bluuebunny/crossref_metadata_2025_split huggingface dataset:
Label-free imaging flow cytometry: analysis and sorting of enzymatically dissociated tissues
Authors: Herbig Maik , Tessmer Karen , Nötzel Martin , Nawaz Ahsan Ahmad , Santos-Ferreira Tiago , Borsch Oliver , Gasparini Sylvia J. , Guck Jochen , Ader Marius 
Published: May 2021

AbstractBiomedical research often relies on identification and isolation of specific cell types using molecular biomarkers and sorting methods such as fluorescence or magnetic activated cell sorting. Labelling processes potentially alter the cells’ properties and should be avoided, especially when purifying cells for clinical applications. A promising alternative is the label-free identification of cells based on their physical properties. Sorting real-time deformability and fluorescence cytometry (soRT-FDC) is a microfluidic technique for label-free analysis and sorting of single cells. In soRT-FDC, bright-field images of cells are analyzed by a deep neural net (DNN) to obtain a sorting decision, but sorting was so far only demonstrated for blood cells which show clear morphological differences and are naturally in suspension. Most cells, however, grow in tissues, requiring dissociation before cell sorting which is associated with additional challenges including survival, changes in morphology, or presence of aggregates. Here, we introduce methods for robust analysis and sorting of single cells from mammalian nervous tissue and provide DNNs which are capable of distinguishing visually similar cells. Exemplarily, we employ the DNN for image-based sorting to enrich photoreceptor cells from dissociated retina for transplantation into the mouse eye. Results provide evidence that the combination of machine learning and soRT-FDC allows label-free enrichment of target cells from dissociated tissues.
Growth-dependent heterogeneity in the DNA damage response inEscherichia coli
Authors: Jaramillo-Riveri Sebastián , Broughton James , McVey Alexander , Pilizota Teuta , Scott Matthew , El Karoui Meriem 
Published: May 2021

ABSTRACTIn natural environments bacteria are frequently exposed to sub-lethal levels of DNA damage which leads to the induction of a stress response (the SOS response inEscherichia coli). Natural environments also vary in nutrient availability, resulting in distinct physiological changes in bacteria which may have direct implications on their capacity to repair their chromosomes. Here, we evaluated the impact of varying the nutrient availability on the expression of the SOS response induced by chronic sub-lethal DNA damage inE. coli. The expression of the SOS regulon was found to be highly heterogeneous at the single-cell level in all growth conditions. Surprisingly, we observed a larger fraction of high SOS-induced cells in slow growth as compared with fast growth, despite a higher rate of SOS induction in fast growth. This counter-intuitive result can be explained by the dynamic balance between the rate of SOS induction and the division rates of cells exposed to DNA damage. Taken together, our data illustrates how cell division and physiology come together to produce growth-dependent heterogeneity in the DNA damage response.
Structures of the human cholecystokinin 1 (CCK1) receptor bound to Gs and Gq mimetic proteins: insight into mechanisms of G protein selectivity
Authors: Mobbs Jesse , Belousoff Matthew J. , Harikumar Kaleeckal G. , Piper Sarah J. , Xu Xiaomeng , Furness Sebastian G.B. , Venugopal Hari , Christopoulos Arthur , Danev Radostin , Wootten Denise , Thal David M. , Miller Laurence J. , Sexton Patrick M. 
Published: May 2021

AbstractG protein-coupled receptors (GPCRs) are critical regulators of cellular function acting via heterotrimeric G proteins as their primary transducers with individual GPCRs capable of pleiotropic coupling to multiple G proteins. Structural features governing G protein selectivity and promiscuity are currently unclear. Here we used cryo-electron microscopy to determine structures of the CCK1R bound to the CCK peptide agonist, CCK-8 and two distinct transducer proteins, its primary transducer Gq, and the more weakly coupled Gs. As seen with other Gq/11-GPCR complexes, the Gq-α5 helix bound to a relatively narrow pocket in the CCK1R core. Surprisingly, the backbone of the CCK1R and volume of the G protein binding pocket was essentially equivalent when Gs was bound, with the Gs α5 helix displaying a conformation that arises from “unwinding” of the far C-terminal residues, compared to canonically Gs coupled receptors. Thus, integrated changes in the conformations of both the receptor and G protein play critical roles in the promiscuous coupling of individual GPCRs.One-Sentence SummaryCryo-EM structures of the CCK-1R reveal key mechanisms for promiscuous G protein coupling.
Changes of the biophysical properties of voltage-gated Na+currents during maturation of the sodium-taste cells in rat fungiform papillae
Authors: Bigiani Albertino , Tirindelli Roberto , Bigiani Lorenzo 
Published: May 2021

