Nevin Manimala

Chaos. 2023 Nov 1;33(11):113111. doi: 10.1063/5.0136673.

ABSTRACT

We study a two-layer energy balance model that allows for vertical exchanges between a surface layer and the atmosphere. The evolution equations of the surface temperature and the atmospheric temperature are coupled by the emission of infrared radiation by one level, that emission being partly captured by the other layer, and the effect of all non-radiative vertical exchanges of energy. Therefore, an essential parameter is the absorptivity of the atmosphere, denoted εa. The value of εa depends critically on greenhouse gases: increasing concentrations of CO2 and CH4 lead to a more opaque atmosphere with higher values of ϵa. First, we prove that global existence of solutions of the system holds if and only if εa∈(0,2) and blow up in finite time occurs if εa>2. (Note that the physical range of values for εa is (0,1].) Next, we explain the long time dynamics for εa∈(0,2), and we prove that all solutions converge to some equilibrium point. Finally, motivated by the physical context, we study the dependence of the equilibrium points with respect to the involved parameters, and we prove, in particular, that the surface temperature increases monotonically with respect to εa. This is the key mathematical manifestation of the greenhouse effect.

PMID:37930684 | DOI:10.1063/5.0136673

Clin J Am Soc Nephrol. 2023 Nov 6. doi: 10.2215/CJN.0000000000000354. Online ahead of print.

ABSTRACT

BACKGROUND: Use of eGFR to determine preemptive waitlisting eligibility may contribute to racial/ethnic disparities in access to waitlisting, which can only occur when the eGFR falls to <20 mL/min1.73m2. Use of an alternate risk-based strategy for waitlisting (e.g.,a Kidney Failure Risk Equation [KFRE] estimated two-year risk of kidney failure) rather than the standard eGFR threshold for determining waitlist eligibility may reduce these inequities. Our objective was to model the amount of preemptive waittime that could be accrued by race and ethnicity, applying two different strategies to determine waitlist eligibility.

METHODS: Using electronic health record data, linear mixed models were used to compare racial/ethnic differences in preemptive waittime that could be accrued using two strategies: estimating the time between an eGFR<20 and 5 mL/min/1.73 m2 versus time between a 25% 2-year predicted risk of kidney failure (using the KFRE, which incorporates age, sex, albuminuria, and eGFR to provide kidney failure risk estimation) and eGFR of 5 mL/min/1.73 m2.

RESULTS: Among 1,290 adults with CKD stage 4-5, using the CKD-EPI equation yielded shorter preemptive waittime between an eGFR of 20 and 5 mL/min/1.732 in Black (-6.8 months;95%CI -11.7, -1.9), Hispanic (-10.2 months;-15.3,-5.1) and Asian/Pacific Islander patients (-10.3; 95%CI -15.3,-5.4) compared with non-Hispanic White patients. Use of a KFRE threshold to determine waittime yielded smaller differences by race and ethnicity than observed when using a single eGFR threshold, with shorter time still noted for Black (-2.5 months;95%CI-7.8,2.7), Hispanic (-4.8 months; 95% CI -10.3,0.6) and Asian/Pacific Islander individuals (-5.4 months;-10.7,-0.1) compared to non-Hispanic White individuals, but findings only met statistical significance criteria in Asian/Pacific Islander individuals. When we compared potential waittime availability using a KFRE versus eGFR threshold, use of the KFRE yielded more equity in waittime for Black (p=0.02), Hispanic (p=0.002) and Asian/Pacific Islander (p=0.002) patients.

CONCLUSIONS: Use of a risk-based strategy was associated with greater racial equity in waittime accrual compared with use of a standard single eGFR threshold to determine eligibility for preemptive waitlisting.

PMID:37930674 | DOI:10.2215/CJN.0000000000000354

JAMA Neurol. 2023 Nov 6. doi: 10.1001/jamaneurol.2023.3810. Online ahead of print.

ABSTRACT

IMPORTANCE: Agitation is a prevalent, distressing, and burdensome manifestation of Alzheimer dementia in need of an efficacious, safe, and well-tolerated treatment.

