bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detecting aspartate isomerization and backbone cleavage after aspartate in intact proteins by NMR spectroscopy
Authors: Hinterholzer Arthur , Stanojlovic Vesna , Regl Christof , Huber Christian G. , Cabrele Chiara , Schubert Mario 
Published: January 2021

AbstractThe monitoring of non-enzymatic post-translational modifications (PTMs) in therapeutic proteins is important to ensure drug safety and efficacy. Together with methionine and asparagine, aspartic acid (Asp) is very sensitive to spontaneous alterations. In particular, Asp residues can undergo isomerization and peptide-bond hydrolysis, especially when embedded in sequence motifs that are prone to succinimide formation or when followed by proline (Pro). As Asp and isoAsp have the same mass, and the Asp-Pro peptide-bond cleavage may lead to an unspecific mass difference of + 18 Da under native conditions or in the case of disulfide-bridged cleavage products, it is challenging to directly detect and characterize such modifications by mass spectrometry (MS). Here we propose a 2D NMR-based approach for the unambiguous identification of isoAsp and the products of Asp-Pro peptide-bond cleavage, namely N-terminal Pro and C-terminal Asp, and demonstrate its applicability to proteins including a therapeutic monoclonal antibody (mAb). To choose the ideal pH conditions under which the NMR signals of isoAsp and C-terminal Asp are distinct from other random coil signals, we determined the pKa values of isoAsp and C-terminal Asp in short peptides. The characteristic 1H-13C chemical shift correlations of isoAsp, N-terminal Pro and C-terminal Asp under standardized conditions were used to identify these PTMs in lysozyme and in the therapeutic mAb rituximab (MabThera) upon prolonged storage under acidic conditions (pH 4–5) and 40 °C. The results show that the application of our 2D NMR-based protocol is straightforward and allows detecting chemical changes of proteins that may be otherwise unnoticed with other analytical methods.
Three-dimensional beam element for pre- and post-buckling analysis of thin-walled beams in multibody systems
Authors: Jonker J. B. 
Published: January 2021

AbstractThis paper presents a three-dimensional beam element for stability analysis of elastic thin-walled open-section beams in multibody systems. The beam model is based on the generalized strain beam formulation. In this formulation, a set of independent deformation modes is defined which are related to dual stress resultants in a co-rotational frame. The deformation modes are characterized by generalized strains or deformations, expressed as analytical functions of the nodal coordinates referred to the global coordinate system. A nonlinear theory of non-uniform torsion of open-section beams is adopted for the derivation of the elastic and geometric stiffness matrices. Both torsional-related warping and Wagner’s stiffening torques are taken into account. Second order approximations for the axial elongation and bending curvatures are included by additional second order terms in the expressions for the deformations. The model allows to study the buckling and post-buckling behaviour of asymmetric thin-walled beams with open cross-section that can undergo moderately large twist rotations. The inertia properties of the beam are described using both consistent and lumped mass formulations. The latter is used to model rotary and warping inertias of the beam cross-section. Some validation examples illustrate the accuracy and computational efficiency of the new beam element in the analysis of the buckling and post-buckling behaviour of thin-walled beams under various loads and (quasi)static boundary conditions. Finally, applications to multibody problems are presented, including the stability analysis of an elementary two-flexure cross-hinge mechanism.
Informal institutions, transaction risk, and firm productivity in Myanmar
Authors: Danquah Michael , Sen Kunal 
Published: January 2021

AbstractIn many low-income transition countries, where formal institutions such as courts do not function effectively, informal institutions are often used by firms to minimize transaction risks. We examine the role of informal institutions, in the forms of relational contracting and social networks, in determining the risks that firms are willing to bear in their transactions with their suppliers and customers, and whether firms that bear such risks have higher productivity. Our country context is Myanmar, a country which is making a transition from a socialist to market-oriented economy. Using a unique dataset of 2496 micro, small, and medium firms, we find that firms that engage in risk taking are significantly more productive than firms that do not, and such firms are more likely to utilize informal institutions, such as acquiring information from informal interaction with customers, and social networks, including information received from business networks by firms, talking to other suppliers of customers, and being a member of a business association. Our findings suggest that informal institutions can be effective substitutes for formal institutions that are often absent or not effective in low-income transition economies.
Multiscale stick-breaking mixture models
Authors: Stefanucci Marco , Canale Antonio 
Published: January 2021

