bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamic microtubules slow down during their shrinkage phase
Authors: Luchniak Anna , Kuo Yin-Wei , McGuinness Catherine , Sutradhar Sabyasachi , Orbach Ron , Mahamdeh Mohammed , Howard Jonathon 
Published: July 2022

AbstractMicrotubules are dynamic polymers that undergo stochastic transitions between growing and shrinking phases. The structural and chemical properties of these phases remain poorly understood. The transition from growth to shrinkage, termed catastrophe, is not a first-order reaction but is rather a multi-step process whose frequency increases with the growth time: the microtubule ages as the older microtubule tip becomes more unstable. Aging shows that the growing phase is not a single state but comprises several substates of increasing instability. To investigate whether the shrinking phase is also multi-state, we characterized the kinetics of microtubule shrinkage following catastrophe using anin vitroreconstitution assay with purified tubulins. We found that the shrinkage speed is highly variable across microtubules and that the shrinkage speed of individual microtubules slows down over time by as much as several fold. The shrinkage slowdown was observed in both fluorescently labeled and unlabeled microtubules as well as in microtubules polymerized from tubulin purified from different species, suggesting that the shrinkage slowdown is a general property of microtubules. These results indicate that microtubule shrinkage, like catastrophe, is time-dependent and that the shrinking microtubule tip passes through a succession of states of increasing stability. We hypothesize that the shrinkage slowdown is due to destabilizing events that took place during growth which led to multi-step catastrophe. This suggests that the aging associated with growth is also manifest during shrinkage with the older, more unstable growing tip being associated with a faster depolymerizing shrinking tip.Statement of SignificanceThe dynamics of the microtubule cytoskeleton is crucial for several functions in eukaryotic cells. Microtubule dynamics is traditionally described by constant growth and shrinkage speeds with first order transitions between the growth and shrinkage phases. However, catastrophe, the transition from growth to shrinkage, increases with microtubule age and is not a first order process. In contrast to the common assumption that microtubules shrink with constant speed, here we show that shrinking microtubule tips undergo step-wise slowdown during depolymerization. Our results suggest that microtubule shrinkage, like catastrophe, is a multi-step process. This finding is important for understanding the molecular nature of microtubule dynamic instability and how microtubule shrinkage can be modulated by microtubule associated proteins.
Subtilases turn on pectin methylesterase activity for a robust apoplastic immunity
Authors: Coculo Daniele , Del Corpo Daniele , Martínez Miguel Ozáez , Vera Pablo , Piro Gabriella , De Caroli Monica , Lionetti Vincenzo 
Published: July 2022

AbstractPlants involve a fine modulation of pectin methylesterase (PME) activity against microbes. PME activity can promote the cell wall stiffening and the production of damage signals able to induce defense responses. However, to date, the knowledge about the molecular mechanisms triggering PME activity during disease remains largely unknown. In this study, we explored the role of subtilases (SBTs), serine proteases consisting of 56 isoforms inArabidopsis thaliana, as activators of PME activity in plant immunity. By using biochemical and reverse genetic approaches, we found that SBT3.3 and SBT3.5 are required to control PME activity and resistance to the fungusBotrytis cinerea. Arabidopsis sbt3.3 and sbt3.5knockout mutants showed a reduced induction of PME activity and an increased susceptibility toB. cinerea. SBT3.3expression is controlled by the damage-associated molecular patterns Oligogalacturonides. TheSBT3.3overexpression overactivates PME activity, but only during fungal infection, resulting in an increased expression of the defense-related genes and in an enhanced resistance toB. cinerea. We revealed that SBT3.3 and the Pro-PME17 isoforms are both secreted in the cell wall exploiting distinct protein secretion pathways and a different kinetic. Our findings point to SBTs as a mechanism to switch on PME activity and the related pectin integrity signaling to strengthen plant immunity against pests, in a timely manner to avoid the growth-defense trade-off.One sentence SummarySubtilases arm pectin methylesterase activity against pathogens to switch on pectin integrity signalling, reinforcing plant immunity and avoiding the growth-defense trade-offs
Effect of Delta and Omicron mutations on the RBD-SD1 domain of the Spike protein in SARS-CoV-2 and the Omicron mutations on RBD-ACE2 interface complex
Authors: Ching Wai-Yim , Adhikari Puja , Jawad Bahaa , Podgornik Rudolf 
Published: July 2022

