bluuebunny/crossref_metadata_2025_split huggingface dataset:
Learning processes in hierarchical pairs regulate entire gene expression in cells
Authors: Yamaguchi Tomoyuki 
Published: May 2022

AbstractExpression of numerous genes is precisely controlled in a cell in various contexts. While genetic and epigenetic mechanisms contribute to this regulation, how each mechanism cooperates to ensure the proper expression patterns of the whole gene remains unclear. Here, I theoretically show that the repetition of simple biological processes makes cells functional with the appropriate expression patterns of all genes if the inappropriateness of current expression ratios is roughly fed back to the epigenetic states. A learning pair model is developed, in which two factors autonomously approach the target ratio by repeating two stochastic processes; competitive amplification with a small addition term and decay depending on the difference between the current and target ratios. Furthermore, thousands of factors are self-regulated in a hierarchical-pair architecture, in which the activation degrees competitively amplify, while transducing the activation signal, and decay at four different probabilities. Changes in whole-gene expression during human early embryogenesis and hematopoiesis are reproduced in simulation using this epigenetic learning process in a single genetically-determined hierarchical-pair architecture of gene regulatory cascades. On the background of this learning process, I propose the law of biological inertia, which means that a living cell basically maintains the expression pattern while renewing its contents.
Physics-informed attention-based neural network for hyperbolic partial differential equations: application to the Buckley–Leverett problem
Authors: Rodriguez-Torrado Ruben , Ruiz Pablo , Cueto-Felgueroso Luis , Green Michael Cerny , Friesen Tyler , Matringe Sebastien , Togelius Julian 
Published: May 2022

AbstractPhysics-informed neural networks (PINNs) have enabled significant improvements in modelling physical processes described by partial differential equations (PDEs) and are in principle capable of modeling a large variety of differential equations. PINNs are based on simple architectures, and learn the behavior of complex physical systems by optimizing the network parameters to minimize the residual of the underlying PDE. Current network architectures share some of the limitations of classical numerical discretization schemes when applied to non-linear differential equations in continuum mechanics. A paradigmatic example is the solution of hyperbolic conservation laws that develop highly localized nonlinear shock waves. Learning solutions of PDEs with dominant hyperbolic character is a challenge for current PINN approaches, which rely, like most grid-based numerical schemes, on adding artificial dissipation. Here, we address the fundamental question of which network architectures are best suited to learn the complex behavior of non-linear PDEs. We focus on network architecture rather than on residual regularization. Our new methodology, called physics-informed attention-based neural networks (PIANNs), is a combination of recurrent neural networks and attention mechanisms. The attention mechanism adapts the behavior of the deep neural network to the non-linear features of the solution, and break the current limitations of PINNs. We find that PIANNs effectively capture the shock front in a hyperbolic model problem, and are capable of providing high-quality solutions inside the convex hull of the training set.
Novel brown adipose tissue candidate genes predicted by the human gene connectome
Authors: Salazar-Tortosa Diego F. , Enard David , Itan Yuval , Ruiz Jonatan R. 
Published: May 2022

AbstractBrown adipose tissue (BAT) is a promising therapeutic target against obesity. Therefore, research on the genetic architecture of BAT could be key for the development of successful therapies against this complex phenotype. Hypothesis-driven candidate gene association studies are useful for studying genetic determinants of complex traits, but they are dependent upon the previous knowledge to select candidate genes. Here, we predicted 107 novel-BAT candidate genes in silico using the uncoupling protein one (UCP1) as the hallmark of BAT activity. We first identified the top 1% of human genes predicted by the human gene connectome to be biologically closest to the UCP1, estimating 167 additional pathway genes (BAT connectome). We validated this prediction by showing that 60 genes already associated with BAT were included in the connectome and they were biologically closer to each other than expected by chance (p < 2.2 × 10−16). The rest of genes (107) are potential candidates for BAT, being also closer to known BAT genes and more expressed in BAT biopsies than expected by chance (p < 2.2 × 10−16; p = 4.39 × 10–02). The resulting new list of predicted human BAT genes should be useful for the discovery of novel BAT genes and metabolic pathways.
Lung function, allergic sensitization and asthma in school-aged children after viral-coinfection bronchiolitis
Authors: Ruiz Sara , Calvo Cristina , Pozo Francisco , Casas Inmaculada , García-García María Luz 
Published: May 2022

