bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-fidelity approximation of grid- and shell-based sampling schemes from undersampled DSI using compressed sensing: Post mortem validation
Authors: Jones Robert , Maffei Chiara , Augustinack Jean , Fischl Bruce , Wang Hui , Bilgic Berkin , Yendiki Anastasia 
Published: February 2021

AbstractWhile many useful microstructural indices, as well as orientation distribution functions, can be obtained from multi-shell dMRI data, there is growing interest in exploring the richer set of microstructural features that can be extracted from the full ensemble average propagator (EAP). The EAP can be readily computed from diffusion spectrum imaging (DSI) data, at the cost of a very lengthy acquisition. Compressed sensing (CS) has been used to make DSI more practical by reducing its acquisition time. CS applied to DSI (CS-DSI) attempts to reconstruct the EAP from significantly undersampled q-space data. We present a post mortem validation study where we evaluate the ability of CS-DSI to approximate not only fully sampled DSI but also multi-shell acquisitions with high fidelity. Human brain samples are imaged with high-resolution DSI at 9.4T and with polarization-sensitive optical coherence tomography (PSOCT). The latter provides direct measurements of axonal orientations at microscopic resolutions, allowing us to evaluate the mesoscopic orientation estimates obtained from diffusion MRI, in terms of their angular error and the presence of spurious peaks. We test two fast, dictionary-based, L2-regularized algorithms for CS-DSI reconstruction. We find that, for a CS acceleration factor of R=3, i.e., an acquisition with 171 gradient directions, one of these methods is able to achieve both low angular error and low number of spurious peaks. With a scan length similar to that of high angular resolution multi-shell acquisition schemes, this CS-DSI approach is able to approximate both fully sampled DSI and multi-shell data with high accuracy. Thus it is suitable for orientation reconstruction and microstructural modeling techniques that require either grid- or shell-based acquisitions. We find that the signal-to-noise ratio (SNR) of the training data used to construct the dictionary can have an impact on the accuracy of CS-DSI, but that there is substantial robustness to loss of SNR in the test data. Finally, we show that, as the CS acceleration factor increases beyond R=3, the accuracy of these reconstruction methods degrade, either in terms of the angular error, or in terms of the number of spurious peaks. Our results provide useful benchmarks for the future development of even more efficient q-space acceleration techniques.
A compact spatial map in V2 visual cortex
Authors: Long Xiaoyang , Deng Bin , Cai Jing , Chen Zhe Sage , Zhang Sheng-Jia 
Published: February 2021

SummaryVision plays a critical role in guiding spatial navigation. A traditional view of the visual cortex is to compute a world-centered map of visual space, and visual neurons exhibit diverse tunings to simple or complex visual features. The neural representation of spatio-visual map in the visual cortex is thought to be transformed from spatial modulation signals at the hippocampal-entorhinal system. Although visual thalamic and cortical neurons have been shown to be modulated by spatial signals during navigation, the exact source of spatially modulated neurons within the visual circuit has never been identified, and the neural correlate underpinning a visuospatial or spatio-visual map remains elusive. To search for direct visuospatial and visuodirectional signals, here we recordin vivoextracellular spiking activity in the secondary visual cortex (V2) from freely foraging rats in a naturalistic environment. We identify that V2 neurons forms a complete spatio-visual map with a wide range of spatial tunings, which resembles the classical spatial map that includes the place, head-direction, border, grid and conjunctive cells reported in the hippocampal-entorhinal network. These spatially tuned V2 neurons display stable responses to external visual cues, and are robust with respect to non- spatial environmental changes. Spatially and directionally tuned V2 neuronal firing persists in darkness, suggesting that this spatio-visual map is not completely dependent on visual inputs. Identification of functionally distinct spatial cell types in visual cortex expands its classical role of information coding beyond a retinotopic map of the eye-centered world.
Substrates modulate charge-reorganization allosteric effects in protein-protein association
Authors: Ghosh Shirsendu , Banerjee-Ghosh Koyel , Levy Dorit , Riven Inbal , Naaman Ron , Haran Gilad 
Published: February 2021

