Nevin Manimala

PLoS One. 2025 Dec 1;20(12):e0336022. doi: 10.1371/journal.pone.0336022. eCollection 2025.

ABSTRACT

BACKGROUND: Malaria is a life-threatening infectious disease caused by parasites of the genus Plasmodium transmitted through the bite of infected female Anopheles mosquitoes, which act as vectors of the disease. It affects approximately 219 million people globally and results in 435,000 deaths each year. Fever, chills, and exhaustion are among of the signs of this illness. If left untreated, these symptoms can develop into serious problems like anemia, respiratory distress, and even organ failure. By identifying determinants related to malaria prevalence, this study supports evidence-based national malaria prevention and control initiatives. The results help improve decision-making for malaria control efforts and guide focused public health initiatives by identifying areas with a high malaria burden.

METHODS: Data from the 2021 Niger Malaria Indicator Survey (NMIS) is used, focusing on RDT-confirmed malaria cases in children aged 6-59 months. The dataset includes individual, household, and community-level variables, such as age, household income, education, healthcare access, and geographic coordinates. Spatial distribution of malaria prevalence is first visualized through maps and hot spot analysis to identify areas with high and low malaria rates. Random effects are incorporated to capture unobserved heterogeneity between regions and communities, allowing for more accurate estimates of malaria prevalence by adjusting for spatial clustering. Multilevel logistic regression models are applied to account for the hierarchical structure of the data. Model fit is evaluated using standard criteria (AIC, BIC and DIC), and diagnostics are performed to ensure reliability.

RESULTS: 1121 (23.7%) of the 4724 children aged 6 to 59 months who were examined had positive RDT results for malaria. Malaria prevalence in Niger among children aged 6-59 months is significantly clustered (Moran’s I = 0.434, p < 0.001), revealing distinct hotspots and cold spots unlikely due to chance. Model III provides a better fit for RDT prevalence among children aged 6-59 months with malaria, as indicated by the smallest AIC, BIC, and deviation statistics compared to other reduced models. Malaria prevalence was associated with factors, including child age, anemia levels, maternal education, the number of children sleeping under bed nets, the use of insecticide-treated nets, the number of children aged 5 and under, as well as residence and region.

CONCLUSION: The findings show that malaria prevalence among children aged 6-59 months in Niger is significantly influenced by factors such as child age, anemia levels, maternal education, and bed net usage, emphasizing the need for improved coverage of insecticide-treated nets and tailored interventions based on local conditions.

PMID:41325497 | DOI:10.1371/journal.pone.0336022

PLoS One. 2025 Dec 1;20(12):e0336495. doi: 10.1371/journal.pone.0336495. eCollection 2025.

ABSTRACT

This paper introduces a novel statistical test, the Policy Effects Lagrange Multiplier (PELM) test, to detect stabilization policy effects in the distribution of forecast errors from dynamic financial models. Traditional analyses of policy impact typically rely on explicit policy information or direct intervention data, which are often unavailable or incomplete. In contrast, the proposed PELM test infers policy footprints from the distribution of forecast errors alone. Empirically applied to sovereign bond yield data from 33 countries before the Russian financial crisis of 2014, the test identifies countries showing stabilization policy footprints. Subsequent analysis shows that significant budgetary improvements were observed for years following the crisis in the group of countries where our test statistically confirmed stabilization policies. This confirms the rationale of test foundations and also indicates its predictive properties. Robustness checks further validate these findings across various model specifications and sensitivity scenarios. The proposed PELM test offers policymakers and researchers a powerful tool for evaluating stabilization policies, facilitating better forecasting and assessing policy efficiency in diverse economic contexts without necessitating detailed policy intervention data.

PMID:41325492 | DOI:10.1371/journal.pone.0336495

PLoS One. 2025 Dec 1;20(12):e0336899. doi: 10.1371/journal.pone.0336899. eCollection 2025.

