bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of viral transport media and freeze-thaw cycling on the sensitivity of qRT-PCR detection of SARS-CoV-2 nucleic acids
Authors: Holohan Cian , Hanarahan Sophia , Feely Nathan , Li Peng , O’Connell John , Moss Catherine , Carr Michael , Tagit Oya , Lee Gil U
Published: June 2021

The events of the last year have highlighted the complexity of implementing large-scale molecular diagnostic testing for novel pathogens. The purpose of this study was to determine the chemical influences of sample collection media and storage on the stability and detection of viral nucleic acids by qRT-PCR. We studied the mechanism(s) through which viral transport media (VTM) and number of freeze-thaw cycles influenced the analytical sensitivity of qRT-PCR detection of SARS-CoV-2. Our goal is to reinforce testing capabilities and identify weaknesses that could arise in resource-limited environments that do not have well-controlled cold chains. The sensitivity of qRT-PCR analysis was studied in four VTM for synthetic single-stranded RNA (ssRNA) and double-stranded DNA (dsDNA) simulants of the SARS-CoV-2 genome. The sensitivity and reproducibility of qRT-PCR for the synthetic ssRNA and dsDNA were found to be highly sensitive to VTM with the best results observed for ssRNA in HBSS and PBS-G. Surprisingly, the presence of epithelial cellular material with the ssRNA increased the sensitivity of the qRT-PCR assay. Repeated freeze-thaw cycling decreased the sensitivity of the qRT-PCR with two noted exceptions. The choice of VTM is critically important to defining the sensitivity of COVID-19 molecular diagnostics assays and this study suggests they can impact upon the stability of the SARS-CoV-2 viral genome. This becomes increasingly important if the virus structure is destabilised before analysis, which can occur due to poor storage conditions. This study suggests that COVID-19 testing performed with glycerol-containing PBS will produce a high level of stability and sensitivity. These results are in agreement with clinical studies reported for patient-derived samples.
Fast alignment and preprocessing of chromatin profiles with Chromap
Authors: Zhang Haowen , Song Li , Wang Xiaotao , Cheng Haoyu , Wang Chenfei , Meyer Clifford A. , Liu Tao , Tang Ming , Aluru Srinivas , Yue Feng , Liu X. Shirley , Li Heng
Published: June 2021

We present Chromap, an ultrafast method for aligning and preprocessing high throughput chromatin profiles. Chromap is comparable to BWA-MEM and Bowtie2 in alignment accuracy and is over 10 times faster than traditional workflows on bulk ChIP-seq / Hi-C profiles and than 10x Genomics’ CellRanger v2.0.0 pipeline on single-cell ATAC-seq profiles.
GRAND: A database of gene regulatory network models across human conditions
Authors: Guebila Marouen Ben , Lopes-Ramos Camila M , Weighill Deborah , Sonawane Abhijeet Rajendra , Burkholz Rebekka , Shamsaei Behrouz , Platig John , Glass Kimberly , Kuijjer Marieke L , Quackenbush John
Published: June 2021

Gene regulation plays a fundamental role in shaping tissue identity, function, and response to perturbation. Regulatory processes are controlled by complex networks of interacting elements, including transcription factors, miRNAs and their target genes. The structure of these networks helps to determine phenotypes and can ultimately influence the development of disease or response to therapy. We developed GRAND (https://grand.networkmedicine.org) as a database for gene regulatory network models that can be compared between biological states, or used to predict which drugs produce changes in regulatory network structure. The database includes 12,468 genome-scale networks covering 36 human tissues, 28 cancers, 1,378 unperturbed cell lines, as well as 173,013 TF and gene targeting scores for 2,858 small molecule-induced cell line perturbation paired with phenotypic information. GRAND allows the networks to be queried using phenotypic information and visualized using a variety of interactive tools. In addition, it includes a web application that matches disease states to potentially therapeutic small molecule drugs using regulatory network properties.

Graphical abstract

Modeling gene regulation across human conditions integrates cancer tissues and cell lines, small molecules, and normal tissue networks.
Extensive protein dosage compensation in aneuploid human cancers
Authors: Schukken Klaske M. , Sheltzer Jason M.
Published: June 2021

Aneuploidy is a hallmark of human cancers, but the effects of aneuploidy on protein expression remain poorly understood. To uncover how chromosome copy number changes influence the cancer proteome, we have conducted an analysis of hundreds of human cancer cell lines with matched copy number, RNA expression, and protein expression data. We found that a majority of proteins exhibit dosage compensation and fail to change by the degree expected based on chromosome copy number alone. We uncovered a variety of gene groups that were recurrently buffered upon both chromosome gain and loss, including protein complex subunits and cell cycle genes. Several genetic and biophysical factors were predictive of protein buffering, highlighting complex post-translational regulatory mechanisms that maintain appropriate gene product dosage. Finally, we established that chromosomal aneuploidy has an unexpectedly moderate effect on the expression of oncogenes and tumor suppressors, demonstrating that these key cancer drivers can be subject to dosage compensation as well. In total, our comprehensive analysis of aneuploidy and dosage compensation across cancers will help identify the key driver genes encoded on altered chromosomes and will shed light on the overall consequences of aneuploidy during tumor development.
Functional characterization of odor responses and gene expression changes in olfactory co-receptor mutants inDrosophila
Authors: Vulpe Alina , Mohapatra Pratyajit , Menuz Karen
Published: June 2021