AbstractTaste cells are a heterogeneous population of sensory receptors that undergoes a continuous turnover. Different chemo-sensitive cell lines rely on action potentials to release the neurotransmitter onto nerve endings. The electrical excitability is due to the presence of a tetrodotoxin-sensitive, voltage-gated sodium current (INa) similar to that found in neurons. Since the biophysical properties ofINachange during neuronal development, we wondered whether the same also occurred in taste cells. Here, we used the patch-clamp recording technique to studyINain sodium sensing cells of rat fungiform papillae. We identified these cells by exploiting the known blocking effect of amiloride on ENaC, the sodium (salt) receptor. Then, based on the amplitude ofINaand a morphological analysis, we subdivided sodium cells into two broad developmental groups, namely immature and mature cells. We found that: the voltage dependence of activation and inactivation changed in the transition from immature to mature state (depolarizing shift); the membrane capacitance significantly decreased in mature cells, enhancing the density ofINa; a persistent sodium current, absent in immature cells, appeared in mature cells. mRNA expression analysis of the α-subunits of voltage-gated sodium channels in fungiform taste buds supported the electrophysiological data. As a whole, our findings provide evidence for a noticeable change in membrane excitability during development, which is consistent with the key role played by electrical signaling in the release of neurotransmitter by mature sodium cells.Key Points SummaryTaste cells are sensory receptors that undergo continuous turnover while they detect food chemicals and communicate with afferent nerve fibers.The voltage-gated sodium current (INa) is a key ion current for generating action potentials in fully differentiated and chemo-sensitive taste cells, which use electrical signaling to release neurotransmitters.Here we report that in rat taste cells involved in salt detection, the properties ofINa, such as voltage dependence of activation and inactivation, undergo significant changes during the transition from immature to mature state.Our results help understand how taste cells gain electrical excitability during turnover, a property critical to operate as chemical detectors that relay sensory information to nerve fibers.
Genomic characterization of endemic and ecdemic non-typhoidalSalmonella entericalineages circulating among animals and animal products in South Africa
Authors: Carroll Laura M. , Pierneef Rian , Mathole Masenyabu , Matle Itumeleng 
Published: May 2021

ABSTRACTNon-typhoidalSalmonella entericaimposes a significant burden on human and animal health in South Africa. However, very little is known about lineages circulating among animals and animal products in the country on a genomic scale. Here, we used whole-genome sequencing (WGS) to characterize 63Salmonella entericastrains (n= 18, 8, 13, and 24 strains assigned to serotypes Dublin, Hadar, Enteritidis, and Typhimurium, respectively) isolated from livestock, companion animals, wildlife, and animal products in South Africa over a 60-year period. Within-serotype phylogenies were constructed using genomes sequenced in this study, as well as publicly available genomes representative of each respective serotype’s (i) global (n= 2,802 and 1,569S.Dublin and Hadar genomes, respectively) and (ii) African (n= 716 and 343S.Enteritidis and Typhimurium genomes, respectively) population. ForS.Dublin, the approaches used here identified a largely antimicrobial-susceptible, endemic lineage circulating among humans, animals, and food in South Africa, as well as a lineage that was likely recently introduced from the United States. ForS.Hadar, multiple South African lineages harboring streptomycin and tetracycline resistance-conferring genes were identified. AfricanS.Enteritidis could be primarily partitioned into one largely antimicrobial-susceptible and one largely multidrug-resistant (MDR) clade, with South African isolates confined to the largely antimicrobial-susceptible clade.S.Typhimurium strains sequenced here were distributed across the AfricanS.Typhimurium phylogeny, representing a diverse range of lineages, including numerous MDR lineages. Overall, this study provides insight into the evolution, population structure, and antimicrobial resistome composition ofSalmonella entericain Africa.IMPORTANCEGlobally,Salmonella entericais estimated to be responsible for more than 93 million illnesses and 150,000 deaths annually. In Africa, the burden of salmonellosis is disproportionally high; however, WGS efforts are overwhelmingly concentrated in world regions with lower salmonellosis burdens. While WGS is being increasingly employed in South Africa to characterizeSalmonella enterica, the bulk of these efforts have centered on characterizing human clinical strains. WGS data derived from non-typhoidalSalmonella entericaserotypes isolated from non-human sources in South Africa is extremely limited. To our knowledge, the genomes sequenced here represent the largest collection of non-typhoidalSalmonella entericaisolate genomes from non-human sources in South Africa to date. Furthermore, this study provides critical insights into endemic and ecdemic non-typhoidalSalmonella entericalineages circulating among animals, foods, and humans in South Africa and showcases the utility of WGS in characterizing animal-associated strains from a world region with a high salmonellosis burden.
CBMOS: a GPU-enabled Python framework for the numerical study of center-based models
Authors: Mathias Sonja , Coulier Adrien , Hellander Andreas 
Published: May 2021

