bluuebunny/crossref_metadata_2025_split huggingface dataset:
P176S polymorphism in Maspin rewires electrostatic interaction that alters Maspin functionality
Authors: Anwar Muhammad Ayaz , Haseeb Muhammad , Choi Sangdun , Kwong-Pyo Kim 
Published: May 2022

AbstractMaspin has been known to regress tumors by inhibiting angiogenesis, however, its roles have been reported to be context and sequence-dependent. There are various proteins and cofactors that bind with maspin possibly explaining the conflicting roles of maspin. Moreover, maspin polymorphic forms have also been linked to tumor regression or survival, for instance, maspin with Ser at 176 (maspin-S176) promotes tumor while maspin with Pro at 176 (maspin-Pro176) has opposing roles in cancer pathogenesis. With the help of long molecular dynamic simulation, a possible link between polymorphic forms and tumor progression has been established. First, the maspin is dynamically stable with either amino acid at 176 position, secondly, differential contacts have been observed among various regions, thirdly, these contacts have significantly altered the electrostatic energetics of various residues, and finally, these altered electrostatics of maspin-S176 and maspin-P176 rewired the polar contacts that abolished the allosteric control in protein. By combining these factors, the altered electrostatics can substantially affect the localization, and the preference of maspin binding partners, thus, culminating in a different maspin-protein (cofactor)-interaction landscape that could have been manifested with conflicting reports in previous studies. Here, the underlying reason has been highlighted and discussed that could be helpful for better therapeutic manipulations.SignificanceProtein altered functions in response to mutations are well documented, however, a slight perturbation in structure can lead to dramatic effects that are being felt at longer distances are rare. Here, we have reported that the substitution of Pro to Ser at 176th position in Maspin can substantially alter the protein electrostatic interactions that can hamper the allosteric control. This could lead to different binding partners, localization preferences, and altered cytoplasmic retention duration resulting in functions that are not associated with normal protein. Moreover, the electrostatic attraction/repulsion can immensely affect the allosteric cohesion of protein resulting in unexpected outcomes.
SpecGlob: rapid and accurate alignment of mass spectra differing from their peptide models by several unknown modifications
Authors: Lysiak Albane , Fertin Guillaume , Jean Géraldine , Tessier Dominique 
Published: May 2022

ABSTRACTBackgroundIn proteomics, mass spectra representing peptides carrying multiple unknown modifications are particularly difficult to interpret, which results in a large number of unidentified spectra.MethodsWe developed SpecGlob, a dynamic programming algorithm that aligns pairs of spectra, each such pair being a Peptide-Spectrum Match (PSM) provided by any Open Modification Search (OMS) method. For each PSM, SpecGlob computes the best alignment according to a given score system, while interpreting the mass delta within the PSM as one or several unspecified modification(s). All alignments are provided in a file, written in a specific syntax.ResultsUsing several sets of simulated spectra generated from the human proteome, we demonstrate that running SpecGlob as a post-analysis of an OMS method can significantly increase the number of correctly interpreted spectra, as SpecGlob is able to correctly and rapidly align spectra that differ by one or more modification(s) without any a priori.ConclusionSince SpecGlob explores all possible alignments that may explain the mass delta within a PSM, it reduces interpretation errors generated by incorrect assumptions about the modifications present in the sample or the number and the specificities of modifications carried by peptides. Our results demonstrate that SpecGlob should be relevant to align experimental spectra, although this consists in a more challenging task.
Crowding induced morphological changes in synthetic lipid vesicles determined using smFRET
Authors: Quinn Steven D. , Dresser Lara , Graham Sarah , Conteduca Donato , Shepherd Jack , Leake Mark C. 
Published: May 2022

