bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computing the electronic circular dichroism spectrum of DNA quadruple helices of different topology: A critical test for a generalized excitonic model based on a fragment diabatization
Authors: Asha Haritha , Green James A. , Esposito Luciana , Santoro Fabrizio , Improta Roberto 
Published: February 2023

AbstractIn this study, we exploit a recently developed fragment diabatization‐based excitonic model, FrDEx, to simulate the electronic circular dichroism (ECD) spectra of three guanine‐rich DNA sequences arranged in guanine quadruple helices with different topologies: thrombin binding aptamer (antiparallel), c‐Myc promoter (parallel), and human telomeric sequence (3+1 hybrid). Starting from time‐dependent density functional theory (TD‐DFT) calculations with the M052X functional, we apply our protocol to parameterize the FrDEX Hamiltonian, which accounts for electron density overlap and includes both the coupling with charge transfer transitions and the effect of the surrounding bases on the local excitation of each chromophore. The TD‐DFT/M052X spectral shapes are in good agreement with the experimental ones, the main source of discrepancy being related to the intrinsic error on the computed transition energies of guanine monomer. FrDEx spectra are fairly close to the reference TD‐DFT ones, allowing a significant advance with respect to a more standard excitonic Hamiltonian. We also show that the ECD spectra are sensitive to the inclusion of the inner K
cation in the calculation.
A new fast entropy‐based method to generate composite centrality measures in complex networks
Authors: Sabah Levent , Şimşek Mehmet 
Published: February 2023

SummaryDetermining the centrality of nodes in complex networks provides practical benefits in many areas such as detecting influencer nodes, viral marketing, and preventing the spread of rumors. On the other hand, there is no consensus for the definition of centrality. Therefore, different centrality measures such as degree, closeness, and betweenness have been developed to measure the centrality of a node. However, each centrality measure highlights the various characteristics of the nodes in the network from its own point of view. This causes each centrality measure to rank the nodes in a different order. In recent years, researchers have focused on approaches that combine multiple centrality measures. Thus, the perspectives of different centrality measures can be considered simultaneously. In this study, we have proposed a fast and efficient method using the analytic hierarchy process and entropy weighting to combine multiple centrality measures. We tested the proposed method with synthetic and real datasets and compared the results with those of state‐of‐the‐art methods. The experimental results showed the proposed method to be competitive with these advanced methods, whereas it performed much better than the other methods in terms of computational speed. This indicated that our proposed method could be applied to large and dynamic complex networks.
Recombineering: Genetic Engineering in Escherichia coli Using Homologous Recombination
Authors: Thomason Lynn C. , Costantino Nina , Li Xintian , Court Donald L. 
Published: February 2023

AbstractThe bacterial chromosome and bacterial plasmids can be engineered in vivo by homologous recombination using either PCR products or synthetic double‐stranded DNA (dsDNA) or single‐stranded DNA as substrates. Multiple linear dsDNA molecules can be assembled into an intact plasmid. The technology of recombineering is possible because bacteriophage‐encoded recombination proteins efficiently recombine sequences with homologies as short as 35 to 50 bases. Recombineering allows DNA sequences to be inserted or deleted without regard to the location of restriction sites and can also be used in combination with CRISPR/Cas targeting systems. © 2023 Wiley Periodicals LLC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.This article was corrected on 12 November 2024. See the end of the full text for details.Basic Protocol: Making electrocompetent cells and transforming with linear DNASupport Protocol 1: Selection/counter‐selections for genome engineeringSupport Protocol 2: Creating and screening for oligo recombinants by PCRSupport Protocol 3: Other methods of screening for unselected recombinantsSupport Protocol 4: Curing recombineering plasmids containing a temperature‐sensitive replication functionSupport Protocol 5: Removal of the prophage by recombineeringAlternate Protocol 1: Using CRISPR/Cas9 as a counter‐selection following recombineeringAlternate Protocol 2: Assembly of linear dsDNA fragments into functional plasmidsAlternate Protocol 3: Retrieval of alleles onto a plasmid by gap repairAlternate Protocol 4: Modifying multicopy plasmids with recombineeringSupport Protocol 6: Screening for unselected plasmid recombinantsAlternate Protocol 5: Recombineering with an intact λ prophageAlternate Protocol 6: Targeting an infecting λ phage with the defective prophage strains
Lung epithelial cells: Upstream targets in type 2‐high asthma
Authors: Lameire Sahine , Hammad Hamida 
Published: February 2023

