bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Pixelation Method for Loads Transfer on Fluid Structure Interface
Authors: Cheng Pan , Sun Yuchen , Zhao Yang , Ding Zekai , Zhang Wu 
Published: April 2021

Abstract
Fluid Structure Interaction (FSI) is widely applied in aircraft aerodynamic and aeroelastic analysis. Iteration between the CFD and FEA will solve the aerodynamic force, flow field, structure stress and deformation under equilibrium state simultaneously. In aircraft product development, the CFD mesh and Finite element model normally do not match each other because the goal of CFD and FEA are different. To connect between unmatched interface, a pixelation method is developed to transfer the aerodynamic loads onto the finite element model correctly. The pixelation method is also easy to be implemented and parallelized.
Direct Numerical Simulation of Particle-laden Flow Around an Obstacle at Different Reynolds Numbers
Authors: Lin Shengxiang , Xia Huanxiong , Zhang Zhenyu , Liu Jianhua , Wang Honglei 
Published: April 2021

Abstract
Inspired by the practical operation of the fluid machineries, direct numerical simulation of fluid with a lot of finite-size particles flowing around a large-size obstacle at three different Reynolds numbers is implemented by using a two-way coupled finite-volume, discrete-element and immersed-boundary method. The results show that, for a low Reynolds number Re=20, the flow is dominated by viscosity, and under the circumstances of a small Stokes number, the particles follow fluid streamlines closely. The flow suggests regular movement characteristics of laminar flow, although the vortices behind the obstacle tend to collapse under the perturbation of particles. For a moderate Reynolds number Re=100, the phenomenon of vortex shedding is also observed. Due to the centrifugal force induced by the vortices, particles are distributed around the main vortices behind the obstacle, forming particle-free zones in these vortices. For a high Reynolds number Re=300, the flow is chaotic. The vortices of many sizes appear irregularly in the domain and the distribution of particles tends to be uniform.
Analysis on technological features of pile foundations construction in frozen and seasonal thawing soils
Authors: Montayeva A , Zhussupbekov A , Kaliakin V N , Montayev S 
Published: April 2021

Abstract
This article assesses the more productive methods for thawing seasonally frozen soils. The most rational and progressive method of thawing seasonally frozen soils involves putting antifreeze additives into the soil. New goals and objectives for the development of pile foundation construction technology in seasonally frozen soils in northern and central regions of Kazakhstan is presented.
Characterization and assessment of crushed limestone powder and its environmental applications
Authors: Dafalla Muawia , Al-Mahbashi Ahmed , Alnuaim Ahmed 
Published: April 2021

Abstract
The subway (metro) and tunnel excavation works are of high demand in today’s large and urban cities. The use of tunnel boring machines resulted in huge quantities of crushed rock powder and generally treated as waste. This work is aimed at the characterization and assessment of Riyadh limestone powder and its possible use as a construction material. The environmental application of this powder as an additive to clay sand liners proved to be useful and efficient. Advanced testing indicated that this material can occupy part of the voids and help in reducing the high expansive nature of the liners and yet maintain a satisfactory hydraulic conductivity. Geotechnical characterization as well as SEM testing was performed. Soil water characteristic curves were established for selected mixtures. The introduction of this material was found environmentally friendly and can reduce the demand for bentonite and highly expansive additives.
The design of geotechnical structures using numerical methods
Authors: Jürgens H. , Henke S. 
Published: April 2021

Abstract
The use of numerical simulations in geotechnical engineering today is often limited to the investigation of the serviceability limit state (SLS). Therefore, the main focus up to now was more on the deformation prognosis for geotechnical constructions than the geotechnical design itself. Nevertheless, numerical methods like the Finite-Element-Method (FEM) for example can be a valuable tool to investigate the bearing capacity of geotechnical structures as well. E.g. existing structures which cannot be calculated using classical analytical approaches can be investigated with numerical simulations to estimate the remaining bearing capacity. In the present paper, the use of numerical methods for the design of geotechnical structures will be discussed. First, the approved ϕ - c reduction method is recalculated and verified with the help of a script based on the Python programming language. Afterwards, the Python script is extended so that the diameter of an Embedded Beam Row element can be successively reduced automatically similar to the ϕ - c reduction. Finally, a short outlook is given in which direction the research project should proceed.
California’s Mental Health Services Act and Mortality Due to Suicide, Homicide, and Acute Effects of Alcohol: A Synthetic Control Application
Authors: Zimmerman Scott C , Matthay Ellicott C , Rudolph Kara E , Goin Dana E , Farkas Kriszta , Rowe Christopher L , Ahern Jennifer 
Published: April 2021