AbstractLipid vesicles are valuable mesoscale molecular confinement vessels for studying membrane mechanics and lipid-protein interactions, and they have found utility among bio-inspired technologies including drug delivery vehicles. While vesicle morphology can be modified by changing the lipid composition and introducing fusion or pore-forming proteins and detergents, the influence of extramembrane crowding on vesicle morphology has remained under explored owing to a lack of experimental tools capable of capturing morphological changes on the nanoscale. Here, we use biocompatible polymers to simulate molecular crowding in vitro, and through combinations of FRET spectroscopy, lifetime analysis, dynamic light scattering and single-vesicle imaging, we characterize how crowding regulates vesicle morphology. We show that both freely-diffusing and surface-tethered vesicles fluorescently tagged with the DiI and DiD FRET pair undergo compaction in response to modest concentrations of sorbitol, polyethylene glycol and Ficoll. A striking observation is that sorbitol results in irreversible compaction, whereas the influence of high molecular weight PEG-based crowders was found to be reversible. Regulation of molecular crowding allows for precise control of vesicle architecture in vitro, with vast implications for drug delivery and vesicle trafficking systems. Furthermore, our observations of vesicle compaction may also serve to act as a mechanosensitive readout of extramembrane crowding.
Mitochondrial pyruvate metabolism regulates the activation of quiescent adult neural stem cells
Authors: Petrelli Francesco , Scandella Valentina , Montessuit Sylvie , Zamboni Nicola , Martinou Jean-Claude , Knobloch Marlen 
Published: May 2022

SummaryCellular metabolism is important for adult neural stem/progenitor cell (NSPC) behavior. However, its role in the transition from quiescence to proliferation is not fully understood. We here show that the mitochondrial pyruvate carrier (MPC) plays a crucial and unexpected part in this process. MPC transports pyruvate into mitochondria, linking cytosolic glycolysis to mitochondrial tricarboxylic acid cycle (TCA) and oxidative phosphorylation (OXPHOS). Despite its metabolic key function, the role of MPC in NSPCs has not been addressed. We show that quiescent NSPCs have an active mitochondrial metabolism and express high levels of MPC. Pharmacological MPC inhibition increases aspartate and triggers NSPC activation. Furthermore, genetic MPC-ablation in vivo also activates NSPCs, which differentiate into mature neurons, leading to overall increased hippocampal neurogenesis in adult and aged mice. These findings highlight the importance of metabolism for NSPC regulation and identify a novel pathway through which mitochondrial pyruvate import controls NSPC quiescence and activation.Highlights•Quiescent NSPCs have high levels of MPC and an active mitochondrial network•The import of pyruvate into mitochondria is necessary to maintain quiescence of NSPCs•MPC inhibition increases intracellular aspartate levels and triggers the activation of quiescent NSPCs•MPC-knockout NSPCs generate mature newborn neurons, leading to overall increased neurogenesis in adult and advanced age miceGraphical abstract
The complex octoploid Craterostigma genome and tissue-specific mechanisms underlying desiccation tolerance
Authors: VanBuren Robert , Wai Ching Man , Giarola Valentino , Župunski Milan , Pardo Jeremy , Kalinowski Michael , Grossmann Guido , Bartels Dorothea 
Published: May 2022

AbstractResurrection plants can survive prolonged anhydrobiosis, and desiccation tolerance has evolved recurrently across land plants as a common adaptation for survival in regions with seasonal drying.Craterostigma plantagineumwas among the first model resurrection plants, and many of the genetic mechanisms underlying desiccation tolerance were discovered in this important system. Here, we analyzed the complex, octoploid Craterostigma (C. plantagineum) genome and surveyed spatial and temporal expression dynamics to identify genetic elements underlying desiccation tolerance. Homeologous genes within the Craterostigma genome have divergent expression profiles, suggesting the subgenomes contribute differently to desiccation tolerance traits. The Craterostigma genome contains almost 200 tandemly duplicated early light induced proteins (ELIPs), a hallmark trait of desiccation tolerance, with massive upregulation under water deficit. We identified a core network of desiccation responsive genes across all tissues but observed almost entirely unique expression dynamics in each tissue during recovery. Roots and leaves have differential responses related to light and photoprotection, autophagy, and nutrient transport, reflecting their divergent functions. Our findings highlight a universal set of likely ancestral desiccation tolerance mechanisms to protect cellular macromolecules under anhydrobiosis, with secondary adaptations related to tissue function.
Rapid and in-depth coverage of the (phospho-)proteome with deep libraries and optimal window design for dia-PASEF
Authors: Skowronek Patricia , Thielert Marvin , Voytik Eugenia , Tanzer Maria C. , Hansen Fynn M. , Willems Sander , Karayel Özge , Brunner Andreas-David , Meier Florian , Mann Matthias 
Published: May 2022

