bluuebunny/crossref_metadata_2025_split huggingface dataset:
Solid‐phase silica‐based extraction leads to underestimation of residual DNA in decellularized tissues
Authors: Schmitz Tara C. , Dede Eren Aysegul , Spierings Janne , de Boer Jan , Ito Keita , Foolen Jasper 
Published: February 2021

AbstractDecellularization of animal tissues is a novel route to obtain biomaterials for use in tissue engineering and organ transplantation. Successful decellularization is required as animal DNA causes inflammatory reactions and contains endogenous retroviruses, which could be transmitted to the patient. One of the criteria for successful decellularization is digestion (fragmentation) and elimination (residual quantity) of DNA from the tissue. Quantification of DNA can be done in many ways, but it has recently been shown that silica‐based solid‐phase extraction methods often do not completely purify in particular small DNA fragments. In the context of decellularization, this means that the measured DNA amount is underestimated, which could compromise safety of the processed tissue for in‐patient use. In this article, we review DNA quantification methods used by researchers and assess their influence on the reported DNA contents after decellularization. We find that underestimation of residual DNA amount after silica‐based solid‐phase extraction may be as large as a factor of ten. We therefore recommend a direct assessment of DNA amount in tissue lysate using dsDNA‐specific binding dyes, such as Picogreen, due to their higher accuracy for small fragment detection as well as ease of use and widespread availability.
MET currents and otoacoustic emissions from mice with a detached tectorial membrane indicate the extracellular matrix regulates Ca2+ near stereocilia
Authors: Jeng Jing‐Yi , Harasztosi Csaba , Carlton Adam J. , Corns Laura F. , Marchetta Philine , Johnson Stuart L. , Goodyear Richard J. , Legan Kevin P. , Rüttiger Lukas , Richardson Guy P. , Marcotti Walter 
Published: February 2021

Key points
The aim was to determine whether detachment of the tectorial membrane (TM) from the organ of Corti in Tecta/Tectb−/− mice affects the biophysical properties of cochlear outer hair cells (OHCs).
Tecta/Tectb−/− mice have highly elevated hearing thresholds, but OHCs mature normally.
Mechanoelectrical transducer (MET) channel resting open probability (Po) in mature OHC is ∼50% in endolymphatic [Ca2+], resulting in a large standing depolarizing MET current that would allow OHCs to act optimally as electromotile cochlear amplifiers.
MET channel resting Po in vivo is also high in Tecta/Tectb−/− mice, indicating that the TM is unlikely to statically bias the hair bundles of OHCs.
Distortion product otoacoustic emissions (DPOAEs), a readout of active, MET‐dependent, non‐linear cochlear amplification in OHCs, fail to exhibit long‐lasting adaptation to repetitive stimulation in Tecta/Tectb−/− mice.
We conclude that during prolonged, sound‐induced stimulation of the cochlea the TM may determine the extracellular Ca2+ concentration near the OHC's MET channels.
AbstractThe tectorial membrane (TM) is an acellular structure of the cochlea that is attached to the stereociliary bundles of the outer hair cells (OHCs), electromotile cells that amplify motion of the cochlear partition and sharpen its frequency selectivity. Although the TM is essential for hearing, its role is still not fully understood. In Tecta/Tectb−/− double knockout mice, in which the TM is not coupled to the OHC stereocilia, hearing sensitivity is considerably reduced compared with that of wild‐type animals. In vivo, the OHC receptor potentials, assessed using cochlear microphonics, are symmetrical in both wild‐type and Tecta/Tectb−/− mice, indicating that the TM does not bias the hair bundle resting position. The functional maturation of hair cells is also unaffected in Tecta/Tectb−/− mice, and the resting open probability of the mechanoelectrical transducer (MET) channel reaches values of ∼50% when the hair bundles of mature OHCs are bathed in an endolymphatic‐like Ca2+ concentration (40 μM) in vitro. The resultant large MET current depolarizes OHCs to near –40 mV, a value that would allow optimal activation of the motor protein prestin and normal cochlear amplification. Although the set point of the OHC receptor potential transfer function in vivo may therefore be determined primarily by endolymphatic Ca2+ concentration, repetitive acoustic stimulation fails to produce adaptation of MET‐dependent otoacoustic emissions in vivo in the Tecta/Tectb−/− mice. Therefore, the TM is likely to contribute to the regulation of Ca2+ levels around the stereocilia, and thus adaptation of the OHC MET channel during prolonged sound stimulation.
Modeling of Axial Compressor With Large Tip Clearances
Authors: Evans Simon , Yi Junsok , Nolan Sean , Joseph Liselle , Ni Michael , Kulkarni Sameer 
Published: February 2021