OBJECTIVE: To confirm the efficacy, safety, and tolerability of brexpiprazole in patients with agitation in Alzheimer dementia.

DESIGN, SETTING, AND PARTICIPANTS: This randomized clinical trial was a 12-week, double-blind, placebo-controlled, fixed-dose, parallel-arm trial that ran from May 2018 to June 2022 at 123 clinical trial sites in Europe and the United States. Participants included patients with agitation in Alzheimer dementia in a care facility or community-based setting. Stable Alzheimer disease medications were permitted.

INTERVENTIONS: In this 2-arm trial, patients were randomized to receive oral brexpiprazole or placebo (2:1 ratio) for 12 weeks. Within the brexpiprazole arm, patients were further randomized to receive fixed doses of 2 mg/d or 3 mg/d in a 1:2 ratio.

MAIN OUTCOMES AND MEASURES: The primary end point was change in Cohen-Mansfield Agitation Inventory total score (which measures the frequency of 29 agitated behaviors) from baseline to week 12 for brexpiprazole, 2 or 3 mg, vs placebo. Safety was assessed by standard measures, including treatment-emergent adverse events.

RESULTS: A total of 345 patients were randomized to receive brexpiprazole (n = 228) or placebo (n = 117); completion rates were 198 (86.8%) for brexpiprazole and 104 (88.9%) for placebo. Mean (SD) age was 74.0 (7.5) years, and 195 of 345 patients were female (56.5%). Patients receiving brexpiprazole, 2 or 3 mg (n = 225), demonstrated statistically significantly greater improvement than those taking placebo (n = 116) in Cohen-Mansfield Agitation Inventory total score from baseline to week 12 (brexpiprazole baseline, 80.6, mean change, -22.6; placebo baseline, 79.2, mean change, -17.3; least-squares mean difference, -5.32; 95% CI, -8.77 to -1.87; P = .003; Cohen d effect size, 0.35). No treatment-emergent adverse events had an incidence of 5% or more with brexpiprazole and greater incidence than placebo. The proportion of patients who discontinued because of adverse events was 12 of 226 (5.3%) for brexpiprazole and 5 of 116 (4.3%) for placebo.

CONCLUSIONS AND RELEVANCE: In this study, patients with Alzheimer dementia who took brexpiprazole, 2 or 3 mg, showed a statistically significant improvement vs placebo in agitation over 12 weeks. Brexpiprazole was generally well tolerated over 12 weeks in this vulnerable patient population.

TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT03548584.

PMID:37930669 | DOI:10.1001/jamaneurol.2023.3810

Monaldi Arch Chest Dis. 2023 Nov 3. doi: 10.4081/monaldi.2023.2778. Online ahead of print.

ABSTRACT

In cancer treatment, programmed death-1 (PD-1) and programmed death ligand-1 (PD-L1) inhibitors are thriving. Activated T lymphocytes expressed PD-1, it works with its ligand PD-L1 to limit T lymphocyte activation and prevent autoimmune disease. The expression of molecular biomarkers and PD-L1 in lung cancer determines the appropriate treatment strategy for patients with lung cancer. The purpose of this study was to look at the prevalence of molecular biomarkers and PD-L1 expression in a large group of Tunisian patients with advanced non-small cell lung cancer. We conducted an observational retrospective study in which medical/treatment history data were extracted retrospectively from medical records and archived tissue samples between January 1st 2019 and December 31st 2021. We gathered 157 patients who had recently been diagnosed with non-small cell lung carcinoma. In 36.9%of the cases, there was no molecular genotyping. EGFR (28.6%), KRAS (5.73%), and ALK gene rearrangement were the most common genotyping mutations (3.8%). ROS1 rearrangement was not present. There was a link between EGFR and gender, HER and age, and KRAS and biopsy tissue origin. Six of the tested cases with PD-L1 met the cut-off (³50%). PD-L1 positivity was more common in solid type adenocarcinoma (1.9%) than in acinar or papillary adenocarcinoma. There were no significant differences in PD-L1 expression across clinical and demographic parameters. High PD-L1 expression and molecular abnormalities were found in 1 case of EGFR, 1 case of BRAF, and 1 case of KRAS (3 cases). All of the other specimens with abnormalities had a PD-L1 <50%. ALK, ROS1, BRAF, KRAS, and MET were found to be significantly associated with PD-L1 expression. Our study is one of the country’s largest, describing a large panel of biomarkers and their clinicopathologic/histopathologic associations in Tunisian lung cancer patients. We have the same molecular profile as European patients with an EGFR mutation, which is not the most common genotype abnormality in Tunisian patients. There is only one mutation at any given time. The expression of PD-L1 is determined by the histologic type and the origin of the biopsy tissue.

