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How and why small volcanic ocean islands collapse and move vertically up and down

Fast and accurate imputation of genotypes from noisy low-coverage sequencing data in bi-parental populations

Motivation Genotyping of bi-parental populations can be performed with low-coverage next-generation sequencing (LC-NGS). This allows the creation of highly saturated genetic maps at reasonable cost, precisely localized recombination breakpoints (i.e., the crossovers), and minimized mapping intervals for quantitative-trait locus analysis. The main issues with these low-coverage genotyping methods are (1) poor performance at heterozygous loci, (2) high percentage of missing data, (3) local errors due to erroneous mapping of sequencing reads and reference genome mistakes, and (4) global, technical errors inherent to NGS itself. Recent methods like Tassel-FSFHap or LB-Impute are excellent at addressing issues 1 and 2, but nonetheless perform poorly when issues 3 and 4 are persistent in a dataset (i.e., “noisy” data). Here, we present a new algorithm for imputation of LC-NGS data that eliminates the need of complex pre-filtering of noisy data, accurately types heterozygous chromosomal regions, precisely estimates crossover positions, corrects erroneous data, and imputes missing data. The imputation of genotypes and recombination breakpoints is based on maximum-likelihood estimation. We compare its performance with Tassel-FSFHap and LB-Impute using simulated data and two real datasets. NOISYmputer is consistently more efficient than the two other software tested and reaches average breakpoint precision of 99.9% and average recall of 99.6% on illumina simulated dataset. NOISYmputer consistently provides precise map size estimations when applied to real datasets while alternative tools may exhibit errors ranging from 3 to 1845 times the real size of the chromosomes in centimorgans. Furthermore, the algorithm is not only highly effective in terms of precision and recall but is also particularly economical in its use of RAM and computation time, being much faster than Hidden Markov Model methods. Availability NOISYmputer and its source code are available as a multiplatform (Linux, macOS, Windows) Java executable at the URL https://gitlab.cirad.fr/noisymputer/noisymputerstandalone/-/tree/1.0.0-RELEASE?reftype=tags.

Deep learning-based malaria parasite detection: convolutional neural networks model for accurate species identification of Plasmodium falciparum and Plasmodium vivax

Abstract Accurate malaria diagnosis with precise identification of Plasmodium species is crucial for an effective treatment. While microscopy is still the gold standard in malaria diagnosis, it relies heavily on trained personnel. Artificial intelligence (AI) advances, particularly convolutional neural networks (CNNs), have significantly improved diagnostic capabilities and accuracy by enabling the automated analysis of medical images. Previous models efficiently detected malaria parasites in red blood cells but had difficulty differentiating between species. We propose a CNN-based model for classifying cells infected by P. falciparum, P. vivax, and uninfected white blood cells from thick blood smears. Our best-performing model utilizes a seven-channel input and correctly predicted 12,876 out of 12,954 cases. We also generated a cross-validation confusion matrix that showed the results of five iterations, achieving 63,654 out of 64,126 true predictions. The model’s accuracy reached 99.51%, a precision of 99.26%, a recall of 99.26%, a specificity of 99.63%, an F1 score of 99.26%, and a loss of 2.3%. We are now developing a system based on real-world quality images to create a comprehensive detection tool for remote regions where trained microscopists are unavailable.

Carotid artery stenosis and ischemic cerebrovascular events after radiotherapy in patients with head and neck cancer

Radiotherapy is the main treatment for patients with head and neck cancer (HNC) and is associated with an increased risk of ischemic cerebrovascular events (ICVE). The purpose of this cross-sectional study was to determine the incidence of ICVE and carotid artery stenosis (CAS) in patients with HNC who receive radiotherapy and the risk factors for CAS. We enrolled 907 patients with HNC who underwent radiotherapy between February 2011 and June 2022 and obtained information on their clinical and tumor characteristics and their treatment from the clinical records. Data on risk factors for atherosclerosis, medications used, and radiotherapy were also collected. The patients were followed through to the end of 2023 unless they died or were lost to follow-up. The overall incidence of ICVE was 1.98%, with a cumulative incidence of 1.65% over 5 years. In patients who did not have a preexisting carotid artery lesion, the cumulative incidence of significant CAS was 1.3% at 12 months, 2.2% at 24 months, and 2.5% at 36 months post-radiotherapy. The most important risk factors for new CAS were age >65 years (aHR = 2.60, p = 0.008, 95% confidence Interval: 1.28–5.30), laryngeal cancer (aHR = 2.36, p<0.017, 95% confidence Interval: 1.01–5.55), and total plaque score (aHR = 1.38, p<0.001, 95% confidence Interval: 1.23–1.56). There was a significant increase in stenosis, plaque score, and wall thickness in all areas in the carotid artery (p<0.001). The incidence of ICVE and the cumulative incidence of CAS was found to be lower in the Thai population than in other populations. The main risk factors for new CAS were age >65 years, laryngeal cancer, and total plaque score. Changes in the carotid artery were detected early and affected all areas in the artery. Patients with HNC treated by radiotherapy should be assessed for risk factors for CAS and undergo vascular surveillance during follow-up.

