bluuebunny/crossref_metadata_2025_split huggingface dataset:
Association of soluble CD40 levels with ‐1 C > T CD40 polymorphism and chronic kidney disease in systemic lupus erythematosus
Authors: Tapia‐Llanos Raziel , Muñoz‐Valle José F. , Román‐Fernández Ilce V. , Marín‐Rosales Miguel , Salazar‐Camarena Diana C. , Cruz Alvaro , Orozco‐Barocio Gerardo , Guareña‐Casillas Jorge A. , Oregon‐Romero Edith , Palafox‐Sánchez Claudia A. 
Published: October 2019

AbstractBackgroundCD40 is a transmembrane protein mainly expressed on the antigen‐presenting cells surface. CD40 plays a crucial role in immunoglobulin class switching and antibodies production. Genetic polymorphisms in the CD40 gene have been associated with increased risk of systemic lupus erythematosus (SLE) in several populations. This study aimed to evaluate the association of CD40 polymorphisms (−1 C > T, rs1883832 and 6,048 G > T, rs4810485) with SLE susceptibility, as well as with mRNA expression and soluble CD40 (sCD40) levels.MethodsThe study included 293 patients with SLE and 294 control subjects (CS). Genotyping was performed by PCR‐RFLP method. CD40 mRNA expression was determined by quantitative real‐time PCR, and ELISA quantified sCD40 levels.ResultsThe CD40 polymorphisms −1 C > T and 6,048 G > T were associated with SLE susceptibility. There was no difference between CD40 mRNA expression and CD40 polymorphisms. The sCD40 levels were lower in SLE patients with TT haplotype, whereas higher sCD40 levels were associated with damage and impaired renal function according to SLICC and KDIGO. The sCD40 levels were negatively correlated with eGFR.ConclusionThe CD40 gene polymorphisms increase the risk of SLE in the western Mexican population. The sCD40 levels are associated with −1 C > T polymorphism and chronic kidney disease.
Chaperones in sporadic inclusion body myositis—Validation of proteomic data
Authors: Güttsches Anne‐Katrin , Jacobsen Frank , Schreiner Anja , Mertens‐Rill Janine , Tegenthoff Martin , Marcus Katrin , Vorgerd Matthias , Kley Rudolf A. 
Published: October 2019

AbstractIntroductionSporadic inclusion body myositis (sIBM) is characterized by myopathological features including rimmed vacuoles (RVs) and proteins associated with protein aggregation, autophagy, and inflammation. Previous proteomic studies of RV areas revealed an overrepresentation of several chaperones and subunits of the T‐complex protein 1 (TCP‐1), which is involved in prevention of protein aggregation.MethodsTo validate our proteomic findings, immunofluorescence analyses of selected chaperones and quantitative Western blot analysis of TCP‐1 proteins were performed in five sIBM patients and five healthy controls.ResultsImmunofluorescence studies confirmed increased immunoreactivity for VCP, UNC45B, GRP‐75, αB‐crystallin, LAMP‐2, Rab‐7a, and TCP‐1α and TCP‐θ in RVs. Quantitative Western blot analysis revealed a significantly higher level of TCP‐1 in sIBM muscle tissue when compared with healthy controls.DiscussionOur study findings validate new insights in protein quality control and degradation processes that seem to be relevant in sIBM. These data provide an important basis for future functional and therapeutic studies.
Intraday and interday reliability of pelvic floor muscles electromyography in continent woman
Authors: Scharschmidt Ronja , Derlien Steffen , Siebert Tobias , Herbsleb Marco , Stutzig Norman 
Published: October 2019

