bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhancer‐mediated reporter gene expression in Arabidopsis thaliana: a forward genetic screen
Authors: Lin Yuan , Zhao Hainan , Kotlarz Magdalena , Jiang Jiming 
Published: February 2021

SUMMARYGene expression is controlled and regulated by interactions between cis‐regulatory DNA elements (CREs) and regulatory proteins. Enhancers are one of the most important classes of CREs in eukaryotes. Eukaryotic genes, especially those related to development or responses to environmental cues, are often regulated by multiple enhancers in different tissues and/or at different developmental stages. Remarkably, little is known about the molecular mechanisms by which enhancers regulate gene expression in plants. We identified a distal enhancer, CREβ, which regulates the expression of AtDGK7, which encodes a diacylglycerol kinase in Arabidopsis. We developed a transgenic line containing the luciferase reporter gene (LUC) driven by CREβ fused with a minimal cauliflower mosaic virus (CaMV) 35S promoter. The CREβ enhancer was shown to play a role in the response to osmotic pressure of the LUC reporter gene. A forward genetic screen pipeline based on the transgenic line was established to generate mutations associated with altered expression of the LUC reporter gene. We identified a suite of mutants with variable LUC expression levels as well as different segregation patterns of the mutations in populations. We demonstrate that this pipeline will allow us to identify trans‐regulatory factors associated with CREβ function as well as those acting in the regulation of the endogenous AtDGK7 gene.
Subgenome evolution in allotetraploid plants
Authors: Schiavinato Matteo , Bodrug‐Schepers Alexandrina , Dohm Juliane C. , Himmelbauer Heinz 
Published: February 2021

SUMMARYPolyploidization is a well‐known speciation and adaptation mechanism. Traces of former polyploidization events were discovered within many genomes, and especially in plants. Allopolyploidization by interspecific hybridization between two species is common. Among hybrid plants, many are domesticated species of agricultural interest and many of their genomes and of their presumptive parents have been sequenced. Hybrid genomes remain challenging to analyse because of the presence of multiple subgenomes. The genomes of hybrids often undergo rearrangement and degradation over time. Based on 10 hybrid plant genomes from six different genera, with hybridization dating from 10,000 to 5 million years ago, we assessed subgenome degradation, subgenomic intermixing and biased subgenome fractionation. The restructuring of hybrid genomes does not proceed proportionally with the age of the hybrid. The oldest hybrids in our data set display completely different fates: whereas the subgenomes of the tobacco plant Nicotiana benthamiana are in an advanced stage of degradation, the subgenomes of quinoa (Chenopodium quinoa) are exceptionally well conserved by structure and sequence. We observed statistically significant biased subgenome fractionation in seven out of 10 hybrids, which had different ages and subgenomic intermixing levels. Hence, we conclude that no correlation exists between biased fractionation and subgenome intermixing. Lastly, domestication may encourage or hinder subgenome intermixing, depending on the evolutionary context. In summary, comparative analysis of hybrid genomes and their presumptive parents allowed us to determine commonalities and differences between their evolutionary fates. In order to facilitate the future analysis of further hybrid genomes, we automated the analysis steps within manticore, which is publicly available at https://github.com/MatteoSchiavinato/manticore.git.
Does the order of intraocular pressure measurement affect tonometry results?
Authors: Pe’er Oren , Chiu Eni , Arad Dikla , Lelescu Cristina , Ross Maya , Ofri Ron 
Published: February 2021