Author Correction: High vulnerability of the endemic Southern Ocean snail Neobuccinum eatoni (Buccinidae) to critical projected oceanographic changes

A new computational framework for simulating airway resistance, fraction of exhaled nitric oxide, and diffusing capacity for nitric oxide

In this paper, we present a new computational framework for the simulation of airway resistance, the fraction of exhaled nitric oxide, and the diffusion capacity for nitric oxide in healthy and unhealthy lungs. Our approach is firstly based on a realistic representation of the geometry of healthy lungs as a function of body mass, which compares well with data from the literature, particularly in terms of lung volume and alveolar surface area. The original way in which this geometry is created, including an individual definition of the airways in the first seven generations of the lungs, makes it possible to consider the heterogeneous nature of the lungs in terms of perfusion and ventilation. In addition, a geometry can be easily modified to simulate various abnormalities, local or global (constriction, inflammation, perfusion defect). The natural variability of the lungs at constant body mass is also considered. The computational framework includes the possibility to simulate, on a given (possibly modified) geometry, a test to measure the flow resistance of the lungs (including its component due to the not fully developed flow in the first generations of lungs), a test to measure the concentration of nitric oxide in the exhaled air, and a test to measure the diffusion capacity for nitric oxide. This is implemented in the framework by solving different transport equations (momentum and convection/diffusion) describing these tests. Through numerous simulations, we demonstrate the ability of our model to reproduce results from the literature, both for healthy lungs and lungs of patients with asthma or chronic obstructive pulmonary disease. Such a computational framework, through the possibilities of numerous and rapid tests that it allows, sheds new light on experimental data by providing information on the phenomena that take place in the distal generations of the lungs, which are difficult to access with imaging.

Analysis of the cardiotoxic and myorelaxant effects of camphor on fish of the Nile tilapia species (Oreochromis niloticus) (Linnaeus 1758)

High pulse pressure is associated with an increased risk of prediabetes in hypertensive individuals: A retrospective study based on an adult Chinese population

Objectives The pulse pressure (PP) is an important factor influencing the outcomes of diabetes. However, the relationship between the PP and prediabetes has been rarely studied and how this association might be impacted by hypertension is not clear. Methods In this study, we retrospectively included 184,252 adults from 32 regions in China, spanning from 2010 to 2016. Cox regression and sensitivity analysis were used to examine the relationship between PP and prediabetes. For the hypertensive population, Cox proportional hazards regression and smooth curve fitting were performed to explore the non-linear relationship between PP and prediabetes. A two-stage Cox proportional hazards regression model was used to determine the inflection point of PP in relation to the risk of prediabetes. Results After adjusting for confounding factors, we found a positive association between PP and prediabetes (HR: 1.11, 95% CI: 1.03–1.19, P = 0.0045). However, we observed that this relationship was not significant in the normal blood pressure group (HR: 1.06, 95% CI: 0.94–1.18, P = 0.3529). We also found a non-linear relationship between PP and the risk of prediabetes in hypertensive individuals. The inflection point of PP was 31 mmHg. When PP ≥ 31 mmHg, there was a positive association with the risk of prediabetes (HR: 1.22, 95% CI: 1.04–2.08, P <0.0001). Conversely, when PP < 31 mmHg, this association was not significant (HR: 0.83, 95% CI: 0.59–1.15, P = 0.2646). Conclusions This study suggests a non-linear relationship between PP and the risk of prediabetes in hypertensive individuals. Maintaining PP within 31 mmHg is crucial for preventing the occurrence of prediabetes.

Kinetic and isothermal study of dye absorption using pre-treated natural fabrics using polyamine compounds

Abstract The study examined the use of cationic polymers (Polyethyleneimine and chitosan) in treating fabrics like cotton, wool, and cotton/wool (70/30) to improve their dyeability and printability. The study examined factors such as dye concentration, time, and temperature for the dyeing process. Results showed that all dyed and printed fabrics treated with polyethyleneimine and chitosan increased color strength by significant percentages. Fastness properties, such as washing, rubbing, acidic and alkaline perspiration, and lightness, improved significantly. Fabric roughness, tensile strength, and elongation decreased by about 4-10% for each fabric. Additionally, the dyed and printed fabrics showed high resistance to bacteria and fungi. The study contributed to reducing chemicals used in traditional dyeing processes by a significant percentage, as the dyeing bath contained only the treated sample and dye solution. Furthermore kintic and isothermal study was investigated to explain the behaviour of treated fabrics for dye absorption.

