bluuebunny/crossref_metadata_2025_split huggingface dataset:
Studies on the synthesis and stability of α-ketoacyl peptides
Authors: Sajapin Johann , Hellwig Michael 
Published: October 2020

AbstractOxidative stress, an excess of reactive oxygen species (ROS), may lead to oxidative post-translational modifications of proteins resulting in the cleavage of the peptide backbone, known as α-amidation, and formation of fragments such as peptide amides and α-ketoacyl peptides (α-KaP). In this study, we first compared different approaches for the synthesis of different model α-KaP and then investigated their stability compared to the corresponding unmodified peptides. The stability of peptides was studied at room temperature or at temperatures relevant for food processing (100 °C for cooking and 150 °C as a simulation of roasting) in water, in 1% (m/v) acetic acid or as the dry substance (to simulate the thermal treatment of dehydration processes) by HPLC analysis. Oxidation of peptides by 2,5-di-tert-butyl-1,4-benzoquinone (DTBBQ) proved to be the most suited method for synthesis of α-KaPs. The acyl side chain of the carbonyl-terminal α-keto acid has a crucial impact on the stability of α-KaPs. This carbonyl group has a catalytic effect on the hydrolysis of the neighboring peptide bond, leading to the release of α-keto acids. Unmodified peptides were significantly more stable than the corresponding α-KaPs. The possibility of further degradation reactions was shown by the formation of Schiff bases from glyoxylic or pyruvic acids with glycine and proven through detection of transamination products and Strecker aldehydes of α-keto acids by HPLC–MS/MS. We propose here a mechanism for the decomposition of α-ketoacyl peptides.
Der Offene Dialog in der Behandlung von Patient_innen mit einer Borderline-Persönlichkeitsstörung
Authors: Giertz Karsten , Aderhold Volkmar 
Published: October 2020

ZusammenfassungIm Beitrag stellen die Autoren das Konzept der bedürfnisangepassten Behandlung und des Offenen Dialoges vor. Hierbei handelt es sich um innovative therapeutische Behandlungskonzepte, die ab den 1980er Jahren in Finnland zunächst für Menschen mit psychotischem Erleben entwickelt wurden und später auch in mehreren nordeuropäischen Ländern in vielen Regionen des öffentlichen psychiatrischen Regelversorgungssystems eingeführt wurden. Mittlerweile wird dieser Ansatz auch bei weiteren Gruppen von Patient_innen erfolgreich angewendet und hat sich weiter regional weltweit verbreitet.Bei Erstbehandlungen und Krisen steht die Frühintervention durch Netzwerkgespräche im Vordergrund. Dabei fokussieren die Netzwerkgespräche auf die Förderung von Dialogen indem jede(r) gehört wird, damit neue psychologische Bedeutungen von Symptomen und eine gemeinsame Erfahrung dieses Prozesses entstehen können. Die Netzwerkmitglieder helfen, damit ein vielstimmiges Bild der Vorgeschichte und wichtiger Ereignisse entsteht und verständigen sich darüber, was zu tun ist, um so die Handlungsfähigkeit der Betroffenen in ihrem eigenen Leben zu fördern. So kann ein individuell angepasster Behandlungsprozess entstehen, bei dem die jeweiligen Akteur_innen im Rahmen von Netzwerkgesprächen miteinander in Verbindung gebracht werden, so dass sich die verschiedenen für sinnvoll erachteten Ansätze gegenseitig ergänzen und eine Konkurrenz vermieden wird.Obwohl sich die Mehrzahl der existierenden naturalistischen Evaluationsstudien auf die Behandlung von Menschen mit erster psychotischer Episode beziehen, werden die Prinzipien dieses Ansatzes seit vielen Jahren bei allen Krisensituationen und bei Bedarf darüber hinaus angewendet und sind daher nicht als diagnosespezifisch anzusehen. Wesentliche evidenzbasierte Elemente multiprofessioneller psychotherapeutischer und psychiatrischer Behandlung werden somit ergänzt durch eine systemisch dialogische Praxis. In diesem Beitrag vertiefen die Autoren die Methodik des Offenen Dialoges im Kontext der psychotherapeutischen und psychiatrischen Behandlung von Borderline-Patient_innen.
Utility of Hounsfield unit in the diagnosis of tandem occlusion in acute ischemic stroke
Authors: Mühl-Benninghaus Ruben , Dressler Julia , Haußmann Alena , Simgen Andreas , Reith Wolfgang , Yilmaz Umut 
Published: October 2020