AbstractPurposeTo determine whether the order of intraocular pressure (IOP) measurement affects readings, regardless of which eye is measured first.MethodsIntraocular pressure was measured in 31 and 41 dogs using applanation and rebound tonometry, respectively. Initially, IOP was measured in the first (randomly chosen) eye (reading A), followed by measurement in the fellow eye (reading B), and a third (repeated) measurement in the first eye (reading C). After 15 minutes, measurements were repeated in reverse order (readings D ‐ F).ResultsApplanation tonometry revealed significant differences between readings A & B (15.6 ± 2.3 and 14.8 ± 2.7 mm Hg, respectively, p = .02), A & C (15.6 ± 2.3 and 14.5 ± 2.4 mm Hg, respectively, p = .002), D & E (14.5 ± 2.3 and 13.7 ± 2.1 mm Hg, respectively, p = .02), D & F (14.5 ± 2.3 and 13.9 ± 1.9 mm Hg, respectively, p = .05), and A & E (15.6 ± 2.3 and 13.7 ± 2.1 mm Hg, respectively, p = .001). Rebound tonometry yielded similar results, with additional differences between B & C (19.1 ± 3.0 and 18.2 ± 2.4 mm Hg, respectively, p = .002) and E & F (18.7 ± 3.3 and 18.2 ± 3.3 mm Hg, respectively, p = .02).ConclusionsIntraocular pressure measured in the first eye, whether right or left, is higher than in the fellow eye. Repeated tonometry in the same visit could result in a significant IOP decrease, though the magnitude may not be clinically appreciable.
Deferasirox‐associated Fanconi syndrome in adult patients with transfusional iron overload
Authors: Yui Jennifer C. , Geara Abdallah , Sayani Farzana 
Published: February 2021

Background and ObjectivesDeferasirox is an oral chelator approved for iron overload, which has a potential side effect of renal Fanconi syndrome, with proximal tubular dysfunction and tubular acidosis. Monitoring of renal function is recommended, though no standard for monitoring exists. We aim to describe cases of deferasirox‐associated Fanconi syndrome in adults and the renal monitoring required to detect these findings.Materials and MethodsWe present a review of the literature and six cases from our institution of deferasirox‐associated partial Fanconi syndrome in adult patients with transfusional iron overload secondary to β‐thalassemia or Diamond Blackfan Anaemia.ResultsWhile prior cases in the literature occurred at high doses of deferasirox, our series included patients on doses as low as deferasirox 10 mg/kg who had been aggressively chelated. All patients had resolution of laboratory abnormalities with drug interruption.ConclusionRather than chelating to normal iron levels, this series supports prior suggestions that deferasirox dose be reduced if ferritin <500–1000 ng/ml, and also supports dose reduction if liver iron content <3 mg iron per g dry weight or for those undergoing aggressive chelation with rapid decrease in iron. Monitoring with metabolic panel and urinalysis were sufficient to detect clinically significant proximal tubular dysfunction, but should be followed up with additional studies to confirm the diagnosis while deferasirox dose is decreased or held.
Effectiveness of pharmacotherapy for depression after traumatic brain injury in adults: an umbrella review protocol
Authors: Hicks Amelia J. , Clay Fiona J. , James Amelia C. , Hopwood Malcolm , Ponsford Jennie L. 
Published: February 2021

ABSTRACT

Objective:
The objective of this review is to synthesize systematic reviews of the effectiveness of pharmacotherapy vs any other comparator for the management of post-traumatic brain injury depression in adults.

Introduction:
Depression following a traumatic brain injury can have a considerable impact on the life of the individual, their family members, and the health care system. There have been several recent systematic reviews and meta-analyses on pharmacologic treatment for depression caused by post-traumatic brain injury. These reviews differ in conduct, quality, and reporting, and have discordant results and conclusions. Therefore, an umbrella review can provide prescribers with a summary of the evidence.

Inclusion criteria:
This review will consider systematic reviews of studies of adults 16 years or older who have sustained a traumatic brain injury of any severity at any time in the past, who are receiving pharmacotherapy for depression of any severity in any health care setting. Studies that include the following outcomes will be considered: change in symptoms of depression and occurrence of harms.

Methods:
MEDLINE, Embase, CINAHL, PsycINFO, Cochrane Database of Systematic Reviews, Epistemonikos, and PROSPERO will be searched, as well as Google Scholar, ResearchGate, TRIP Medical Database, and hand searching journals. There will be no restriction on publication date. Only systematic reviews published in English will be considered. Screening of articles, assessment of methodological quality, and data extraction will be performed independently by two reviewers. A Grading of Recommendations, Assessment, Development and Evaluation Summary of Findings will be presented. Data will be summarized in narrative form with supporting tables.