AbstractCell-based models are becoming increasingly popular for applications in developmental biology. However, the impact of numerical choices on the accuracy and efficiency of the simulation of these models is rarely meticulously tested. We present CBMOS, a Python framework for the simulation of the center-based or cell-centered model. Contrary to other implementations, CBMOS’ focus is on facilitating numerical study of center-based models by providing access to multiple ODE solvers and force functions through a flexible, user-friendly API. We show-case its potential by evaluating the use of the backward Euler method for calculating the trajectories of two-dimensional cell populations. We confirm that although for moderate accuracy levels the backward Euler method allows for larger time step sizes than the commonly used forward Euler method, its additional computational cost due to being an implicit method prohibits its use for practical test cases.CBMOS is available on GitHub1 and PyPI under an MIT license. It allows for fast prototyping on a CPU for small systems through the use of NumPy. Using CuPy on a GPU, cell populations of up to 10,000 cells can be simulated within a few seconds. As such, we hope it can also be of use to modelers interested in testing preliminary hypotheses before committing to more complex center-based model frameworks.AMS subject classification65Z05, 92C15, 92-10
The dynamic interplay of PIP2and ATP in the regulation of the KATPchannel
Authors: Pipatpolkai Tanadet , Usher Samuel G. , Vedovato Natascia , Ashcroft Frances M , Stansfeld Phillip J. 
Published: May 2021

AbstractATP-sensitive potassium (KATP) channels couple the intracellular ATP concentration to insulin secretion. KATPchannel activity is inhibited by ATP binding to the Kir6.2 tetramer and activated by phosphatidylinositol-4,5-bisphosphate (PIP2). Here, we use molecular dynamics (MD) simulation, electrophysiology and fluorescence spectroscopy to show that ATP and PIP2occupy different binding pockets that share a single amino acid residue, K39. When both ligands are present, K39 shows a greater preference to co-ordinate with PIP2than ATP. A neonatal diabetes mutation at K39 (K39R) increases the number of hydrogen bonds formed between K39 and PIP2, reducing ATP inhibition. We also find direct effects on nucleotide binding from mutating E179, a residue proposed to interact with PIP2. Our work suggests PIP2and ATP interact allosterically to regulate KATPchannel activity.
A novel class of TMPRSS2 inhibitors potently block SARS-CoV-2 and MERS-CoV viral entry and protect human epithelial lung cells
Authors: Mahoney Matthew , Damalanka Vishnu C. , Tartell Michael A. , Chung Dong Hee , Lourenco André Luiz , Pwee Dustin , Mayer Bridwell Anne E. , Hoffmann Markus , Voss Jorine , Karmakar Partha , Azouz Nurit , Klingler Andrea M. , Rothlauf Paul W. , Thompson Cassandra E. , Lee Melody , Klampfer Lidija , Stallings Christina , Rothenberg Marc E. , Pöhlmann Stefan , Whelan Sean P. , O’Donoghue Anthony J. , Craik Charles S. , Janetka James W. 
Published: May 2021