ABSTRACTData-independent acquisition (DIA) methods have become increasingly attractive in mass spectrometry (MS)-based proteomics, because they enable high data completeness and a wide dynamic range. Recently, we combined DIA with parallel accumulation – serial fragmentation (dia-PASEF) on a Bruker trapped ion mobility separated (TIMS) quadrupole time-of-flight (TOF) mass spectrometer. This requires alignment of the ion mobility separation with the downstream mass selective quadrupole, leading to a more complex scheme for dia-PASEF window placement compared to DIA. To achieve high data completeness and deep proteome coverage, here we employ variable isolation windows that are placed optimally depending on precursor density in them/zand ion mobility plane. ThisAutomatic IsolationDesign procedure is implemented in the freely available py_diAID package. In combination with in-depth project-specific proteomics libraries and the Evosep LC system, we reproducibly identified over 7,700 proteins in a human cancer cell line in 44 minutes with quadruplicate single-shot injections at high sensitivity. Even at a throughput of 100 samples per day (11 minutes LC gradients), we consistently quantified more than 6,000 proteins in mammalian cell lysates by injecting four replicates. We found that optimal dia-PASEF window placement facilitates in-depth phosphoproteomics with very high sensitivity, quantifying more than 35,000 phosphosites in a human cancer cell line stimulated with an epidermal growth factor (EGF) in triplicate 21 minutes runs. This covers a substantial part of the regulated phosphoproteome with high sensitivity, opening up for extensive systems-biological studies.
Corrosion behavior of typical hot rolled sheets in humid storage environments
Authors: Bai Yun , Sun Baozhuang , Huangfu Wenzhu , Sun Xianjin , Liu Zhiyong , Du Cuiwei , Li Xiaogang 
Published: May 2022

Purpose
The purpose of this paper was to study the relationship between safe storage life and storage mode of hot-rolled sheet (Q235, X70) in humid environment, and a prediction model of safe storage life under different storage modes was established.

Design/methodology/approach
The corrosion behavior of hot-rolled sheets under different storage conditions was studied with immersion experiment and morphology observation.

Findings
The results show that pitting occurs on the hot-rolled sheets in humid environment, and the corrosion behavior is strongly related with the storage mode. When they are stored separately, the number and depth of pits first increase and then decrease as the Cl− concentration rises, while for the stack storage, pit depth increases with increasing Cl− concentration. The safe storage time of separate storage is longer than that of stack storage. Based on this, a model of chloride ion concentration and storage life was established.

Originality/value
A storage safe life model of hot-rolled sheet in humid environment is proposed.
Collaboration, trust and performance in agri-food supply chains: a bibliometric analysis
Authors: Gajdić Dušanka , Kotzab Herbert , Petljak Kristina 
Published: May 2022