ABSTRACT

Previous research has shown that the causal structure of events influences how well they are recalled in episodic memory later on. Here, we aimed to investigate whether these effects apply not only to events that are passively observed but also situations directly shaped by an individual’s decisions. We designed a task in which participants had to traverse decision trees of varying causal structure: ‘Coherent’ trees where each decision followed from the consequences of the preceding decision, and ‘fragmented’ trees where each subsequent decision was only statistically (but not causally) contingent on the preceding decision. In a between-subjects experiment, participants first completed an exploration phase in which they had to explore the decision trees without a specific goal; in a subsequent search phase, they had to reach a target outcome in as few attempts as possible. Analyses of participants’ performance showed that those in the coherent group required significantly fewer attempts to reach a correct outcome than those in the fragmented group. A follow-up experiment surprisingly found that the advantage of causal structure does not depend on episodic memory: Removing the exploration phase barely diminished the positive effect causal coherence had on participants’ performance. In further follow-up experiments without an exploration phase, neither the additional removal of ‘process images’ that show how a choice leads to an outcome, nor the removal of text labels describing decisions, was individually sufficient to equalize performances. Only when both were eliminated at once did participants perform equally well on coherent and fragmented trees. This indicates that cues relating to causal mechanisms (images) and predictive cues (text) each facilitate goal-directed decision making without relying on extensive learning, and that only the absence of both is sufficient to suppress the advantage causal structure provides.

PMID:41325484 | DOI:10.1371/journal.pone.0336899

PLoS One. 2025 Dec 1;20(12):e0337076. doi: 10.1371/journal.pone.0337076. eCollection 2025.

ABSTRACT

Shale samples from source rocks of the Upper Triassic Yanchang Formation (Chang 9 member) in the Ansai area, Ordos Basin, North China, were analyzed using gas chromatography – mass spectrometry (GC-MS) to investigate the distribution, abundance, and enrichment mechanisms of rearranged hopanes. Four rearranged hopane series were detected, with all four present simultaneously in individual samples. Analysis of the C₃₀ hopane series (regular C₃₀H, diahopane C₃₀D, and neohopane C₃₀E) using a ternary diagram revealed a distinct linear trend, demonstrating a systematic, inverse relationship between the abundance of regular hopane and the combined abundance of its rearranged counterparts. These results provide strong evidence that C₃₀D and C₃₀E in the Chang 9 shales are diagenetic products derived from C₃₀H, sharing a common biological precursor. Both diasteranes and regular steranes with the ββ configuration were correlated positively in abundance with rearranged hopanes, further supporting a common origin linked to specific organism assemblages rather than widespread organisms. Samples deposited under highly saline, suboxic sedimentary environments displayed relatively high abundances of rearranged hopanes, indicating the critical role of depositional conditions in their enrichment. Multi-proxy analysis revealed a complex, non-linear control of thermal maturity on rearranged hopane abundance. The C₃₀ Rearranged Hopane Index showed statistically significant positive correlations with multiple maturity parameters (including sterane and hopane isomerization ratios), indicating maturity as a primary driver in the early oil window. However, this trend diverged at higher maturity levels, suggesting that other factors, such as the catalytic activity of the mineral matrix, become dominant. Our findings establish a robust biomarker-based framework for interpreting oil-source correlations and informing petroleum exploration in the Ordos Basin, particularly for the Chang 9 member source rocks.

PMID:41325482 | DOI:10.1371/journal.pone.0337076

PLoS Comput Biol. 2025 Dec 1;21(12):e1013758. doi: 10.1371/journal.pcbi.1013758. Online ahead of print.