AbstractBayesian nonparametric density estimation is dominated by single-scale methods, typically exploiting mixture model specifications, exception made for Pólya trees prior and allied approaches. In this paper we focus on developing a novel family of multiscale stick-breaking mixture models that inherits some of the advantages of both single-scale nonparametric mixtures and Pólya trees. Our proposal is based on a mixture specification exploiting an infinitely deep binary tree of random weights that grows according to a multiscale generalization of a large class of stick-breaking processes; this multiscale stick-breaking is paired with specific stochastic processes generating sequences of parameters that induce stochastically ordered kernel functions. Properties of this family of multiscale stick-breaking mixtures are described. Focusing on a Gaussian specification, a Markov Chain Monte Carlo algorithm for posterior computation is introduced. The performance of the method is illustrated analyzing both synthetic and real datasets consistently showing competitive results both in scenarios favoring single-scale and multiscale methods. The results suggest that the method is well suited to estimate densities with varying degree of smoothness and local features.
Parametric Mapping for TSPO PET Imaging with Spectral Analysis Impulsive Response Function
Authors: Veronese Mattia , Tuosto Marcello , Marques Tiago Reis , Howes Oliver , Pascual Belen , Yu Meixiang , Masdeu Joseph C. , Turkheimer Federico , Bertoldo Alessandra , Zanotti-Fregonara Paolo 
Published: January 2021

Abstract
Purpose
The aim of this study was to investigate the use of spectral analysis (SA) for voxel-wise analysis of TSPO PET imaging studies. TSPO PET quantification is methodologically complicated by the heterogeneity of TSPO expression and its cell-dependent modulation during neuroinflammatory response. Compartmental models to account for this complexity exist, but they are unreliable at the high noise typical of voxel data. On the contrary, SA is noise-robust for parametric mapping and provides useful information about tracer kinetics with a free compartmental structure.

Procedures
SA impulse response function (IRF) calculated at 90 min after tracer injection was used as main parameter of interest in 3 independent PET imaging studies to investigate its sensitivity to (1) a TSPO genetic polymorphism (rs6971) known to affect tracer binding in a cross-sectional analysis of healthy controls scanned with [11C]PBR28 PET; (2) TSPO density with [11C]PBR28 in a competitive blocking study with a TSPO blocker, XBD173; and (3) the higher affinity of a second radiotracer for TSPO, by using data from a head-to-head comparison between [11C]PBR28 and [11C]ER176 scans.

Results
SA-IRF produced parametric maps of visually good quality. These were sensitive to TSPO genotype (mean relative difference between high- and mixed-affinity binders = 25 %) and TSPO availability (mean signal displacement after 90 mg oral administration of XBD173 = 39 %). Regional averages of voxel-wise IRF estimates were strongly associated with regional total distribution volume (VT) estimated with a 2-tissue compartmental model with vascular compartment (Pearson’s r = 0.86 ± 0.11) but less strongly with standard 2TCM-VT (Pearson’s r = 0.76 ± 0.32). Finally, SA-IRF estimates for [11C]ER176 were significantly higher than [11C]PBR28 ones, consistent with the higher amount of specific binding of the former tracer.