AbstractAimsVaginal surface electromyography (sEMG) is a tool used for the diagnosis and therapeutic intervention of urinary incontinence. Current sEMG systems differ in regard to electrode arrangement and data reproducibility. The aim of this study was to determine the intrasession, intraday, and interday reliabilities of sEMG parameters using a probe with circumferential electrode‐position.MethodsThe intrasession, intraday, and interday reliabilities of maximum isometric voluntary contractions (MVC) of the pelvic floor muscles were assessed for 19 healthy continent women. Three sEMG parameters that are used to describe muscle activity were verified: maximal EMG (EMGmax), mean over 500 ms around EMGmax (EMGA0.5), and mean over 2 seconds during MVC plateau (EMGA2‐4). Relative and absolute reliability parameters were calculated, and the statistical methods described by Bland and Altman were applied to the data.ResultsWe observed substantial reliabilities for all obtained parameters (EMGmax, EMGA2‐4, and EMGA0.5) in regard to the intrasession measurements (ICC = 0.93‐0.97; CI = 0.86‐0.99). Overall, the intraday reliability has been moderate (ICC = 0.64‐0.75; CI = 0.27‐0.90). EMGmax (ICC = 0.75; CI = 0.45‐0.90) and EMGA2‐4 (ICC = 0.73, CI = 0.42‐0.89) were higher than EMGA0.5 (ICC = 0.64; CI = 0.27‐0.85). However, the interday reliability was only fair for EMGmax (ICC = 0.48; CI = 0.04‐0.77) and EMGA0.5 (ICC = 0.51; CI = 0.07‐0.78) but moderate for EMGA2‐4 (ICC = 0.65; CI = 0.28‐0.85).ConclusionsThis intrasession, intraday, and interday reliability results are similar to the results reported in the literature using probes with longitudinally oriented bars. The mean sEMG signal over 2 seconds (EMGA2‐4) exhibited the highest reliability and is recommended for further studies. The interday reliability might be enhanced by considering the menstruation cycle.
Complete implicit stress integration algorithm with extended subloading surface model for elastoplastic deformation analysis
Authors: Anjiki Takuya , Oka Masanori , Hashiguchi Koichi 
Published: October 2019

SummaryThe subloading surface model released from a purely elastic domain is capable of describing not only monotonic but also cyclic loading behaviors accurately. It is expected that elastoplastic deformation analyses can be performed with high accuracy and efficiency by the complete implicit stress integration algorithm with a return‐mapping projection. Various implicit stress integration algorithms for the subloading surface model have been proposed. However, they are applicable only to the monotonic loading behavior since they adopt the incorrect loading criterion presuming that the subloading surface expands in the plastic loading process. In fact, however, the plastic strain rate is induced even when the subloading surface contracts in the elastic trial step. Therefore, erroneous results in the descriptions of unloading‐reloading and cyclic loading behaviors are caused in the calculations with the existing algorithms. The complete implicit stress integration method is formulated adopting the rigorous loading criterion and implemented in Abaqus in this study. Numerical analyses for the elastoplastic deformation behaviors in the single‐element are performed by the present and the existing algorithms. In addition, the deformation analysis of the R‐notched cylinder is performed by the present algorithm. High performability of the present algorithm is confirmed by these numerical calculation results.
Adjoint Hamiltonian Monte Carlo algorithm for the estimation of elastic modulus through the inversion of elastic wave propagation data
Authors: Koch Michael C. , Fujisawa Kazunori , Murakami Akira 
Published: October 2019

SUMMARYEfficient inversion of noisy seismic waveform data produced due to elastic wave propagation for the estimation of a high‐dimensional elastic modulus vector is achieved. Estimation is carried out in a Bayesian framework using Hamiltonian Monte Carlo (HMC) that enables efficient statistical estimation over high‐dimensional parameters. The truncated Karhunen‐Loève (K‐L) expansion is introduced to reduce the dimensionality of the elastic modulus vector. Expensive computations of the gradient of the state vector with respect to the parameter vector at every step are also eliminated through the adjoint method, which is developed from a general one‐step discretization of the governing second‐order ordinary differential equations (ODEs). An Adjoint HMC algorithm that employs a truncated K‐L expansion of the elastic modulus vector is presented. The efficacy of the algorithm is investigated with respect to two representative problems with varying geometric complexity. Adjoint HMC offers a significant speed up in gradient calculation time over the direct differentiation counterpart as the number of terms in the K‐L expansion increases. The algorithm is able to estimate the true elastic modulus within the credible intervals for both cases.
A numerical integration approach for fractional‐order viscoelastic analysis of hereditary‐aging structures
Authors: Beltempo Angela , Bonelli Alessio , Bursi Oreste S. , Zingales Massimiliano 
Published: October 2019