ABSTRACT

Antibodies play a crucial role in adaptive immunity. They develop as B cell receptors (BCRs): membrane-bound forms of antibodies that are expressed on the surfaces of B cells. BCRs are refined through affinity maturation, a process of somatic hypermutation (SHM) and natural selection, to improve binding to an antigen. Computational models of affinity maturation have developed from two main perspectives: molecular evolution and language modeling. The molecular evolution perspective focuses on nucleotide sequence context to describe mutation and selection; the language modeling perspective involves learning patterns from large data sets of protein sequences. In this paper, we compared models from both perspectives on their ability to predict the course of antibody affinity maturation along phylogenetic trees of BCR sequences. This included models of SHM, models of SHM combined with an estimate of selection, and protein language models. We evaluated these models for large human BCR repertoire data sets, as well as an antigen-specific mouse experiment with a pre-rearranged cognate naive antibody. We demonstrated that precise modeling of SHM, which requires the nucleotide context, provides a substantial amount of predictive power for predicting the course of affinity maturation. Notably, a simple nucleotide-based convolutional neural network modeling SHM outperformed state-of-the-art protein language models, including one trained exclusively on antibody sequences. Furthermore, incorporating estimates of selection based on a custom deep mutational scanning experiment brought only modest improvement in predictive power. To support further research, we introduce EPAM (Evaluating Predictions of Affinity Maturation), a benchmarking framework to integrate evolutionary principles with advances in language modeling, offering a road map for understanding antibody evolution and improving predictive models.

PMID:41325480 | DOI:10.1371/journal.pcbi.1013758

Biotech Histochem. 2025 Dec 1:1-9. doi: 10.1080/10520295.2025.2583966. Online ahead of print.

ABSTRACT

The ability to escape immune surveillance is a hallmark of malignancy. Programmed death ligand 1 (PD-L1) facilitates tumor progression by binding to the immune inhibitory receptor known as programmed cell death protein 1 (PD1) on immune cells, resulting in suppression of the cytotoxic T lymphocyte function. The degree of PD-L1 expression may have a prognostic value in some cancer types, and it may vary according to the genetic makeup and the ethnicity of patients. The expression level of PD-L1 in 63 cases of primary head and neck squamous cell carcinoma (HNSCC) tumor tissues was evaluated using immunohistochemistry (IHC). Also, PD-L1 association with various clinicopathologic characteristics and overall survival was studied. The positive expression rate of PD-L1 in HNSCC was 85.7%, 60.3%, and 52.3% of the total number of cases using combined positive score (CPS) ≥ 1, CPS ≥ 5, and CPS ≥ 20 cutoff values, respectively. Statistical analysis revealed no significant relationship between the expression of PD-L1 protein and clinicopathological features except for tobacco use using a cutoff CPS ≥ 20. The log-rank chi-square results showed that PD-L1 was not a significant factor affecting the 4-year overall survival of HNSCC patients. Also, the overall survival rate was not significantly affected by the patient’s age, tumor differentiation, tumor size, and lymphovascular invasion. However, survival curves demonstrated lower overall survival in HNSCC female patients, disease recurrence, and positive perineural invasion. Our findings showed relatively high PDL-1 expression in most HNSCC patients. No significant association was found between PD-L1 protein expression and overall survival.

PMID:41324994 | DOI:10.1080/10520295.2025.2583966

JAMA Netw Open. 2025 Dec 1;8(12):e2545712. doi: 10.1001/jamanetworkopen.2025.45712.

ABSTRACT

IMPORTANCE: Home hospital provides hospital-level care at home for patients with acute illness who would traditionally be cared for in a brick-and-mortar (BAM) hospital. While most home hospital programs have been implemented in urban areas, its feasibility in rural areas, where access to care is a major challenge, is unknown.

OBJECTIVE: To compare home hospital care with BAM hospital care for patients residing in rural areas.

DESIGN, SETTING, AND PARTICIPANTS: This randomized clinical trial took place from 2022 to 2023 with a 30-day follow-up in 3 rural areas in the US and Canada. Participants were adults recruited in the emergency department who required hospital-level care for select acute conditions (infections, heart failure, chronic obstructive pulmonary disease or asthma, and other diagnoses).

INTERVENTIONS: Patients in the home hospital group received acute care at home, including in-home nurse and/or paramedic visits, remote physician care, intravenous medications, remote monitoring, video communication, and point-of-care testing. Patients in the BAM group received services at a rural BAM hospital.

MAIN OUTCOMES AND MEASURES: The primary outcome was the relative change in the acute care episode’s direct cost. Secondary outcomes were 30-day readmission, days at home within 30 days of discharge, and physical activity. Exploratory outcomes included the Picker Experience Score and Net Promoter Score.

