bluuebunny/crossref_metadata_2025_split huggingface dataset:
S protein-reactive IgG and memory B cell production after human SARS-CoV-2 infection includes broad reactivity to the S2 subunit
Authors: Nguyen-Contant Phuong , Embong A. Karim , Kanagaiah Preshetha , Chaves Francisco A. , Yang Hongmei , Branche Angela R. , Topham David J. , Sangster Mark Y. 
Published: July 2020

ABSTRACTThe high susceptibility of humans to SARS-CoV-2 infection, the cause of COVID-19, reflects the novelty of the virus and limited preexisting B cell immunity. IgG against the SARS-CoV-2 spike (S) protein, which carries the novel receptor binding domain (RBD), is absent or at low levels in unexposed individuals. To better understand the B cell response to SARS-CoV-2 infection, we asked whether virus-reactive memory B cells (MBCs) were present in unexposed subjects and whether MBC generation accompanied virus-specific IgG production in infected subjects. We analyzed sera and PBMCs from non-SARS-CoV-2-exposed healthy donors and COVID-19 convalescent subjects. Serum IgG levels specific for SARS-CoV-2 proteins (S, including the RBD and S2 subunit, and nucleocapsid [N]) and non-SARS-CoV-2 proteins were related to measurements of circulating IgG MBCs. Anti-RBD IgG was absent in unexposed subjects. Most unexposed subjects had anti-S2 IgG and a minority had anti-N IgG, but IgG MBCs with these specificities were not detected, perhaps reflecting low frequencies. Convalescent subjects had high levels of IgG against the RBD, S2, and N, together with large populations of RBD- and S2-reactive IgG MBCs. Notably, IgG titers against the S protein of the human coronavirus OC43 in convalescent subjects were higher than in unexposed subjects and correlated strongly with anti-S2 titers. Our findings indicate cross-reactive B cell responses against the S2 subunit that might enhance broad coronavirus protection. Importantly, our demonstration of MBC induction by SARS-CoV-2 infection suggests that a durable form of B cell immunity is maintained even if circulating antibody levels wane.IMPORTANCERecent rapid worldwide spread of SARS-CoV-2 has established a pandemic of potentially serious disease in the highly susceptible human population. Key questions are whether humans have preexisting immune memory that provides some protection against SARS-CoV-2 and whether SARS-CoV-2 infection generates lasting immune protection against reinfection. Our analysis focused on pre- and post-infection IgG and IgG memory B cells (MBCs) reactive to SARS-CoV-2 proteins. Most importantly, we demonstrate that infection generates both IgG and IgG MBCs against the novel receptor binding domain and the conserved S2 subunit of the SARS-CoV-2 spike protein. Thus, even if antibody levels wane, long-lived MBCs remain to mediate rapid antibody production. Our study also suggests that SARS-CoV-2 infection strengthens preexisting broad coronavirus protection through S2-reactive antibody and MBC formation.
CENP-A overexpression drives distinct cell fates depending on p53 status
Authors: Jeffery Daniel , Podsypanina Katrina , Gatto Alberto , Landete Rebeca Ponce , Bonneville Lorraine , Dumont Marie , Fachinetti Daniele , Almouzni Geneviève 
Published: July 2020

AbstractTumour evolution is driven by both genetic and epigenetic changes. CENP-A, the centromeric histone H3 variant, is an epigenetic mark that directly perturbs genetic stability and chromatin when overexpressed. Although CENP-A overexpression is a common feature of many cancers, how this impacts cell fate and response to therapy remains unclear. Here, we established a tunable system of inducible and reversible CENP-A overexpression combined with a switch in p53 status in human cell lines. Through clonogenic survival assays and single-cell RNA-sequencing over time, we uncover the tumour suppressor p53 as a key determinant of how CENP-A impacts cell state, cell identity and therapeutic response. If p53 is functional, CENP-A overexpression promotes senescence and radiosensitivity. But, when we inactivate p53, CENP-A overexpression instead promotes epithelial-mesenchymal transition, an essential precursor for tumour cell invasion and metastasis. Thus, CENP-A overexpression drives distinct cell fates depending on p53 status, with important implications for tumour evolution.
DeepTracer: Fast Cryo-EM Protein Structure Modeling and Special Studies on CoV-related Complexes
Authors: Pfab Jonas , Phan Nhut Minh , Si Dong 
Published: July 2020