Two large families of olfactory receptors, the Odorant Receptors (ORs) and the Ionotropic Receptors (IRs), mediate responses to most odors in the insect olfactory system. Individual odor binding “tuning” OR receptors are expressed by olfactory neurons in basiconic and trichoid sensilla and require the co-receptor Orco to function. The situation for IRs is more complex. Different tuning IR receptors are expressed by olfactory neurons in coeloconic sensilla and rely on either the Ir25a or Ir8a co-receptors; some evidence suggests that Ir76b may also act as a coreceptor, but its function has not been systematically examined. This is particularly important as recent data indicate that nearly all coeloconic olfactory neurons co-express Ir25a, Ir8a, and Ir76b. Here, we report the effects ofDrosophilaolfactory co-receptor mutants on odor detection by coeloconic olfactory neurons and determine their broader impact on gene expression through RNASeq analysis. We demonstrate that Ir76b and Ir25a function together in all amine-sensing olfactory receptor neurons. In most neurons, loss of either co-receptor abolishes amine responses, whereas in ac1 sensilla, amine responses persist in the absence of Ir76b or Ir25a, but are lost in a double-mutant. Such responses do not require Ir8a. Conversely, acid-sensing ORNs require Ir8a, but not Ir76b or Ir25a. Using antennal transcriptional profiling, we find that the expression of acid-sensing IR receptors is significantly reduced inIr8amutants, but is unaffected by the loss ofIr25aorIr76b.Similarly, select OR tuning receptors are also downregulated inOrco2mutants. In contrast, expression of amine-sensing IR receptors is mostly unchanged inIr25aandIr76bmutants. Together, our data reveal new aspects of co-receptor function in the olfactory system.

Insect vectors of human disease rely on their sense of smell to locate humans for blood meals. A critical first step in olfaction is the odorant-induced activation of receptors on olfactory neurons. There are two major olfactory receptor families in insects, with each species having dozens of different odorant-binding “tuning” receptors. The receptor complexes also contain non-tuning co-receptors, which are highly conserved across insect species and are required for function. Here we characterize co-receptor mutants with electrophysiological recordings and transcriptome analysis inDrosophila. Our findings resolve the differential co-receptor dependence of olfactory neuron responses to volatile amines and acids. We also report changes in antennal gene expression that result from the absence of these co-receptors. Most notably, the absence of some co-receptors leads to a selective loss of transcript expression for the tuning olfactory receptors whose function depends on the missing co-receptors. Together our data provide new insight into the roles of co-receptors in insect olfaction.
Geometric machine learning informed by ground truth: Recovery of conformational continuum from single-particle cryo-EM data of biomolecules
Authors: Seitz Evan , Acosta-Reyes Francisco , Maji Suvrajit , Schwander Peter , Frank Joachim
Published: June 2021

This work is based on the manifold-embedding approach to study biological molecules exhibiting continuous conformational changes. Previous work established a method capable of reconstructing 3D movies and accompanying energetics of atomic-level structures from single-particle cryo-EM images of macromolecules displaying multiple conformational degrees of freedom. Here, we introduce an unsupervised geometric machine learning approach that is informed by detailed heuristic analysis of manifolds formed by simulated heterogeneous cryo-EM datasets generated from an atomic structure. These simulated data were generated with increasing complexity to account for multiple conformational motions, state occupancies and typical microscope parameters in a wide range of signal-to-noise ratios. Using these datasets as ground-truth, we provide detailed exposition of our findings using several conformational motions while exploring the available parameter space. Guided by these insights, we build a framework to leverage the high-dimensional geometric information obtained towards reconstituting a quasi-continuum of conformational states in the form of a free-energy landscape and respective 3D density maps for all states therein. As shown by a direct comparison of results, this framework offers substantial improvements relative to the previous work.
Single nucleus pituitary transcriptomic and epigenetic landscape reveals human stem cell heterogeneity with diverse regulatory mechanisms
Authors: Zhang Zidong , Zamojski Michel , Smith Gregory R. , Willis Thea L. , Yianni Val , Mendelev Natalia , Pincas Hanna , Seenarine Nitish , Amper Mary Anne S. , Vasoya Mital , Nair Venugopalan D. , Turgeon Judith L. , Bernard Daniel J. , Troyanskaya Olga G. , Andoniadou Cynthia L. , Sealfon Stuart C. , Ruf-Zamojski Frederique
Published: June 2021

