bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting cancer stages from tissue energy dissipation
Authors: Arango-Restrepo A. , Rubi J. M. 
Published: September 2023

AbstractUnderstanding cancer staging in order to predict its progression is vital to determine its severity and to plan the most appropriate therapies. This task has attracted interest from different fields of science and engineering. We propose a computational model that predicts the evolution of cancer in terms of the intimate structure of the tissue, considering that this is a self-organised structure that undergoes transformations governed by non-equilibrium thermodynamics laws. Based on experimental data on the dependence of tissue configurations on their elasticity and porosity, we relate the cancerous tissue stages with the energy dissipated, showing quantitatively that tissues in more advanced stages dissipate more energy. The knowledge of this energy allows us to know the probability of observing the tissue in its different stages and the probability of transition from one stage to another. We validate our results with experimental data and statistics from the World Health Organisation. Our quantitative approach provides insights into the evolution of cancer through its different stages, important as a starting point for new and integrative research to defeat cancer.
DRCNN: decomposing residual convolutional neural networks for time series forecasting
Authors: Zhu Yuzhen , Luo Shaojie , Huang Di , Zheng Weiyan , Su Fang , Hou Beiping 
Published: September 2023

AbstractRecent studies have shown great performance of Transformer-based models in long-term time series forecasting due to their ability in capturing long-term dependencies. However, Transformers have their limitations when training on small datasets because of their lack in necessary inductive bias for time series forecasting, and do not show significant benefits in short-time step forecasting as well as that in long-time step as the continuity of sequence is not focused on. In this paper, efficient designs in Transformers are reviewed and a design of decomposing residual convolution neural networks or DRCNN is proposed. The DRCNN method allows to utilize the continuity between data by decomposing data into residual and trend terms which are processed by a designed convolution block or DR-Block. DR-Block has its strength in extracting features by following the structural design of Transformers. In addition, by imitating the multi-head in Transformers, a Multi-head Sequence method is proposed such that the network is enabled to receive longer inputs and more accurate forecasts are obtained. The state-of-the-art performance of the presented model are demonstrated on several datasets.
Differential relationship between decreased muscle oxygenation and blood pressure recovery during supraventricular and ventricular tachycardia
Authors: Ishii Kei , Machino Takeshi , Hatori Yasuhiro , Gwak Jongseong , Izaki Tsubasa , Komine Hidehiko 
Published: September 2023

AbstractVasoconstriction during tachyarrhythmia contributes to maintenance of arterial pressure (AP) by decreasing peripheral blood flow. This cross-sectional observational study aimed to ascertain whether the relationship between peripheral blood flow and AP recovery occurs during both paroxysmal supraventricular (PSVT, n = 19) and ventricular tachycardias (VT, n = 17). Peripheral blood flow was evaluated using forearm tissue oxygen index (TOI), and mean AP (MAP) was measured using a catheter inserted in the brachial or femoral artery during an electrophysiological study. PSVT and VT rapidly decreased MAP with a comparable heart rate (P = 0.194). MAP recovered to the baseline level at 40 s from PSVT onset, but not VT. The forearm TOI decreased during both tachyarrhythmias (P ≤ 0.029). The TOI response was correlated with MAPrecovery (i.e., MAP recovery from the initial rapid decrease) at 20–60 s from PSVT onset (r = -– 0.652 to – 0.814, P ≤ 0.0298); however, this association was not observed during VT. These findings persisted even after excluding patients who had taken vasoactive drugs. Thus, restricting peripheral blood flow was associated with MAP recovery during PSVT, but not VT. This indicates that AP recovery depends on the type of tachyarrhythmia: different cardiac output and/or vasoconstriction ability during tachyarrhythmia.
Continuous aerosol monitoring and comparison of aerosol exposure based on smoke dispersion distance and concentrations during oxygenation therapy
Authors: Wu Chih-Chieh , Chen Wei-Lun , Tseng Cheng-Wei , Su Yung-Cheng , Chen Hsin-Ling , Lin Chun-Lung , Hung Tzu-Yao 
Published: September 2023