Abstract
Background
Tandem occlusions can complicate medical and endovascular stroke treatment. To identify these occlusions, computed tomography angiography (CTA) represents the best imaging modality. However, CTA is still not initially performed in some patients not admitted directly to stroke centers. Early identification of an additional occlusion of the proximal extracranial internal carotid artery may improve the best suitable treatment strategy. The purpose of this study was to find a valuable threshold of thrombus attenuation in a non-contrast head CT (NCCT) scan to facilitate a safe diagnosis of tandem occlusions.

Materials and methods
Consecutive patients with acute middle cerebral artery (MCA) occlusions who underwent endovascular treatment were identified from our registry of neuroendovascular interventions. Thrombus attenuations of the affected MCA and contralateral vessel were measured by NCCT. To compare individual baseline blood attenuations, the difference between the thrombus attenuation and the contralateral MCA attenuation (referred to as ΔTM) was calculated.

Results
Three hundred and twenty-five patients were included. There was a highly significant difference between mean thrombus attenuation with isolated MCA occlusion and additional extracranial internal carotid artery (ICA) occlusion (49.9 ± 8 vs. 56.2 ± 10 Hounsfield units (HU); P < 0.001). The area under the receiver operating characteristic curve of ΔTM was 0.72. The optimal threshold value was 13.5 HU, with a sensitivity of 67.5% and a specificity of 68.6%.

Conclusion
Despite a significant difference in thrombus attenuation in MCA occlusions with an additional extracranial ICA occlusion compared with isolated MCA occlusions, a relevant threshold of thrombus attenuation was not found.
Secondary metabolites from the Burkholderia pseudomallei complex: structure, ecology, and evolution
Authors: Klaus Jennifer R , Coulon Pauline M L , Koirala Pratik , Seyedsayamdost Mohammad R , Déziel Eric , Chandler Josephine R 
Published: October 2020

Abstract
Bacterial secondary metabolites play important roles in promoting survival, though few have been carefully studied in their natural context. Numerous gene clusters code for secondary metabolites in the genomes of members of the Bptm group, made up of three closely related species with distinctly different lifestyles: the opportunistic pathogen Burkholderia pseudomallei, the non-pathogenic saprophyte Burkholderia thailandensis, and the host-adapted pathogen Burkholderia mallei. Several biosynthetic gene clusters are conserved across two or all three species, and this provides an opportunity to understand how the corresponding secondary metabolites contribute to survival in different contexts in nature. In this review, we discuss three secondary metabolites from the Bptm group: bactobolin, malleilactone (and malleicyprol), and the 4-hydroxy-3-methyl-2-alkylquinolines, providing an overview of each of their biosynthetic pathways and insight into their potential ecological roles. Results of studies on these secondary metabolites provide a window into how secondary metabolites contribute to bacterial survival in different environments, from host infections to polymicrobial soil communities.
Production of d-Glyceric acid from d-Galacturonate in Escherichia coli
Authors: Fox Kevin J , Prather Kristala L J 
Published: October 2020

Abstract
A microbial production platform has been developed in Escherichia coli to synthesize d-glyceric acid from d-galacturonate. The expression of uronate dehydrogenase (udh) from Pseudomonas syringae and galactarolactone isomerase (gli) from Agrobacterium fabrum, along with the inactivation of garK, encoding for glycerate kinase, enables d-glyceric acid accumulation by utilizing the endogenous expression of galactarate dehydratase (garD), 5-keto-4-deoxy-D-glucarate aldolase (garL), and 2-hydroxy-3-oxopropionate reductase (garR). Optimization of carbon flux through the elimination of competing metabolic pathways led to the development of a ΔgarKΔhyiΔglxKΔuxaC mutant strain that produced 4.8 g/l of d-glyceric acid from d-galacturonate, with an 83% molar yield. Cultivation in a minimal medium produced similar yields and demonstrated that galactose or glycerol serve as possible carbon co-feeds for industrial production. This novel platform represents an alternative for the production of d-glyceric acid, an industrially relevant chemical, that addresses current challenges in using acetic acid bacteria for its synthesis: increasing yield, enantio-purity and biological stability.
Angiogenesis, hereditary hemorrhagic telangiectasia and COVID-19
Authors: Riera-Mestre Antoni , Iriarte Adriana , Moreno Manuela , del Castillo Raul , López-Wolf Daniel 
Published: October 2020