AbstractOur main objective was to compare the lung function, the rate of allergic sensitization and the prevalence of asthma at 7–9 years in children hospitalized for bronchiolitis with viral coinfection versus single viral infection. Observational study in children with previous bronchiolitis and current age 7–9 years. Clinical data were collected. Fraction of exhaled nitric oxide (FeNO) determination, spirometry and skin prick test for common aeroallergens were performed. A total of 181 children hospitalized for bronchiolitis (40 coinfections and 141 single infections), with median age of 8.3 years (IQR:7.5–9.1) were included. Single-HRV-infections showed lower basal FEV1(%) than coinfections (p = 0.04) and lower z-score FEV1than single-RSV-infections (p = 0.04) or coinfections (p = 0.02). Also, single-HRV-infections had lower post-bronchodilator FEV1(%) and z-score FEV1values than coinfections (p = 0.03 andp = 0.03). Single-HRV-bronchiolitis was an independent risk factor for FEV1 < 80% (p = 0.007). FeNO value > 25 ppb was detected in 21(12.5%) cases, without differences between viral groups (p = 0.768). The prevalence of allergic sensitization was similar in coinfections (31.4%) versus single infections (38.7%), (p = 0.428). The highest frequency of allergic rhinitis was observed in single-HRV patients (p = 0.004). The respiratory morbidity at 7–9 years of coinfected patients was similar to the single-HRV ones. In contrast, the likelihood of current asthma was up to 5 times higher in RSV/HRV coinfections than in the single-RSV-infections ones (p = 0.012). The respiratory morbidity at 7–9 years of age after severe bronchiolitis is significantly higher in single-HRV or viral coinfection patients that in single-RSV ones. Single-HRV-bronchiolitis is independently associated with lower lung function at school-age.
The influence of grain shape and size on the relationship between porosity and permeability in sandstone: a digital approach
Authors: Payton Ryan L. , Chiarella Domenico , Kingdon Andrew 
Published: May 2022

AbstractAn accurate and reliable description of the porosity–permeability relationship in geological materials is valuable in understanding subsurface fluid movement. This is important for reservoir characterisation, energy exploitation, geological carbon storage (GCS) and groundwater contamination and remediation. Whilst the relationship between pore characteristics and porosity and permeability are well examined, further investigation into the influence of grain characteristics on porosity and permeability would be beneficial due to the inherent relationship between grains and pores. This work aims to determine whether incorporation of grain characteristics into a porosity–permeability model is effective in constraining this relationship. Two fully digital approaches to individual 3D grain analysis based upon watershed segmentation are compared to determine the most effective, yet simple, workflow applicable to core plugs of significantly compacted grains. The identification of an effective segmentation workflow will facilitate future work on similarly complex materials, removing the need for traditional time-consuming and manual techniques. We use the most effective approach of measuring grain shape (sphericity) and size (Feret diameter) alongside an established fully digital workflow to measure porosity and permeability to investigate the impact of grain characteristics on porosity and permeability. We show that grain sphericity and porosity exhibit a positive relationship whereas no such relationship exists with grain size. Measurements of grain sphericity are applied to calculate a Kozeny–Carman (K–C) type porosity–permeability fit which was found to be unsatisfactory, compared to a simpler fit excluding any grain parameters. This is possibly due to the lower sphericity of the studied grains, deviating significantly from the K–C assumption that grains are entirely spherical. The simpler fit is most suitable for the studied materials, showing that inclusion of grain characteristics is not effective for better defining the porosity–permeability relationship in a K–C paradigm for these samples. This highlights the need for a model capable of considering a range of grain sphericities to further constrain the porosity–permeability relationship.
Modeling of energy consumption factors for an industrial cement vertical roller mill by SHAP-XGBoost: a "conscious lab" approach
Authors: Fatahi Rasoul , Nasiri Hamid , Dadfar Ehsan , Chehreh Chelgani Saeed 
Published: May 2022