PurposeThis paper identifies, evaluates and structures research that focuses on “collaboration” (C), “trust” (T) and “performance” (P) in the agri-food supply chain (AFSC) and reveals its intellectual foundation. It aims to synthesize research published over a period of 18 years (from 2003 to the beginning of 2020) and provide a platform for practitioners and researchers in their efforts to identify the existing state of work, gaps in current research and future directions in the area of collaboration–trust–performance (CTP) in the AFSC.Design/methodology/approachPrior to carrying out a bibliometric analysis (BA), literature search was performed, identifying 69 related papers focused on CTP in the AFSC. The content of the papers was further analysed in a systematic literature review (SLR) with regard to the subject area, theoretical lenses, research methodology, supply chain (SC) category and other relevant categories.FindingsCTP in the AFSC are based on a relationship marketing and operations management fundament but show specific particularities. AFSCM is a multi-dimensional design task, and collaboration is considered a necessity, whereas trust significantly affects the AFSC effectiveness. The paper also develops a conceptual CTP model, which shows the interrelations between all identified construct variables, where the authors were able to see also bi-directional relations. Furthermore, the paper presents viable future research opportunities, e.g. focus on organic food chains or multi-actor analysis.Research limitations/implicationsResults of the conducted BA refer to the CTP discussion within a preselected number of peer-reviewed academic articles, which are provided by the WoS CC (Web of Science Core Collection) database.Practical implicationsCTP measurements within the AFSC context are a relevant subject with increasing academic interest in the area of agricultural economics as well as operations and supply chain management (SCM). Therefore, further studies are necessary to develop the related theory and ascertain the practical implications of collaboration, trust and performance among members in the consistently complex AFSC.Originality/valueCTP have been recognized as important factors for designing a sustainable SCM strategy, particularly in the case of the AFSC. However, although previous studies have addressed the AFSC, there is insufficient knowledge regarding all three pillars (CTP) and how they enable successful AFSCM. The originality of this paper lies in systematically mapping the intellectual base of CTP research and providing path forward for research in AFSCM.
Leader reward omission and employee knowledge sharing: the moderating role of proactive personality and perceived organizational unfairness
Authors: Zhong Xi , Peng Qiuping , Wang Tian 
Published: May 2022

PurposeBased on social dilemma theory, the authors analyze the impact of leader reward omission on employee knowledge sharing and the boundary conditions in their relationship.Design/methodology/approachThis study tested the theoretical hypotheses based on empirical data obtained from 264 employees using a two-wave survey method.FindingsThe results indicate that leader reward omission significantly negatively affects employee knowledge sharing. An employee's proactive personality weakens the negative relationship between them; the weakening effects of an employee's proactive personality would decrease along with the perceived increase in organizational unfairness.Originality/valueThis study provides the first insight that leader reward omission can inhibit employee knowledge-sharing behavior. In addition, this study shows that an individual proactive personality and perceived organizational unfairness moderate the relationship between leader reward omission and employee knowledge behavior. Thus, this study provides a more comprehensive understanding of whether and when leader reward omission affects employee knowledge sharing.
The contributions of agritourism to the local food system
Authors: Pehin Dato Musa Siti Fatimahwati , Chin Wei Lee 
Published: May 2022

Purpose
This study aims to evaluate the contributions of agritourism towards the local food system (LFS) by studying three small-scale agritourism farms in Brunei. More specifically, it looks at the role of farm agribusinesses and heritagisation efforts of indigenous farmers.

Design/methodology/approach
This qualitative study uses semi-structured interviews to collect data. This method is widely seen as more suitable to gain the unexplored perspectives of the agriculture community at the three agritourism farms.

Findings
The results suggest that the agritourism farms contribute to mild local food activism through their small-scale production of sustainable food products. Another significant finding affirms that these farms also contribute to preserving ethno-culinary heritage through heritagisation of indigenous food and their ancestral agriculture knowledge. The farms’ involvement in agribusiness and efforts in food heritagisation contributes towards a more sustainable LFS and stimulates the rural area as a reinvigorated space for agritourism transactions.