AbstractInformation about macromolecular structure of protein complexes such as SARS-CoV-2, and related cellular and molecular mechanisms can assist the search for vaccines and drug development processes. To obtain such structural information, we present DeepTracer, a fully automatic deep learning-based method for fast de novo multi-chain protein complex structure determination from high-resolution cryo-electron microscopy (cryo-EM) density maps. We applied DeepTracer on a previously published set of 476 raw experimental density maps and compared the results with a current state of the art method. The residue coverage increased by over 30% using DeepTracer and the RMSD value improved from 1.29Å to 1.18Å. Additionally, we applied DeepTracer on a set of 62 coronavirus-related density maps, among them 10 with no deposited structure available in EMDataResource. We observed an average residue match of 84% with the deposited structures and an average RMSD of 0.93Å. Additional tests with related methods further exemplify DeepTracer’s competitive accuracy and efficiency of structure modeling. DeepTracer allows for exceptionally fast computations, making it possible to trace around 60,000 residues in 350 chains within only two hours. The web service is globally accessible athttps://deeptracer.uw.edu.
3D-Visualization of Amyloid-β Oligomer and Fibril Interactions with Lipid Membranes by Cryo-Electron Tomography
Authors: Tian Yao , Liang Ruina , Kumar Amit , Szwedziak Piotr , Viles John H. 
Published: July 2020

ABSTRACTAmyloid-β (Aβ) monomers assemble into mature fibrils via a range of metastable oligomeric and protofibrillar intermediates. These Aβ assemblies have been shown to bind to lipid bilayers. This can disrupt membrane integrity and cause a loss of cellular homeostasis, that triggers a cascade of events leading to Alzheimer’s disease. However, molecular mechanisms of Aβ cytotoxicity and how the different assembly forms interact with the membrane remain enigmatic. Here we use cryo-electron tomography (cryoET) to obtain three-dimensional nano-scale images of various Aβ assembly types and their interaction with liposomes. Aβ oligomers bind extensively to the lipid vesicles, inserting and carpeting the upper-leaflet of the bilayer. Furthermore, curvilinear protofibrils also insert into the bilayer, orthogonally to the membrane surface. Aβ oligomers concentrate at the interface of vesicles and form a network of Aβ-linked liposomes. While crucially, monomeric and fibrillar Aβ have relatively little impact on the membrane. Changes to lipid membrane composition highlights a significant role for GM1-ganglioside in promoting Aβ-membrane interactions. The different effects of Aβ assembly forms observed align with the highlighted cytotoxicity reported for Aβ oligomers. The wide-scale incorporation of Aβ oligomers and curvilinear protofibrils into the lipid bilayer suggests a mechanism by which membrane integrity is lost.
Bioactivity descriptors for uncharacterized compounds
Authors: Bertoni Martino , Duran-Frigola Miquel , Badia-i-Mompel Pau , Pauls Eduardo , Orozco-Ruiz Modesto , Guitart-Pla Oriol , Alcalde Víctor , Diaz Víctor M , Berenguer-Llergo Antoni , García de Herreros Antonio , Aloy Patrick 
Published: July 2020

AbstractChemical descriptors encode the physicochemical and structural properties of small molecules, and they are at the core of chemoinformatics. The broad release of bioactivity data has prompted enriched representations of compounds, reaching beyond chemical structures and capturing their known biological properties. Unfortunately, ‘bioactivity descriptors’ are not available for most small molecules, which limits their applicability to a few thousand well characterized compounds. Here we present a collection of deep neural networks able to infer bioactivity signatures for any compound of interest, even when little or no experimental information is available for them. Our ‘signaturizers’ relate to bioactivities of 25 different types (including target profiles, cellular response and clinical outcomes) and can be used as drop-in replacements for chemical descriptors in day-to-day chemoinformatics tasks. Indeed, we illustrate how inferred bioactivity signatures are useful to navigate the chemical space in a biologically relevant manner, unveiling higher-order organization in natural product collections, and to enrich mostly uncharacterized chemical libraries for activity against the drug-orphan target Snail1. Moreover, we implement a battery of signature-activity relationship (SigAR) models and show a substantial improvement in performance, with respect to chemistry-based classifiers, across a series of biophysics and physiology activity prediction benchmarks.
Unmanned aircraft automatic flight control algorithm in a spin maneuver
Authors: Rogalski Tomasz , Rzucidło Paweł , Prusik Jacek 
Published: July 2020