SummaryIn this paper, a novel numerical integration scheme is proposed for fractional‐order viscoelastic analysis of hereditary‐aging structures. More precisely, the idea of aging is first introduced through a new phenomenological viscoelastic model characterized by variable‐order fractional operators. Then, the presented fractional‐order viscoelastic model is included in a variational formulation, conceived for any viscous kernel and discretized in time by employing a discontinuous Galerkin method. The accuracy of the resulting finite element (FE) scheme is analyzed through a model problem, whose exact solution is known; and the most significant variables affecting the solution quality, such as the number of Gaussian quadrature points and time subintervals, are then investigated in terms of error and computational cost. Moreover, the proposed FE integration scheme is applied to study the short‐ and long‐term behavior of concrete structures, which, due to the severe aging exhibited during their service life, represents one of the most challenging time‐dependent behavior to be investigated. Eventually, also the Euler implicit method, commonly used in commercial software, is compared.
Distributed optimal control of viscous Burgers' equation via a high‐order, linearization, integral, nodal discontinuous Gegenbauer‐Galerkin method
Authors: Elgindy Kareem T. , Karasözen Bülent 
Published: October 2019

SummaryWe developed a novel direct optimization method to solve distributed optimal control of viscous Burgers' equation over a finite‐time horizon by minimizing the distance between the state function and a desired target state profile along with the energy of the control. Through a novel linearization strategy, well‐conditioned integral reformulations, optimal Gegenbauer barycentric quadratures, and nodal discontinuous Galerkin discretizations, the method reduces such optimal control problems into finite‐dimensional, nonlinear programming problems subject to linear algebraic system of equations and discrete mixed path inequality constraints that can be solved easily using standard optimization software. The proposed method produces “an auxiliary control function” that provides a useful model to explicitly define the optimal controller of the state variable. We present an error analysis of the semidiscretization and full discretization of the weak form of the reduced equality constraint system equations to demonstrate the exponential convergence of the method. The accuracy of the proposed method is examined using two numerical examples for various target state functions in the existence/absence of control bounds. The proposed method is exponentially convergent in both space and time, thus producing highly accurate approximations using a significantly small number of collocation points.
Synthetic Activators of Cell Migration Designed by Constructive Machine Learning
Authors: Bruns Dominique , Merk Daniel , Santhana Kumar Karthiga , Baumgartner Martin , Schneider Gisbert 
Published: October 2019

AbstractConstructive machine learning aims to create examples from its learned domain which are likely to exhibit similar properties. Here, a recurrent neural network was trained with the chemical structures of known cell‐migration modulators. This machine learning model was used to generate new molecules that mimic the training compounds. Two top‐scoring designs were synthesized, and tested for functional activity in a phenotypic spheroid cell migration assay. These computationally generated small molecules significantly increased the migration of medulloblastoma cells. The results further corroborate the applicability of constructive machine learning to the de novo design of druglike molecules with desired properties.
Insights revealed by the co‐crystal structure of the Saccharomyces cerevisiae histidine phosphotransfer protein Ypd1 and the receiver domain of its downstream response regulator Ssk1
Authors: Branscum Katie M. , Menon Smita K. , Foster Clay A. , West Ann H. 
Published: October 2019

AbstractTwo‐component signaling systems are the primary means by which bacteria, archaea, and certain plants and fungi react to their environments. The model yeast, Saccharomyces cerevisiae, uses the Sln1 signaling pathway to respond to hyperosmotic stress. This pathway contains a hybrid histidine kinase (Sln1) that autophosphorylates and transfers a phosphoryl group to its own receiver domain (R1). The phosphoryl group is then transferred to a histidine phosphotransfer protein (Ypd1) that finally passes it to the receiver domain (R2) of a downstream response regulator (Ssk1). Under normal conditions, Ssk1 is constitutively and preferentially phosphorylated in the phosphorelay. Upon detecting hyperosmotic stress, Ssk1 rapidly dephosphorylates and activates the high‐osmolarity glycerol (HOG) pathway, initiating a response. Despite their distinct physiological roles, both Sln1 and Ssk1 bind to Ypd1 at a common docking site. Co‐crystal structures of response regulators in complex with their phosphorelay partners are scarce, leaving many mechanistic and structural details uncharacterized for systems like the Sln1 pathway. In this work, we present the co‐crystal structure of Ypd1 and a near wild‐type variant of the receiver domain of Ssk1 (Ssk1‐R2‐W638A) at a resolution of 2.80 Å. Our structural analyses of Ypd1‐receiver domain complexes, biochemical determination of binding affinities for Ssk1‐R2 variants, in silico free energy estimates, and sequence comparisons reveal distinctive electrostatic properties of the Ypd1/Ssk1‐R2‐W638A complex that may provide insight into the regulation of the Sln1 pathway as a function of dynamic osmolyte concentration.
IsCT‐based analogs intending better biological activity
Authors: Acevedo Isabel Cristina Chica , Silva Jr Pedro Ismael , Silva Fernanda Dias , Araújo Iris , Alves Flávio Lopes , Oliveira Cyntia Silva , Oliveira Jr Vani Xavier 
Published: October 2019