Conclusions
SA-IRF can be used for voxel-wise quantification of TSPO PET data because it generates high-quality parametric maps, it is sensitive to TSPO availability and genotype, and it accounts for the complexity of TSPO tracer kinetics with no additional assumptions.
Degradation of naturally produced hydroxylated polybrominated diphenyl ethers in Baltic Sea sediment via reductive debromination
Authors: Lindqvist Dennis , Gustafsson Johan 
Published: January 2021

AbstractOver the last two decades, the occurrence of hydroxylated polybrominated diphenyl ethers (OH-PBDEs) has been observed to be nearly ubiquitous among Baltic Sea filamentous macroalgae. High concentrations are continuously recorded among red, green, and brown filamentous algae. Several of these algae species are ephemeral, and when large parts of the colonies decay at the end of their lifecycles, the OH-PBDEs are expected to largely partition to the sediment. In this study, the fate of OH-PBDEs in Baltic Sea sediment was investigated, with focus on the effect of reductive debromination. During chemical debromination, it was observed that the half-life could differ with as much as two orders of magnitude between a pentabrominated and a tetrabrominated congener. Using collected Baltic Sea sediment, it was further observed that the half-life of spiked pentabrominated OH-PBDEs spanned from a few days up to a few weeks in room temperature. At 4 °C, it took 6 months to achieve a 50% decrease in concentration of the fasted degrading congener. Clear differences in selectivity between chemical debromination and debromination in sediment were also observed when studying the major reaction products. Baltic Sea sediment seems to have a good capacity for reducing naturally produced OH-PBDEs.
Carbon footprint of plastic from biomass and recycled feedstock: methodological insights
Authors: Tonini Davide , Schrijvers Dieuwertje , Nessi Simone , Garcia-Gutierrez Pelayo , Giuntoli Jacopo 
Published: January 2021

AbstractPurposeA circular (bio)economy is sustained through use of secondary raw material and biomass feedstock. In life cycle assessment (LCA), the approach applied to address the impact of these feedstocks is often unclear, in respect to both handling of the recycled content and End-of-Life recyclability and disposal. Further, the modelling approach adopted to account for land use change (LUC) and biogenic C effects is crucial to defining the impact of biobased commodities on global warming.MethodWe depart from state-of-the-art approaches proposed in literature and apply them to the case of non-biodegradable plastic products manufactured from alternative feedstock, focusing on selected polymers that can be made entirely from secondary raw material or biomass. We focus on global warming and the differences incurred by recycled content, recyclability, LUC, and carbon dynamics (effects of delayed emission of fossil C and temporary storage of biogenic C). To address the recycled content and recyclability, three formulas recently proposed are compared and discussed. Temporary storage of biogenic C is handled applying methods for dynamic accounting. LUC impacts are addressed by applying and comparing a biophysical, global equilibrium and a normative-based approach. These methods are applied to two case studies (rigid plastic for packaging and automotive applications) involving eight polymers.Results and discussionDrawing upon the results, secondary raw material is the feedstock with the lowest global warming impact overall. The results for biobased polymers, while promising in some cases (polybutylene succinate), are significantly affected by the formulas proposed to handle the recycled content and recyclability. We observe that some of the proposed formulas in their current form do not fully capture the effects associated with the biogenic nature of the material when this undergoes recycling and substitutes fossil materials. Furthermore, the way in which the recycled content is modelled is important for wastes already in-use. LUC factors derived with models providing a combined direct and indirect impact contribute with 15–30% of the overall life cycle impact, which in magnitude is comparable to the savings from temporary storage of biogenic C, when included.ConclusionEnd-of-Life formulas can be improved by addition of corrective terms accounting for the relative difference in disposal impacts between the recycled and market-substituted product. This affects the assessment of biobased materials. Inclusion of LUCs effects using economic/biophysical models in addition to (direct) LUC already embedded in commercial datasets may result in double-counting and should be done carefully. Dynamic assessment allows for detailed modelling of the carbon cycle, providing useful insights into the impact associated with biogenic C storage.
Therapeutic and toxicological aspects of the use of cannabis and cannabinoids in medicine
Authors: Parolaro Daniela 
Published: January 2021