Systematic review registration number:
PROSPERO CRD42020184915
Liquid Desiccant Air Conditioning Using Single Storage Solution Tank, Evaporative Cooling, and Marquise-Shaped Solar Collector
Authors: Sajesh M. , Fekadu Geleta , Kalpana  , Subudhi Sudhakar 
Published: February 2021

Abstract
The present paper deals with the experimental study of the liquid desiccant air conditioning system using the single storage solution tank. The novelty of the system is that the dehumidification and regeneration are carried out in a single compact unit. The regeneration of solution is done using the marquise-shaped solar collector. The liquid desiccant solution used here is calcium chloride and water. The moisture removal rate (MRR), moisture, and enthalpy effectiveness are used as the performance parameters. The effects of mass flowrate of solution, solution temperature, inlet air temperature, and relative humidity (RH) on the performance are investigated. The experimental outcome shows that when the solution flowrate is increased from 0.263 to 0.437 kg/s, the MRR is improved from 5.08 to 7.82 g/kg and when the RH is increased from 70% to 92%, the MRR is enhanced from 5.56 to 12.45 g/kg. The new correlation for moisture effectiveness is developed based on the experimental values and depending parameters, and also another correlation is developed based on Chung’s correlation (Chung, T.-W., 1994, “Predictions of Moisture Removal Efficiencies for Packed-Bed Dehumidification Systems,” Gas Sep. Purif., 8(4), pp. 265–268).
Energetically Consistent Computation of Combustor Stability With a Model Consisting of a Helmholtz Finite Element Method Domain and a Low-Order Network
Authors: Heilmann Gerrit , Hirsch Christoph , Sattelmayer Thomas 
Published: February 2021

Abstract
An efficient approach for the detection of the acoustic damping of gas turbine combustors is the combination of spatially resolved finite element method (FEM) approaches based on the Helmholtz equation with low-order networks for all elements leading to acoustic damping. A fundamental problem of such hybrid approaches is that the flow is considered in the networks, but not in the spatially resolved FEM area. Without special treatment of the coupling plane and the boundary conditions, this leads to serious errors in the calculation of the damping rate. The purpose of the paper is the derivation of the required correction procedures, which allow the energetically consistent formulation of such hybrid models and lead to correct damping rates. The time-averaged equation of acoustic energy flux for nonuniform fluid flows is expressed in terms of reflection coefficients and compared to the equivalent formulation for vanishing mean flows. An existing transformation for boundary conditions to obtain equal energy flux at the interface between network and Helmholtz domain is analyzed in detail. The findings are then used to derive an energetically consistent transformation of transfer matrices to couple two FEM domains via a network model. The relevance of energetically consistent transfer matrices for stability analysis is demonstrated with a generic test case. The central partition is acoustically characterized via a low-order model considering mean flow. The resulting acoustic two-port is transformed to obtain an energetically consistent transfer matrix for a subsequent FEM discretized eigenvalue analysis of the remaining geometry. The eigenvalues of energetically consistent calculations are finally compared to eigenvalues of energetically inconsistent setups.
A Methodology to Evaluate the Effects of Kinematic Measurement Uncertainties on Knee Ligament Properties Estimated From Laxity Measurements
Authors: Andersen Michael Skipper , Dzialo Christine Mary , Marra Marco Antonio , Pedersen Dennis 
Published: February 2021

Abstract
Ligaments are important joint stabilizers but assessing their mechanical properties remain challenging. We developed a methodology to investigate the effects of kinematic measurement uncertainty during laxity tests on optimization-based estimation of ligament properties. We applied this methodology to a subject-specific knee model with known ligament properties as inputs and compared the estimated to the known knee ligament properties under the influence of noise. Four different sets of laxity tests were simulated with an increasing number of load cases, capturing anterior/posterior, varus/valgus, and internal/external rotation loads at 0 deg and 30 deg of knee flexion. 20 samples of uniform random noise ([−0.5,0.5] mm and degrees) were added to each set and fed into an optimization routine that subsequently estimated the ligament properties based on the noise targets. We found a large range of estimated ligament properties (stiffness ranges of 5.97 kN, 7.64 kN, 8.72 kN, and 3.86 kN; reference strain ranges of 3.11%, 2.53%, 1.88%, and 1.58% for anterior cruciate ligament (ACL), posterior cruciate ligament (PCL), medical collateral ligament (MCL), and lateral collateral ligament (LCL), respectively) for three sets of laxity tests, including up to 22 load cases. A set of laxity tests with 60 load cases kept the stiffness and reference strain ranges below 470 N per unit strain and 0.85%, respectively. These results illustrate that kinematic measurement noise have a large impact on estimated ligament properties and we recommend that future studies assess and report both the estimated ligament properties and the associated uncertainties due to kinematic measurement noise.
The Potential for Quantifying Regional Distributions of Radial and Shear Strain in the Thoracic and Abdominal Aortic Wall Using Spiral Cine DENSE Magnetic Resonance Imaging
Authors: Jones Patrick A. , Wilson John S. 
Published: February 2021