Purpose
The paper aims to present an idea of automatic control algorithms dedicated to both small manned and unmanned aircraft, capable to perform spin maneuver automatically. This is a case of maneuver far away from so-called standard flight. The character of this maneuver and the range of aircraft flight parameters changes restrict application of standard control algorithms. Possibility of acquisition full information about aircraft flight parameters is limited as well in such cases. This paper analyses an alternative solution that can be applied in some specific cases.

Design/methodology/approach
The paper uses theoretical discussion and breakdowns to create basics for development of structures of control algorithms. Simplified analytical approach was applied to tune regulators. Results of research were verified in series of software-in-the loop, computer simulations.

Findings
The structure of the control system enabling aerobatic flight (spin flight as example selected) was found and the method how to tune regulators was presented as well.

Practical implications
It could be a fundament for autopilots working in non-conventional flight states and aircraft automatic recovery systems.

Originality/value
The paper presents author’s original approach to aircraft automatic control when high control precision is not the priority, and not all flight parameters can be precisely measured.
Authorial voice(s): the writing styles of Francis X. Carty
Authors: McGrath Conor 
Published: July 2020

PurposeThe paper aims to analyse the published work of Ireland's pre-eminent public relations (PR) educator, across a number of literary genres in which he has written. More broadly, it considers the writing life of academics.Design/methodology/approachThis paper examines Carty's writings about his own history, Irish history, the development of church-state relations in Ireland and PR. It seeks to make connections between Carty's subjects and his writing styles.FindingsThrough detailed analysis of a number of key texts, the paper explores the writing styles used by Carty to discern the nature of his distinctive “voice(s)”.Research limitations/implicationsThere is considerable research into a handful of (mostly American) “great men” in PR' history and development. But every nation has its own PR pioneers about whom little is known outside that country and who deserve to be more widely recognised.Originality/valueThis paper hopes to stimulate future work by other colleagues in other nations, reflecting on the contribution of their own PR educators and practitioners.
Development of assembly techniques for connection of AlGaN/GaN/Si chips to DBC substrate
Authors: Kisiel Ryszard , Guziewicz Marek , Taube Andrzej , Kaminski Maciej , Sochacki Mariusz 
Published: July 2020

PurposeThis paper aims to investigate the sintering and solid liquid interdiffusion bonding (SLID) techniques to attach AlGaN/GaN-on-Si chips to direct bond copper (DBC) substrate. The influence of metal layers deposited on the backside of AlGaN/GaN-on-Si dies on the assembly process is also investigated.Design/methodology/approachThe authors assumed the value of the shear strength to be a basic parameter for evaluation of mechanical properties. Additionally, the surface condition after shearing was assessed by SEM photographs and the shear surface was studied by X-ray diffraction method. The SLID requires Sn-plated DBC substrate and can be carried out at temperature slightly higher than 250°C and pressure reduced to 4 MPa, while the sintering requires process temperature of 350°C and the pressure at least 7.5 MPa.FindingsAg-, Au-backside covered high electron mobility transistor (HEMT) chips can be assembled on Sn-plated DBC substrates by SLID technology. In case of sintering technology, Cu- or Ag-backside covered HEMT chips can be assembled on Ag- or Ni/Au-plated DBC substrates. The SLID process can be realized at lower temperature and decreased pressure than sintering process.Research limitations/implicationsFor SLID technology, the adhesion between Cu-backside covered HEMT die and DBC with Sn layer loses its operational properties after short-term ageing in air at temperature of 300°C.Originality/valueIn the SLID process, Sn-Cu and Sn-Ag intermetallic compounds and alloys are responsible for creation of the joint between Sn-plated DBC and micropowder Ag layer, while the sintered joint between the chip and Ag-based micropowder is formed in diffusion process.
Computational design of resonant phononic crystal for aperiodic stress wave attenuation
Authors: Luo Chengcheng , Ning Shaowu , Liu Zhanli , Li Xiang , Zhuang Zhuo 
Published: July 2020

Purpose
This paper aims to propose a design method for attenuating stress waves pressure using soft matrix embedded with particles.