Despite their importance in tissue homeostasis and renewal, human pituitary stem cells (PSCs) are incompletely characterized. We describe a human single nucleus (sn) RNAseq and ATACseq resource from pediatric, adult, and aged pituitaries (snpituitaryatlas.princeton.edu) and characterize cell type-specific gene expression and chromatin accessibility programs for all major pituitary cell lineages. We identify uncommitted PSCs, committing progenitor cells, and sex differences. Pseudotime trajectory analysis indicates that early life PSCs are distinct from the other age groups. Linear modeling of same-cell multiome data identifies regulatory domain accessibility sites and transcription factors (TFs) that are significantly associated with gene expression in PSCs compared to other cell types and within PSCs. Modeling the heterogeneous expression of two markers for committing cell lineages among PSCs shows significant correlation with regulatory domain accessibility forGATA3, but with TF expression forPOMC. These findings characterize human stem cell lineages and reveal diverse mechanisms regulating key PSC genes.
2.5D Tractions in monocytes reveal mesoscale mechanics of podosomes during substrate indenting cell protrusion
Authors: Schürmann H , Russo A , Hofemeier AD , Brandt M , Roth J , Vogl T , Betz T
Published: June 2021

Degradation and protrusion are key to cellular barrier breaching in cancer metastasis and leukocyte extravasation. Cancerous invadopodia and myelomonocytic podosomes are widely considered as structural tools facilitating these processes and are thus summarized under the term invadosomes. Despite similar behaviour on the individual scale, substantial differences have been reported to arise on the collective scale. They are considered to be a result of podosome mesoscale-connectivity. In this study, we investigated global in-plane and out-of-plane mechanical forces of podosome clusters in ER-Hoxb8 cell derived monocytes. We are able to correlate these forces with the interpodosomal connectivity. The observed traction and protrusion patterns fail to be explained by summation of single podosome mechanics. Instead, they appear to originate from superimposed mesoscale effects. Based on mechanistic and morphological similarities with epithelial monolayer mechanics, we propose a spatiotemporal model of podosome cluster mechanics capable of relating single to collective podosome mechanical behaviour. Our results suggest that network contraction-driven (in-plane) tractions lead to a buckling instability that contributes to the out-of-plane indentation into the substrate. First assigning an active mechanical role to the dorsal podosome actomyosin network, we aim at translating actomyosin hierarchy into scale dependency of podosome mechanics.
Endothelial Resolution of Inflammation is Delayed Following JAK-driven but not NFκB-dependent Activation
Authors: Valenzuela Nicole M
Published: June 2021

Blood endothelial cells actively regulate egress of leukocytes into peripheral tissues in response to inflammatory insult. The resolution of inflammation is critical for healing and return to homeostasis, but the timing and mechanisms involved in return to a non-inflamed state are not well-understood. We examined vascular endothelial activation comparing NFκB-driven TNFα and JAK/STAT-mediated IFNγ. Pro-adhesive gene expression, phenotype and secretome of human endothelial cells from 6 vascular beds were measured under chronic cytokine stimulation, and after short-term cytokine priming followed by withdrawal. The majority of inducible TNFα effectors require continuous exposure for reinforcement of the altered phenotype. NFκB and target genes are quickly down-regulated in the absence of cytokine. In contrast, the consequences of even short exposure to IFNγ are long-lasting and broad, with sustained elevation of adhesion molecules and chemokines up to 48hr later. JAK/STAT and interferon response factor expression are likewise durable, dependent on new transcription and autonomous of continuous IFNγ. Finally, intact persistent STAT expression and JAK signaling in the endothelium is required to maintain a pro-adhesive phenotype after IFNγ withdrawal, which could be prevented by the JAK1/2 inhibitor ruxolitinib. Our results reveal a sustained JAK-dependent perturbation of endothelial function after exposure to IFNγ, but not after NFκB-driven inflammation.
Preferential lipolysis of DGAT1 over DGAT2 generated triacylglycerol in Huh7 hepatocytes
Authors: Selvaraj Rajakumar , Zehnder Sarah V. , Watts Russell , Lian Jihong , Nelson Randal , Lehner Richard
Published: June 2021

Hepatic steatosis is defined by accumulation of neutral lipids in lipid droplets (LDs) including triacylglycerol (TG) and steryl esters. Two distinct diacylglycerol acyltransferases (DGAT1 and DGAT2) catalyze synthesis of TG in hepatocytes. TG formed through either DGAT1 or DGAT2 appears to be preferentially directed to distinct intercellular fates, such as fatty acid production for oxidation or very-low density lipoprotein assembly, respectively. Because of the preferential use of TG generated by DGAT1 and DGAT2, we hypothesized that targeting/association of lipolytic machinery to LDs would differ depending on whether the TG stores were generated through DGAT1 or DGAT2 activities. Inhibition of DGAT1 or DGAT2 in human hepatoma cells (Huh7) incubated with oleic acid resulted in only a small change in TG accretion suggesting that the two DGATs can compensate for each other in fatty acid esterification. This compensation was not accompanied by changes in DGAT1 or DGAT2 mRNA expression. DGAT1 inhibition (TG synthesized by DGAT2) resulted in large LDs, whereas DGAT2 inhibition (TG synthesized by DGAT1) caused the accumulation of numerous small LDs. Oleic acid treatment increased mRNA and protein expression of the LD-associated protein PLIN2 but not PLIN5 or the lipase ATGL and its activator ABHD5/CGI-58. Inactivation of DGAT1 or DGAT2 did not alter expression (mRNA or protein) of ATGL, ABHD5/CGI-58, PLIN2 or PLIN5, but inactivation of both DGATs increased PLIN2 abundance despite a dramatic reduction in the number of LDs. ATGL localized preferentially to DGAT1-made LDs rather than to DGAT2-made LDs, and TG in these LDs was preferentially used for fatty acid (FA) oxidation. A combination of DGAT2 inhibitor and the pan lipase inhibitor E600 resulted in large LDs, suggesting that the small size of DGAT1-made LDs is due to a lipolytic process.
The non-canonical interaction between calmodulin and calcineurin contributes to the differential regulation of plant-derived calmodulins on calcineurin
Authors: Sun Bin , Fang Xuan , Johnson Christopher N. , Hauck Garrett , Davis Jonathan P. , Kekenes-Huskey Peter M.
Published: June 2021