Abstract
In the drive for lower fuel consumption through increased bypass ratio and increased overall pressure ratio (OPR), engine designs for the next generation of single-aisle aircraft will require core sizes below 3 lb/s and OPRs above 50. Traditionally, these core sizes are the domain of centrifugal compressors, but materials limit pressure ratio in these machines to well below 50. An all-axial high-pressure compressor (HPC) at this core size, however, comes with limitations associated with the small blade spans at the back of the HPC, as clearances, fillets, and leading edges do not scale with the core size. The result is a substantial efficiency penalty, driven primarily by the tip leakage flow produced by the larger clearance-to-span ratio, which negates the cycle efficiency benefits of the high OPR. In order to enable small-core, high-OPR, all-axial compressors mitigating technologies need to be developed and implemented to reduce the large clearance-to-span efficiency penalty. However, for this technology development to be successful, it is imperative that predictive design tools accurately model the overall flow physics and trends of the technologies developed. In this paper, we describe an effort to determine whether different modeling standards are required for a large clearance-to-span ratio, and if so, identify criteria for an appropriate solver and/or mesh. Multiple models are run and results compared with data collected in the NASA Glenn Research Center’s low-speed axial compressor. These comparisons show that steady Reynolds-averaged Navier–Stokes (RANS) solvers can predict the pressure-rise characteristic to an acceptable level of accuracy, if careful attention is paid to mesh topology in the tip region. However, unsteady tools are necessary to accurately capture radial profiles of blockage and total pressure. The Delayed-Detached Eddy Simulation model was also used to run this geometry, but did not resolve any additional features not captured by the unsteady RANS simulation near stall.
Angular Velocity Control of Pneumatic Soft Robotic Digits
Authors: Shi W. Y. , Wijesundara Muthu B. J. 
Published: February 2021

Abstract
The paper presents an angular velocity controller for the pneumatic soft robotic gloves which are applied to medical hand rehabilitation and performance augmentation. In order to configure the reliable control parameters, linear dynamic second-order state-space models of five robotic digits were identified by the experimental data. Using the identified models, proportional-integral (PI) control parameters were tuned by simulation studies. The tuned PI parameters were verified by experiment, which demonstrates that the system identification and simulation studies are reliable and can reduce the manual tuning time and prevent tuning hardware wear.
Code Verification of Non-Newtonian Fluid Solvers for Single- and Two-Phase Laminar Flows
Authors: Lovato Stefano , Toxopeus Serge L. , Settels Just W. , Keetels Geert H. , Vaz Guilherme 
Published: February 2021

Abstract
The presence of complex fluids in nature and industrial applications combined with the rapid growth of computer power over the past decades has led to an increasing number of numerical studies of non-Newtonian flows. In most cases, non-Newtonian models can be implemented in existing Newtonian solvers by relatively simple modifications of the viscosity. However, due to the scarcity of analytical solutions for non-Newtonian fluid flows and the widespread use of regularization methods, performing rigorous code verification is a challenging task. The method of manufactured solutions (MMS) is a powerful tool to generate analytical solutions for code verification. In this article, we present and discuss the results of three verification exercises based on MMS: (i) steady single-phase flow; (ii) unsteady two-phase flow with a smooth interface; (iii) unsteady two-phase flow with a free surface. The first and second exercises showed that rigorous verification of non-Newtonian fluid solvers is possible both on single- and two-phase flows. The third exercise revealed that “spurious velocities” typical of free-surface calculations with the Volume-of-Fluid model lead to “spurious viscosities” in the non-Newtonian fluid. The procedure is illustrated herein on a second-order finite volume flow solver, using the regularized Herschel-Bulkley fluid model as an example. The same methodology is however applicable to any flow solver and to all the rheological models falling under the class of generalized Newtonian fluid models.
Modeling of Reversed Austenite Formation and Its Effect on Performance of Stainless Steel Components
Authors: Green Sadie Louise , Yeddu Hemantha Kumar 
Published: February 2021