AbstractThis study evaluated the aerosol exposure risks while using common noninvasive oxygenation devices. A simulated mannequin was designed to breathe at a minute ventilation of 20 L/min and used the following oxygen-therapy devices: nasal cannula oxygenation (NCO) at 4 and 15 L/min, nonrebreathing mask (NRM) at 15 L/min, simple mask at 6 L/min, combination of NCO at 15 L/min and NRM at 15 L/min, high-flow nasal cannula (HFNC) at 50 L/min, and flush rate NRM. Two-dimension of the dispersion distance and the aerosol concentrations were measured at head, trunk, and foot around the mannequin for over 10 min. HFNC and flush-rate NRM yielded the longest dispersion distance and highest aerosol concentrations over the three sites of the mannequin than the other oxygenation devices and should use with caution. For flow rates of < 15 L/min, oxygenation devices with mask-like effects, such as NRM or NCO with NRM, decreased aerosol dispersion more effectively than NCO alone or a simple mask. In the upright position, the foot area exhibited the highest aerosol concentration regardless of the oxygenation device than the head–trunk areas of the mannequin. Healthcare workers should be alert even at the foot side of the patient while administering oxygenation therapy.
Prevalence and predictors of post-abortion modern contraceptive utilization among reproductive age women in Ethiopia
Authors: Belachew Tadele Biresaw , Negash Wubshet Debebe , Asmamaw Desale Bihonegn , Fetene Samrawit Mihret , Addis Banchlay , Baykeda Tsegaw Amare , Kidie Atitegeb Abera , Endawkie Abel , Zegeye Alebachew Ferede , Tamir Tadesse Tarik , Fentie Elsa Awoke , Wubante Sisay Maru 
Published: September 2023

AbstractThe development of a post-abortion family plan is an integral part of comprehensive abortion care. In spite of this, it received insufficient attention as a means of breaking the cycle of repeated abortions, unintended pregnancies, and maternal deaths resulting from abortion. Therefore, this study examined post abortion modern contraceptive utilization among Ethiopian women as well as associated factors. The study was based on secondary data analysis of the Ethiopian Demographic and Health Survey 2016 data. A total weighted sample of 1236 reproductive age women was included. A multilevel mixed-effect binary logistic regression model was fitted to identify the significant associated factors of post abortion contraceptive use. Statistical significance was determined using Adjusted Odds Ratio (AOR) with 95% confidence interval. Overall prevalence of post abortion contraceptive use was observed to be 25.6% (95% CI: 23.24, 28.12). Women's age 15–24 (AOR = 2.34; 95% CI: 1.11, 4.93), and 25–34 (AOR = 1.94; 95% CI: 1.27, 2.98), married women (AOR = 2.6; 95% CI: 1.43, 4.96), women who had 1–4 (AOR = 4.13; 95% CI: 1.79, 9.57) and ≥ 5 number of children (AOR = 8.80; 95% CI: 3.30, 13.49), Being in metropolitan region (AOR = 9.14; 95% CI: 1.79, 12.48), women being in urban area (AOR = 1.85; 95% CI: 1.32, 2.24), and community media exposure (AOR = 1.75; 95% CI: 1.11, 3.56) were associated with post abortion modern contraceptive use. Post abortion modern contraceptive use in this study was low. Women age, current marital status, number of living children, residency, community media exposure, and region were significantly associated with post abortion modern contraceptive utilization. Therefore, it is better to provide ongoing health information about post-abortion family planning and its benefits, especially for people who live in rural and small peripheral regions, and public health policymakers should take both individual and community level factors into account when designing family planning programmes.
Cutaneous wound healing promoted by topical administration of heat-killed Lactobacillus plantarum KB131 and possible contribution of CARD9-mediated signaling
Authors: Ishi Shinyo , Kanno Emi , Tanno Hiromasa , Kurosaka Shiho , Shoji Miki , Imai Toshiro , Yamaguchi Kenji , Kotsugai Kanna , Niiyama Momoko , Kurachi Haruko , Makabe Fuko , Watanabe Takumi , Sato Ko , Ishii Keiko , Hara Hiromitsu , Imai Yoshimichi , Kawakami Kazuyoshi 
Published: September 2023