Abstract
Aortic displacement encoding with stimulated echoes (DENSE) magnetic resonance imaging (MRI) was recently developed to assess heterogeneities in aortic wall circumferential strain (CS). However, previous studies neglected potential radial and shear strain (RSS) distributions. Herein, we present an improved aortic DENSE MRI postprocessing method to assess the feasibility of quantifying all components of the two-dimensional (2D) strain tensor. 32 previously acquired 2D DENSE scans from three distinct aortic locations were re-analyzed. Contrasting previous studies, displacements of the inner and outer aortic wall layers were processed separately to preserve RSS. Differences in regional strain between the new and old postprocessing methods were evaluated, along with interobserver, intraobserver, and interscan repeatability for all strain components. The new postprocessing method revealed an overall mean absolute difference in regional CS of 0.01 ± 0.01 compared to the prior method, with minimal impact on CS repeatability. Mean absolute magnitudes of regional RSS increased significantly compared to changes in CS (radial 0.04 ± 0.05, p &lt; 0.001; shear 0.04 ± 0.04, p = 0.02). Most repeatability metrics for RSS were significantly worse than for CS. The unique distributions of RSS for each axial location associated well with local periaortic structures and mean aortic displacement. The new postprocessing method captures heterogeneous distributions of nonzero RSS which may provide new information for improving clinical diagnostics and computational modeling of heterogeneous aortic wall mechanics. However, future studies are required to improve the repeatability of RSS and assess the influence of partial volume effects.
Application of Proper Orthogonal Decomposition to Study Coherent Flow Structures in a Saccular Aneurysm
Authors: Yu Paulo , Durgesh Vibhav , Xing Tao , Budwig Ralph 
Published: February 2021

Abstract
Aneurysms are localized expansions of weakened blood vessels that can be debilitating or fatal upon rupture. Previous studies have shown that flow in an aneurysm exhibits complex flow structures that are correlated with its inflow conditions. Therefore, the objective of this study was to demonstrate the application of proper orthogonal decomposition (POD) to study the impact of different inflow conditions on energetic flow structures and their temporal behavior in an aneurysm. To achieve this objective, experiments were performed on an idealized rigid sidewall aneurysm model. A piston pump system was used for precise inflow control, i.e., peak Reynolds number (Rep) and Womersley number (α) were varied from 50 to 270 and 2 to 5, respectively. The velocity flow field measurements at the midplane location of the idealized aneurysm model were performed using particle image velocimetry (PIV). The results demonstrate the efficacy of POD in decomposing complex data, and POD was able to capture the energetic flow structures unique to each studied inflow condition. Furthermore, the time-varying coefficient results highlighted the interplay between the coefficients and their corresponding POD modes, which in turn helped explain how POD modes impact certain flow features. The low-order reconstruction results were able to capture the flow evolution and provide information on complex flow in an aneurysm. The POD and low-order reconstruction results also indicated that vortex formation, evolution, and convection varied with an increase in α, while vortex strength and formation of secondary structures were correlated with an increase in Rep.
Comparison of the Trueness of Fits of the Biphasic Transverse Isotropic and Kelvin Models to the Tensile Behavior of Temporomandibular Joint Disc
Authors: Li Wuyang , Trbojevic Sara , Almarza Alejandro J. 
Published: February 2021