Design/methodology/approach
Based on the phononic crystal theory, the particle composed of hard core and soft coating can form a spring oscillator structure. When the frequency of the wave is close to the resonance frequency of the spring oscillator, it can cause the resonance of the particle and absorb a lot of energy. In this paper, the resonant phononic crystal with three phases, namely, matrix, particle core and coating, is computationally designed to effectively mitigate the stress wave with aperiodic waveform.

Findings
The relationship between the center frequency and width of the bandgap and the geometric and physical parameters of particle core are discussed in detail, and the trend of influence is analyzed and explained by a spring oscillator model. Increasing the radius of hard core could effectively enhance the bandgap width, thus enhancing the effect of stress wave attenuation. In addition, it is found that when the wave is in the bandgap, adding viscosity into the matrix will not further enhance the stress attenuation effect, but will make the stress attenuation effect of the material worse because of the competition between viscous dissipation mechanism and resonance mechanism.

Research limitations/implications
This study will provide a reference for the design of stress wave protection materials with general stress waves.

Originality/value
This study proposes a design method for attenuating stress waves pressure using soft matrix embedded with particles.
Chemical characteristics of groundwater in Ardabil region, Iran
Authors: Pazand Kamran , Pazand Kaveh 
Published: July 2020

Purpose
The chemical analysis of wells in the Ardabil area, Ardabil Province NW of Iran, was evaluated to determine the hydrogeochemical processes and ion concentration background in the region. The purpose of this study is to analyze the hydrochemical quality of groundwater in Ardabil aquifer in order to assess the suitability of the waters for different uses.

Design/methodology/approach
The chemical analysis of 75 water wells in the Ardabil area, was evaluated. Over the entire area, the dominated hydrochemical types are: Na-Cl, Na-HCO3-Cl-Mg, Ca-SO4, Ca-Mg-SO4-Cl and Ca-Mg-HCO3. The abundance of the major ions is as follows: Na+>Ca2+>Mg2+>K+ and SO42–> Cl–>HCO3– and major ion concentrations are below the acceptable level for drinking water. Most of groundwater samples fell in the soft water category. All of groundwaters belong to the excellent category and can be used safely for irrigation.

Findings
The chemical analysis of 75 water wells in the Ardabil area, Ardabil Province NW of Iran, was evaluated to determine the hydrogeochemical processes and ion concentration background in the region. Over the entire area, the dominated hydrochemical types are: Na-Cl, Na-HCO3-Cl-Mg, Ca-SO4, Ca-Mg-SO4-Cl and Ca-Mg-HCO3. The abundance of the major ions is as follows: Na+>Ca2+>Mg2+>K+ and SO42–> Cl–>HCO3– and major ion concentrations are below the acceptable level for drinking water. Most of groundwater samples fell in the soft water category. All of groundwaters belong to the excellent category and can be used safely for irrigation.

Originality/value
The chemical analysis of 75 water wells in the Ardabil area, Ardabil Province NW of Iran, was evaluated to determine the hydrogeochemical processes and ion concentration background in the region. Over the entire area, the dominated hydrochemical types are: Na-Cl, Na-HCO3-Cl-Mg, Ca-SO4, Ca-Mg-SO4-Cl and Ca-Mg-HCO3. The abundance of the major ions is as follows: Na+>Ca2+>Mg2+>K+ and SO42–> Cl–>HCO3– and major ion concentrations are below the acceptable level for drinking water. Most of groundwater samples fell in the soft water category. All of groundwaters belong to the excellent category and can be used safely for irrigation.
Workplace learning and foreign workers' commitment to host cultural organization: the effects of cross-cultural adjustment and supervisor trust
Authors: Dang Van Thac , Vu Thinh Truong , Nguyen Phuoc-Thien 
Published: July 2020