Abstract
The kinetics of reversed austenite formation in 301 stainless steel and its effect on the deformation of an automobile front bumper beam are studied by using modeling approaches at different length scales. The diffusion-controlled reversed austenite formation is studied by using the Johnson–Mehl–Avrami–Kolmogorov (JMAK) model, based on the experimental data. The model can be used to predict the volume fraction of reversed austenite in a temperature range of 650–750 °C. A three-dimensional elastoplastic phase-field model is used to study the diffusionless shear-type reversed austenite formation in 301 steel at 760 °C. The phase-field simulations show that reversion initiates at martensite lath boundaries and proceeds inwards of laths due to the high driving force at such high temperature. The effect of reversed austenite (RA) and martensite on the deformation of a bumper beam subjected to front and side impacts is studied by using finite element (FE) analysis. The FE simulations show that the presence of reversed austenite and martensite increased the critical speed at which the beam yielded and failed. RA fraction also affects the performance of the bumper beam.
Simulation of Flow Through Variable Permeability Darcy–Brinkman Layers
Authors: Alokaily Samer A. 
Published: February 2021

AbstractIn this paper, coupled parallel flow in a triple layer channel is studied numerically. The channel consists of a clear fluid sandwiched between two Darcy–Brinkman permeable layers of variable porousness. A single binary equation is presented, in which, the penetrability within transition porous layers is portrayed by a nth degree objective capacity. However, because of the absence of explanatory arrangement of the issue, direct numerical simulations are performed in order to give a novel knowledge into the fluid dynamics inside permeable media of variable porousness. These simulations are carried out through utilizing a modified steady-state finite volume solver from the open source programing bundle openfoam. After check and approval of the solver and mathematical technique, parametric investigation is acted in which the Darcy number, intensity of the penetrability degree, transition layer thickness, channel depth, fluid viscosity, and pressure gradient vary. The findings of this study show that velocity increases when: first, the Darcy number, the degree, or the channel depth increases; second, when the transition layer thickness decreases. Also, strain rate is almost independent of both Darcy number and degree and nearly doubles when either the thickness of transition layer halves or the channel depth doubles. In addition, velocity and strain rate are found to scale with viscosity and pressure gradient.
Characterization, Design, and Experimentation of a Fabric-Based Wearable Joint Sensing Device on Human Elbow
Authors: Lau Jun Liang , Soh Gim Song 
Published: February 2021

Abstract
The use of conductive fabrics (CFs) in the design of wearables for joint sensing has recently received much interest in a wide range of applications such as robotics, rehabilitation, personal wellness, and sports. However, one key limitation in the existing measurement approach is that the user’s anthropometric information is required to relate the joint parameters to the CF sensor strain reading. This paper seeks to address this limitation by evaluating a new wearable device concept that comprises a CF strain–voltage sensor embedded as part of an inverted slider-crank (ISC) mechanism for joint extension sensing. This benefits from not requiring anthropometric information from the user to relate the joint parameters to the fabric strain readings, as opposed to an existing design. We first characterize the electromechanical property of a commercially available CF. Second, we formulate the joint sensing device’s geometric synthesis procedure as a constrained revolute joint system, where the CF is designed and introduced as an RPR chain to obtain an ISC linkage. Lastly, we designed our wearable sensing device and validated against an ISC linkage fixture representing an elbow joint and an actual healthy human subject’s left elbow. The ISC linkage fixture experimental setup shows that our designed joint sensing device can track the elbow extension motion of 140 deg with a maximum error of 7.66%. The results from our human subject’s left elbow show that it can track the elbow flexion–extension at various angular motion, with error ranges between 8.24 deg and 12.86 deg, and have provided us with an acceptable average Spearman’s coefficient values rs at 0.95.
Impact of Turbine-Strut Clocking on the Performance of a Turbine Center Frame
Authors: Sterzinger P. Z. , Merli F. , Peters A. , Behre S. , Heitmeir F. , Göttlich E. 
Published: February 2021