PMID:37930659 | DOI:10.4081/monaldi.2023.2778

Clin Rheumatol. 2023 Nov 6. doi: 10.1007/s10067-023-06804-4. Online ahead of print.

ABSTRACT

BACKGROUND: It has been proved that rheumatoid arthritis (RA) patients have high incidence of atrial fibrillation (AF). Nevertheless, whether they have causal relevance is uncertain. This study aimed to explore and verify the authenticity of causal relationship between RA and AF using Mendelian randomization (MR).

METHODS: The genome-wide association study (GWAS) summary data from Biobank Japan Project (BBJ) (RA, 4199 cases and 208,254 controls) were regarded as exposure data and the GWAS data from European Bio-informatics Institute database (EBI) (AF, 15,979 cases and 102,776 controls) as outcome data. The causal effect was appraised by the inverse variance weighted (IVW) method, MR-Egger regression, and weighted median estimator. MR-robust adjusted profile score (MR-RAPS) method was delivered to examine the robustness of causal relationship and MR Pleiotropy Residual Sum and Outlier (MR-PRESSO) method to control horizontal (directional) pleiotropy.

RESULTS: The results indicated that RA increased the risk of AF (IVW, the odds ratio (OR) = 1.060; 95% confidence interval (CI), 1.028 to 1.092; p = 1.411 × 10^-4; weighted median, OR = 1.046, 95% CI, 1.002 to 1.093, p = 0.047). The MR analysis also showed this causal effect through all four IVW methods with various statistical algorithms. Both MR-RAPS and MR-PRESSO supported the causality of RA and AF. Also, the MR-PRESSO result indicated the absence of apparent pleiotropy.

CONCLUSION: There is a causal association between RA and AF. RA patients are genetically more vulnerable to AF. This study may contribute to further exploring early clinical prevention and fundamental mechanism of AF in patients with RA. Key Points • We provided some genetic evidence for the causal link between rheumatoid arthritis (RA) and atrial fibrillation (AF) with multiple Mendelian randomization (MR) methods. • RA patients were genetically more vulnerable to AF. • This study partly shed light on latent fundamental mechanisms underlying RA-induced AF and inspired future studies on RA-AF relationship.

PMID:37930596 | DOI:10.1007/s10067-023-06804-4

Psychometrika. 2023 Nov 6. doi: 10.1007/s11336-023-09935-4. Online ahead of print.

ABSTRACT

The key assumption of conditional independence of item responses given latent ability in item response theory (IRT) models is addressed for multistage adaptive testing (MST) designs. Routing decisions in MST designs can cause patterns in the data that are not accounted for by the IRT model. This phenomenon relates to quasi-independence in log-linear models for incomplete contingency tables and impacts certain types of statistical inference based on assumptions on observed and missing data. We demonstrate that generalized residuals for item pair frequencies under IRT models as discussed by Haberman and Sinharay (J Am Stat Assoc 108:1435-1444, 2013. https://doi.org/10.1080/01621459.2013.835660 ) are inappropriate for MST data without adjustments. The adjustments are dependent on the MST design, and can quickly become nontrivial as the complexity of the routing increases. However, the adjusted residuals are found to have satisfactory Type I errors in a simulation and illustrated by an application to real MST data from the Programme for International Student Assessment (PISA). Implications and suggestions for statistical inference with MST designs are discussed.