AbstractOptimal conditions for wound healing require a smooth transition from the early stage of inflammation to proliferation, and during this time alternatively activated (M2) macrophages play a central role. Recently, heat-killed lactic acid bacteria (LAB), such as Lactobacillus plantarum (L. plantarum) have been reported as possible modulators affecting the immune responses in wound healing. However, how signaling molecules regulate this process after the administration of heat-killed LAB remains unclear. In this study, we examined the effect of heat-killed L. plantarum KB131 (KB131) administration on wound healing and the contribution of CARD9, which is an essential signaling adaptor molecule for NF-kB activation upon triggering through C-type lectin receptors, in the effects of this bacterium. We analyzed wound closure, histological findings, and inflammatory responses. We found that administration of KB131 accelerated wound closure, re-epithelialization, granulation area, CD31-positive vessels, and α-SMA-positive myofibroblast accumulated area, as well as the local infiltration of leukocytes. In particular, M2 macrophages were increased, in parallel with CCL5 synthesis. The acceleration of wound healing responses by KB131 was canceled in CARD9-knockout mice. These results indicate that the topical administration of KB131 accelerates wound healing, accompanying increased M2 macrophages, which suggests that CARD9 may be involved in these responses.
Two-dimensional analytical description of the plasma potential in a magnetron discharge
Authors: Costin Claudiu , Minea Tiberiu M. 
Published: September 2023

AbstractSimple analytical formulas are proposed to describe the plasma potential in a steady-state magnetron discharge, based on the results of various experiments and numerical simulations reported in the literature. The description is two-dimensional (2D), covering two main regions, the cathode sheath and the ionization region, both contributing to electron energization. A parabolic potential in the axial direction governs the cathode sheath. The thickness of the cathode sheath is obtained from the 1D collisionless Child–Langmuir law. A parabolic or linear potential in the axial direction characterizes the ionization region. The local ion current density to the cathode, estimated from the target erosion profile, sets the radial dependence of the potential. The proposed formulas use a set of input parameters that can be experimentally obtained. The analytical description captures all characteristics of the highly inhomogeneous plasma potential of a steady-state magnetron discharge operated in a reduced magnetic field BRT/p lower than 0.1 T/Pa, as revealed by the comparison to self-consistent 2D numerical simulations.
Resistance–capacitance optimizer: a physics-inspired population-based algorithm for numerical and industrial engineering computation problems
Authors: Ravichandran Sowmya , Manoharan Premkumar , Jangir Pradeep , Selvarajan Shitharth 
Published: September 2023

AbstractThe primary objective of this study is to delve into the application and validation of the Resistance Capacitance Optimization Algorithm (RCOA)—a new, physics-inspired metaheuristic optimization algorithm. The RCOA, intriguingly inspired by the time response of a resistance–capacitance circuit to a sudden voltage fluctuation, has been earmarked for solving complex numerical and engineering design optimization problems. Uniquely, the RCOA operates without any control/tunable parameters. In the first phase of this study, we evaluated the RCOA's credibility and functionality by deploying it on a set of 23 benchmark test functions. This was followed by thoroughly examining its application in eight distinct constrained engineering design optimization scenarios. This methodical approach was undertaken to dissect and understand the algorithm's exploration and exploitation phases, leveraging standard benchmark functions as the yardstick. The principal findings underline the significant effectiveness of the RCOA, especially when contrasted against various state-of-the-art algorithms in the field. Beyond its apparent superiority, the RCOA was put through rigorous statistical non-parametric testing, further endorsing its reliability as an innovative tool for handling complex engineering design problems. The conclusion of this research underscores the RCOA's strong performance in terms of reliability and precision, particularly in tackling constrained engineering design optimization challenges. This statement, derived from the systematic study, strengthens RCOA's position as a potentially transformative tool in the mathematical optimization landscape. It also paves the way for further exploration and adaptation of physics-inspired algorithms in the broader realm of optimization problems.
Integrated transcriptomic meta-analysis and comparative artificial intelligence models in maize under biotic stress
Authors: Nazari Leyla , Aslan Muhammet Fatih , Sabanci Kadir , Ropelewska Ewa 
Published: September 2023