Calmodulin (CaM) is an important Ca2+ signaling hub that regulates many protein signaling pathways. In recent years, several CaM homologs expressed in plants have been shown to regulate mammalian targets and they are attractive for gene therapy. However, the molecular basis of how the CaM homologs mutations impact target activation is unclear, which limits efforts to engineer their functional properties. To understand these mechanisms, we examined two CaM isoforms found in soybean plants that differentially regulate a mammalian target, calcineurin (CaN). These CaM isofroms, sCaM-1 and sCaM-4 share >90% and ~ 78% identity with the mammalian CaM (mCaM), respectively, activate CaN with comparable or reduced activity relative to mCaM. We used molecular simulations and experimental assays to probe whether calcium and protein-protein binding interactions are altered in plant CaMs relative to mCaM as a basis for differential CaN regulations. We found that the two sCaMs’ Ca2+-binding properties such as coordination and affinity are comparable to mCaM. Further, the binding of CaM to the CaM binding region (CaMBR) in CaN is also comparable among the three CaMs, as evidenced by calculated binding free energies and experimental measured EC50 [CaM]. However, mCaM and sCaM-1 exhibited stronger binding with a secondary region of CaN’s regulatory domain that is weakened for sCaM-4. This secondary interaction is likely to affect the turnover rate (kcat) of CaN based on our modeling of enzyme activity and is consistent with our experimental data. Together, our data show how plant-derived CaM variants can alter target activation through interactions beyond Ca2+-binding and canonical CaMBR binding, which may extend beyond the mammalian CaN target.
LD-CNV: rapid and simple discovery of chromosomal translocations using linkage disequilibrium between copy number variable loci
Authors: Comai Luca , Amundson Kirk , Ordonez Benny , Zhao Xin , Braz Guilherme Tomaz , Jiang Jiming , Henry Isabelle
Published: June 2021

Large scale structural variations, such as chromosomal translocations, can have profound effects on fitness and phenotype, but are difficult to identify and characterize. Here, we describe a simple and effective method aimed at identifying translocations using only the dosage of sequence reads mapped on the reference genome. We binned reads on genomic segments sized according to sequencing coverage and identified instances when copy number segregated in populations. For each dosage-polymorphic 1Mb bin, we tested linkage disequilibrium with other variable bins. In nine potato (Solanum tuberosum) dihaploid families translocations affecting pericentromeric regions were common and in two cases were due to genomic misassembly. In two populations, we found evidence for translocation affecting euchromatic arms. In cv. PI 310467, a non-reciprocal translocation between chromosome 7 and 8 resulted in a 5-3 copy number change affecting several Mb at the respective chromosome tips. In cv. “Alca Tarma”, the terminal arm of chromosome 4 translocated to the tip of chromosome 1. Using oligonucleotide-based fluorescent in situ hybridization painting probes (oligo-FISH), we tested and confirmed the predicted arrangement in PI 310467. In 192 natural accessions of Arabidopsis thaliana, dosage haplotypes tended to vary continuously and resulted in higher noise, but we identified pericentromeric LD suggesting the effect of repeats. This method should be useful in species where translocations are suspected because it tests linkage without the need for genotyping.
Mechanism of CFTR correction by type I folding correctors
Authors: Fiedorczuk Karol , Chen Jue
Published: June 2021

Small molecule chaperones have been exploited as therapeutics for the hundreds of diseases caused by protein misfolding. The most successful examples are the CFTR correctors, which transformed cystic fibrosis therapy. These molecules revert folding defects of the ΔF508 mutant and are widely used to treat patients. However, their mechanism of action is unknown. Here we present cryo-electron microscopy structures of CFTR in complex with two FDA-approved correctors: lumacaftor and tezacaftor. Both drugs insert into a hydrophobic pocket in the first transmembrane domain (TMD1), linking together four helices that are thermodynamically unstable. Mutating residues at the binding site rendered ΔF508-CFTR insensitive to lumacaftor and tezacaftor, underscoring the functional significance of the structural discovery. These results support a mechanism in which the correctors stabilize TMD1 at an early stage of biogenesis, prevent its pre-mature degradation, and thereby allosterically rescue a large number of disease-causing mutations.
Phenotypic plasticity in floral scent in response to nutrient, but not water, availability in the perennial plant Arabis alpina
Authors: Luizzi Victoria J. , Friberg Magne , Petrén Hampus
Published: June 2021

Floral scent is an important mediator of plant–pollinator interactions. Multiple recent studies report ample intraspecific scent variation among populations and individuals. Yet, few studies have estimated effects of phenotypic plasticity on floral scent in response to differing environmental factors.