PMID:37930558 | DOI:10.1007/s11336-023-09935-4

Qual Life Res. 2023 Nov 6. doi: 10.1007/s11136-023-03548-1. Online ahead of print.

ABSTRACT

PURPOSE: To examine differences in health-related quality of life (HRQoL) between native and foreign-born gynaecological cancer patients in Sweden, taking into account clinical, demographic, and socioeconomic factors.

METHODS: The 30-item European Organisation for Research and Treatment of Cancer quality of life questionnaire (QLQ-C30) and a study-specific questionnaire covering demographic and socioeconomic factors were answered by 684 women aged ≥ 18 years old, diagnosed in 2014, 2016, or 2018 with gynaecological cancer in the Stockholm-Gotland health care region, Sweden. Clinical data were obtained from the Swedish Cancer Register. Data were analysed using the Kruskal-Wallis test and linear regression.

RESULTS: The women had a mean age of 65.4 years, with 555 (81.1%) born in Sweden, 54 (7.9%) in other Nordic countries (ONC), 43 (6.3%) in other European countries (OEC), and 32 (4.7%) in non-European countries (NEC). HRQoL differed significantly between the four groups for 14 of the 15 QLQ-C30 scales/items. On average, Swedish-born women scored 2.0, 15.2, and 16.7 points higher for QoL/functioning scales/items and 2.2, 14.1, and 18.7 points lower for symptom scales/items, compared with ONC-, OEC-, and NEC-born women, respectively. In adjusted analyses, none of the differences between Swedish-born and ONC-born women were significant, while for OEC- and NEC-born women the differences were significant for most QLQ-C30 scales/items.

CONCLUSION: HRQoL differs between native and foreign-born gynaecological cancer patients in Sweden, with lower HRQoL the further from Sweden the women are born. A more individualised cancer care, with tailored support to optimize HRQoL is needed for this vulnerable group of patients.

PMID:37930556 | DOI:10.1007/s11136-023-03548-1

Methods Mol Biol. 2024;2715:471-483. doi: 10.1007/978-1-0716-3445-5_28.

ABSTRACT

Membrane proteins data analysis by cryoEM shows some specificities, as can be found in other typical investigations such as biochemistry, biophysics, or X-ray crystallography. Membrane proteins are typically surrounded by an amphipathic belt that will have some degree of influence on the 3D reconstruction and analysis. In this chapter, we review our experience with the ABC transporter BmrA, as well as our statistical analysis of amphipathic belts around membrane proteins, to bring awareness on some particular features of membrane protein investigations by cryoEM.

PMID:37930545 | DOI:10.1007/978-1-0716-3445-5_28

Methods Mol Biol. 2024;2715:431-470. doi: 10.1007/978-1-0716-3445-5_27.