ABSTRACTProtein function may be modulated by an event occurring far away from the functional site, a phenomenon termed allostery. While classically allostery involves conformational changes, we recently observed that charge redistribution within an antibody can also lead to an allosteric effect, modulating the kinetics of binding to target antigen. In the present study, we study the association of a poly-histidine tagged enzyme (phosphoglycerate kinase, PGK) to surface-immobilized anti-His antibodies, finding a significant Charge-Reorganization Allostery (CRA) effect. We further observe that PGK’s negatively charged nucleotide substrates modulate CRA substantially, even though they bind far away from the His-tag-antibody interaction interface. In particular, binding of ATP reduces CRA by more than 50%. The results indicate that CRA may be affected by charged substrates bound to a protein and provide further insight into the role of charge redistribution in protein function.TOC GRAPHIC
Functional and taxonomic comparison of mouse and human gut microbiotas using extensive culturing and metagenomics
Authors: Beresford-Jones Benjamin S. , Forster Samuel C. , Stares Mark D. , Notley George , Viciani Elisa , Browne Hilary P. , Kumar Nitin , Vervier Kevin , Almeida Alexandre , Lawley Trevor D. , Pedicord Virginia A. 
Published: February 2021

AbstractMouse models are essential for biomedical science and drug discovery, yet it is not known how the bacteria in the mouse microbiota – important determinants of phenotypes of health and disease –affect their relevance to human disease. To interrogate the taxonomic and functional differences between the human and mouse gut microbiotas, we developed the Mouse Microbial Genome Collection (MMGC), a compilation of 276 genomes from cultured isolates and 45,218 metagenome-assembled genomes (MAGs) from 1,960 publicly available mouse metagenomes. The MMGC reveals that while only 2.65% of bacterial species are shared between mouse and human, over 80% of annotatable functions are present in both microbiomes. Using drug metabolism and butyrate synthesis as examples, we illustrate that although the species harbouring these key functions can differ between hosts, the MMGC enables identification of functionally equivalent taxa in the mouse and human microbiotas. The MMGC thereby facilitates the informed use of mice in biomedical research by providing access to the conservation and taxonomic locations of bacterial functions of interest.
Release of extracellular DNA byPseudomonasspecies as a major determinant for biofilm switching and an early indicator for cell population control
Authors: Kakahi Fatemeh Bajoul , Martinez Juan Andres , Avitia Fabian Moreno , Telek Samuel , Volke Daniel C. , Wirth Nicolas T. , Nikel Pablo I. , Delvigne Frank 
Published: February 2021

AbstractThe different steps involved in biofilm formation have been the subjects of intensive researches. However, the very early cell decision-making process related to the switch from planktonic to sessile state still remains uncharacterized. Based on the use ofPseudomonas putidaKT2440 and derivatives with varying biofilm-forming capabilities, we observed a subpopulation of cells bound to extracellular DNA (eDNA) in the planktonic phase, as indicated by propidium iodide (PI) staining. Strikingly, the size of this eDNA-bound/PI-positive subpopulation correlated with the overall biofilm forming capability of the bacterial population. This finding challenges the conventional view of phenotypic switching and suggests that, inPseudomonas, biofilm switching is determined collectively based on the quantity of eDNA released in the supernatant. The whole process can be followed based on automated flow cytometry, and the appearance of PI-positive cells was considered as an early-warning indicator for biofilm formation. For this purpose, automated glucose pulsing was used successfully to interfere with the proliferation of PI-positive cells, resulting in a reduction of biofilm formation. This study provides insights into the collective determinants of biofilm switching inPseudomonasspecies and introduces a potential strategy for controlling biofilm formation.
Optimal Linkage Disequilibrium Splitting
Authors: Privé Florian 
Published: February 2021

AbstractA few algorithms have been developed for splitting the genome in nearly independent blocks of linkage disequilibrium. Due to the complexity of this problem, these algorithms rely on heuristics, which makes them sub-optimal. Here we develop an optimal solution for this problem using dynamic programming. This is now implemented as functionsnp_ldplitas part of R package bigsnpr.
The relational embeddedness as the differentiator of the cluster supply chain collaboration – a multidimensional comparative analysis
Authors: Frankowska Marzena , Cheba Katarzyna 
Published: February 2021

Purpose
The purpose of this paper is to fill the research and cognitive gap by comparative analyzing of the cluster supply chain (CSC) and supply chains not belonging to the clusters to examine the relational embeddedness as the differentiator of supply chains operating in the clusters.

Design/methodology/approach
The conceptual model was tested with data collected from 475 industrial companies cooperating with their partners within supply chains, including 135 CSC. To identify the livraisons between different indicators, the correspondence analysis was applied.

Findings
The division of enterprises participating in this study into groups allows for the determination of relatively clear boundaries between enterprises belonging to the cluster and those that do not declare such affiliation. The obtained results confirmed that the relational embeddedness is the differentiator of the CSC collaboration.

Research limitations/implications
The main limitations are referred to as the static character of the data.