In this study, we investigated the effects of nutrient and water availability on floral scent in self‐compatible and self‐incompatible populations of the perennial herb Arabis alpina. We subjected greenhouse grown plants to different nutrient and water treatments in a crossed design, examined the effects on floral scent emission rate and composition, compared the level of plasticity to that of other plant traits, and conducted hand‐pollinations of nutrient‐limited individuals to test for a potential allocation cost of scent production.

For both self‐compatible and self‐incompatible populations, the per‐flower scent emission rate was 1.2–4 times higher when nutrients were abundant, but this effect explained little variation in scent emission rate and was limited compared to plasticity in flower number. There was no effect of water treatment on scent emission. Additionally, neither treatment had an effect on the composition of the floral scent, and there was no detectable trade‐off between scent and seed production that would imply a cost of floral scent production.

Overall, while per‐flower floral scent emission displayed limited phenotypic plasticity in response to nutrient conditions, the total amount of scent emitted by plants may increase more strongly at higher nutrient availabilities due to an increase in flower production. Therefore, our results suggest that fitness benefits due to increased scent emission rates under favourable nutrient conditions might depend on the extent to which floral scent serves as a long‐ or short‐distance pollinator attractant for the focal plant species.

A free Plain Language Summary can be found within the Supporting Information of this article.
Thinking Globally about Attitudes to Immigration: Concerns about Social Conflict, Economic Competition and Cultural Threat
Authors: Dennison James , Geddes Andrew
Published: June 2021

This article looks globally at the motivations behind attitudes to immigration. Such motivations have been typically conceptualised by academics either in terms of the ‘economic competition’ or ‘cultural threat’ that immigrants are perceived to pose to the individual or their ‘in‐group’. We propose and test a third possibility: that support for or opposition to immigration is determined by one's perceptions of immigration's effects on social conflict. Using the 2017–2020 World Values Survey (WVS) for forty‐nine countries, we show that: in most countries, globally, citizens are more likely to agree than disagree that immigration leads to social conflict; levels of concern about the effects of immigration on social conflict are higher than those regarding unemployment or culture in sixteen—disproportionately economically developed—countries; concern about social conflict is conceptually and distributionally distinct; belief that immigration leads to social conflict predicts immigration policy preferences; but, uniquely, is positively predicted by higher education. Our findings highlight the importance of institutional conflict resolution capacity, including those related to integration, for the politics of migration.
Beyond deficit: ‘strengths‐based approaches’ in Indigenous health research
Authors: Bryant Joanne , Bolt Reuben , Botfield Jessica R. , Martin Kacey , Doyle Michael , Murphy Dean , Graham Simon , Newman Christy E. , Bell Stephen , Treloar Carla , Browne Annette J. , Aggleton Peter
Published: June 2021

Health research concerning Indigenous peoples has been strongly characterised by deficit discourse—a ‘mode of thinking’ that is overly focused on risk behaviours and problems. Strengths‐based approaches offer a different perspective by promoting a set of values that recognise the capacities and capabilities of Indigenous peoples. In this article, we seek to understand the conceptual basis of strengths‐based approaches as currently presented in health research. We propose that three main approaches exist: ‘resilience’ approaches concerned with the personal skills of individuals; ‘social–ecological’ approaches, which focus on the individual, community and structural aspects of a person's environment; and ‘sociocultural’ approaches, which view ‘strengths’ as social relations, collective identities and practices. We suggest that neither ‘resilience’ nor ‘social–ecological’ approaches sufficiently problematise deficit discourse because they remain largely informed by Western concepts of individualised rationality and, as a result, rest on logics that support notions of absence and deficit. In contrast, sociocultural approaches tend to view ‘strengths’ not as qualities possessed by individuals, but as the structure and character of social relations, collective practices and identities. As such, they are better able to capture Indigenous ways of knowing and being and provide a stronger basis on which to build meaningful interventions.
Competing revolutionaries: Legitimacy and leadership in revolutionary situations
Authors: Rasit Huseyin
Published: June 2021