Video-based estimation of blood pressure

In this work, we propose a non-contact video-based approach that estimates an individual’s blood pressure. The estimation of blood pressure is critical for monitoring hypertension and cardiovascular diseases such as coronary artery disease or stroke. Estimation of blood pressure is typically achieved using contact-based devices which apply pressure on the arm through a cuff. Such contact-based devices are cost-prohibitive as well as limited in their scalability due to the requirement of specialized equipment. The ubiquity of mobile phones and video-based capturing devices motivates the development of a non-contact blood pressure estimation method—Video-based Blood Pressure Estimation (V-BPE). We leverage the time difference of the blood pulse arrival at two different locations in the body (Pulse Transit Time) and the inverse relation between the blood pressure and the velocity of blood pressure pulse propagation in the artery to analytically estimate the blood pressure. Through statistical hypothesis testing, we demonstrate that Pulse Transit Time-based approaches to estimate blood pressure require knowledge of subject specific blood vessel parameters, such as the length of the blood vessel. We utilize a combination of computer vision techniques and demographic information (such as the height and the weight of the subject) to capture and incorporate the aforementioned subject specific blood vessel parameters into our estimation of blood pressure. We demonstrate the robustness of V-BPE by evaluating the efficacy of blood pressure estimation in demographically diverse, outside-the-lab conditions. V-BPE is advantageous in three ways; 1) it is non-contact-based, reducing the possibility of infection due to contact 2) it is scalable, given the ubiquity of video recording devices and 3) it is robust to diverse demographic scenarios due to the incorporation of subject specific information.

Mechanistic study of the effect of a high-salt diet on the intestinal barrier

The impact of intermittent preventive treatment in school aged children with dihydroartemisinin piperaquine and artesunate amodiaquine on IgG response against six blood stage Plasmodium falciparum antigens

Several interventional strategies have been implemented in malaria endemic areas where the burden is high, that include among others, intermittent preventive treatment (IPT), a tactic that blocks transmission and can reduce disease morbidity. However, the implementation IPT strategies raises a genuine concern, intervening the development of naturally acquired immunity to malaria which requires continuous contact with parasite antigens. This study investigated whether dihydroartemisinin-piperaquine (DP) or artesunate-amodiaquine (ASAQ) IPT in schoolchildren (IPTsc) impairs IgG reactivity to six malaria antigens. An IPTsc trial in north-eastern Tanzania administered three doses of DP or ASAQ at four-monthly intervals and the schoolchildren were followed up. This study compared IgG reactivity against GLURP-R2, MSP1, MSP3, and CIDR domains (CIDRa1.1, CIDRa1.4, and CIDRa1.5) of Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP-1) in intervention and control groups using enzyme linked immunosorbent assay (ELISA) technique. During the study, 369 schoolchildren were available for analysis, 119, 134 and 116 participants in the control, DP and ASAQ groups, respectively. Breadth of malaria antigen recognition increased significantly during and after the intervention phases and did not differ between the study groups (Trend test: DP, z-score = 5.92, p < 0.001, ASAQ, z-score = 6.64, p < 0.001 and control, z-score = 5.85, p < 0.001). There were no differences between the control and ASAQ group in the recognition of any of the tested antigens at all visits. In the DP group, however, during the intervention period IPTsc did not impair antibody against MSP1, MSP3, CIDRa1.1, CIDRa1.4 and CIDRa1.5, but it did impair against GLURP-R2. The current study has shown that effective IPTsc with DP or ASAQ does not interfere with the development of antibodies against malaria antigens of the blood stages, suggesting that the advancement of naturally acquired immunity to malaria is not impeded by IPTsc interventions.

Chromosome distribution of four LTR retrotransposons and 18 S rDNA in coffea eugenioides

Application of attenuated total reflection–Fourier transform infrared spectroscopy in semi-quantification of blood lipids and characterization of the metabolic syndrome