ABSTRACTThe receptor-binding domain (RBD) is the essential part in the Spike-protein (S-protein) of SARS-CoV-2 virus that directly binds to the human ACE2 receptor, making it a key target for many vaccines and therapies. Therefore, any mutations at this domain could affect the efficacy of these treatments as well as the viral-cell entry mechanism. We introduceab initioDFT-based computational study that mainly focuses on two parts: (1) Mutations effects of both Delta and Omicron variants in the RBD-SD1 domain. (2) Impact of Omicron RBD mutations on the structure and properties of the RBD-ACE2 interface system. The in-depth analysis is based on the novel concept ofamino acid-amino acid bond pair units(AABPU) that reveal the differences between the Delta and/or Omicron mutations and its corresponding wild-type strain in terms of the role played by non-local amino acid interactions, their 3D shapes and sizes, as well as contribution to hydrogen bonding and partial charge distributions. Our results also show that the interaction of Omicron RBD with ACE2 significantly increased its bonding between amino acids at the interface providing information on the implications of penetration of S-protein into ACE2, and thus offering a possible explanation for its high infectivity. Our findings enable us to present in more conspicuous atomic level detail the effect of specific mutations that may help in predicting and/or mitigating the next variant of concern.
The Chemical Features of Polyanions Modulate Tau Aggregation and Conformational States
Authors: Montgomery Kelly M. , Carroll Emma C. , Thwin Aye , Hodges Paige , Southworth Daniel R. , Gestwicki Jason E. 
Published: July 2022

AbstractThe aggregation of tau into insoluble fibrils is a defining feature of neurodegenerative tauopathies. However, tau has a positive overall charge and is highly soluble; so polyanions, such as heparin, are typically required to promote its aggregation in vitro. There are dozens of polyanions in living systems and it is not clear which ones might promote this process. Here, we systematically measure the ability of 30 diverse, anionic biomolecules to initiate tau aggregation, using either wild type (WT) tau or the disease associated P301S mutant. We find that polyanions from many different structural classes can promote fibril formation and that P301S tau is sensitive to a greater number of polyanions (19/30) than WT tau (16/30). We also find that some polyanions preferentially reduce the lag time of the aggregation reactions, while others enhance the elongation rate, suggesting that they act on partially distinct steps. From the resulting structure-activity relationships, the valency of the polyanion seems to be an important chemical feature, such that anions with low valency tend to be weaker aggregation inducers, even at the same overall charge. Finally, the identity of the polyanion influences fibril morphology, based on electron microscopy and limited proteolysis. These results provide insight into the crucial role of polyanion—tau interactions in modulating tau conformational dynamics with implications for understanding the tau aggregation landscape in a complex cellular environment.
Augmenting the Signal Peptide of the Ag43 Autotransporter for the improved heterologous display of sfGFP using Fluorescence-Activated Cell Sorting (FACs)-assisted natural selection
Authors: Koh Darius Wen-Shuo , Tay Jian-Hua , Gan Samuel Ken-En 
Published: July 2022

AbstractProtein display, secretion and export in prokaryotes are essential for utilizing microbial systems as engineered living materials for medicines, biocatalysts, and protein factories. To select for improved signal peptides forEscherichia coliprotein display, we utilized error-prone polymerase chain reaction (epPCR) coupled with single-cell sorting and microplate titer to generate, select, and detect improved Ag43 signal peptides. Through three rounds of mutagenesis and selection using green fluorescence from the 56 kDa sfGFP-beta-lactamase, we isolated clones that increased surface display from 1.4 to 3 folds as detected by the microplate plate-reader and native SDS-PAGE assays. To establish that the protein was displayed extracellularly, we trypsinised the bacterial cells to release the surface displayed proteins for analysis. This workflow demonstrated a fast and high-throughput method leveraging on epPCR and single-cell sorting to rapidly augment bacterial surface display, a method that could be applied to other bacterial proteins.
Exploring the effects of problem- and solution-related knowledge sharing in internal crowdsourcing
Authors: Chen Qian , Magnusson Mats , Björk Jennie 
Published: July 2022