AbstractThe legalization of cannabis products for recreational and/or medical use means that our society is now clearly more open to its diffusion. Thus, it is particularly important for people to understand what is known about both the adverse health effects and the potential therapeutic benefits linked to cannabis. The evaluation of the benefit vs adverse effect of cannabis use is generally referred to its recreational use; however, medicinal cannabis is now authorized in several countries, and therefore, it has become a public safety issue. In this article, the acute and long-lasting consequences of recreational cannabis use as well as the therapeutic vs toxicological effect of medicinal cannabis will be summarized.Graphic abstract
Discovery and function exploration of microRNA-155 as a molecular biomarker for early detection of breast cancer
Authors: Liu Xuemin , Chang Qingyu , Wang Haiqiang , Qian Hairong , Jiang Yikun 
Published: January 2021

Abstract
Background
MicroRNA-155 (miR-155) may function as a diagnostic biomarker of breast cancer (BC). Nevertheless, the available evidence is controversial. Therefore, we performed this study to summarize the global predicting role of miR-155 for early detection of BC and preliminarily explore the functional roles of miR-155 in BC.

Methods
We first collected published studies and applied the bivariate meta-analysis model to generate the pooled diagnostic parameters of miR-155 in diagnosing BC such as sensitivity, specificity and area under curve (AUC). Then, we applied function enrichment and protein–protein interactions (PPI) analyses to explore the potential mechanisms of miR-155.

Results
A total of 21 studies were finally included. The results indicated that miR-155 allowed for the discrimination between BC patients and healthy controls with a sensitivity of 0.87 (95% CI 0.78–0.93), specificity of 0.82 (0.72–0.89), and AUC of 0.91 (0.88–0.93). In addition, the overall sensitivity, specificity and AUC for circulating miR-155 were 0.88 (0.76–0.95), 0.83 (0.72–0.90), and 0.92 (0.89–0.94), respectively. Function enrichment analysis revealed several vital ontologies terms and pathways associated with BC occurrence and development. Furthermore, in the PPI network, ten hub genes and two significant modules were identified to be involved in some important pathways associated with the pathogenesis of BC.

Conclusions
We demonstrated that miR-155 has great potential to facilitate accurate BC detection and may serve as a promising diagnostic biomarker for BC. However, well-designed cohort studies and biological experiments should be implemented to confirm the diagnostic value of miR-155 before it can be applied to routine clinical procedures.
Significance of the particle physical properties and the Geldart group in the use of correlations for the prediction of minimum fluidization velocity of biomass–sand binary mixtures
Authors: Cáceres-Martínez Louis Edwards , Guío-Pérez Diana Carolina , Rincón-Prat Sonia Lucía 
Published: January 2021

AbstractThe present study explores the relevance of the physical properties of biomass particles on the determination of the minimum fluidization velocity (Umf) of binary mixtures. Fluidization experiments were performed in a cold flow unit with diverse biomasses mixed with sand in different mass fractions. Gas velocity and pressure drop across the bed were used to determine Umf. Different correlations reported in the literature were evaluated on their ability to accurately predict Umf of the mixtures. Results showed satisfactory predictions when appropriately identifying correlations according to the corresponding Geldart groups for the biomass particles. This perspective opens new possibilities toward the generalization of correlation factors and helps in improving the accuracy of the prediction for highly heterogeneous mixtures. The methodology also allows the analysis of mixtures for which the experimental approach is difficult, such as those including char particle, with the only requirement of carefully measuring the physical properties of the particles.
Using climate reanalysis data in conjunction with multi-temporal satellite thermal imagery to derive supraglacial debris thickness changes from energy-balance modelling
Authors: Stewart Rebecca L. , Westoby Matthew , Pellicciotti Francesca , Rowan Ann , Swift Darrel , Brock Benjamin , Woodward John 
Published: January 2021