AbstractCalifornia’s Mental Health Services Act (MHSA) substantially expanded funding of county mental health services through a state tax, and led to broad prevention efforts and intensive services for individuals experiencing serious mental disorders. We estimated the associations between MHSA and mortality due to suicide, homicide, and acute effects of alcohol. Using annual cause-specific mortality data for each US state and the District of Columbia from 1976–2015, we used a generalization of the quasi-experimental synthetic control method to predict California’s mortality rate for each outcome in the absence of MHSA using a weighted combination of comparison states. We calculated the association between MHSA and each outcome as the absolute difference and percentage difference between California’s observed and predicted average annual rates over the postintervention years (2007–2015). MHSA was associated with modest decreases in average annual rates of homicide (−0.81/100,000 persons, corresponding to a 13% reduction) and mortality from acute alcohol effects (−0.35/100,000 persons, corresponding to a 12% reduction). Placebo test inference suggested that the associations were unlikely to be due to chance. MHSA was not associated with suicide. Protective associations with mortality due to homicide and acute alcohol effects provide evidence for modest health benefits of MHSA at the population level.
Network-based identification of key master regulators associated with an immune-silent cancer phenotype
Authors: Mall Raghvendra , Saad Mohamad , Roelands Jessica , Rinchai Darawan , Kunji Khalid , Almeer Hossam , Hendrickx Wouter , M Marincola Francesco , Ceccarelli Michele , Bedognetti Davide 
Published: April 2021

AbstractA cancer immune phenotype characterized by an active T-helper 1 (Th1)/cytotoxic response is associated with responsiveness to immunotherapy and favorable prognosis across different tumors. However, in some cancers, such an intratumoral immune activation does not confer protection from progression or relapse. Defining mechanisms associated with immune evasion is imperative to refine stratification algorithms, to guide treatment decisions and to identify candidates for immune-targeted therapy. Molecular alterations governing mechanisms for immune exclusion are still largely unknown. The availability of large genomic datasets offers an opportunity to ascertain key determinants of differential intratumoral immune response. We follow a network-based protocol to identify transcription regulators (TRs) associated with poor immunologic antitumor activity. We use a consensus of four different pipelines consisting of two state-of-the-art gene regulatory network inference techniques, regularized gradient boosting machines and ARACNE to determine TR regulons, and three separate enrichment techniques, including fast gene set enrichment analysis, gene set variation analysis and virtual inference of protein activity by enriched regulon analysis to identify the most important TRs affecting immunologic antitumor activity. These TRs, referred to as master regulators (MRs), are unique to immune-silent and immune-active tumors, respectively. We validated the MRs coherently associated with the immune-silent phenotype across cancers in The Cancer Genome Atlas and a series of additional datasets in the Prediction of Clinical Outcomes from Genomic Profiles repository. A downstream analysis of MRs specific to the immune-silent phenotype resulted in the identification of several enriched candidate pathways, including NOTCH1, TGF-$\beta $, Interleukin-1 and TNF-$\alpha $ signaling pathways. TGFB1I1 emerged as one of the main negative immune modulators preventing the favorable effects of a Th1/cytotoxic response.
Biological Field Stations Promote Science Literacy through Outreach
Authors: Struminger Rhonda , Short Rachel A , Zarestky Jill , Vilen Lauren , Lawing A Michelle 
Published: April 2021