AbstractIsCT1‐NH2 is a cationic antimicrobial peptide isolated from the venom of the scorpion Opisthacanthus madagascariensis that has a tendency to form an α‐helical structure and shows potent antimicrobial activity and also inopportunely shows hemolytic effects. In this study, five IsCT1 (ILGKIWEGIKSLF)‐based analogs with amino acid modifications at positions 1, 3, 5, or 8 and one analog with three simultaneous substitutions at the 1, 5, and 8 positions were designed. The net charge of each analog was between +2 and +3. The peptides obtained were characterized by mass spectrometry and analyzed by circular dichroism for their structure in different media. Studies of antimicrobial activity, hemolytic activity, and stability against proteases were also carried out.Peptides with a substitution at position 3 or 5 ([L]3‐IsCT1‐NH2, [K]3‐IsCT1‐NH2, or [F]5‐IsCT1‐NH2) showed no significant change in an activity relative to IsCT1‐NH2. The addition of a proline residue at position 8 ([P]8‐IsCT1‐NH2) reduced the hemolytic activity as well as the antimicrobial activity (MIC ranging 3.13‐50 μmol L−1), and the addition of a tryptophan residue at position 1 ([W]1‐IsCT1‐NH2) increased the hemolytic activity (MHC = 1.56 μmol L−1) without an improvement in antimicrobial activity. The analog [A]1[F]5[K]8‐IsCT1‐NH2, which carries three simultaneous modifications, presented increasing or equivalent values in antimicrobial activity (MIC approximately 0.38 and 12.5 μmol L−1) with a reduction in hemolytic activity. In addition, this analog presented the best resistance against proteases. This kind of strategy can find functional hotspots in peptide molecules in an attempt to generate novel potent peptide antibiotics.
Nature of mercury inclusion in intermediate 6‐valence electron [M@Au8Hgx(PPh3)8]n+ (M = Au, Pd, Pt; x = 0‐2) protected gold superatoms: Insights from relativistic density functional theory calculations
Authors: Quintana Constanza G. , Ocayo Fernanda , Guajardo Maturana Raul , Hurtado John J. , Muñoz‐Castro Alvaro 
Published: October 2019

AbstractSuperatomic clusters offer useful templates displaying distinctive physical and chemical characteristics. Here, we explore the [M@Au8(PPh3)8]n+ (M = Au, n = 3; Pd, Pt, n = 2) robust framework to gain an understanding of the nature of the inclusion of mercury atoms at Au4 faces, leading to [M@Au8Hgx(PPh3)8]n+ (x = 1, 2). Our results show a weak interaction of about 25 kcal mol−1 per Hg atom, which is mainly of electrostatic character, followed by orbital and London dispersion‐type interactions. This weak interaction can be understood as the formation of host‐guest species, for which the inherent electronic and optical properties of the [M@Au8(PPh3)8] cluster along the series do not vary to a large extent. This demonstrates that, in [M@Au8Hgx(PPh3)8], each Hg can be considered an inclusion atom rather than a dopant element, where the parent cluster is able to act as a Lewis acid host. Furthermore, the viable formation of such species can serve as useful examples to stimulate future experimental characterization of inclusion complexes involving related superatomic structures with available open faces.
Structural Characterization of Controlled Decrystallization of Cassava Starch
Authors: Lin Ri‐Hui , Fan Yan‐Ye , Liu Tao , Yang Hui , Ma Li‐Juan , Huang Xia‐Jie , Liu Yue 
Published: October 2019