AbstractSurface energy-balance models are commonly used in conjunction with satellite thermal imagery to estimate supraglacial debris thickness. Removing the need for local meteorological data in the debris thickness estimation workflow could improve the versatility and spatiotemporal application of debris thickness estimation. We evaluate the use of regional reanalysis data to derive debris thickness for two mountain glaciers using a surface energy-balance model. Results forced using ERA-5 agree with AWS-derived estimates to within 0.01 ± 0.05 m for Miage Glacier, Italy, and 0.01 ± 0.02 m for Khumbu Glacier, Nepal. ERA-5 data were then used to estimate spatiotemporal changes in debris thickness over a ~20-year period for Miage Glacier, Khumbu Glacier and Haut Glacier d'Arolla, Switzerland. We observe significant increases in debris thickness at the terminus for Haut Glacier d'Arolla and at the margins of the expanding debris cover at all glaciers. While simulated debris thickness was underestimated compared to point measurements in areas of thick debris, our approach can reconstruct glacier-scale debris thickness distribution and its temporal evolution over multiple decades. We find significant changes in debris thickness over areas of thin debris, areas susceptible to high ablation rates, where current knowledge of debris evolution is limited.
CULTURE, PERIOD OR STYLE? RECONSIDERATION OF EARLY AND MIDDLE COPPER AGE CHRONOLOGY OF THE GREAT HUNGARIAN PLAIN
Authors: Siklósi Zsuzsanna , Szilágyi Márton 
Published: January 2021

ABSTRACTThe main goal of our research project was to date the Early and Middle Copper Age (4500/4450–3800 cal BC) of the Great Hungarian Plain more precisely. In our project, we took samples for accelerator mass spectrometry (AMS) dating from both settlement features and burials, and the data were analyzed using Bayesian modeling. We examined the Early and Middle Copper Age finds of the Great Hungarian Plain on several levels (site, microregional, and regional levels) using a bottom-up approach. The AMS measurements were supplemented by statistics-based pottery analysis in order to make our understanding of the relationship between the Tiszapolgár and Bodrogkeresztúr cultures more detailed. As a result, we can see a significant, 130 (68.2%) 230 years overlap between the two types of find assemblages, which contradicts to the earlier accepted chronological sequences created by the traditional culture-historical approach. According to the stylistic analyzes, the two ceramic styles are not clearly distinguishable.
Does Free-Market Reform Induce Protest? Selection, Post-Treatment Bias, and Depoliticization
Authors: Kurtz Marcus J. , Lauretig Adam 
Published: January 2021

AbstractAcross myriad literatures, it is widely held that expanding economic grievances induce violence, protest, or other forms of backlash. In Latin America, where economic liberalization deepened the downturn of the ‘lost decade’ of the 1980s (and 1990s), reform has been tightly associated with protest and mobilization. At the same time, liberal economic reforms have proven to be remarkably durable, even where long-promised benefits are hard to discern. This article makes the case that economically liberal reforms, despite inducing or deepening severe and sustained economic downturns, have actually undermined political protest. Previous work confirming the conventional wisdom foundered on two main methodological problems. First, selection into economic reform was a consequence of the very economic pain and macroeconomic imbalances it also served to induce. Secondly, because of this, these key (macro)economic characteristics are both pre- and post-treatment. Utilizing a marginal structural model approach to assess the impact of economic liberalization on protest outcomes net of this selection process, and the prior history of treatment, the study finds that painful reform reduces political protest even as it heightens grievances. This depoliticizing dynamic helps to explain the surprising durability of liberal reforms in Latin America.
e-Navigating in highly-constrained waters: a case study of the Vistula Lagoon
Authors: Weintrit Adam , Pietraszkiewicz Jacek , Piotrzkowski Wiesław , Tycholiz Wojciech 
Published: January 2021

AbstractIn recent years the transition of marine navigation to the digital era has been gaining momentum. Implementation of e-Navigation solutions varies from country to country in terms of their priorities, goals, levels and effects. Maritime authorities in Poland have been setting the pace in this transition process, not only in Poland but also in general as a global solution. The most recent example is the planned deployment of a variety of e-Navigation tools in the Vistula Lagoon: from GNSS-RTK Ground-Based Augmentation System, to virtual and synthetic aids to navigation, high-resolution bathymetry and advanced navigational software for piloting. The major objectives of this paper are, first, to summarise recent dynamics in the e-Navigation field, and second, to present a practical implementation of the e-Navigation concept in the Vistula Lagoon area.