Practical implications
The paper contains implications for cluster facilitators, as well as for cluster policy decision makers, to better design support for cluster organizations.

Originality/value
This research is a contribution to the literature on inter-organizational structures, such as clusters and supply chains, and in particular, contributes to the creation of the scientific ground of SCS theory. The research allowed to better understand the nature of collaboration taking into consideration the fact of the relational embeddedness of the companies operating within supply chains located in clusters. It proves the existence of a new type of inter-organizational form that is CSC.
Strategies to manage product recalls in the COVID-19 pandemic: an exploratory case study of PPE supply chains
Authors: Schumacher Roman , Glew Rob , Tsolakis Naoum , Kumar Mukesh 
Published: February 2021

PurposeThe purpose of this paper is to investigate strategies to manage product recalls where shortages are a critical threat, with impacts such as loss of life. The authors aim to identify key supply chain strategies and opportunities for theoretical advancement by taking a resilience perspective on temporary supply chain design.Design/methodology/approachFirst, the authors conducted an impact event analysis of product recalls by exploring the RAPEX database and official statements of individual country regulators. Second, the authors conducted an exploratory case study with the Cambridge University Hospitals on Personal Protective Equipment to explore product recall risks, utilising an action research methodology.FindingsAdditional processes, mainly testing, can compensate for the risks that may arise from temporary supply chains, where changes in location and product design are not possible due to the immediate nature of demand caused by COVID-19 pandemic. This finding reflects on the resilience of designing and implementing temporary supply chains from the perspective of product, process and location.Research limitations/implicationsThis paper does not employ an in-depth multiple case study methodology. However, the authors argue that the role of institutional actors in global supply chains and its implications on product safety needs to be empirically studied in order to expand existing supply chain management theories to cover resilience in emerging, mature and temporary supply chain.Practical implicationsManagers can learn from the Cambridge University Hospitals case study that a downstream quality inspection system can be deployed to manage product quality and safety risks where recalls are not an option, such as during critical situations in the COVID-19 pandemic.Social implicationsThe authors’ observations suggest that governments may be socially responsible for implementing rigorous mechanisms to manage product recall risks that compromise consumer safety.Originality/valueThe authors’ study is uniquely designed and studies various specific phenomena of product recalls risks in COVID-19. The unique design features include a dynamic and recent database analysis involving a product, process and location centric perspective complemented with a Cambridge University Hospitals case study.
Challenges and enabling features of small and medium infrastructure public–private partnerships (P3s): a case study of the US P3 infrastructure market
Authors: Liang Yunping , Ashuri Baabak 
Published: February 2021

PurposeIn classical perspective, projects under a certain size are not feasible for P3. However, there is an emerging trend on using P3 to deliver projects which are frequently at small- to medium- size to meet ever-increasingly complex social needs, including enhancing lifecycle performance of existing facilities, designing and building for resilience and sustainability, ensuring cost effectiveness of public spending and fostering innovation. In contrast with the increasing implementation, small and medium P3s, especially those in the United States, receive little attention in existing studies. This study aims at answering the question: in the context of US, what features of those small- to medium- sized P3s with success records enable the selection of P3 as delivery method.Design/methodology/approachBy critically reviewing the literature, this study synthesizes and discusses the challenges in classical perspective. The authors use a framework drawn from the transaction cost to propose two types of enabling features that could contribute to the success of small and medium P3s. The proposed enabling features are supported by case study of twelve identified small- to medium- sized P3s which have reached financial closure as of 2018 in the United States.FindingsThe results show how the identified enabling opportunities have been used in these cases to enhance the viability of the P3 model in the infrastructure market. The two types of features are high tolerance enabler explained by the expectations on indirect and non-monetary compensations, and cost reduction enablers including: (1) being in the sectors with well-established traditions on using private investments; (2) having developers with expertise on infrastructure finance; (3) being in the jurisdictions with favorable legislative environment and (4) having less-uncertain future project revenue.Originality/valueThis study, for the first time, critically examines the enabling features of the P3 model for delivering small and medium infrastructure projects in the United States. This research sheds light on the credibility and viability of small- to medium- sized P3 and increases the confidence in policy makers to promote this model.
Propaganda analysis in social media: a bibliometric review
Authors: Chaudhari Deptii Devendra , Pawar Ambika Vishal 
Published: February 2021

Purpose
This paper aims to examine the trends in research studies in the past decade which address the use and analysis of propaganda in social media using natural language processing. The purpose of this study is to conduct a comprehensive bibliometric review of studies focusing on the use, identification and analysis of propaganda in social media.