RESULTS: A total of 161 patients (79 home; 82 BAM) with mean (SD) age of 64.4 (17.2) years (home) and 64.9 (14.1) years (control) were included. Most were female (home, 52 [65.8%]; BAM, 50 [61.0%]). The adjusted mean cost of the acute episode was not significantly different (home vs BAM, 14% greater; 95% CI, -6% to 39%; P = .19). There were no significant differences in 30-day readmission (home vs BAM: 8 [10.1%] vs 14 [17.1%]) or mean (SD) days at home within 30 days of discharge (home vs BAM: 28.6 [3.4] vs 28.4 [3.4] days). Patients in the home hospital group were less sedentary, according to accelerometer measurements, than those in the BAM group (mean [SD], 78.0% [10.4%] vs 86.0% [7.2%] of the day sedentary; mean difference, -8.0%; 95% CI, -12.8% to -3.3%; P < .001) and had more mean (SD) steps daily (834.1 [1219.6] vs 120.4 [206.0] steps; mean difference, 713.7 steps; 95% CI, 290.2 to 1137.2 steps; P < .001). Total mean (SD) length of stay (ie, BAM and home hospital days for intervention patients and BAM days for control patients) was not significantly different (home vs BAM: 6.7 [5.0] days vs 5.4 [4.4] days), although patients receiving care at home transferred late in their course (mean [SD] day of transfer, 4.2 [4.3] of 6.7 days). Patients in the home hospital group reported better experiences than those in the BAM hospital group: the mean (SD) Picker experience score was 13.4 (2.6) vs 11.0 (3.8) (mean difference, 2.4; 95% CI, 1.0 to 3.8; P < .001), and the mean (SD) net-promoter score was 88.4 (32.3) vs 45.5 (69.9) (mean difference, 43.0; 95% CI, 17.5 to 68.5; P < .001). Safety events occurred in 11 (14.1%) home patients vs 10 (12.4%) BAM patients (mean difference, 1.8%; 95% CI, -8.1% to 11.6%; P = .74).

CONCLUSIONS AND RELEVANCE: In this randomized clinical trial of home hospital care in rural settings, cost and readmission were unchanged while patient activity and experience improved. Late transfer home likely attenuated the intervention’s effect.

TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT05256303.

PMID:41324962 | DOI:10.1001/jamanetworkopen.2025.45712

JAMA Netw Open. 2025 Dec 1;8(12):e2545826. doi: 10.1001/jamanetworkopen.2025.45826.

ABSTRACT

IMPORTANCE: State policies provide variable health insurance coverage for the 3 million immigrant children in the US, with limited understanding of associations with health care access.

OBJECTIVES: To (1) examine disparities in health insurance and health care access between immigrant and US-born children and (2) analyze associations of state insurance policies with health care access outcomes for immigrant children.

DESIGN, SETTING, AND PARTICIPANTS: This population-based, retrospective cross-sectional study sampled from the National Survey of Children’s Health (2016 to 2022) to facilitate national estimates. Caregivers of children aged 0 to 17 years completed the survey. Data were analyzed from May to December 2024.

EXPOSURES: Child immigration status and state-level health insurance policies for immigrant children, categorized as least inclusive (5-year waiting period and eligibility restricted by immigration status), moderately inclusive (waived 5-year waiting period), and most inclusive (waived 5-year waiting period and all immigrant children eligible).

MAIN OUTCOMES AND MEASURES: Primary outcomes were (1) uninterrupted health insurance in the past 12 months, (2) usual place for primary care, (3) usual place for sick care, (4) having foregone medical care, and (5) having difficulty with referrals. For each outcome, multivariable logistic regression models examined the association with immigration status, adjusting for state-level policies and individual variables, reporting adjusted odds ratios (aORs) and 95% CIs.