Abstract
Biological field stations (BFSs) are well positioned through their informal STEM (science, technology, engineering, and mathematics) education programs to improve levels of science literacy and support environmental sustainability. A survey of 223 US BFSs revealed that their outreach programs strive to promote conservation and environmental stewardship in addition to disseminating place-based knowledge and/or skills. In this article, we unpack the educational approaches that BFSs use to engage learners, the aspects of science literacy most often addressed, and the perceived learning outcomes. Most notably, the BFSs reported that their participants develop an interest in and excitement for science, increase or change their knowledge of program topics, identify more with the scientific enterprise, and engage in scientific practices. The results indicate opportunities for BFSs to conduct more rigorous assessments of participant learning and program impact. By focusing on learner engagement, science learning, and participant outcomes, BFSs and other place-based informal education venues can expand their efforts and better support conservation and science learning.
Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in Intercollegiate Athletics Not Fully Mitigated With Daily Antigen Testing
Authors: Moreno Gage K , Braun Katarina M , Pray Ian W , Segaloff Hannah E , Lim Ailam , Poulsen Keith , Meiman Jonathan , Borcher James , Westergaard Ryan P , Moll Michael K , Friedrich Thomas C , O’Connor David H 
Published: April 2021

Abstract

Background
High-frequency, rapid-turnaround severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing continues to be proposed as a way of efficiently identifying and mitigating transmission in congregate settings. However, 2 SARS-CoV-2 outbreaks occurred among intercollegiate university athletic programs during the fall 2020 semester, despite mandatory directly observed daily antigen testing.

Methods
During the fall 2020 semester, athletes and staff in both programs were tested daily using Quidel’s Sofia SARS Antigen Fluorescent Immunoassay, with positive antigen results requiring confirmatory testing with real-time reverse-transcription polymerase chain reaction. We used genomic sequencing to investigate transmission dynamics in these 2 outbreaks.

Results
In the first outbreak, 32 confirmed cases occurred within a university athletics program after the index patient attended a meeting while infectious, despite a negative antigen test on the day of the meeting. Among isolates sequenced from that outbreak, 24 (92%) of 26 were closely related, suggesting sustained transmission following an initial introduction event. In the second outbreak, 12 confirmed cases occurred among athletes from 2 university programs that faced each other in an athletic competition, despite receipt of negative antigen test results on the day of the competition. Sequences from both teams were closely related and distinct from viruses circulating in the community for team 1, suggesting transmission during intercollegiate competition in the community for team 2.

Conclusions
These findings suggest that antigen testing alone, even when mandated and directly observed, may not be sufficient as an intervention to prevent SARS-CoV-2 outbreaks in congregate settings, and they highlight the importance of vaccination to prevent SARS-CoV-2 outbreak in congregate settings.
The role of cation diffusion facilitator CDF-1 in lipid metabolism in Caenorhabditis elegans
Authors: Hu Ying , Wang Yanli , Wang Xuanjun , Wu Xiaoyun , Fu Lin , Liu Xiayu , Wen Yu , Sheng Jun , Zhang Jingjing 
Published: April 2021

Abstract
Zinc is one of the most important trace elements as it plays a vital role in many biological processes. As well, aberrant zinc metabolism has been implicated in lipid-related metabolic diseases. Previously, we showed that zinc antagonizes iron to regulate sterol regulatory element-binding proteins and the stearoyl-CoA desaturase (SREBP-SCD) pathway in lipid metabolism in the model organism Caenorhabditis elegans. In this study, we present the identification of another cation diffusion facilitator, CDF-1, which regulates lipid metabolism along with SUR-7 in response to zinc. Inactivation of SBP-1, the only homolog of SREBPs, leads to an increased zinc level but decreased lipid accumulation. However, either the cdf-1(n2527) or sur-7(tm6523) mutation could successfully restore the altered fatty acid profile, fat content, and zinc level of the sbp-1(ep79) mutant. Furthermore, we found that CDF-1/SUR-7 may functionally bypass SBP-1 to directly affect the conversion activity of SCD in the biosynthesis of unsaturated fatty acids and lipid accumulation. Collectively, these results consistently support the link between zinc homeostasis and lipid metabolism via the SREBP-SCD axis by the cation diffusion facilitators CDF-1 and SUR-7.
Caenorhabditis elegansjunctophilin has tissue-specific functions and regulates neurotransmission with extended-synaptotagmin
Authors: Piggott Christopher A , Wu Zilu , Nurrish Stephen , Xu Suhong , Kaplan Joshua M , Chisholm Andrew D , Jin Yishi 
Published: April 2021