Abstract
Previous studies have indicated a potential for improving the performance of a turbine center frame (TCF) duct by optimizing the clocking position between the high-pressure turbine (HPT) vanes and TCF struts. To assess the impact of clocking on the performance, a new test vehicle with a clockable ratio of HPT vanes to TCF struts, consisting of an HPT stage (aerodynamically representative of the second-stage HPT engine), a TCF duct with nonturning struts, and a first-stage low-pressure turbine vane, was designed and tested in the transonic test turbine facility (TTTF) at Graz University of Technology. This article quantifies the performance impact of clocking and describes the mechanisms causing TCF flow field changes, leveraging both experimental and numerical data. Other areas in the TCF duct impacted by the choice of the HPT vane circumferential position including the strength of unsteady HPT-TCF interaction modes, TCF strut incidence changes, and carryover effects to the first low-pressure turbine (LPT) vane are additionally highlighted. Five-hole-probe (5HP) area traverses and kielhead-rake traverses were used to assess the flow field at the TCF exit and to calculate the pressure loss. The flow field at the TCF exit shows significant differences depending on the circumferential position of the HPT vane. A relative performance benefit of 5% was achieved. A series of unsteady RANS simulations were performed to support the measured results, understand, and characterize the relevant loss mechanisms. The observed performance improvement was related to interaction between the HPT secondary-flow structures and the TCF struts. The impact of the HPT vane clocking on the unsteady flow field downstream of the TCF was investigated using fast-response aerodynamic pressure probe (FRAPP) area traverses and analyzed by means of modal decomposition. In this way, the individual azimuthal modes were ranked by their amplitude, and a dependency of the clocking position was observed and quantified.
Impaired brain fractalkine-CX3CR1 signaling is implicated in cognitive dysfunction in diet-induced obese mice
Authors: Kawamura Namiko , Katsuura Goro , Yamada-Goto Nobuko , Novianti Ela , Inui Akio , Asakawa Akihiro 
Published: February 2021

IntroductionA diet high in saturated fat is well known to affect neuronal function and contribute to cognitive decline in experimental animals and humans. Fractalkine released from neurons acts on its receptor, CX3C chemokine receptor 1 (CX3CR1), in the microglia to regulate several brain functions. The present study addressed whether fractalkine-CX3CR1 signaling in the brain, especially the hippocampus, contributes to the cognitive deficits observed in diet-induced obese (DIO) mice.Research design and methodsMice were given 60% high-fat diet for 16 weeks. The expression of fractalkine and CX3CR1 in the hippocampus, amygdala and prefrontal cortex of DIO mice was analyzed. Cognitive ability in the Y-maze test and hippocampal glutamate receptors and synaptic markers were observed in DIO and CX3CR1 antagonist-treated mice. Regulation of fractalkine and CX3CR1 expression in the hippocampus was examined following administration of a selective insulin-like growth factor-1 (IGF-1) receptor inhibitor and a tyrosine receptor kinase B (TrkB) antagonist in normal mice.ResultsDIO mice exhibited significant cognitive deficits in the Y-maze test and decrease in fractalkine and CX3CR1 in the hippocampus and amygdala compared with mice fed a control diet (CD mice). Administration of the CX3CR1 antagonist 18a in normal mice induced significant cognitive deficits in the Y-maze test. DIO mice and CX3CR1 antagonist-treated mice exhibited significant decreases in protein levels of NMDA (N-methyl-D-aspartate) receptor subunit (NR2A), AMPA (α-amino-5-methyl-3-hydroxy-4-isoxazole propionate) receptor subunit (GluR1) and postsynaptic density protein 95 in the hippocampus compared with their respective controls. Furthermore, plasma IGF-1 and hippocampal brain-derived neurotrophic factor were significantly decreased in DIO mice compared with CD mice. Administration of a selective IGF-1 receptor inhibitor and a TrkB antagonist in normal mice significantly decreased fractalkine and CX3CR1 in the hippocampus.ConclusionsThese findings indicate that the cognitive decline observed in DIO mice is due, in part, to reduced fractalkine-CX3CR1 signaling in the corticolimbic system.
Adolescent sexual and reproductive health research in sub-Saharan Africa: a scoping review of substantive focus, research volume, geographic distribution and Africa-led inquiry
Authors: Ajayi Anthony Idowu , Otukpa Emmanuel Oloche , Mwoka Meggie , Kabiru Caroline W. , Ushie Boniface Ayanbekongshie 
Published: February 2021