AbstractOver the last years, technological advances in the field of asthma have led to the identification of two disease endotypes, namely, type 2‐high and type 2‐low asthma, characterized by different pathophysiologic mechanisms at a cellular and molecular level. Although specific immune cells are important contributors to each of the recognized asthma endotype, the lung epithelium is now regarded as a crucial player able to orchestrate responses to inhaled environmental triggers such as allergens and microbes. The impact of the epithelium goes beyond its physical barrier. It is nowadays considered as a part of the innate immune system that can actively respond to insults. Activated epithelial cells, by producing a specific set of cytokines, trigger innate and adaptive immune cells to cause pathology. Here, we review how the epithelium contributes to the development of Th2 sensitization to allergens and asthma with a “type 2‐high” signature, in both murine models and human studies of this asthma endotype. We also discuss epithelial responses to respiratory viruses, such as rhinovirus, respiratory syncytial virus, and SARS‐CoV‐2, and how these triggers influence not only asthma development but also asthma exacerbation. Finally, we also summarize the results of promising clinical trials using biologicals targeting epithelial‐derived cytokines in asthmatic patients.
An adjoint‐based solver with adaptive mesh refinement for efficient design of coupled thermal‐fluid systems
Authors: Gallorini Emanuele , Hèlie Jerome , Piscaglia Federico 
Published: February 2023

AbstractA multi‐objective continuous adjoint strategy based on the superposition of boundary functions for topology optimization of problems where the heat transfer must be enhanced and the dissipated mechanical power controlled at the same time, has been here implemented in a finite volume (FV), incompressible, steady flow solver supporting a dynamic adaptive mesh refinement (AMR) strategy. The solver models the transition from fluid to solid by a porosity field, that appears in the form of penalization in the momentum equation; the material distribution is optimized by the method of moving asymptotes (MMA). AMR is based on a hierarchical nonconforming h‐refinement strategy and is applied together with a flux correction to enforce conservation across topology changes. It is shown that a proper choice of the refinement criterium favors a mesh‐independent solution. Finally, a Pareto front built from the components of the objective function is used to find the best combination of the weights in the optimization cycle. Numerical experiments on two‐ and three‐dimensional test cases, including the aero‐thermal optimization of a simplified layout of a cooling system, have been used to validate the implemented methodology.
A graphic processing unit implementation for the moment representation of the lattice Boltzmann method
Authors: Ferrari Marco A. , de Oliveira Waine B. , Lugarini Alan , Franco Admilson T. , Hegele Luiz A. 
Published: February 2023

AbstractWe implement the moment representation of the lattice Boltzmann method in a graphic processing unit (GPU) environment to study the computational performance of three‐dimensional fluid flows. The moment representation of the lattice Boltzmann method (MRLBM) uses up to second‐order moments of the particle distribution function to regularize and reconstruct it. By adopting this method, there is a reduction in memory usage and global memory transfer and, therefore, increased performance. The results show an increase of up to 40% in speed compared to population schemes. The validation results show there was no loss of accuracy when using single precision for turbulent flows. The adoption of single‐precision also enables higher processing speed for GPUs with low double‐precision capability and reduces the memory footprint, which can further increase performance. The implementation here presented provides a fast and straightforward environment for fluid simulation by combining single‐precision and the MRLBM.
Deep learning model for temperature prediction: A case study in New Delhi
Authors: Shrivastava Virendra Kumar , Shrivastava Aastik , Sharma Nonita , Mohanty Sachi Nandan , Pattanaik Chinmaya Ranjan 
Published: February 2023

AbstractThis study is based on temperature prediction in the capital of India (New Delhi). We have adopted different ML models such as (MPR and DNN) which are designed and implemented for temperature prediction. The MPR models are varied on the degree of the polynomial, whereas the DNN models differ in the number of input parameters. DNNM‐1 takes date, time, and temperature as input, and DNNM‐2 receives date, time, temperature, pressure, humidity, and dew point as input parameters, whereas DNNM‐3, is a complex model that takes date, time, temperature, pressure, humidity, dew point, and 32 weather conditions as input. To evaluate the accuracy of the predictions, a comparison of the predicted temperature and the actual recorded temperature is done, and the performance and accuracy of the models are examined. The MPR models work well in case of fewer input features, but as the number of input features grows, the DNN model outperforms the MPR models. The DNN model (DNNM‐3) outperformed the other models with better accuracy as compared to past evidence.
Effect of women's literacy on maternal and child health: Evidence from demographic Health Survey data in Senegal
Authors: Diallo Mamadou Abdoulaye , Mbaye Ngoné , Aidara Ibrahima 
Published: February 2023