AbstractThe host cell serine protease TMPRSS2 is an attractive therapeutic target for COVID-19 drug discovery. This protease activates the Spike protein of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and of other coronaviruses and is essential for viral spread in the lung. Utilizing rational structure-based drug design (SBDD) coupled to substrate specificity screening of TMPRSS2, we have discovered a novel class of small molecule ketobenzothiazole TMPRSS2 inhibitors with significantly improved activity over existing irreversible inhibitors Camostat and Nafamostat. Lead compound MM3122 (4) has an IC50of 340 pM against recombinant full-length TMPRSS2 protein, an EC50of 430 pM in blocking host cell entry into Calu-3 human lung epithelial cells of a newly developed VSV SARS-CoV-2 chimeric virus, and an EC50of 74 nM in inhibiting cytopathic effects induced by SARS-CoV-2 virus in Calu-3 cells. Further, MM3122 blocks Middle East Respiratory Syndrome Coronavirus (MERS-CoV) cell entry with an EC50of 870 pM. MM3122 has excellent metabolic stability, safety, and pharmacokinetics in mice with a half-life of 8.6 hours in plasma and 7.5 h in lung tissue, making it suitable for in vivo efficacy evaluation and a promising drug candidate for COVID-19 treatment.
Accuracy in near-perfect virus phylogenies
Authors: Wertheim Joel O. , Steel Mike , Sanderson Michael J. 
Published: May 2021

AbstractPhylogenetic trees from real-world data often include short edges with very few substitutions per site, which can lead to partially resolved trees and poor accuracy. Theory indicates that the number of sites needed to accurately reconstruct a fully resolved tree grows at a rate proportional to the inverse square of the length of the shortest edge. However, when inferred trees are partially resolved due to short edges, “accuracy” should be defined as the rate of discovering false splits (clades on a rooted tree) relative to the actual number found. Thus, accuracy can be high even if short edges are common. Specifically, in a “near-perfect” parameter space in which trees are large, the tree length ξ (the sum of all edge lengths), is small, and rate variation is minimal, the expected false positive rate is less than ξ/3; the exact value depends on tree shape and sequence length. This expected false positive rate is far below the false negative rate for small ξ and often well below 5% even when some assumptions are relaxed. We show this result analytically for maximum parsimony and explore its extension to maximum likelihood using theory and simulations. For hypothesis testing, we show that measures of split “support” that rely on bootstrap resampling consistently imply weaker support than that implied by the false positive rates in near-perfect trees. The near-perfect parameter space closely fits several empirical studies of human virus diversification during outbreaks and epidemics, including Ebolavirus, Zika virus, and SARS-CoV-2, reflecting low substitution rates relative to high transmission/sampling rates in these viruses.
Strategic management, management control practices and public value creation: the strategic triangle in the Swedish public sector
Authors: Höglund Linda , Mårtensson Maria , Thomson Kerstin 
Published: May 2021

PurposeThe purpose of this paper is to enhance understanding of the conceptualisation and operationalisation of public value in practice by applying Moore's (1995) strategic triangle as an analytical framework to study strategic management and management control practices in relation to public value.Design/methodology/approachThe paper uses an interpretative longitudinal case study approach including qualitative methods of document studies and interviews between 2017 and 2019.FindingsIn the strategic triangle, the three nodes of authorising environment, public value creation and operational capacity are interdependent, and alignment is a necessity for a strategy to be successful. But this alignment is vulnerable. The findings suggest three propositions: (1) strategic alignment is vulnerable to management control practices having a strong focus on performance measurements, (2) strategic alignment is vulnerable to standardised management control practices and (3) strategic alignment is vulnerable to politically driven management control practices.Originality/valueWith the strategic triangle as a base, this paper tries to understand what kind of management control practices enable and/or constrain public value, as there has been a call for this kind of research. In this way it adds to earlier research on public value, to the growing interest in the strategic triangle as an analytical framework in analysing empirical material and to the request for more empirical studies on the subject. The strategic triangle also embraces political factors, government agendas and political leadership for which there has also been a call for more research.
Corporate social responsibility advertising in social media: a content analysis of the fashion industry's CSR advertising on Instagram
Authors: Kwon Kyeongwon , Lee Jaejin 
Published: May 2021