Originality/value
There are lack of research on the contributions of agritourism towards the LFS, especially in Brunei. This study will provide evidence of the overlooked significance of agribusiness and heritagisation efforts conducted by the local farms.
Expanding advanced work packaging to include commissioning and startup for industrial projects
Authors: O'Connor James T. , Leite Fernanda , Ma Jong Won 
Published: May 2022

Purpose
The purpose of this paper is to present a comprehensive analysis on how the advanced work packaging (AWP) managerial paradigm could be advanced by incorporating and integrating the post-construction commissioning and startup (CSU) phases.

Design/methodology/approach
This study was implemented with the support of consolidated knowledge from industry subject matter experts and an exhaustive literature review to provide a knowledge foundation for the developments. The findings were further validated and strengthened by external subject matter experts.

Findings
A new operating system-oriented work package, systems work package (SWP), is devised with a set of definitions and models of how it relates to AWPs with three-dimensional visualizations. SWP-related constraints, key roles and responsibilities are thoroughly investigated.

Research limitations/implications
A new SWP concept would pose potential challenges for its adoption because of inherent organizational culture and hesitation to change. A systematic reorganization of existing practices is considered as a key strategy to alleviate the limitation, and short- and long-term validity of SWP is currently being investigated by organizations.

Practical implications
This research provides practical implementation strategies on CSU integration which lead to benefits including: better alignment and collaboration of stakeholders, reduced costs for associating AWPs to SWP and improved predictability.

Originality/value
AWP-related studies have primarily focused on the construction phase, with minimal integration of CSU considerations. Highlighting the importance of the philosophy “start with the end in mind,” this research describes how the AWP managerial paradigm can be expanded to include CSU, by placing a strong emphasis on understanding CSU priorities, sequences and constraints.
Expectation management in AI implementation projects: a case study
Authors: Buschmeyer Katharina , Hatfield Sarah , Heine Ina , Jahn Svenja , Markus Antonia Lea 
Published: May 2022

PurposeThe aim of this case study is to exemplify the application of a change story to facilitate the user centered introduction of an AI-based assistance system. Thereby, user expectations considered critical for technology acceptance and continuance intention are actively taken into account.Design/methodology/approachSemi-structured interviews are conducted with future users of the AI-based assistance system. Data are analysed by means of inductive and deductive qualitative content analysis. The resulting categories are considered as communicational core messages and included in the developed change story.FindingsParadox user expectations were revealed and answered in the change story by informational and motivational means. Thus, accurate expectation management is enabled and, additionally, the users are prepared for the upcoming change process, i.e., the implementation of the AI-based assistance system.Originality/valueThe added value lies in the psychological handling of expectation management in addition to technical aspects, which are usually primarily focused but are not sufficient to guarantee a successfully continued use of human-AI-systems.
The impact of apartment vacancies on nearby housing rents over multiple time periods: application of smart meter data
Authors: Baba Hiroki , Shimizu Chihiro 
Published: May 2022

Purpose
This study aims to explore the spatial externalities of apartment vacancy rates on housing rent by considering multiple vacancy durations.

Design/methodology/approach
This research uses smart meter data to measure unobservable vacant houses. This study made a significant contribution by applying building-level smart meter data to housing market analysis. It examined whether vacancy duration significantly affected apartment rent and whether the relationship between apartment rent and vacancy rate differed depending on the level of housing rent.

Findings
The primary finding indicates that there is a significant negative correlation between apartment rent and vacancy duration. Considering the spatial externalities of apartment vacancy rates, the apartment vacancy rates of surrounding buildings did not show any statistical significance. Moreover, quantile regression results indicate that although the bottom 10% of apartment rent levels showed a negative correlation with all vacancy durations, the top 10% showed no statistical significance related to vacancies.

Practical implications
This study measures the extent of spatial externalities that can differentiate taxation based on housing vacancies.

Originality/value
The findings indicate that landlords have asymmetric information about their buildings compared with the surrounding buildings, and the extent to which price adjusts for long-term vacancies differs depending on the level of apartment rent.