ABSTRACT

Structural studies of bio-complexes using single particle cryo-Electron Microscopy (cryo-EM) is nowadays a well-established technique in structural biology and has become competitive with X-ray crystallography. Development of digital registration systems for electron microscopy images and algorithms for the fast and efficient processing of the recorded images and their following analysis has facilitated the determination of structures at near-atomic resolution. The latest advances in EM have enabled the determination of protein complex structures at 1.4-3 Å resolution for an extremely broad range of sizes (from ~100 kDa up to hundreds of MDa (Bartesaghi et al., Science 348(6239):1147-1151, 2015; Herzik et al., Nat Commun 10:1032, 2019; Wu et al., J Struct Biol X 4:100020, 2020; Zhang et al., Nat Commun 10:5511, 2019; Zhang et al., Cell Res 30(12):1136-1139, 2020; Yip et al., Nature 587(7832):157-161, 2020; https://www.ebi.ac.uk/emdb/statistics/emdb_resolution_year )). In 2022, nearly 1200 structures deposited to the EMDB database were at a resolution of better than 3 Å ( https://www.ebi.ac.uk/emdb/statistics/emdb_resolution_year ).To date, the highest resolutions have been achieved for apoferritin, which comprises a homo-oligomer of high point group symmetry (O432) and has rigid organization together with high stability (Zhang et al., Cell Res 30(12):1136-1139, 2020; Yip et al., Nature 587(7832):157-161, 2020). It has been used as a test object for the assessments of modern cryo-microscopes and processing methods during the last 5 years. In contrast to apoferritin bacterial secretion systems are typical examples of multi protein complexes exhibiting high flexibility owing to their functions relating to the transportation of small molecules, proteins, and DNA into the extracellular space or target cells. This makes their structural characterization extremely challenging (Barlow, Methods Mol Biol 532:397-411, 2009; Costa et al., Nat Rev Microbiol 13:343-359, 2015). The most feasible approach to reveal their spatial organization and functional modification is cryo-electron microscopy (EM). During the last decade, structural cryo-EM has become broadly used for the analysis of the bio-complexes that comprise multiple components and are not amenable to crystallization (Lyumkis, J Biol Chem 294:5181-5197, 2019; Orlova and Saibil, Methods Enzymol 482:321-341, 2010; Orlova and Saibil, Chem Rev 111(12):7710-7748, 2011).In this review, we will describe the basics of sample preparation for cryo-EM, the principles of digital data collection, and the logistics of image analysis focusing on the common steps required for reconstructions of both small and large biological complexes together with refinement of their structures to nearly atomic resolution. The workflow of processing will be illustrated by examples of EM analysis of Type IV Secretion System.

PMID:37930544 | DOI:10.1007/978-1-0716-3445-5_27

Target Oncol. 2023 Nov 6. doi: 10.1007/s11523-023-01008-x. Online ahead of print.

ABSTRACT

BACKGROUND: Delta-like ligand 3 (DLL3), a member of the Notch pathway, has been identified as a potential therapeutic target as it is highly expressed in small cell lung cancer (SCLC), a subtype accounting for 15% of lung cancer cases.

OBJECTIVE: A systematic literature review (SLR) was conducted to understand the prevalence and prognostic impact of DLL3 expression on survival of patients with SCLC and treatment response.

PATIENTS AND METHODS: Systematic literature searches were conducted across multiple databases to capture studies of any SCLC population that evaluated DLL3 expression. Specific outcomes of interest included prevalence of DLL3 expression, method of expression analysis, and impact on outcome, including treatment response and survival (overall, progression-free, disease-free) according to varying levels of DLL3 expression/positivity. Standard risk of bias tools were used to evaluate study quality.

RESULTS: Among the 30 included studies, the most common DLL3 testing method was immunohistochemistry (N = 26, 86.7%). For comparability, results focused on the 13 (22.3%) studies that used the Ventana DLL3 (SP347) immunohistochemistry assay. The prevalence of DLL3 positivity ranged from 80.0-93.5% for studies using a threshold of ≥ 1% of tumor cells (N = 4) and 58.3-91.1% for studies with a ≥ 25% threshold (N = 4). DLL3 expression was generally categorized as high using cutoffs of ≥ 50% (prevalence range: 45.8-79.5%; N = 6) or ≥ 75% (prevalence range: 47.3-75.6%; N = 5) of cells with positivity. Two studies used an H-score of ≥ 150 to define high DLL3 expression with prevalence ranging from 33.3-53.1%. No consistent associations were seen between DLL3 expression level and patient age, sex, smoking history, or disease stage. Two studies reported change in DLL3 expression category (high versus low) before and after chemotherapy. No statistically significant differences were reported between DLL3 expression groups and survival (overall, progression-free, or disease-free) or treatment response.

CONCLUSIONS: There is a high prevalence of DLL3 expression in SCLC. Further research and analytical methods may help to characterize different populations of patients with SCLC based on DLL3 expression. While no significant prognostic factor in the included studies was identified, additional cohort studies using standardized methodology, with longer follow-up, are needed to better characterize any potential differences in patient survival or response by DLL3 expression level in SCLC.

PMID:37930513 | DOI:10.1007/s11523-023-01008-x