AbstractThe junctophilin family of proteins tether together plasma membrane (PM) and endoplasmic reticulum (ER) membranes, and couple PM- and ER-localized calcium channels. Understanding in vivo functions of junctophilins is of great interest for dissecting the physiological roles of ER-PM contact sites. Here, we show that the sole Caenorhabditis elegans junctophilin JPH-1 localizes to discrete membrane contact sites in neurons and muscles and has important tissue-specific functions. jph-1 null mutants display slow growth and development due to weaker contraction of pharyngeal muscles, leading to reduced feeding. In the body wall muscle, JPH-1 colocalizes with the PM-localized EGL-19 voltage-gated calcium channel and ER-localized UNC-68 RyR calcium channel, and is required for animal movement. In neurons, JPH-1 colocalizes with the membrane contact site protein Extended-SYnaptoTagmin 2 (ESYT-2) in the soma, and is present near presynaptic release sites. Interestingly, jph-1 and esyt-2 null mutants display mutual suppression in their response to aldicarb, suggesting that JPH-1 and ESYT-2 have antagonistic roles in neuromuscular synaptic transmission. Additionally, we find an unexpected cell nonautonomous effect of jph-1 in axon regrowth after injury. Genetic double mutant analysis suggests that jph-1 functions in overlapping pathways with two PM-localized voltage-gated calcium channels, egl-19 and unc-2, and with unc-68 for animal health and development. Finally, we show that jph-1 regulates the colocalization of EGL-19 and UNC-68 and that unc-68 is required for JPH-1 localization to ER-PM puncta. Our data demonstrate important roles for junctophilin in cellular physiology, and also provide insights into how junctophilin functions together with other calcium channels in vivo.
A chromosome-level reference genome of the hazelnut, Corylus heterophylla Fisch
Authors: Zhao Tiantian , Ma Wenxu , Yang Zhen , Liang Lisong , Chen Xin , Wang Guixi , Ma Qinghua , Wang Lujun 
Published: April 2021

Abstract

Background
Corylus heterophylla Fisch. is a species of the Betulaceae family native to China. As an economically and ecologically important nut tree, C. heterophylla can survive in extremely low temperatures (–30 to –40 °C). To deepen our knowledge of the Betulaceae species and facilitate the use of C. heterophylla for breeding and its genetic improvement, we have sequenced the whole genome of C. heterophylla.

Findings
Based on &gt;64.99 Gb (∼175.30×) of Nanopore long reads, we assembled a 370.75-Mb C. heterophylla genome with contig N50 and scaffold N50 sizes of 2.07 and 31.33  Mb, respectively, accounting for 99.23% of the estimated genome size (373.61 Mb). Furthermore, 361.90 Mb contigs were anchored to 11 chromosomes using Hi-C link data, representing 97.61% of the assembled genome sequences. Transcriptomes representing 4 different tissues were sequenced to assist protein-coding gene prediction. A total of 27,591 protein-coding genes were identified, of which 92.02% (25,389) were functionally annotated. The phylogenetic analysis showed that C. heterophylla is close to Ostrya japonica, and they diverged from their common ancestor ∼52.79 million years ago.

Conclusions
We generated a high-quality chromosome-level genome of C. heterophylla. This genome resource will promote research on the molecular mechanisms of how the hazelnut responds to environmental stresses and serves as an important resource for genome-assisted improvement in cold and drought resistance of the Corylus genus.
Adjoint slip inversion under a constrained optimization framework: revisiting the 2006 Guerrero slow slip event
Authors: Tago J , Cruz-Atienza V M , Villafuerte C , Nishimura T , Kostoglodov V , Real J , Ito Y 
Published: April 2021