RESULTS: There were 277 386 children included (population estimate, 72 473 052 children) with 8835 immigrant children (population estimate, 3 097 329 children [4.3%]; 1 513 509 [48.9%] aged 12-17 years; 1 542 412 female [49.8%]) and 268 551 US-born children (population estimate, 69 375 723 children [95.7%]; 23 450 439 [33.8%] aged 12-17 years; 33 876 023 female [48.8%]). In multivariable analyses, immigrant compared with US-born children had lower odds of uninterrupted health insurance (aOR, 0.48; 95% CI, 0.41-0.56), usual place for primary care (aOR, 0.44; 95% CI, 0.38-0.52), and usual place for sick care (aOR, 0.62; 95% CI, 0.55-0.70), and increased odds of having foregone medical care (aOR, 1.61; 95% CI, 1.22-2.14) and difficulty with subspecialty referral (aOR, 1.54; 95% CI, 1.16-2.04). Immigrant children in the most compared with least inclusive policy states had increased odds of uninterrupted health insurance (aOR, 3.01; 95% CI, 1.89-4.79) and usual place for primary care (aOR, 1.61; 95% CI, 1.07-2.41).

CONCLUSIONS AND RELEVANCE: In this cross-sectional study of US children, immigrant compared with US-born children had disparities in health care access, which were attenuated in states with the most inclusive state insurance policies, suggesting that inclusive state insurance eligibility policies for immigrant children may improve health care access outcomes for this population.

PMID:41324961 | DOI:10.1001/jamanetworkopen.2025.45826

JAMA Netw Open. 2025 Dec 1;8(12):e2545996. doi: 10.1001/jamanetworkopen.2025.45996.

ABSTRACT

IMPORTANCE: Medicaid expansion under the Affordable Care Act broadened eligibility for government-funded health coverage. This may have improved access to early diagnosis and rapid treatment, potentially impacting survival in patients with resectable non-small cell lung cancer (NSCLC), a leading cause of cancer-related death in the US.

OBJECTIVE: To evaluate the association between state-level Medicaid expansion and all-cause mortality in patients with resectable NSCLC.

DESIGN, SETTING, AND PARTICIPANTS: This cohort study of patients aged 20 to 64 years who were diagnosed with stage I to IIIA NSCLC used data from the Surveillance, Epidemiology, and End Results registry collected between January 1, 2006, to December 31, 2019, with outcomes administratively censored at 2 and 4 years. Data were analyzed between March 1 and September 10, 2025.

EXPOSURE: Medicaid expansion status of patients’ state of residence at diagnosis. Patients’ states of residence were categorized as nonexpansion, early expansion (2011), 2014 expansion, or late expansion (after 2014).

MAIN OUTCOMES AND MEASURES: Primary outcomes were 2- and 4-year all-cause mortality. Cox proportional hazards regression models within a difference-in-differences framework were used to estimate adjusted hazard ratios (HRs) for death. Secondary analyses evaluated postexpansion mortality trends and changes in early-stage (I-II) diagnoses using logistic regression.

RESULTS: Among 53 842 patients included in the analysis (24 849 [46.2%] 60-64 years of age; 27 027 [50.2%] male), propensity score-matched analyses showed lower 2-year mortality in states with early expansion (HR, 0.95; 95% CI, 0.91-0.99; P = .02) and 2014 expansion (HR, 0.91; 95% CI, 0.86-0.95; P < .001) compared with nonexpansion control states, whereas no significant difference was observed in late expansion states (HR, 0.95; 95% CI, 0.89-1.02; P = .15). All expansion groups showed decreased mortality. Mortality decreases were observed after the first 3 years and persisted throughout the study period. The proportion of early-stage diagnoses did not change post expansion, suggesting benefits may have been mediated by improved postdiagnostic care rather than earlier detection.

CONCLUSIONS AND RELEVANCE: In this cohort study of patients with stage I to IIIA NSCLC, Medicaid expansion was associated with lower mortality at 2 and 4 years. These findings suggest that expanded insurance coverage may have enhanced access to effective cancer care and improved population-level outcomes.

PMID:41324959 | DOI:10.1001/jamanetworkopen.2025.45996