AbstractBiotic stress imposed by pathogens, including fungal, bacterial, and viral, can cause heavy damage leading to yield reduction in maize. Therefore, the identification of resistant genes paves the way to the development of disease-resistant cultivars and is essential for reliable production in maize. Identifying different gene expression patterns can deepen our perception of maize resistance to disease. This study includes machine learning and deep learning-based application for classifying genes expressed under normal and biotic stress in maize. Machine learning algorithms used are Naive Bayes (NB), K-Nearest Neighbor (KNN), Ensemble, Support Vector Machine (SVM), and Decision Tree (DT). A Bidirectional Long Short Term Memory (BiLSTM) based network with Recurrent Neural Network (RNN) architecture is proposed for gene classification with deep learning. To increase the performance of these algorithms, feature selection is made from the raw gene features through the Relief feature selection algorithm. The obtained finding indicated the efficacy of BiLSTM over other machine learning algorithms. Some top genes ((S)-beta-macrocarpene synthase,zealexin A1 synthase,polyphenol oxidase I,chloroplastic,pathogenesis-related protein 10,CHY1,chitinase chem 5,barwin, and uncharacterizedLOC100273479were proved to be differentially upregulated under biotic stress condition.
NOXA expression is downregulated in human breast cancer undergoing incomplete pathological response and senescence after neoadjuvant chemotherapy
Authors: Al Shboul Sofian , El-Sadoni Mohammed , Alhesa Ahmad , Abu Shahin Nisreen , Abuquteish Dua , Abu Al Karsaneh Ola , Alsharaiah Elham , Ismail Mohammad A. , Tyutyunyk-Massey Liliya , Alotaibi Moureq R. , Neely Victoria , Harada Hisashi , Saleh Tareq 
Published: September 2023

AbstractNeoadjuvant chemotherapy (NAC) is a frequently utilized approach to treat locally advanced breast cancer, but, unfortunately, a subset of tumors fails to undergo complete pathological response. Apoptosis and therapy-induced senescence (TIS) are both cell stress mechanisms but their exact role in mediating the pathological response to NAC is not fully elucidated. We investigated the change in expression of PAMIP1, the gene encoding for the pro-apoptotic protein, NOXA, following NAC in two breast cancer gene datasets, and the change in NOXA protein expression in response to NAC in 55 matched patient samples (pre- and post-NAC). PAMIP1 expression significantly declined in post-NAC in the two sets, and in our cohort, 75% of the samples exhibited a downregulation in NOXA post-NAC. Matched samples that showed a decline in NOXA post-NAC were examined for TIS based on a signature of downregulated expression of Lamin-B1 and Ki-67 and increased p16INK4a, and the majority exhibited a decrease in Lamin B1 (66%) and Ki-67 (80%), and increased p16INK4a (49%). Since our cohort consisted of patients that did not develop complete pathological response, such findings have clinical implications on the role of TIS and NOXA downregulation in mediating suboptimal responses to the currently established NAC.
A computationally optimized broadly reactive hemagglutinin vaccine elicits neutralizing antibodies against influenza B viruses from both lineages
Authors: Carlock Michael A. , Ross Ted M. 
Published: September 2023

AbstractInfluenza B viruses (IBV) can cause severe disease and death much like influenza A viruses (IAV), with a disproportionate number of infections in children. Despite moving to a quadrivalent vaccine to include strains from both the B/Victoria and B/Yamagata lineages, vaccine effectiveness rates continue to be variable and low in many past seasons. To develop more effective influenza B virus vaccines, three novel IBV hemagglutinin (HA) vaccines were designed using a computationally optimized broadly reactive antigen (COBRA) methodology. These IBV HA proteins were expressed on the surface of a virus-like particle (VLP) and used to vaccinate ferrets that were pre-immune to historical B/Victoria or B/Yamagata lineage viruses. Ferrets vaccinated with B-COBRA HA vaccines had neutralizing antibodies with high titer HAI titer against all influenza B viruses regardless of pre-immunization history. Conversely, VLPs expressing wild-type IBV HA antigens preferentially boosted titers against viruses from the same lineage and there was little-to-no seroprotective antibodies detected in ferrets with mismatched IBV pre-immune infections. Overall, a single IBV HA developed using the COBRA methodology elicited protective broadly-reactive antibodies against current and future drifted IBVs from both lineages.
Mechanosensitive ion channel gene survey suggests potential roles in primary open angle glaucoma
Authors: Liu Wendy W. , Kinzy Tyler G. , Cooke Bailey Jessica N. , Xu Zihe , Hysi Pirro , Wiggs Janey L. ,   NEIGHBORHOOD Consortium, Allingham R. Rand , Brilliant Murray , Budenz Donald L. , Fingert John H. , Gaasterland Douglas , Gaasterland Teresa , Haines Jonathan L. , Hauser Michael A. , Lee Richard K. , Lichter Paul R. , Liu Yutao , Moroi Syoko , Myers Jonathan , Pasquale Louis R. , Pericak-Vance Margaret , Realini Anthony , Rhee Doug , Richards Julia E. , Ritch Robert , Schuman Joel S. , Scott William K. , Singh Kuldev , Sit Arthur J. , Vollrath Douglas , Weinreb Robert N. , Wollstein Gadi , Zack Donald J. 
Published: September 2023