Purpose
Firms increasingly rely on both external and internal crowdsourcing to capture ideas more broadly and enhance innovative problem-solving. Especially in internal crowdsourcing, knowledge sharing that contributes to develop or further the understanding of the problem the idea is focused on solving can take place between critical employees, and in that way improve ideas generated by others. This far, most crowdsourcing practices have focused on identifying solutions to proposed problems, whereas much less is known about how crowds can be used to share problem-related knowledge. There is thus an untapped potential in leveraging crowds not just to generate solution-oriented ideas but also to share knowledge to improve ideas and even to reframe problems. This paper aims to explore the effect of problem- and solution-related knowledge sharing in internal crowdsourcing for idea development.

Design/methodology/approach
Data on ideas and comments were collected from an idea management system in a Swedish multinational company. The investigation captures the influences of the problem- and solution-related knowledge sharing on ideas based on content analysis and logistic regression analysis.

Findings
The results from this study show that sharing knowledge related to solutions in idea development impacts idea acceptance positively, whereas sharing knowledge related to problems in idea development has a negative effect on the likelihood of idea acceptance and these effects of knowledge sharing are moderated by the active author responses.

Practical implications
This research provides managerial implications for firms to deliberately manage knowledge sharing in peer communities in internal crowdsourcing, especially by providing suggestions on problem reframing and solution refining for ideas.

Originality/value
The results contribute to existing theory in terms of extending the view of crowdsourcing in ideation to include how crowds contribute to the development of the problem and the solution during the development of ideas and providing new insights on knowledge sharing in internal crowdsourcing based on problem-solving theory.
Mechanisms of knowledge development in a knowledge ecosystem
Authors: Öberg Christina , Lundberg Heléne 
Published: July 2022

Purpose
Although ecosystems have been researched extensively over the past decade, we know little about how they should be organised. Focusing on a knowledge ecosystem comprising a university and a regional strategic network (RSN), this paper aims to describe and discuss the mechanisms for knowledge development in knowledge ecosystems.

Design/methodology/approach
This paper studies the integration of a university into a Swedish RSN. Data were collected through interviews with representatives of the university, the RSN and all firms comprising the RSN. A qualitative content analysis helped to detect mechanisms for knowledge development.

Findings
Two reinforcing mechanisms for knowledge development in the knowledge ecosystem are identified: structure and openness, which relate to insight and outlook, respectively. The findings also indicate a knowledge division, with the university representing the transfer of knowledge capabilities as a linear process, whereas the content-related knowledge is collaborative.

Originality/value
This paper contributes to research on knowledge ecosystems by describing how their organisation is based on a number of contradictions (structure and openness, insight and outlook, linearity and collaboration) to accomplish the development of knowledge capabilities and content-related knowledge.
CFD simulations for evaluating the wind effects on high-rise buildings having varying cross-sectional shape
Authors: Rukhaiyar Ark , Jayant Bhagya , Dahiya Kunal , Meena Rahul Kumar , Raj Ritu 
Published: July 2022

PurposeIn this study the comparison is presented for the variation in cross-sectional shape along the height of the building model. For this purpose Model B and Model C are having the considerable variation and Model A result can be easily predicted on the basis of the result of Model B and C while Model X is considered for the validation purposes only and it is well established that the results are within the allowable limit. This paper aims to discuss these wind generated effects in the tall building model.Design/methodology/approachComputational Fluid Dynamics (CFD) in ANSYS: CFX is used to investigate the wind effects on varying cross-sectional shape along the height of the building model.FindingsFrom pressure contours, it was observed that shape and size of the face is independent of the pressure distribution. It is also observed that pressure distribution for the windward face (A) was less than the magnitude of the leeward face for both models. The leeward face and lateral faces had similar pressure distribution. Also slight changes in pressure distribution were observed at the periphery of the models.Originality/valueThis study has been performed to analyse and compare the wind effect on tall buildings having varying cross sections with variation of different cross sections along the height. Most of the studies done in the field of tall buildings are concentrated to one particular cross-sectional shape while the present study investigates wind effects for combination of two types of cross sections along the height. This analysis is performed for wind incidence angles ranging from 0° to 90° at an interval of 30°. Analysis of wind flow characteristics of two models, Models B and C will be computed using CFD. These two models are the variation of Model A which is a combination of two types of cross section that is square and plus. Square and plus cross-sectional heights for Model B are 48 m and 144 m, respectively. Similarly, square and plus cross-sectional heights for Model C are 144 m and 48 m, respectively. The results are interpreted using pressure contours and streamlines, and comparative graphs of drag and lift forces are presented.
Effects of the substitution of wheat flour with raw or germinated ayocote bean (Phaseolus coccineus) flour on the nutritional properties and quality of bread
Authors: Espinosa‐Ramírez Johanan , Mariscal‐Moreno Rosa María , Chuck‐Hernández Cristina , Serna‐Saldivar Sergio O. , Espiricueta‐Candelaria Rosa Selene 
Published: July 2022