PurposeThe purpose of this study is to investigate the relationship between workplace learning and organizational commitment with the mediating role of cross-cultural adjustment and the moderating role of supervisor trust for the case of foreign workers in a new cultural setting.Design/methodology/approachThis study uses structural equation modeling to analyze a sample data of 367 Vietnamese and Philippine workers in Taiwan.FindingsResults show that workplace learning enhances foreign workers' organizational commitment. Cross-cultural adjustment is found to have a mediating effect in the link between workplace learning and organizational commitment. Furthermore, supervisor trust moderates the link between cross-cultural adjustment and organizational commitment. In addition, supervisor trust moderates the indirect effect of workplace learning on organizational commitment through cross-cultural adjustment.Originality/valuePrior literature often focuses on expatriates who are high-skilled employees. This study investigates low-skilled workers who come from less-developed country working in a more developed economy. This study is one of the first researches examining the issue of foreign workers' commitment in new cultural environment. Our findings shed a new light to the effect of workplace learning on organizational commitment. Our findings also help to clarify the roles of cross-cultural adjustment and supervisor trust into the workplace learning–organizational commitment relationship. This study provides implications for researchers and managers regarding to management and development of foreign workers for local organizations.
Ambiguity and its coping mechanisms in supply chains lessons from the Covid-19 pandemic and natural disasters
Authors: Gunessee Saileshsingh , Subramanian Nachiappan 
Published: July 2020

PurposeThe first purpose of this paper is to situate and conceptualise ambiguity in the operations management (OM) literature, as connected to supply chain decision-making (SCDM). The second purpose is to study the role of ambiguity-coping mechanisms in that context.Design/methodology/approachThis research uses the behavioural decision theory (BDT) to better embed ambiguity in a generic SCDM framework. The framework explicates both behavioural and non-behavioural antecedents of ambiguity and enables us to also ground the “coping” mechanisms as individual and organisational level strategies. Properties of the framework are illustrated through two “ambiguous” events – the 2011 Thai flood and Covid-19 pandemic.FindingsThree key findings are documented. First, ambiguity is shown to distinctively affect supply chain decisions and having correspondence with specific coping mechanisms. Second, the conceptual framework shows how individual coping mechanisms can undermine rational-based organisational coping mechanisms, leading to “sub-optimal” (poor) supply chain decisions. Third, this study highlights the positive role of visibility but surprisingly organisational “experiential” learning is imperfect, due to the focus on “similar” past experience and what is known.Originality/valueThe paper is novel in two ways. First, it introduces ambiguity – an often neglected concept in operations management – into the supply chain lexicon, by developing a typology of ambiguity. Second, ambiguity-coping mechanisms are also introduced as both individual and organisational strategies. This enables the study to draw distinctive theoretical and practical implications.
A multicommodity unpaired pickup and delivery vehicle routing problem with split loads and unloads
Authors: Dongyang Xu , Kunpeng Li , Jiehui Yang , Ligang Cui 
Published: July 2020

PurposeThis paper aims to explore the commodity transshipment planning among customers, which is commonly observed in production/sales enterprises to save the operational costs.Design/methodology/approachA mixed integer programming (MIP) model is built and five types of valid inequalities for tightening the solution space are derived. An improved variable neighborhood search (IVNS) algorithm is presented combining the developed multistart initial solution strategy and modified neighborhood local search procedure.FindingsExperimental results demonstrate that: with less decision variables considered, the proposed model can solve more instances compared to the existing model in previous literature. The valid inequalities utilized to tighten the searching space can efficiently help the model to obtain optimal solutions or high-quality lower bounds. The improved algorithm is efficient to obtain optimal or near-optimal solutions and superior to the compared algorithm in terms of solution quality, computational time and robustness.ractical implicationsThis research not only can help reduce operational costs and improve logistics efficiency for relevant enterprises, but also can provide guidance for constructing the decision support system of logistics intelligent scheduling platform to cater for centralized management and control.Originality/valueThis paper develops a more compact model and some stronger valid inequalities. Moreover, the proposed algorithm is easy to implement and performs well.