AbstractAlthough glaucoma is a disease modulated by eye pressure, the mechanisms of pressure sensing in the eye are not well understood. Here, we investigated associations between mechanosensitive ion channel gene variants and primary open-angle glaucoma (POAG). Common (minor allele frequency > 5%) single nucleotide polymorphisms located within the genomic regions of 20 mechanosensitive ion channel genes in the K2P, TMEM63, PIEZO and TRP channel families were assessed using genotype data from the NEIGHBORHOOD consortium of 3853 cases and 33,480 controls. Rare (minor allele frequency < 1%) coding variants were assessed using exome array genotyping data for 2606 cases and 2606 controls. Association with POAG was analyzed using logistic regression adjusting for age and sex. Two rare PIEZO1 coding variants with protective effects were identified in the NEIGHBOR dataset: R1527H, (OR 0.17, P = 0.0018) and a variant that alters a canonical splice donor site, g.16-88737727-C-G Hg38 (OR 0.38, P = 0.02). Both variants showed similar effects in the UK Biobank and the R1527H also in the FinnGen database. Several common variants also reached study-specific thresholds for association in the NEIGHBORHOOD dataset. These results identify novel variants in several mechanosensitive channel genes that show associations with POAG, suggesting that these channels may be potential therapeutic targets.
Manganese nanoparticles control the gene regulations against multiple stresses in Pangasianodon hypophthalmus
Authors: Kumar Neeraj , Thorat Supriya Tukaram , Singh Ajay Kumar , Kochewad Sanjivkumar Angadrao , Reddy Kotha Sammi 
Published: September 2023

AbstractAmmonia and arsenic pollution, along with the impact of climate change, represent critical factors influencing both the quantity and quality of aquaculture production. Recent developments have underscored the significance of these issues, as they not only disrupt aquatic ecosystems but also have far reaching consequences for human health. To addressed above challenges, an experiment was conducted to delineate the potential of manganese nanoparticles (Mn-NPs) to mitigate arsenic and ammonia pollution as well as high temperature stress in Pangasianodon hypophthalmus. The fish were exposed to different combination of arsenic and ammonia pollution as well as high temperature stress, while simultaneously incorporating diets enriched with Mn-NPs. The inclusion of Mn-NPs at 3 mg kg−1 in the diet led to a noteworthy downregulation of cortisol and HSP 70 gene expression, indicating their potential in mitigating stress responses. Furthermore, immune related gene expressions were markedly altered in response to the stressors but demonstrated improvement with the Mn-NPs diet. Interestingly, the expression of inducible nitric oxide synthase (iNOS), caspase (CAS), metallothionine (MT) and cytochrome P450 (CYP450) genes expression were prominently upregulated, signifying a stress response. Whereas, Mn-NPs at 3 mg kg−1 diet was significantly downregulated theses gene expression and reduces the stress. In addition to stress-related genes, we evaluated the growth-related gene expressions such as growth hormone (GH), growth hormone regulator 1 (GHR1 and GHRβ), Insulin like growth factor (IGF1 and IGF2) were significantly upregulated whereas, myostatin and somatostatin were downregulated upon the supplementation of dietary Mn-NPs with or without stressors in fish. The gene expression of DNA damage inducible protein and DNA damage in response to head DNA % and tail DNA % was protected by Mn-NPs diets. Furthermore, Mn-NPs demonstrated a capacity to enhance the detoxification of arsenic in different fish tissues, resulting in reduced bioaccumulation of arsenic in muscle and other tissues. This finding highlights Mn-NPs as a potential solution for addressing bioaccumulation associated risks. Our study aimed to comprehensively examined the role of dietary Mn-NPs in mitigating the multiple stressors using gene regulation mechanisms, with enhancing the productive performance of P. hypophthalmus.