When the Arab Spring gave way to demonstrations in Syria in 2011, the Kurds in the country were also full of hope. While they were going into the streets, the Kurdish political parties were debating what their people should do and offering competing visions for the future. Then in July 2012, the regime unexpectedly withdrew its forces from the Kurdish regions (Rojava). Suddenly, a revolutionary situation emerged in Rojava: a mobilized population and several political parties claiming leadership and offering competing political projects for a new society. Among these parties, only the Democratic Union Party (PYD) managed to move into the power vacuum and establish its control over large areas. Its rivals were unable to stop the rapid rise of this relatively young organization and fast erosion of their own base. How did the PYD manage to become the dominant organization even though it had rarely drawn attention before the civil war? This question raises the larger problem of how a revolutionary organization becomes the dominant one among competitors. Even though multiple organizations competing in a single revolution is a recurrent phenomenon, we still lack a comprehensive framework specifically focusing on this issue. In this paper, I argue for an approach based on legitimation: for people to follow a certain organization over others, they should see it as a legitimate leader. Bringing together the insights of the political and organizational legitimacy literatures, I identify three processes of legitimation for revolutionary organizations: ideological/normative congruence, effective organizational capacity, and accumulation of prestige. Drawing upon participant observation and 30 in‐depth interviews with Kurdish individuals collected during fieldwork in Iraq, Germany, and the United States between 2016 and 2019, I demonstrate that the PYD has outperformed its contenders and managed to legitimate its leadership through these three processes.
Rallying in fear? Estimating the effect of the UK COVID‐19 lockdown with a natural experiment
Authors: EGGERS ANDREW C. , HARDING ROBIN
Published: June 2021

We use a natural experiment to study how the announcement of the UK COVID‐19 lockdown affected citizens' attitudes towards the pandemic and the government's response to it. On the day of the lockdown announcement, YouGov ran a survey that captured responses before and after the announcement. Comparison of these responses suggests that the lockdown announcement made people more supportive of the government's response to the crisis but also (perhaps surprisingly) more concerned about the pandemic. Analysis of heterogeneous treatment effects suggests that the announcement narrowed gaps in perceptions of the crisis, increasing support for the government's response especially among those who had been least supportive and increasing concern about the pandemic especially among those who had been least concerned. Overall, the findings highlight a tension inherent in governing during times of crisis: actions that increase people's confidence in government and induce compliance with government directives may also tend to increase anxiety among the population.
Challenges associated with spray drying of lactic acid bacteria: Understanding cell viability loss
Authors: Moreira Maria Tereza Cratiú , Martins Evandro , Perrone Ítalo Tuler , de Freitas Rosângela , Queiroz Lucas Sales , de Carvalho Antônio Fernandes
Published: June 2021

Lactic acid bacteria (LAB) cultures used in food fermentation are often dried to reduce transportation costs and facilitate handling during use. Dried LAB ferments are generally lyophilized to ensure high cell viability. Spray drying has come to the forefront as a promising technique due to its versatility and lower associated energy costs. Adverse conditions during spray drying, such as mechanical stress, dehydration, heating, and oxygen exposure, can lead to low LAB cell viability. This reduced viability has limited spray drying's industrial applications thus far. This review aims to demonstrate the operations and thermodynamic principles that govern spray drying, then correlate them to the damage suffered by LAB cells during the spray‐drying process. The particularities of spray drying that might cause LAB cell death are detailed in this review, and the conclusion may enhance future studies on ways to improve cell viability.
Sensory evaluation of fresh/frozen mackerel products: A review
Authors: Huang Yi‐Zhen , Liu Yu , Jin Zheng , Cheng Qiaofen , Qian Michael , Zhu Bei‐Wei , Dong Xiu‐Ping
Published: June 2021

Mackerel has received considerable attention in the global food market as one of the most important pelagic commercial fish species. The quality of mackerel is influenced by species, season, fishing area, nutritional status, catching method, handling, and storage. Due to the mackerel's perishability, its quality is mainly measured by sensory procedures. Although considerable effort has been made to explore quick and reliable quality analysis, developing a practical and scientific sensory evaluation of mackerel has been an active ongoing study area to meet the quality evaluation demand of the industry. Different sensory evaluation methods have been used to assess the mackerel fish quality, including Palatability and Spoilage test, Torry scheme, EU scheme, Quality Index Method, Catch damage index and Processed fish damage index, Affective test, Discriminative test, and Descriptive test. Each method has its strength and weakness. Despite mackerel sensory evaluation protocols having undergone partial harmonization, specific sample process needs to be carefully followed to minimize the change during sample preparation. This review summarizes the sensory evaluation methods in mackerel research, the factors affecting sensory evaluation, and then updates the latest advances in mackerel sensory evaluation and offers guidance for presenting its application in the mackerel chain. Also, each technique's advantages and limitations are discussed. In our opinion, the future trends for sensory evaluation of mackerel should be consumer‐centric.
Avocado oil: Production and market demand, bioactive components, implications in health, and tendencies and potential uses
Authors: Cervantes‐Paz Braulio , Yahia Elhadi M.
Published: June 2021