AbstractCement production is one of the most energy-intensive manufacturing industries, and the milling circuit of cement plants consumes around 4% of a year's global electrical energy production. It is well understood that modeling and digitalizing industrial-scale processes would help control production circuits better, improve efficiency, enhance personal training systems, and decrease plants' energy consumption. This tactical approach could be integrated using conscious lab (CL) as an innovative concept in the internet age. Surprisingly, no CL has been reported for the milling circuit of a cement plant. A robust CL interconnect datasets originated from monitoring operational variables in the plants and translating them to human basis information using explainable artificial intelligence (EAI) models. By initiating a CL for an industrial cement vertical roller mill (VRM), this study conducted a novel strategy to explore relationships between VRM monitored operational variables and their representative energy consumption factors (output temperature and motor power). Using SHapley Additive exPlanations (SHAP) as one of the most recent EAI models accurately helped fill the lack of information about correlations within VRM variables. SHAP analyses highlighted that working pressure and input gas rate with positive relationships are the key factors influencing energy consumption. eXtreme Gradient Boosting (XGBoost) as a powerful predictive tool could accurately model energy representative factors by R-square ever 0.80 in the testing phase. Comparison assessments indicated that SHAP-XGBoost could provide higher accuracy for VRM-CL structure than conventional modeling tools (Pearson correlation, Random Forest, and Support vector regression.
Experience sampling self-reports of social media use have comparable predictive validity to digital trace measures
Authors: Verbeij Tim , Pouwels J. Loes , Beyens Ine , Valkenburg Patti M. 
Published: May 2022

AbstractResearch agrees that self-reported measures of time spent with social media (TSM) show poor convergent validity, because they correlate modestly with equivalent objective digital trace measures. This experience sampling study among 159 adolescents (12,617 self-reports) extends this work by examining the comparative predictive validity of self-reported and digital trace measures of TSM, that is, the extent to which self-reported and digital trace measures of TSM correspond in their effects on self-esteem, well-being, and friendship closeness. Using an N = 1 method of analysis, we investigated the correspondence on a between-person, within-person, and person-specific level. Although our results confirmed the poor convergent validity of self-reported TSM reported earlier, we found that self-reports of TSM had comparable predictive validity to digital trace measures on all three levels. Because comparative predictive validity of self-reported TSM is crucial for investigating social media effects, our results have important implications for future research using self-reported TSM.
The value of Ki67 for the diagnosis of LSIL and the problems of p16 in the diagnosis of HSIL
Authors: Liu Jixuan , Su Sanmei , Liu Yafang 
Published: May 2022

Abstractp16 and Ki67 are immunohistochemical markers related to cervical squamous intraepithelial lesions. p16 has been widely used to assist in the diagnosis of high-grade squamous intraepithelial lesions. However, a conclusion about the role of Ki67 in the diagnosis of squamous intraepithelial lesions has not been established. The aim of this study was to analyze the role of p16 and Ki67 immunohistochemical staining in assisting cervical squamous intraepithelial lesions. This study performed immunohistochemical staining for p16 and Ki67 on 1024 cervical biopsy specimens at our hospital to compare the differences between p16 and Ki67 in different cervical lesions using the chi-squared test and Fisher’s exact test. This study also evaluated the value of Ki67 for the diagnosis of low-grade squamous intraepithelial lesions (LSILs) using the receiver operating characteristic curve. The results indicated that Ki67 had high specificity and sensitivity in distinguishing LSIL from normal cervix. p16 was diffusely and strongly positive in some LSILs, and some problems were encountered in the interpretation of p16 staining. Therefore, we believe that Ki67 can be used as an immunohistochemical marker to help in the diagnosis of LSIL, to distinguish lesions that are difficult to morphologically determine and to avoid misdiagnosis. The practical application of p16 staining is still problematic. It may be necessary to find other auxiliary means to distinguish this small proportion of cervical lesions.
The effect of reducing per capita water and energy uses on renewable water resources in the water, food and energy nexus
Authors: Kheirinejad Shima , Bozorg-Haddad Omid , Singh Vijay P. , Loáiciga Hugo A. 
Published: May 2022