AbstractBackgroundSenegal has certainly made significant efforts in adult literacy and in the fight against maternal and infant mortality. However, a large proportion of the female population is illiterate, and the country's maternal and infant mortality rates are still higher than WHO recommendations. This article examined the effect of women's literacy on maternal and child health in Senegal.MethodsData were extracted from the last Senegal Demographic and Health Surveys (DHS) collected in 2019. A binary logistic model was performed to assess the effect of women's literacy on ten outcomes of maternal and child health indicators.ResultsResults indicate that women's literacy has a positive and significant effect on nine of key indicators outcomes. For instance, women's literacy increases the odds of contraceptive use by 1.29 (95% Confidence Interval [CI], 1.13–1.48; p < 0.01), compliance with the number of prenatal visits by 1.57 (95% CI, 1.35–1.83; p < 0.01) and consultation in the first trimester of pregnancy by 1.52 (95% CI, 1.31–1.78; p < 0.01). Literacy is associated with increased odds of breastfeeding up to six months (Odds Ratio [OR], 1.17; 95% CI, 0.97–1.42; p < 0.1) and healthy birth interval (OR, 1.18; 95% CI, 0.97–1.44; p < 0.1) only in rural areas. Women literacy reduces the risk of stunting by 0.81 (95% CI, 0.68–0.96; p < 0.05) and the risk of underweight by 0.72 (95% CI, 0.59–0.87; p < 0.01) among children under five years. The mother's ability to read and write favors compliance with the increase of odds of DPT vaccination record of her children, especially in rural areas (OR, 1.69; 95% CI, 1.05–2.74; p < 0.05). Moreover, there are serval other factors influencing positively the maternal and child health, like health insurance access, media exposure, and clean water and improved sanitation facilities access.ConclusionsThis study emphasizes on the need to strengthen adult literacy programs, especially for women in rural areas. Indeed, this could help generalize health insurance by income‐sensitive premiums or exemptions for the poor as well as increased awareness campaigns to promote reproductive and maternal health benefits, via the radio or television. Furthermore, improving access to clean water supply and improved sanitation facilities would greatly ameliorate maternal and child health.
Thrombocytopenia and clinical outcomes among patients with COVID‐19 disease: A cohort study
Authors: Alkhalifa Hussain , Alsalman Zaenb , Alfaraj Aman , Algaraash Mohammed , Alsalman Mortadah 
Published: February 2023

AbstractBackground and AimsThrombocytopenia is increasingly recognized among patients with critical illness and plays a role in several diseases affecting different organ systems. Therefore, we studied the prevalence of thrombocytopenia among hospitalized COVID‐19 patients and its correlation with disease severity and clinical outcomes.MethodsThis was an observational retrospective cohort study conducted on 256 hospitalized COVID‐19 patients. Thrombocytopenia is defined as a platelet count below 150,000/μL. Disease severity was classified based on the five‐point CXR scoring tool.ResultsThrombocytopenia was found in 66 (25.78%) patients. In outcomes, 41 (16%) patients were admitted to intensive care unit, 51 (19.9%) died, and 50 (19.5%) had acute kidney injury (AKI). Of the total patients with thrombocytopenia, 58 (87.9%) had early thrombocytopenia, while 8 (12.1%) had late thrombocytopenia. Notably, mean survival time was markedly decreased in late‐onset thrombocytopenia cases (p < 0.0001). Patients with thrombocytopenia showed a significant increase in creatinine compared to those with normal platelet counts (p < 0.05). Moreover, thrombocytopenia was more prevalent in patients with chronic kidney disease compared to other comorbidities (p < 0.05). In addition, hemoglobin was significantly lower in the thrombocytopenia group (p < 0.05).ConclusionThrombocytopenia is a common finding among COVID‐19 patients, with a predilection toward a specific group of patients, though the exact reasons are unclear. It predicts poor clinical outcomes and is closely linked to mortality, AKI, and the need for mechanical ventilation. These findings suggest that more research is required to study the mechanism of thrombocytopenia and the possibility of thrombotic microangiopathy in COVID‐19 patients.
Prognostic artificial intelligence model to predict 5 year survival at 1 year after gastric cancer surgery based on nutrition and body morphometry
Authors: Chung Heewon , Ko Yousun , Lee In‐Seob , Hur Hoon , Huh Jimi , Han Sang‐Uk , Kim Kyung Won , Lee Jinseok 
Published: February 2023