Avocado is a subtropical/tropical fruit with creamy texture, peculiar flavor, and high nutritional value. Due to its high oil content, a significant quantity of avocado fruit is used for the production of oil using different methods. Avocado oil is rich in lipid‐soluble bioactive compounds, but their content depends on different factors. Several phytochemicals in the oil have been linked to prevention of cancer, age‐related macular degeneration, and cardiovascular diseases and therefore have generated an increase in consumer demand for avocado oil. The aim of this review is to critically and systematically analyze the worldwide production and commercialization of avocado oil, its extraction methods, changes in its fat‐soluble phytochemical content, health benefits, and new trends and applications. There is a lack of information on the production and commercialization of the different types of avocado oil, but there are abundant data on extraction methods using solvents, centrifugation‐assisted aqueous extraction, mechanical extraction by cold pressing (varying concentration and type of enzymes, temperature and time of reaction, and dilution ratio), ultrasound‐assisted extraction, and supercritical fluid to enhance the yield and quality of oil. Extensive information is available on the content of fatty acids, although it is limited on carotenoids and chlorophylls. The effect of avocado oil on cancer, diabetes, and cardiovascular diseases has been demonstrated through in vitro and animal studies, but not in humans. Avocado oil continues to be of interest to the food, pharmaceutical, and cosmetic industries and is also generating increased attention in other areas including structured lipids, nanotechnology, and environmental care.
Recent developments of natural antimicrobials and antioxidants on fish and fishery food products
Authors: Rathod Nikheel Bhojraj , Ranveer Rahul Chudaman , Benjakul Soottawat , Kim Se‐Kwon , Pagarkar Asif Umar , Patange Surendra , Ozogul Fatih
Published: June 2021

Fish and fishery products (FFP) are highly perishable due to their high nutritional value and moisture content. The spoilage is mainly caused by microorganisms and chemical reactions, especially lipid oxidation, leading to losses in quality and market value. Microbiological and lipid deteriorations of fishery‐derived products directly lower their nutritive value and pose the risk of toxicity for human health. Increasing demand for safe FFP brings about the preservation using additives from natural origins without chemical additives due to their safety and strict regulation. Antimicrobials and antioxidants from natural sources have exhibited an excellent control over the growth of microorganisms causing fish spoilage via different mechanisms. They also play a major role in retarding lipid oxidation by acting at various stages of oxidation. Antimicrobials and antioxidants from natural sources are usually regarded as safe with no detrimental effects on the quality attributes of FFP. This review provides recent literature on the different antioxidant and antimicrobial agents from natural sources, focusing on microbial and oxidative spoilage mechanisms, their inhibition system, and their applications to retard spoilage, maintain safety, and extend the shelf life of FFP. Their applications and benefits have been revisited.
Wine phenolic profile altered by yeast: Mechanisms and influences
Authors: Zhang Pangzhen , Ma Wen , Meng Yiqi , Zhang Yifan , Jin Gang , Fang Zhongxiang
Published: June 2021

Grape phenolic compounds undergo various types of transformations during winemaking under the influences of yeasts, which further impacts the sensory attributes, thus the quality of wine. Understanding the roles of yeasts in phenolics transformation is important for controlling wine quality through fermentation culture selection. This literature review discusses the mechanisms of how yeasts alter the phenolic compounds during winemaking, summarizes the effects of Saccharomyces cerevisiae and non‐Saccharomyces yeasts on the content and composition of phenolics in wine, and highlights the influences of mixed cultural fermentation on the phenolic profile of wine. Collectively, this paper aims to provide a deeper understanding on yeast–phenolics interactions and to identify the current literature gaps for future research.
Bacillus spore germination at moderate high pressure: A review on underlying mechanisms, influencing factors, and its comparison with nutrient germination
Authors: Delbrück Alessia I. , Zhang Yifan , Heydenreich Rosa , Mathys Alexander
Published: June 2021

Spore‐forming bacteria are resistant to stress conditions owing to their ability to form highly resistant dormant spores. These spores can survive adverse environmental conditions in nature, as well as decontamination processes in the food and related industries. Bacterial spores may return to their vegetative state through a process called germination. As spore germination is critical for the loss of resistance, outgrowth, and development of pathogenicity and spoilage potential, the germination pathway has piqued the interest of the scientific community. The inhibition and induction of germination have critical applications in the food industry. Targeted germination can aid in decreasing the resistance of spores and allow the application of milder inactivation procedures. This germination‐inactivation strategy allows better maintenance of important food quality attributes. Different stimuli are reported to trigger germination. Among those, isostatic high pressure (HP) has gained increasing attention due to its potential applications in industrial processes. However, pressure‐mediated spore germination is extremely heterogeneous as some spores germinate rapidly, while others exhibit slow germination or do not undergo germination at all. The successful and safe implementation of the germination‐inactivation strategy, however, depends on the germination of all spores. Therefore, there is a need to elucidate the mechanisms of HP‐mediated germination. This work aimed to critically review the current state of knowledge on Bacillus spore germination at a moderate HP of 50–300 MPa. In this review, the germination mechanism, heterogeneity, and influencing factors have been outlined along with knowledge gaps.
Food polysaccharides and roles of rheology and tribology in rational design of thickened liquids for oropharyngeal dysphagia: A review
Authors: Methacanon Pawadee , Gamonpilas Chaiwut , Kongjaroen Akapong , Buathongjan Chonchanok
Published: June 2021