Background/Purpose Dyslipidemia, a hallmark of metabolic syndrome (MetS), contributes to atherosclerotic and cardiometabolic disorders. Due to days-long analysis, current clinical procedures for cardiotoxic blood lipid monitoring are unmet. This study used AI-assisted attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy to identify MetS and precisely quantify multiple blood lipid levels with a blood sample of 0.5 µl and the assaying time is approximately 10 minutes. Methods ATR-FTIR spectroscopy with 1738 data points in the spectral range of 4000–650 cm−1 was used to analyze the blood samples. An adaptive synthetic technique was used to establish a prevalence-balanced dataset. LDL-C, HDL-C, TG, VLDL-C, and cholesterol levels were defined as the predicted targets of lipid absorption profiles. Linear regression (LR), gradient boosting regression tree (GBT), and histogram-based gradient boosting regression tree (HGBTR) were used to train the models. Lipid profile value prediction was evaluated using R2 and MAE, whereas MetS prediction was evaluated using area under the ROC curve. Results A total of 150 blood samples from 25 individuals without MetS and 25 with MetS yielded 491 spectral measurements. In the regression models, HGBT best predicted the targets of TG, CHOL, HDL-C, LDL-C, and VLDL-C with R2 values of 0.854 (0.12), 0.684 (0.08), 0.758 (0.10), and 0.419 (0.11), respectively. The classification model with the greatest AUC was RF (0.978), followed by HGBT (0.972) and GBT (0.967). Conclusion The results of this study revealed that predicting MetS and determining blood lipid levels with high R2 values and limited errors are feasible for monitoring during therapy and intervention.

Publisher Correction: Comparative lipidome and transcriptome provide novel insights into zero-valent iron nanoparticle-treated Fremyella diplosiphon

Study on the cooling effect of the parallel perforated ventilation subgrade in permafrost regions based on the numerical model

The runway in permafrost regions has remarkable temperature sensitivity. Therefore, this paper puts forward to the parallel perforated ventilation subgrade. The reliability and validity of the finite element model of the runway with the parallel perforated ventilation subgrade are verified by comparing with the previous studies. And the cooling effect of the parallel perforated ventilation subgrade is analyzed. Results show that the parallel perforated ventilation subgrade has a significant cooling effect on the pavement and has little cooling effect in the natural ground. Compared with the non-ventilation subgrade, temperature time-history curves for the parallel perforated ventilation subgrade change periodically each year and are gradually lower with the growth of time. Temperature-depth curves for the parallel perforated ventilation subgrade change significantly at the insulation layer, the crushed rock layer, and the perforated ventilation. The air velocity and working time of the parallel perforated ventilation have no effect on the temperature of the surface layer, base layer, and subbase layer, have little effect on the temperature of the insulation layer, and have great effect on the temperature of the crushed rock layer and subgrade. This study provides scientific support for the design, construction, and maintenance of the runway in permafrost regions.

Genes related to neural tube defects and glioblastoma

Correction: Estimation of crossbreeding and genetic parameters for reproductive traits of Boer x Central Highland goats in Ethiopia

Microstructure evolution during solution annealing of an Al–Zn–Mg–Cu alloy with La additions

IL-34 aggravates myocardial ischemia-reperfusion injury by upregulating the HMGB1-IL-17A-IL-6 axis through the JAK signaling pathway

Interleukin-34 (IL-34) was recently reported to be a new biomarker for atherosclerosis diseases, such as coronary artery disease and vascular dementia. IL-34 regulates the expression of proinflammatory cytokines (IL-17A, IL-1 and IL-6), which are classical cytokines involved in myocardial ischemia‒reperfusion (MI/R) injury. However, the exact role of IL-34 in MI/R remains unknown. In this study, a rat MI/R model was used to explore the effect of IL-34 on modulating inflammatory processes during MI/R injury. First, eighteen rats were subjected to 30 min of LAD ligation followed by 0 h, 1 h, 2 h, 4 h, 8 h or 24 h of reperfusion (n = 3 for each group). The level of IL-34 peaked at 4 h after MI/R in the ischemic myocardium. Next, ischemia for 30min and reperfusion for 4h (I/R) model was used. 24 rats were randomly divided into I/R group (n = 8), IL-34+IR group (n = 8) and IL-34+ab12+IR group (n = 8). We found that IL-34 pretreatment increased the expression of inflammatory cytokines, including high mobility group Box 1 (HMGB1), IL-17A, and IL-6; the expression of the apoptosis protein cleaved caspase-3; and the Bcl-2/Bax ratio within the ischemic myocardium. We also observed increased serum cardiac enzymes and a larger myocardial injury area. Treatment with a Janus kinase (JAK) pathway inhibitor, however, partially reduced the expression of these proteins and attenuated myocardial injury. Together, these results showed that IL-34 aggravates MI/R injury by inducing the expression of the HMGB1-IL-17A-IL-6 axis and apoptosis after MI/R, which is partially dependent on the JAK pathway. Therefore, blocking the JAK signaling pathway or inhibiting IL-34 expression might provide a new idea to reduce MI/R injury, but further researches are needed.