Abstract
This technical brief explores the validity and trueness of fit for using the transverse isotropic biphasic and Kelvin models (first and second order generalized) for characterization of the viscoelastic tensile properties of the temporomandibular joint (TMJ) discs from pigs and goats at a strain rate of 10 mm/min. We performed incremental stress-relaxation tests from 0 to 12% strain, in 4% strain steps on pig TMJ disc samples. In addition, to compare the outcomes of these models between species, we also performed a single-step stress-relaxation test of 10% strain. The transverse isotropic biphasic model yielded reliable fits in reference to the least root mean squared error method only at low strain, while the Kelvin models yielded good fits at both low and high strain, with the second order generalized Kelvin model yielding the best fit. When comparing pig to goat TMJ disc in 10% strain stress-relaxation test, unlike the other two Kelvin models, the transverse isotropic model did not fit well for this larger step. In conclusion, the second order Kelvin model showed the best fits to the experimental data of both species. The transverse isotropic biphasic model did not fit well with the experimental data, although better at low strain, suggesting that the assumption of water flow only applies while uncrimping the collagen fibers. Thus, it is likely that the permeability from the biphasic model is not truly representative, and other biphasic models, such as the poroviscoelastic model, would likely yield more meaningful outputs and should be explored in future works.
An Equilibrium Prediction Method for Control and Fault Detection of Energy Systems
Authors: Rogers Austin , Guo Fangzhou , Rasmussen Bryan 
Published: February 2021

Abstract
Many fault detection, optimization, and control logic methods rely on sensor feedback that assumes the system is operating at steady-state conditions, despite persistent transient disturbances. While filtering and signal processing techniques can eliminate some transient effects, this paper proposes an equilibrium prediction method for first-order dynamic systems using an exponential regression. This method is particularly valuable for many commercial and industrial energy system, whose dynamics are dominated by first-order thermo-fluid effects. To illustrate the basic advantages of the proposed approach, Monte Carlo simulations are used. This is followed by three distinct experimental case studies to demonstrate the practical efficacy of the proposed method. First, the ability to predict the carbon dioxide level in classrooms allows for energy efficient control of the ventilation system and ensures occupant comfort. Second, predicting the optimal time to end the cool-down of an industrial sintering furnace allows for maximum part throughput and worker safety. Finally, fault detection and diagnosis (FDD) methods for air conditioning systems typically use static system models; however, the transient response of many air conditioning signals may be approximated as first-order, and therefore, the prediction model enables the use of static fault detection methods with transient data (a need that has not been addressed in over 20 years of air conditioning FDD research). In this paper, the equilibrium prediction method's performance will be quantified using both Monte Carlo simulations and case studies.
Ignition Studies of C1–C7 Natural Gas Blends at Gas-Turbine-Relevant Conditions
Authors: Sahu Amrit Bikram , Mohamed A. Abd El-Sabor , Panigrahy Snehasish , Bourque Gilles , Curran Henry 
Published: February 2021

Abstract
New ignition delay time measurements of natural gas mixtures enriched with small amounts of n-hexane and n-heptane were performed in a rapid compression machine to interpret the sensitization effect of heavier hydrocarbons on auto-ignition at gas-turbine relevant conditions. The experimental data of natural gas mixtures containing alkanes from methane to n-heptane were carried out over a wide range of temperatures (840–1050 K), pressures (20–30 bar), and equivalence ratios (φ = 0.5 and 1.5). The experiments were complimented with numerical simulations using a detailed kinetic model developed to investigate the effect of n-hexane and n-heptane additions. Model predictions show that the addition of even small amounts (1–2%) of n-hexane and n-heptane can lead to an increase in reactivity by ∼40–60 ms at compressed temperature (TC) = 700 K. The ignition delay time (IDT) of these mixtures decreases rapidly with an increase in concentration of up to 7.5% but becomes almost independent of the C6/C7 concentration beyond 10%. This sensitization effect of C6 and C7 is also found to be more pronounced in the temperature range 700–900 K compared to that at higher temperatures (&gt;900 K). The reason is attributed to the dependence of IDT primarily on H2O2(+M) ↔ 2ȮH(+M) at higher temperatures while the fuel-dependent reactions such as H-atom abstraction, RȮ2 dissociation, or Q˙OOH + O2 reactions are less important compared to 700–900 K, where they are very important.