AbstractHereditary hemorrhagic telangiectasia (HHT) is a rare autosomal-dominant disease characterized by pathologic angiogenesis that provokes vascular overgrowth. The evidence about the influence of Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in patients with rare diseases is scarce. We aimed to know the prevalence of coronavirus disease 2019 (COVID-19) in HHT patients. The HHT pathogenic angiogenesis and endothelial injury in COVID-19 are discussed using data from RiHHTa (Computerized Registry of Hereditary Hemorrhagic Telangiectasia) registry. RiHHTa is an open, multicenter, prospective, observational registry including adult patients with HHT. A 27-item survey that captured clinical data of admitted HHT patients for COVID-19 was distributed to all RiHHTa investigators from June 8th to June 24th 2020. Only one out of 1177 HHT patients was admitted for COVID-19 pneumonia. She is a 74 years-old woman with a pathogenic variant in ACVRL1 gene. Her clinical course did not involve mechanical ventilation or worsening epistaxis, and she was successfully discharged after two weeks. The endothelial damage and the consequent angiogenic process in COVID-19 patients deserve further investigation.
Empirical vulnerability curves for Italian mansory buildings: evolution of vulnerability model from the DPM to curves as a function of accelertion
Authors: Zuccaro Giulio , Perelli Francesca Linda , De Gregorio Daniela , Cacace Francesco 
Published: October 2020

AbstractIn the framework of the emergency management in the case of seismic events, the evaluation of the expected damage represents a basic requirement for risk informed planning. Seismic risk is defined by the probability to reach a level of damage on given exposed elements caused by seismic events occurring in a fixed period and in a fixed area. To this purpose, the expected seismic input, the exposed elements and their vulnerability have to be correctly evaluated. The aim of the research is to define a correct model of vulnerability curves, in PGA, for masonry structures in Italy, by heuristic approach starting from damage probability matrices (DPMs). To this purpose, the PLINIVS database, containing data on major Italian seismic events, has been used and supported by “critical” assumption on missing data. To support the reliability of this assumption, two vulnerability models, considering or not the hypothesis on the missing data, have been estimated and used to calculate the seismic scenario of the L’Aquila 2009 earthquake through the IRMA (Italian Risk MAp) platform. Finally, a comparison between the outcomes elaborated by IRMA platform and the observed damage collected in the AEDES forms, has been done.
PorePy: an open-source software for simulation of multiphysics processes in fractured porous media
Authors: Keilegavlen Eirik , Berge Runar , Fumagalli Alessio , Starnoni Michele , Stefansson Ivar , Varela Jhabriel , Berre Inga 
Published: October 2020

AbstractDevelopment of models and dedicated numerical methods for dynamics in fractured rocks is an active research field, with research moving towards increasingly advanced process couplings and complex fracture networks. The inclusion of coupled processes in simulation models is challenged by the high aspect ratio of the fractures, the complex geometry of fracture networks, and the crucial impact of processes that completely change characteristics on the fracture-rock interface. This paper provides a general discussion of design principles for introducing fractures in simulators, and defines a framework for integrated modeling, discretization, and computer implementation. The framework is implemented in the open-source simulation software PorePy, which can serve as a flexible prototyping tool for multiphysics problems in fractured rocks. Based on a representation of the fractures and their intersections as lower-dimensional objects, we discuss data structures for mixed-dimensional grids, formulation of multiphysics problems, and discretizations that utilize existing software. We further present a Python implementation of these concepts in the PorePy open-source software tool, which is aimed at coupled simulation of flow and transport in three-dimensional fractured reservoirs as well as deformation of fractures and the reservoir in general. We present validation by benchmarks for flow, poroelasticity, and fracture deformation in porous media. The flexibility of the framework is then illustrated by simulations of non-linearly coupled flow and transport and of injection-driven deformation of fractures. All results can be reproduced by openly available simulation scripts.
Understanding design-based learning context and the associated emotional experience
Authors: Zhang Feiran , Markopoulos Panos , Bekker Tilde , Paule-Ruíz Mpuerto , Schüll Martine 
Published: October 2020