AbstractNative starch granule has a complex crystalline structure. Controlled decrystallization cassava starch (CDCS) was prepared by the alcohol–alkali method. Polarized microscopy, scanning electron microscopy (SEM), X‐ray diffraction (XRD), and Fourier transform infrared spectroscopy (FTIR) analysis of the CDCS are carried out to investigate its structural information. The results show that the relative crystallinity (RC) of the processed cassava starches can be reduced from 25.56% to 17.90% by adjusting the concentration of sodium hydroxide while keeping the integrity of the starch granule. During the decrystallization process, as the sodium hydroxide concentration is increased from 0.25 to 1.25 mol L−1, the polarized light of the starch granules disappear from the inside to the outside, and the X‐ray diffraction peaks of native cassava starch (NCS) disappear sequentially from 17.16°, 23.04°, 15.08°, to 17.83°. On the other hand, the FTIR peaks of the NCS centered at 1645 cm−1 is shifted to about 1600 cm−1, and the intensity of the peaks at 3424, 2929, 1645, and 1017 cm−1 become weaker with decrystallization process. This study provides valuable data and a theoretical basis to understand the mechanism of the controlled decrystallization of cassava starch.
Ecosystem engineers: Biofilms and the ontogeny of glacier floodplain ecosystems
Authors: Roncoroni Matteo , Brandani Jade , Battin Tom I. , Lane Stuart N. 
Published: October 2019

AbstractThe term “ecosystem engineering” emerged in the 1990s and is commonly used to refer to the activities of larger organisms like beavers and trees in rivers and streams. The focus on larger organisms may be motivated by their more visible effects on the environment. However, while it may be intuitive to suggest that the bigger the organism the bigger its potential engineering effects, there may be microscale organisms who through their number rather than their size can act simultaneously to result in significant impacts. This paper considers biofilms as a candidate ecosystem engineer. It is well known that biofilms play an important role in enriching the sediment matrix of nutrients and in stabilizing sediments. Biofilms may be critical in increasing the habitability of the benthic substratum. In this paper, we consider their potential role in the ontogeny of ecosystems in recently deglaciated terrain. We show how by changing sediment stoichiometry, decreasing sediment erodibility, and reducing surface sediment permeability they may promote primary succession on lateral, incised terraces, which are less perturbed compared with the main active floodplain.This article is categorized under:
Water and Life > Nature of Freshwater Ecosystems
Science of Water > Water and Environmental Change
Nitrogen release and plant available nitrogen of composted and un‐composted biosolids
Authors: Oladeji Olawale , Tian Guanglong , Lindo Pauline , Kumar Kuldip , Cox Albert , Hundal Lakhwinder , Zhang Heng , Podczerwinski Edward 
Published: October 2019

AbstractThe nitrogen (N) release from composted and un‐composted biosolids and plant available N (PAN) of the biosolids were quantified to evaluate if composting can contribute to stabilize biosolids N and reduce the nitrate () leaching potential in biosolids‐amended soil. Biosolids were composted at >55°C for 21 days after mixing the biosolids with yard waste at 1:1 (w/w) ratio. In the N release study, we installed field lysimeters filled with soil (sand and clay) amended with composted and un‐composted biosolids at two rates (30 and 150 dry Mg/ha) and measured the inorganic N in leachate after each rainfall and soil inorganic N monthly. The N released from composted biosolids during the two‐year study period were lower (6% of organic N added for clay and 11% for sandy loam soil) as compared to un‐composted biosolids (14% of organic N added for clay and 21% for sandy soils). Composted biosolids showed a lower N release rate constant k value of 0.0014 and 0.0027 month−1 for clay and sandy soil, respectively, compared to corresponding values of 0.0035 and 0.0068 month−1 for un‐composted biosolids. We used greenhouse bioassay with corn (Zea mays), ryegrass (Lolium perenne), and Miscanthus (Miscanthus giganteus) as test plants grown for six months with reference to N chemical fertilizer ranging from 0, 75, 150 to 300 kg N/ha to evaluate the PAN of the biosolids. Based on our study, plant growth was not affected by using either composted or un‐composted biosolids but the PAN was lower in composted biosolids (4.0%–5.9%) than un‐composted biosolids (11.4%–13.6%). Composting results in higher N‐retention efficiency in biosolids and composted biosolids are a valuable source of N to support the plant growth with lower N released to the environment. Thus, the potential of N leaching would still be low in the situations where a high rate of biosolids needs to be applied for land reclamation or landscaping soil reconstruction.Practitioner points

Composting enhances N‐retention efficiency in biosolids and composted biosolids are a valuable source of N to support the plant growth with lower N released to the environment.

Potential of N leaching would still be low in the situations where a high rate of biosolids needs to be applied for land reclamation or landscaping soil reconstruction.

N released from composted and un‐composted biosolids can be adequately described by first‐order kinetic model.