AbstractThis study aimed to evaluate the potential of 10%, 20%, and 30% of raw (ARF) and germinated (AGF) ayocote bean flour as a partial substitute for wheat flour in breadmaking. Substitution with both ayocote bean flours modified the water absorption and development time while maintaining the dough stability. Supplemented breads had 13%, 51%, and 132% higher protein, mineral, and crude fiber content, respectively, than control bread (100% wheat). The breadmaking features, color and crumb firmness, were affected by the substitution level. Sensory analysis revealed that germination could improve the taste and smell of breads produced with ayocote bean flour. The sensory attribute scores of 10% AGF bread were comparable to those of the control bread. Supplementation reduced the in vitro protein digestibility, although the effect was less pronounced in 10% ARF and 20% AGF breads. The limiting amino acid score of supplemented breads increased up to 70%, which improved their protein digestibility‐corrected amino acid scores. Supplementation with 20% or 30% of both ARF and AGF increased resistant starch values and decreased the total digestible starch of breads. Thus, the results showed that substituting wheat with ARF or AGF improves the nutritional properties of bread. However, low substitution levels should be selected to avoid a considerable decrease in physical and sensory properties.Practical Application
Substituting wheat flour with ayocote bean flour improved the nutritional value of bread.
Germination of ayocote beans decreased the cooking stability of composite dough.
Bread fortified with ayocote flour had high levels of essential amino acids.
Bread with raw or germinated ayocote flours had high limiting amino acid scores.
Composite bread had high resistant starch and low total digestible starch.
Colchicine resistance: Associated factors and its effect on health‐related quality of life in patients with familial Mediterranean fever
Authors: Erdem Gürsoy Didem , Gezer Halise Hande , Öz Nuran , Özer Aygün , Acer Kasman Sevtap , Duruöz Mehmet Tuncay 
Published: July 2022

AbstractAimTo determine the factors associated with colchicine resistance and the effect of colchicine resistance on health‐related quality of life (QoL) in patients with familial Mediterranean fever (FMF).MethodsDemographic and clinical features, MEFV gene mutations, and Pras disease severity scores were recorded. QoL was assessed using the Short Form‐36 (SF‐36) and FMF‐QoL scales. Colchicine resistance was defined as at least 1 attack per month for 6 months at the maximum tolerated dose of colchicine in fully compliant patients.ResultsThe mean age of 118 patients (90 female, 28 male) with FMF was 38.4 ± 12.5 years. The percentage of colchicine‐resistant patients was 19.5%. In univariable analysis, smoking (odds ratio [OR] = 2.885; 95% confidence interval [CI] = 1.104–7.539; P = 0.031), attack duration (OR = 1.955; 95% CI = 1.137–3.360; P = 0.015), presence of arthritis (OR = 5.235; 95% CI = 1.508–18.179; P = 0.009), and disease severity score (OR = 1.790; 95% CI = 1.334–2.402; P < 0.001) were associated with colchicine resistance. The FMF‐QoL and subscales of SF‐36 except for role emotional and vitality, were different between colchicine‐resistant and non‐resistant patients (P < 0.05).ConclusionSmoking, attack duration, presence of arthritis, and disease severity were associated with colchicine resistance in fully compliant FMF patients. Colchicine‐resistant patients had poorer health‐related QoL.
Using disaster‐induced closures to evaluate discrete choice models of hospital demand
Authors: Raval Devesh , Rosenbaum Ted , Wilson Nathan E. 
Published: July 2022