AbstractEducational settings are emotional places where students experience diverse emotions in relation to academic activities and their outcomes. Emotions, in turn, greatly influence students’ learning process and engagement. Research on emotions in Design-Based Learning (DBL) has so far been coarse-grained examining how students evaluate their overall feelings towards the DBL project. As yet, little is known regarding how specific DBL activities influence students’ emotional experience. Therefore, we report a three-month field study of a DBL project involving 30 middle school students (aged 13–14) addressing dual research purposes: (1) to faithfully reconstruct the manner and sequence of activities during DBL from a fine-grained perspective; and (2) to examine the relationship between these activities and students’ emotional experience. This study used a mixed research method and collected multiple data sources, including experience sampling surveys, classroom observations, and interviews. The research outcomes in this study are multiple. First, this paper reveals detailed inspection regarding the types of task students performed, the strategies of shifting, and executing tasks during the process student experienced. Second, this paper identifies specific types of activities that have a significant positive or negative relationship with students’ emotional experiences. Derived from reported empirical evidence in the present study, this paper furtherly proposes an Activity-and-Affect model of DBL. This model provides a fine-grained description of DBL activity as continuous along three dimensions: task (design thinking process, project management, social interaction) task strategy (single-tasking vs. multitasking), and collaboration strategy (individual or group). Our analysis highlights the variability in how different DBL activities can be associated with different emotions.
A simplified approach to control cell adherence on biologically derived in vitro cell culture scaffolds by direct UV-mediated RGD linkage
Authors: Porras Hernández A. M. , Pohlit H. , Sjögren F. , Shi L. , Ossipov D. , Antfolk M. , Tenje M. 
Published: October 2020

AbstractIn this work, we present a method to fabricate a hyaluronic acid (HA) hydrogel with spatially controlled cell-adhesion properties based on photo-polymerisation cross-linking and functionalization. The approach utilises the same reaction pathway for both steps meaning that it is user-friendly and allows for adaptation at any stage during the fabrication process. Moreover, the process does not require any additional cross-linkers. The hydrogel is formed by UV-initiated radical addition reaction between acrylamide (Am) groups on the HA backbone. Cell adhesion is modulated by functionalising the adhesion peptide sequence arginine–glycine–aspartate onto the hydrogel surface via radical mediated thiol–ene reaction using the non-reacted Am groups. We show that 10 × 10 µm2 squares could be patterned with sharp features and a good resolution. The smallest area that could be patterned resulting in good cell adhesion was 25 × 25 µm2 squares, showing single-cell adhesion. Mouse brain endothelial cells adhered and remained in culture for up to 7 days on 100 × 100 µm2 square patterns. We see potential for this material combination for future use in novel organ-on-chip models and tissue engineering where the location of the cells is of importance and to further study endothelial cell biology.
Motif: an open-source R tool for pattern-based spatial analysis
Authors: Nowosad Jakub 
Published: October 2020

AbstractContextPattern-based spatial analysis provides methods to describe and quantitatively compare spatial patterns for categorical raster datasets. It allows for spatial search, change detection, and clustering of areas with similar patterns.ObjectivesWe developed an R packagemotifas a set of open-source tools for pattern-based spatial analysis.MethodsThis package provides most of the functionality of existing software (except spatial segmentation), but also extends the existing ideas through support for multi-layer raster datasets. It accepts larger-than-RAM datasets and works across all of the major operating systems.ResultsIn this study, we describe the software design of the tool, its capabilities, and present four case studies. They include calculation of spatial signatures based on land cover data for regular and irregular areas, search for regions with similar patterns of geomorphons, detection of changes in land cover patterns, and clustering of areas with similar spatial patterns of land cover and landforms.ConclusionsThe methods implemented inmotifshould be useful in a wide range of applications, including land management, sustainable development, environmental protection, forest cover change and urban growth monitoring, and agriculture expansion studies. Themotifpackage homepage ishttps://nowosad.github.io/motif.
Upscaling the interplay between diffusion and polynomial drifts through a composite thin strip with periodic microstructure
Authors: Cirillo Emilio N. M. , de Bonis Ida , Muntean Adrian , Richardson Omar 
Published: October 2020

