1990-2021). Signalment, examination findings and treatments were recorded. Descriptive statistics were performed, and breed over-representations were determined using Chi-squared or Fisher’s exact tests.

RESULTS: Thirty-one (Cornell) and 70 (UCD) horses with congenital or juvenile cataracts were identified, for a total of 101 affected horses. Seventy-eight horses were affected bilaterally and 23 were affected unilaterally, for a total of 179 affected eyes. Standardbreds were significantly over-represented at both institutions, comprising 32.5% of congenital/juvenile cataract cases and 10% of the equine hospital population at Cornell (p < 0.001) and 4.3% of cataract cases and 1.3% of the equine hospital population at UCD (p = 0.03). Thoroughbreds were under-represented for congenital and juvenile cataracts at both institutions (p = 0.03 Cornell, p = 0.01 UCD).

MAIN LIMITATIONS: Retrospective study, potential for selection bias.

CONCLUSIONS: The over-representation of the Standardbred breed for congenital and juvenile cataracts at two institutions suggests an underlying genetic basis in the breed. Future genetic and genomic studies are warranted to investigate heritable cataracts in Standardbred horses.

PMID:38095155 | DOI:10.1111/evj.14034