SUMMARYTo shed light on the prevalently slow, aseismic slip interaction between tectonic plates, we developed a new static slip inversion strategy, the ELADIN (ELastostatic ADjoint INversion) method, that uses the adjoint elastostatic equations to compute the gradient of the cost function. ELADIN is a 2-step inversion algorithm to efficiently handle plausible slip constraints. First it finds the slip that best explains the data without any constraint, and then refines the solution by imposing the constraints through a Gradient Projection Method. To obtain a self-similar, physically consistent slip distribution that accounts for sparsity and uncertainty in the data, ELADIN reduces the model space by using a von Karman regularization function that controls the wavenumber content of the solution, and weights the observations according to their covariance using the data precision matrix. Since crustal deformation is the result of different concomitant interactions at the plate interface, ELADIN simultaneously determines the regions of the interface subject to both stressing (i.e. coupling) and relaxing slip regimes. For estimating the resolution, we introduce a mobile checkerboard analysis that allows to determine lower-bound fault resolution zones for an expected slip-patch size and a given stations array. We systematically test ELADIN with synthetic inversions along the whole Mexican subduction zone and use it to invert the 2006 Guerrero Slow Slip Event (SSE), which is one of the most studied SSEs in Mexico. Since only 12 GPS stations recorded the event, careful regularization is thus required to achieve reliable solutions. We compared our preferred slip solution with two previously published models and found that our solution retains their most reliable features. In addition, although all three SSE models predict an upward slip penetration invading the seismogenic zone of the Guerrero seismic gap, our resolution analysis indicates that this penetration might not be a reliable feature of the 2006 SSE.
Changes in infection-related hospitalizations in children following pandemic restrictions: an interrupted time-series analysis of total population data
Authors: Todd Isobel M F , Miller Jessica E , Rowe Stacey L , Burgner David P , Sullivan Sheena G 
Published: April 2021

Abstract

Background
Infectious diseases are a leading cause of hospitalization during childhood. The various mitigation strategies implemented to control the coronavirus disease (COVID-19) pandemic could have additional, unintended benefits for limiting the spread of other infectious diseases and their associated burden on the health care system.

Methods
We conducted an interrupted time-series analysis using population-wide hospitalization data for the state of Victoria, Australia. Infection-related hospitalizations for children and adolescents (aged &lt;18 years, total source population ∼1.4 million) were extracted using pre-defined International Classification of Diseases 10th Revision Australian Modification (ICD-10-AM) codes. The change in weekly hospitalization rates (incidence rate ratio, IRR) for all infections following the introduction of pandemic-related restrictions from 15 March 2020 was estimated.

Results
Over 2015–19, the mean annual incidence of hospitalization with infection among children less than 18 years was 37 per 1000 population. There was an estimated 65% (95% CI 62-67%) reduction in the incidence of overall infection-related hospitalizations associated with the introduction of pandemic restrictions. The reduction was most marked in younger children (at least 66% in those less than 5 years of age) and for lower respiratory tract infections (relative reduction 85%, 95% CI 85-86%).

Conclusions
The wider impacts of pandemic mitigation strategies on non-COVID-19 infection-related hospitalizations are poorly understood. We observed marked and rapid decreases in hospitalized childhood infection. In tandem with broader consequences, sustainable measures, such as improved hand hygiene, could reduce the burden of severe childhood infection post-pandemic and the social and economic costs of hospitalization.
A structured model for COVID-19 spread: modelling age and healthcare inequities
Authors: James A , Plank M J , Binny R N , Lustig A , Hannah K , Hendy S C , Steyn N 
Published: April 2021

Abstract
We use a stochastic branching process model, structured by age and level of healthcare access, to look at the heterogeneous spread of COVID-19 within a population. We examine the effect of control scenarios targeted at particular groups, such as school closures or social distancing by older people. Although we currently lack detailed empirical data about contact and infection rates between age groups and groups with different levels of healthcare access within New Zealand, these scenarios illustrate how such evidence could be used to inform specific interventions. We find that an increase in the transmission rates among children from reopening schools is unlikely to significantly increase the number of cases, unless this is accompanied by a change in adult behaviour. We also find that there is a risk of undetected outbreaks occurring in communities that have low access to healthcare and that are socially isolated from more privileged communities. The greater the degree of inequity and extent of social segregation, the longer it will take before any outbreaks are detected. A well-established evidence for health inequities, particularly in accessing primary healthcare and testing, indicates that Māori and Pacific peoples are at a higher risk of undetected outbreaks in Aotearoa New Zealand. This highlights the importance of ensuring that community needs for access to healthcare, including early proactive testing, rapid contact tracing and the ability to isolate, are being met equitably. Finally, these scenarios illustrate how information concerning contact and infection rates across different demographic groups may be useful in informing specific policy interventions.