BackgroundPrevious review studies have not systematically mapped the existing body of knowledge on adolescent sexual and reproductive health (ASRH) in sub-Saharan Africa (SSA). Our scoping review addresses this gap by examining how the body of research on ASRH in SSA has evolved over the past decade, and its present profile, in terms of trends in volume, geographic and substantive focus, and Africa-led inquiry.MethodsWe used a three-step search strategy to identify English and French peer-reviewed publications and relevant grey literature on ASRH in SSA published between January 2010 and December 2019. Two reviewers screened the titles, abstracts and full texts of publications for eligibility and inclusion.ResultsA total of 1302 articles were published over the period, rising from 91 in 2010 to 183 in 2015. However, the bulk of the studies (63.9%) focused on six (South Africa, Kenya, Nigeria, Tanzania, Uganda and Ethiopia) of the 46 SSA countries. Ten countries had no ASRH papers, while five others each had only one publication. While issues like HIV (17.2%), sexual behaviours (17.4%) and access to sexual and reproductive health services (13.0%) received substantial attention, only a few studies focused on early adolescence (10–14 years), programme interventions, scaling up of interventions and policy evaluation. Just over half of publications had authors with African institutional affiliations as first authors (51.1%) or last author (53.0%). Sixteen per cent of papers did not include any authors from institutions in Africa.ConclusionsOur review demonstrated that research on ASRH is limited in focus and is unevenly distributed across SSA countries. The identified gaps can guide future research and funding to advance ASRH policies and programmes. It is also vital for stakeholders in the research enterprise, including researchers, donors, ethical review boards, and journal editors and reviewers, to implement measures that foster national investigators’ inclusion.
How do patient feedback systems work in low-income and middle-income countries? Insights from a realist evaluation in Bangladesh
Authors: Mirzoev Tolib , Kane Sumit , Al Azdi Zunayed , Ebenso Bassey , Chowdhury Ayesha Afroz , Huque Rumana 
Published: February 2021

BackgroundWell-functioning patient feedback systems can contribute to improved quality of healthcare and systems accountability. We used realist evaluation to examine patient feedback systems at health facilities in Bangladesh, informed by theories of citizenship and principal–agent relationships.MethodsWe collected and analysed data in two stages, using: document review; secondary analysis of data from publicly available web-portals; in-depth interviews with patients, health workers and managers; non-participant observations of feedback environments; and stakeholder workshops. Stage 1 focused on identifying and articulating the initial programme theory (PT) of patient feedback systems. In stage 2, we iteratively tested and refined this initial theory, through analysing data and grounding emerging findings within substantive theories and empirical literature, to arrive at a refined PT.ResultsMultiple patient feedback systems operate in Bangladesh, essentially comprising stages of collection, analysis and actions on feedback. Key contextual enablers include political commitment to accountability, whereas key constraints include limited patient awareness of feedback channels, lack of guidelines and documented processes, local political dynamics and priorities, institutional hierarchies and accountability relationships. Findings highlight that relational trust may be important for many people to exercise citizenship and providing feedback, and that appropriate policy and regulatory frameworks with clear lines of accountability are critical for ensuring effective patient feedback management within frontline healthcare facilities.ConclusionTheories of citizenship and principal–agent relationships can help understand how feedback systems work through spotlighting the citizenship identity and agency, shared or competing interests, and information asymmetries. We extend the understanding of these theories by highlighting how patients, health workers and managers act as both principals and agents, and how information asymmetry and possible agency loss can be addressed. We highlight the importance of awareness raising and non-threatening environment to provide feedback, adequate support to staff to document and analyse feedback and timely actions on the information.