AbstractWe study the upscaling of a system of many interacting particles through a heterogenous thin elongated obstacle as modeled via a two-dimensional diffusion problem with a one-directional nonlinear convective drift.
Assuming that the obstacle can be described well by a thin composite strip with periodically placed microstructures, we aim at deriving the upscaled model equations as well as the effective transport coefficients for suitable scalings in terms of both the inherent thickness at the strip and the typical length scales of the microscopic heterogeneities. Aiming at computable scenarios, we consider that the heterogeneity of the strip is made of an array of periodically arranged impenetrable solid rectangles and identify two scaling regimes what concerns the small asymptotics parameter for the upscaling procedure: the characteristic size of the microstructure is either significantly smaller than the thickness of the thin obstacle or it is of the same order of magnitude.
We scale up the diffusion–polynomial drift model and list computable formulas for the effective diffusion and drift tensorial coefficients for both scaling regimes. Our upscaling procedure combines ideas of two-scale asymptotics homogenization with dimension reduction arguments. Consequences of these results for the construction of more general transmission boundary conditions are discussed. We illustrate numerically the concentration profile of the chemical species passing through the upscaled strip in the finite thickness regime and point out that trapping of concentration inside the strip is likely to occur in at least two conceptually different transport situations: (i) full diffusion/dispersion matrix and nonlinear horizontal drift, and (ii) diagonal diffusion matrix and oblique nonlinear drift.
The Limits of Theoretical Disagreements in Jurisprudence
Authors: Dyrda Adam , Gizbert-Studnicki Tomasz 
Published: October 2020

AbstractThis paper discusses the “positivistic” idea of the limits of law in various contexts: the conceptual problem of the “limits of law”, the limits of legal interpretation and the limits of theoretical disagreements in jurisprudence. In the latter case, we briefly show how contemporary “reflective” or “critical” positivist theories approach the possibility and limits of disagreements over the “grounds” of law. In what follows, we argue that these theories, which argue for a form of an “institutional” limit for admissible “legal” reasons as built upon theories of basic concepts or normative theories of interpretation, are themselves actually underdetermined by “legal culture” or, so to speak, a “folk theory of law”. In the final section, we outline how a folk theory of law constrains both conceptual and interpretive enterprises in jurisprudence.
Using scaffolding to formalize digital coach support for low-literate learners
Authors: Schouten Dylan G. M. , Massink Pim , Donker Stella F. , Neerincx Mark A. , Cremers Anita H. M. 
Published: October 2020

AbstractIn this study, we attempt to specify the cognitive support behavior of a previously designed embodied conversational agent coach that provides learning support to low-literates. Three knowledge gaps are identified in the existing work: an incomplete specification of the behaviors that make up ‘support,’ an incomplete specification of how this support can be personalized, and unclear speech recognition rules. We use the socio-cognitive engineering method to update our foundation of knowledge with new online banking exercises, low-level scaffolding and user modeling theory, and speech recognition. We then refine the design of our coach agent by creating comprehensive cognitive support rules that adapt support based on learner needs (the ‘Generalized’ approach) and attune the coach’s support delay to user performance in previous exercises (the ‘Individualized’ approach). A prototype is evaluated in a 3-week within- and between-subjects experiment. Results show that the specified cognitive support is effective: Learners complete all exercises, interact meaningfully with the coach, and improve their online banking self-efficacy. Counter to hypotheses, the Individualized approach does not improve on the Generalized approach. Whether this indicates suboptimal operationalization or a deeper problem with the Individualized approach remains as future work.