In today's market environment, an aging society is recognized as one of the megatrends in the world. The demographic change in the world population age structure has driven a huge demand in healthcare products as well as services that include the technological innovation for the health and wellness of the elderly. Dysphagia or swallowing difficulty is a common problem in the elderly as many changes in swallowing function come with aging. The presence of a strong relationship between swallowing ability, nutritional status, and health outcomes in the elderly leads to the importance of dysphagia management in the population group. Modification of solid food and/or liquid is a mainstay of compensatory intervention for dysphagia patients. In this regard, texture‐modified foods are generally provided to reduce risks associated with choking, while thickened liquids are recommended for mitigating risks associated with aspiration. In this review, we discuss thickened liquids and other issues including the importance of their rheological and tribological properties for oropharyngeal dysphagia management in the elderly. The review focuses on both commercial thickeners that are either based on modified starch or xanthan gum and other potential polysaccharide alternatives, which have been documented in the literature in order to help researchers develop or improve the characteristic properties of thickened liquids required for safe swallowing. Furthermore, some research gaps and future perspectives, particularly from the nutrition aspect related to the interaction between thickeners and other food ingredients, are suggested as such interaction may considerably control the rate of nutrient absorption and release within our body.
Fatal jellyfish envenoming—Pediatric and geographic vulnerabilities
Authors: Tiemensma Marianne , Currie Bart J. , Byard Roger W.
Published: June 2021

Lethal jellyfish envenoming is a very rare event. Two illustrative cases of fatalities following envenomation from the multi‐tentacled box jellyfish, Chironex fleckeri, are reported that involved a six‐year‐old boy and a three‐year‐old girl, both of whom had been playing in shallow beach waters in remote Northern Territory communities (Australia). A recommended approach to autopsy in suspected cases is described, which should include examination of the clothing and skin surfaces for the fine tentacles of Chironex fleckeri. In addition, the combined length and maximum width of tentacle marks should be measured/calculated and collection of unfixed tentacles with adhesive tape onto a glass slide should be undertaken to check for nematocysts. Such rare cases show that children are at higher risk of a lethal outcome, particularly if they are resident in remote coastal tropical communities.
A spectroscopic approach for rapid and simple serial number restoration on polyamide 6 parts of firearms: The use of video spectral comparator 8000
Authors: Uysal Serdar , Armutcu Canan , Mercan Mustafa , Uzun Lokman
Published: June 2021

Serial numbers have forensic value as they help to identify firearms. While the serial numbers are mostly stamped on the metal parts of firearms, the characters on polymer parts involve non‐serial number information such as caliber, brand, model, or proof marks, which also serve for identification purposes. The forensic evidence indicates that the polymer frames of firearms bearing non‐serial number information are obliterated through heating and scraping. Although the destructive restoration techniques for polymers are well‐documented, there is little theoretical and practical knowledge regarding the non‐destructive restoration techniques applied on polymers. In view of this gap, this study aims to devise a non‐destructive spectral technique to recover the obliterated characters on Polyamide 6. Considering its wide use on polymers, the numbering is carried out by hot stamping and the numbers are defaced through heating, scraping, and hammering both superficially and deeply at varying depths. Herein, we focused on imitating the manual obliteration techniques used by criminals instead of the deepness‐controlled techniques preferred by previous studies. The samples are then viewed under the UV and IR lights in the Video Spectral Comparator 8000 for the first time. The results suggest that spectral imaging provided restoration to a good extent after heating and scraping which made the characters invisible at a relatively low depth of deformation compared to hammering. The recovery of characters with this novel technique brings a new perspective forensic marks examination literature by producing quick, successful and reliable results and facilitating reexamination by not harming the sample.
Furfural and organic acid targeted carbon dot sensor array for the accurate identification of Chinese baijiu
Authors: Li Ailan , Jia Junjie , Fan Yao , Chen Hengye , Wang Songtao , Shen Caihong , Dai Hupiao , Zhou Chunsong , Fu Haiyan , She Yuanbin
Published: June 2021

Baijiu quality control has always been a major challenge for researchers. In this paper, taking furfural which is closely related to baijiu brewing process and organic acids related to baijiu fermentation process and microorganism types as the main discriminating factors, a carbon dot (CDs) sensor array targeting furfural and organic acids was constructed to identify 41 kinds of baijiu. Through the fluorescence response investigation of CDs synthesized by isomers of benzenediol, aminophenol, and phenylenediamine to different baijiu, two CDs synthesized by meta‐benzene substitutions containing ‐NH2 were selected to build a fluorescence sensor array. Due to the aggregation‐induced enhancement effect between furfural and the CDs, and the protonation of organic acid and the CDs, different fluorescence changes were observed, the sensor array combined with partial least squares regression could quantitatively analyze furfural and organic acids. What is more, semi‐quantitative analysis of furfural and lactic acid in baijiu was performed. Owing to the interaction of the two CDs with furfural and organic acids in baijiu, the sensor array could accurately identify different baijiu through linear discriminant analysis. This sensor array has potential applications in the quantitative analysis of flavor substances in other alcoholic beverages, moreover, this method could provide a quick response and practical tool for real‐time quality control monitoring in the baijiu industry.