Design/methodology/approach
This work investigates and examines the research papers acquired from the Scopus database which has huge number of peer reviewed literature and also provides interfaces to access required for bibliometric study. This paper has covered subject papers from 2010 to early 2020 and using tools such as VOSviewer and Biblioshiny.

Findings
This bibliometric survey shows that propaganda in social media is more studied in the area of social sciences, and the field of computer science is catching up. The evolution of research for propaganda in social media shows positive trends. This subject is primarily rooted in the social sciences. Also this subject has shown a recent shift in the area of computer science. The keyword analysis shows that the propaganda in social media is being studied in conjunction with issues such as fake news, political astroturfing, terrorism and radicalization.

Research limitations/implications
The lack of highly cited papers and co-citation analysis implies intermittent contributions by the researchers. Propaganda in social media is becoming a global phenomenon, and ill effects of this are evident in developing countries as well. This denotes a great deal of scope of work for researchers in other countries focusing on their territorial issues. This study was conducted in the confines of data captured from the Scopus database. Hence, it should be noted that some vital publications in recent times could not be included in this study.

Originality/value
The uniqueness of this work is that a thorough bibliometric analysis of the topic is demonstrated using several forms such as mind map, co-occurrence, co-citations, Sankey plot and topic dendrograms by using bibliometric tools such as VOSviewer and Biblioshiny.
Evaluation of the influence of ambient air temperature and air velocity on mortar cement durability using a forced convection solar dryer
Authors: Bahammou Younes , Kouhila Mounir , Moussaoui Haytem , Lamsyehe Hamza , Tagnamas Zakaria , Lamharrar Abdelkader , Idlimam Ali 
Published: February 2021

PurposeThis work aims to study the hydrothermal behavior of mortar cement toward certain environmental factors (ambient air temperature and air velocity) based on its drying kinetics data. The objective is to provide a better understanding and controlling the stability of mortar structures, which integrate the sorption phenomenon, drying process, air pressure and intrinsic characteristics. This leads to predict the comportment of mortar structures in relation with main environmental factors and minimize the risk of cracking mortar structures at an early age.Design/methodology/approachThermokinetic study was carried out in natural and forced convection solar drying at three temperatures 20, 30 and 40°C and three air velocities (1, 3 and 5 m.s-1). The empirical and semiempirical models tested successfully describe the drying kinetics of mortar. These models simulate the drying process of water absorbed by capillarity, which is the most common humidity transfer mechanism in building materials and contain parameters with physical significance, which integrate the effect of several environmental factors and intrinsic characteristics of mortar structures.FindingsThe models simulate the drying process of water absorbed by capillarity, which is the most common humidity transfer mechanism in building materials and contain parameters with physical significance, which integrate the effect of several environmental factors and intrinsic characteristics of mortar structures. The average activation energy obtained expressed the temperature effect on the mortar diffusivity. The drying constant and the diffusion coefficient can be used to predict the influence of these environmental factors on the drying behavior of various building materials and therefore on their durability.Originality/valueEvaluation of the effect of several environmental factors and intrinsic characteristics of mortar structures on their durability.
Management of variations in the public-sector building construction projects in Sri Lanka
Authors: Perera B.A.K.S. , Sirimewan D.C. , Senadeera A.D. 
Published: February 2021

Purpose
Many public-sector building projects in developing countries are prone to variations owing to the changes made to their original project scopes, and economic depressions and stagnations. Cost and time-overruns are consequences of such variations. Thus, variation management in these projects is important. Hence, this paper aims to analyse the methods of managing variations in public-sector building projects in Sri Lanka.

Design/methodology/approach
The study adopted a mixed research approach. Seventeen expert interviews and a questionnaire survey were conducted to identify the causes and consequences of the variations, and the strategies that will help manage those variations. Manual content analysis and mean weighted rankings (MWR) were used to analyse the collected quantitative and qualitative data, respectively.

Findings
The employer, consultant, contractor and several other factors are mostly responsible for the variations in public-sector building projects in Sri Lanka. Cost and time-overruns, rework and demolition and disputes are the major consequences of such variations. The study findings reveal that a detailed employer’s brief, clearly defined project objectives, a comprehensive design and set of specifications, and preliminary investigations are the strategies that will mostly minimise the variations in public-sector building projects in Sri Lanka.

Originality/value
The study proposes strategies to avoid or minimise the adverse impact of variations, which the industry practitioners can adopt for variation management in public-sector building projects. The study theoretically contributes to knowledge by revealing how variations in public-sector building projects in Sri Lanka can be managed by identifying their causes and consequences.