AbstractBackgroundPersonalized survival prediction is important in gastric cancer patients after gastrectomy based on large datasets with many variables including time‐varying factors in nutrition and body morphometry. One year after gastrectomy might be the optimal timing to predict long‐term survival because most patients experience significant nutritional change, muscle loss, and postoperative changes in the first year after gastrectomy. We aimed to develop a personalized prognostic artificial intelligence (AI) model to predict 5 year survival at 1 year after gastrectomy.MethodsFrom a prospectively built gastric surgery registry from a tertiary hospital, 4025 gastric cancer patients (mean age 56.1 ± 10.9, 36.2% females) treated gastrectomy and survived more than a year were selected. Eighty‐nine variables including clinical and derived time‐varying variables were used as input variables. We proposed a multi‐tree extreme gradient boosting (XGBoost) algorithm, an ensemble AI algorithm based on 100 datasets derived from repeated five‐fold cross‐validation. Internal validation was performed in split datasets (n = 1121) by comparing our proposed model and six other AI algorithms. External validation was performed in 590 patients from other hospitals (mean age 55.9 ± 11.2, 37.3% females). We performed a sensitivity analysis to analyse the effect of the nutritional and fat/muscle indices using a leave‐one‐out method.ResultsIn the internal validation, our proposed model showed AUROC of 0.8237, which outperformed the other AI algorithms (0.7988–0.8165), 80.00% sensitivity, 72.34% specificity, and 76.17% balanced accuracy. In the external validation, our model showed AUROC of 0.8903, 86.96% sensitivity, 74.60% specificity, and 80.78% balanced accuracy. Sensitivity analysis demonstrated that the nutritional and fat/muscle indices influenced the balanced accuracy by 0.31% and 6.29% in the internal and external validation set, respectively. Our developed AI model was published on a website for personalized survival prediction.ConclusionsOur proposed AI model provides substantially good performance in predicting 5 year survival at 1 year after gastric cancer surgery. The nutritional and fat/muscle indices contributed to increase the prediction performance of our AI model.
Sarcopenia is associated with a greater risk of polypharmacy and number of medications: a systematic review and meta‐analysis
Authors: Prokopidis Konstantinos , Giannos Panagiotis , Reginster Jean Yves , Bruyere Olivier , Petrovic Mirko , Cherubini Antonio , Triantafyllidis Konstantinos K. , Kechagias Konstantinos S. , Dionyssiotis Yannis , Cesari Matteo , Ibrahim Kinda , Scott David , Barbagallo Mario , Veronese Nicola ,   Special interest group in Systematic Reviews and Meta‐analyses and the Task Force on Pharmaceutical Strategy of the European Geriatric Medicine Society (EuGMS)
Published: February 2023

AbstractPolypharmacy in older adults is associated with multiple negative consequences that may affect muscular function, independently from the presence of medical conditions. The aim of this systematic review and meta‐analysis was to investigate the association of sarcopenia with polypharmacy and higher number of medications. A systematic literature search of observational studies using PubMed, Web of Science, Scopus and Cochrane Library databases was conducted from inception until June 2022. To determine if sarcopenia is associated with a higher risk of polypharmacy and increased number of medications, a meta‐analysis using a random‐effects model was used to calculate the pooled effects (CRD42022337539). Twenty‐nine studies were included in the systematic review and meta‐analysis. Sarcopenia was associated with a higher prevalence of polypharmacy (odds ratio [OR]: 1.65, 95% confidence interval [CI] [1.23, 2.20], I2 = 84%, P < 0.01) and higher number of medications (mean difference: 1.39, 95% CI [0.59, 2.19], I2 = 95%, P < 0.01) compared with individuals without sarcopenia. Using meta‐regression, a high variance was observed due to different populations (i.e., community‐dwelling, nursing home residents, inpatients, outpatients) for both outcomes of polypharmacy (r = −0.338, SE = 0.1669, 95% CI [−0.67, −0.01], z = −2.03, P = 0.04) and number of medications (r = 0.589, SE = 0.2615, 95% CI [0.08, 1.10], z = 2.25, P = 0.02). This systematic review and meta‐analysis reported a significantly increased risk of polypharmacy and higher number of medications in people with sarcopenia compared with individuals without this condition. Future research should clarify whether the specificity and number of medications is a direct contributor in accelerating the progression of muscle wasting and dysfunction contributing to sarcopenia in older adults.
Current attitudes toward carrier screening for spinal muscular atrophy among pregnant women in Eastern China
Authors: Li Yerong , Wang Lulu , Tan Jianxin , Huang Mingtao , Wang Yuguo , Shao Binbin , Lv Juan , Zhang Jingjing 
Published: February 2023