PurposeCorporate social responsibility (CSR) has received significant attention and has become a global trend that challenges the role of business. The purpose of this study is to examine how the fashion industry responds to public pressure in terms of sustainability by promoting its CSR commitments through CSR advertising.Design/methodology/approachA quantitative content analysis was conducted to examine how the fashion industry advertises its CSR commitments on social media. To explore the trend and various perspectives of CSR advertising presented by the fashion industry, the top six fashion brands that are well known for their sustainability performance were selected and their Instagram posts from 2019 were fully investigated.FindingsThe findings from the study indicate that the fashion industry uses different strategies for CSR advertising campaigns. It provides evidence that fashion brands, overall, focus on sustainability efforts for the environment and visually communicate their CSR practices through a framework that highlights greenness and environmentally friendly messages in CSR advertising.Originality/valueCSR allows organizations to communicate with consumers about how business can be operated for a sustainable future. CSR advertising is an emerging field as company's CSR practices can create strategic benefits when the practices have high visibility. However, little work has been done to analyze CSR advertising on social media. Therefore, the present study adds values to the existing literature on CSR advertising, which is important to both academic researchers and practitioners.
An exploration of obstacles to identity play during unemployment
Authors: Mühlhaus Julia , Bouwmeester Onno , Khapova Svetlana N. 
Published: May 2021

PurposeThis study seeks to explore the key themes in identity play during unemployment and the potential obstacles faced by unemployed individuals.Design/methodology/approachThis qualitative study is based on 23 interviews with unemployed individuals in Germany.FindingsThe authors identify three obstacles to identity play during unemployment: a lack of psychological safety to explore possible selves, a lack of opportunity to try out possible selves and a lack of social validation for possible selves. Several interviewees highlight the impact of social context, creating an absence of institutional support and a limited identity “playspace.” As such, the authors illustrate that when faced with these obstacles, the unemployed individuals of this study predominantly focus on identity work instead of identity play. Only a few interviewees seem to engage in and sustain identity play. The authors propose that the elaborate nature of their possible selves and their focus on future opportunities may overshadow the present self and immediate obstacles.Originality/valueThe authors argue that identity play is not readily available to all individuals in all situations. Instead, they suggest that some psychologically and socially threatening contexts such as unemployment are characterized by obstacles that constrain individuals' identity play and prevent the adoption of new work identities. Hence, the authors call for a more balanced and localized understanding of identity play.
The transformative role of firm information transparency in triggering retail investor's perceived financial well-being
Authors: Naveed Muhammad , Farah Maya F. , Hasni Muhammad Junaid Shahid 
Published: May 2021

PurposeBased on transformative service research (TSR), the study explores the mechanisms by which a firm's information transparency influences a retail investor's perceived financial well-being (PFW). It proposes a model exploring the mediating roles of the investor's financial risk tolerance (RT) and financial self-efficacy (FSE) in the relationship between a firm's information transparency and the consumer's PFW.Design/methodology/approachA survey was conducted by including a sample of 310 retail investors from Pakistan Stock Exchange (PSX) to test the proposed hypotheses. Data analysis was based on a series of multiple regressions, moderation and serial mediation analyses.FindingsThe findings show that a firm's information transparency harnesses investors' PFW. Information transparency also positively affects investors' RT toward the firm and their FSE while dealing with financial challenges.Research limitations/implicationsThe findings call for a deeper understanding of financial services' interventions and their underlying mechanisms to improve consumer’s financial well-being (FWB). On a methodology level, future studies could apply a mixed-method approach and SEM to explore new avenues for predicting investors' FWB.Practical implicationsBesides validating TSR, the study has several implications for listed firms to adopt more transparent information reporting practices to improve investors' PFW. Accordingly, regulators should take initiatives to compel firms to comply with higher standards of information transparency.Originality/valueThe proposed model explores a concrete mechanism that helps listed firms to strengthen investors' PFW via information transparency.