AbstractAlthough diversion ratios are important inputs to merger evaluation, there is little evidence about how accurately discrete choice models predict diversions. Using a series of natural disasters that unexpectedly closed hospitals, we compare observed post‐disaster diversion ratios to those predicted from pre‐disaster data using standard models of hospital demand. We find that all standard models consistently underpredict large diversions. Both unobserved heterogeneity in preferences over travel and post‐disaster changes to physician practice patterns can explain some of the underprediction of large diversions. We find a significant improvement using models with a random coefficient on distance.
Archaeometric analysis of the ‘greco scritto’ marble slabs from the Edificio dei Triclinii at Murecine (Pompeii, Italy)
Authors: Perna Simona , Antonelli Fabrizio , Lazzarini Lorenzo 
Published: July 2022

AbstractThis paper presents the results of the archaeometric analysis of the greco scritto marble slabs from the Edificio dei Triclinii, an inn or statio negotiatorum discovered at Murecine in Pompeii’s suburbs in 1999–2000. A total of 14 samples were collected and subjected to standard X‐ray diffraction (XRD), optical microscopy (OM) on thin sections and stable isotope ratio analysis (SIRA) to assess the stone’s identity and provenance. The results of this study substantiate the hypothesis (already put forward and based on a macroscopic identification by Perna and Scognamiglio) that the stone originates from the Hasançavuşlar quarries near Ephesus in Asia Minor, and represent the first step towards a systematic contextual and geochemical study of Ephesian greco scritto in Roman contexts and its respective contribution to the Roman stone trade.
Fault zone fluid pathways in the carbonate Irecê basin, NE Brazil
Authors: Gomes Cleber Peralta , Santos Roberto Ventura , Vieira Lucieth Cruz , Dantas Elton Luiz , Taveira Igor Pureza , Barbosa Paola Ferreira , Couto Diego Canídia , Rasbury Troy , Abbots Frances , Bezerra Francisco Hilário 
Published: July 2022

AbstractWe applied field structural data and isotope geochemical (δ13C, δ18O and 87Sr/86Sr) analyses to understand the relationship among calcite veins, fault damage zones and carbonate host rocks in a thrust fault damage zone in the Achado quarry, Irecê Basin in the São Francisco Craton, NE Brazil. Our results reveal three hydrological packages with different rheological behaviours in a stratified carbonate succession. The upper package includes the Achado fault damage zone that is characterised by interlayered dolomitised grainstones and mudstones. These rocks display high positive δ13C values (10‰–13‰), negative δ18O values (mean −6.34‰) and radiogenic (87Sr/86Sr) isotope values (0.70885–0.71519). A second package is marked by a cataclastic brittle shear zone lateral parallel to dolograinstones bedding. These rocks show low to positive δ13C values (−3.41‰ to +8.85‰), more positive δ18O values (mean −3.73‰) and radiogenic (87Sr/86Sr) isotope values (0.71039–0.71373). The lower package is characterised by well‐preserved pristine limestone succession that shows δ13C values ranging between −0.46‰ and +3.17‰, mean δ18O = −5.41‰ and less radiogenic 87Sr/86Sr values (0.70762–0.70818). In contrast to the upper and intermediate packages, rocks from the lower one exhibit very low permeability and behaved as a seal for fluid migration. Fluid flow occurred several times during basin evolution, for example along syn‐rift fault damage zones, bedding‐parallel carbonate breccia, thrust faults, cataclastic shear zones, synorogenic conjugate shear fractures or joints and opening mode I fracture‐fill calcite veins. These fractures allowed pervasive fluid flow in the porous intermediate cataclastic shear zone where fluids flowed and formed veins, as diffuse fluid flow in randomly oriented fracture swarms, or channelised fluid flow in aligned fracture corridors. They record significant centimetre‐scale to km‐scale hydrological behaviour within carbonate layers. Most carbonates that are associated with veins, fault damage zones and hydraulic breccia were formed by fluids of the same origin with low δ13C (−6.0 to −2.0‰) and δ18O (−6.0 to −8.5‰) values, and more radiogenic 87Sr/86Sr values compared to the carbonate host rocks.