AbstractThis study assesses the feedbacks between water, food, and energy nexus at the national level with a dynamic-system model, taking into account the qualitative and quantitative environmental water needs. Surface and groundwater resources are considered jointly in the water resources subsystem of this dynamic system. The developed model considers the effects of reducing the per capita use water and energy on its system’s components. Results indicate that due to feedbacks the changes in per capita uses of water and energy have indirect and direct effects. About 40% of the total water savings achieved by the per capita change policy was related to energy savings, in other words, it is an indirect saving. Implementation of per capita use reductions compensates for 9% of the decline of Iran's groundwater reservoirs (non-renewable resources in the short term) that occur during the five-year study period. The Manageable and Exploitable Renewable Water Stress Index (MRWI) corresponding to water and energy savings equals 214.5%, which is better than its value under the current situation (which is equal to 235.1%).
Analyzing historical and future acute neurosurgical demand using an AI-enabled predictive dashboard
Authors: Pandit Anand S. , Jalal Arif H. B. , Toma Ahmed K. , Nachev Parashkev 
Published: May 2022

AbstractCharacterizing acute service demand is critical for neurosurgery and other emergency-dominant specialties in order to dynamically distribute resources and ensure timely access to treatment. This is especially important in the post-Covid 19 pandemic period, when healthcare centers are grappling with a record backlog of pending surgical procedures and rising acute referral numbers. Healthcare dashboards are well-placed to analyze this data, making key information about service and clinical outcomes available to staff in an easy-to-understand format. However, they typically provide insights based on inference rather than prediction, limiting their operational utility. We retrospectively analyzed and prospectively forecasted acute neurosurgical referrals, based on 10,033 referrals made to a large volume tertiary neurosciences center in London, U.K., from the start of the Covid-19 pandemic lockdown period until October 2021 through the use of a novel AI-enabled predictive dashboard. As anticipated, weekly referral volumes significantly increased during this period, largely owing to an increase in spinal referrals (p < 0.05). Applying validated time-series forecasting methods, we found that referrals were projected to increase beyond this time-point, with Prophet demonstrating the best test and computational performance. Using a mixed-methods approach, we determined that a dashboard approach was usable, feasible, and acceptable among key stakeholders.
Association between bronchopulmonary dysplasia and early respiratory morbidity in children with respiratory distress syndrome: a case–control study using nationwide data
Authors: Shin Jeong Eun , Jang Haerin , Han Jung Ho , Park Joonsik , Kim Soo Yeon , Kim Yoon Hee , Eun Ho Seon , Lee Soon Min , Park Kook In , Sohn Myung Hyun , Park Min Soo , Kim Kyung Won 
Published: May 2022

AbstractBronchopulmonary dysplasia (BPD) can cause respiratory morbidity beyond the neonatal period. We aimed to analyze the association of BPD on childhood lower respiratory illness (LRI) and asthma among patients diagnosed with respiratory distress syndrome (RDS). This case–control study analyzed data between 2002 and 2015 from a nationwide database. We included 55,066 children with RDS. Two-year LRI and asthma at ages 3 and 5 were assessed. Readmission for LRIs within 2 years of birth occurred in 53.9% and 37.9% of the BPD (n = 9470) and non-BPD (n = 45,596) cases, respectively. In the BPD group, the median number of hospitalizations, mechanical ventilation and oxygen use rates were significantly higher, while the hospitalization duration was significantly longer (P < 0.001 for all). The relative risk of BPD was 1.42 (1.39–1.45) on total readmission and 6.53 (5.96–7.15) on intensive care unit readmission. Asthma prevalence was significantly higher in BPD group (57.6% vs. 48.9% at age 3 and 44.3% vs. 38.2% at age 5, P < 0.001). In children with RDS, BPD could affect repetitive and worse LRI as an independent risk factor for respiratory morbidity during the first 2 years of life. BPD may also be a crucial risk factor for asthma in preschoolers.
T-shaped double-strip spoof surface plasmon polariton transmission lines and application to microwave resonators
Authors: Choi Wonseok , Jeong Jinho 
Published: May 2022