AbstractSpinal muscular atrophy (SMA) is an autosomal recessive and often fatal neurological disease. However, very little is known about the attitudes toward SMA carrier screening among Chinese pregnant people. In this study, pregnant women in Eastern China who were undergoing routine chromosomal screening programs were invited to view an educational video about SMA and complete a 26‐item survey regarding their attitudes toward SMA screening by scanning a specific quick response code. A total of 1673 questionnaires were collected, and 81.1% of respondents were willing to undergo self‐funded screening. If the screening program were included in the medical insurance, 97.8% of respondents were willing to accept screening. The important reasons for supporting SMA screening were a belief that it could help them make better reproductive decisions and avoid having a child with SMA. The key reason for declining SMA screening was not having a family history of genetic diseases. A higher score for SMA genetics knowledge was associated with a greater willingness to undergo SMA screening. We concluded that pregnant women in Eastern China had positive attitudes toward SMA carrier screening. Improving genetic knowledge and including the screening program in medical insurance would support the widespread implementation of SMA carrier screening. Steps should be taken to offer SMA carrier screening along with pre‐ and posttest education and genetic counseling to raise awareness and reduce misconceptions regarding SMA.
Oxidative stress—A key determinant of complications and negative outcome in hepatitis E virus infected pregnancies: A comprehensive account involving cases from northeast India
Authors: Kashyap Natasha , Islam Mafidul , Kaur Harpreet , Tiwari Diptika , Begum Anjuma , Bose Moumita , Das Chandana Ray , Saikia Anjan Kumar , Kalita Pankaj , Bose Purabi Deka , Bose Sujoy 
Published: February 2023

AbstractRegulated oxidative stress (OS) is important during pregnancy. Sporadic studies suggest the significance of deregulated OS in hepatitis E virus (HEV) infected pregnancy, but with limited reactive oxygen species (ROS) or antioxidant markers. The present novel study, therefore, aimed to evaluate the significance of ROS‐antioxidant imbalance and resulting altered OS in HEV infected pregnancy complications like preterm delivery (PTD) and outcome. Difference in serum levels of ROS and antioxidant panel of markers were evaluated by ELISA for HEV immunoglobulin M RNA positive genotype 1 cases (including acute [acute viral hepatitis, AVH] and fulminant [fulminant hepatic failure, FHF] cases) and healthy term delivery subjects, and analyzed statistically. Direct ROS marker H2O2 levels and indirect OS marker for DNA damage 8‐hydroxy‐2′‐deoxyguanosine was significantly increased in HEV‐cases compared to controls, and was associated and prognostic factor for PTD and fetal death in HEV cases. A comparatively lower total serum antioxidant capacity was observed in the FHF cases compared to the control subjects and the AVH cases. Glutathione (GSH) levels and superoxide dismutase (SOD) activity were significantly associated with PTD in the FHF sub‐cohorts (p = 0.017) and AVH sub‐cohorts (p < 0.001), respectively, and was associated with poor prognosis in HEV cases. The serum H2O2 levels were found to be negatively correlated with SOD activity (p = 0.016) and GSH levels (p = 0.001) in the HEV‐AVH cases; and positively correlated with the viral load in HEV cases (p = 0.023). The ROS‐antioxidant imbalance resulting OS plays a detrimental associative role in HEV infected pregnancy complications like PTD and adverse pregnancy outcomes; and holds therapeutic significance.