AbstractA microwave double-strip spoof surface plasmon polariton (DS SSPP) is proposed for high-speed interconnects and high-performance microwave circuits. Based on the dispersion analysis, a T-shaped double-strip structure is designed to provide strong surface- and slow-wave properties from very low to very high frequencies (~ 40 GHz). It allows the tight field confinement and greatly reduces the electromagnetic wave leakage. It exhibits broadband performance with reduced ripples in the insertion loss. It also shows more constant group delay and impedance than counterpart single-strip SSPP. The compact coaxial-to-microstrip-to-DS SSPP transition are designed using gradient grooves. The measurement shows that the DS SSPP lines can exhibit the lower coupling and lower insertion loss than the microstrip lines, so that the former is well-suited for the densely packed high-speed interconnects. The designed DS SSPP is utilized for high quality (Q)-factor microwave ring resonator. The measured unloaded Q-factor is 107.9 at the resonant frequency of 8.7 GHz, which is 1.3 times higher than the microstrip ring resonator. It is found to be caused by the reduction of the radiation loss, according to the loss analysis. The size is also reduced due to the short wavelength, occupying 56.8% of that of the microstrip ring resonator. Therefore, the proposed T-shaped DS SSPP can be also applied for high-performance miniaturized microwave circuits.
The comparison of efficacy and safety between transradial and transfemoral approach for chronic total occlusions intervention: a meta-analysis
Authors: Lee Wei-Chieh , Wu Po-Jui , Fang Chih-Yuan , Fang Hsiu-Yu , Wu Chiung-Jen , Liu Ping-Yen 
Published: May 2022

AbstractThis meta-analysis compared the outcomes of transradial access (TRA) and transfemoral access (TFA) in chronic total occlusion (CTO) percutaneous coronary intervention (PCI) in recent decades. We searched multiple databases for articles published between January 1, 2015, and December 31, 2020. Six observational studies with 11,736 patients were analyzed. Data included baseline demographics, Japan-chronic total occlusion (J-CTO) score, sheath size, PCI vessel, retrograde method, procedural time, fluoroscopy time, and contrast volume. The more prevalent target CTO vessel was the left coronary artery in the TRA group and the right coronary artery in the TFA group. Higher J-CTO score, longer procedural time, and more contrast volume were seen in the TFA group. In comparison, the TRA group had better procedural success rate (odds ratio (OR), 0.846; 95% confidence interval (CI) 0.749–0.956) and less vascular complications (OR, 0.323; 95% CI 0.203–0.515), but similar retrograde success rate (OR, 0.965; 95% CI 0.382–2.435). In-hospital death (OR, 0.527; 95% CI 0.187–1.489) and major adverse cardiovascular events (OR, 0.729; 95% CI 0.504–1.054) did not differ between the groups. Overall, fewer vascular complications and higher procedural success rates were noted in the TRA CTO PCI population. However, similar retrograde success rates and clinical outcomes were noted between the groups.
Associations of interpersonal trust with juvenile offending/conduct disorder, callous-unemotional traits, and criminal recidivism
Authors: Aebi Marcel , Haynes Melanie , Bessler Cornelia , Hasler Gregor 
Published: May 2022

AbstractInterpersonal trust has been described as a core dimension of cooperative, mutually beneficial interpersonal relationships but it is unclear if it is related to antisocial behaviours in youth. The present study aimed at analysing a subsample of male juveniles who committed serious violent offenses and met criteria of conduct disorder (JO/CD), and a subsample of healthy controls (HC) using a series of trust games (TGs). Twenty-four male JO/CD and 24 age matched male HC performed a series of eight one-shot TGs against different unknown human respectively computer opponents. Mixed model analyses found a non-significant trend that JO/CD invested less points than HC during TGs. In the subsample of JO/CD, the overall investment in TGs was found to be negatively associated with self-reported uncaring behaviours and officially reported general re-offenses. Our findings suggest some indication of an impaired ability of JO/CD to initiate mutually trusting relationships to others that should be addressed in further research. Trust is a promising factor to predict general criminal recidivism and can be a target for treatment of juveniles who committed violent offenses, for example through the building of stable relationships to care givers. This study encourages future studies to investigate the effects of trust-increasing psychosocial interventions.