bluuebunny/crossref_metadata_2025 huggingface dataset:
Natural Language Processing for Clinical Laboratory Data Repository Systems: Implementation and Evaluation for Respiratory Viruses
Authors: Dolatabadi Elham , Chen Branson , Buchan Sarah A. , Marchand-Austin Alex , Azimaee Mahmoud , McGeer Allison J. , Mubareka Samira , Kwong Jeffrey C.
Published: November 2022

Background

With the growing volume and complexity of laboratory repositories, it has become tedious to parse unstructured data into structured and tabulated formats for secondary uses such as decision support, quality assurance, and outcome analysis. However, advances in Natural Language Processing (NLP) approaches have enabled efficient and automated extraction of clinically meaningful medical concepts from unstructured reports.

Objective

In this study, we aimed to determine the feasibility of using the NLP model for information extraction as an alternative approach to a time-consuming and operationally resource-intensive handcrafted rule-based tool. Therefore, we sought to develop and evaluate a deep learning-based NLP model to derive knowledge and extract information from text-based laboratory reports sourced from a provincial laboratory repository system.

Methods

The NLP model, a hierarchical multi-label classifier, was trained on a corpus of laboratory reports covering testing for 14 different respiratory viruses and viral subtypes. The corpus included 85kunique laboratory reports annotated by eight Subject Matter Experts (SME). The model’s performance stability and variation were analyzed across fine-grained and coarse-grained classes. Moreover, the model’s generalizability was also evaluated internally and externally on various test sets.

Results

The NLP model was trained several times with random initialization on the development corpus, and the results of the top ten best-performing models are presented in this paper. Overall, the NLP model performed well on internal, out-of-time (pre-COVID-19), and external (different laboratories) test sets with micro-averaged F1 scores >94% across all classes. Higher Precision and Recall scores with less variability were observed for the internal and pre-COVID-19 test sets. As expected, the model’s performance varied across categories and virus types due to the imbalanced nature of the corpus and sample sizes per class. There were intrinsically fewer classes of viruses beingdetectedthan thosetested; therefore, the model’s performance (lowest F1-score of 57%) was noticeably lower in the “detected” cases.

Conclusions

We demonstrated that deep learning-based NLP models are promising solutions for information extraction from text-based laboratory reports. These approaches enable scalable, timely, and practical access to high-quality and encoded laboratory data if integrated into laboratory information system repositories.
Development of an Interactive Web Dashboard to Facilitate the Reexamination of Pathology Reports for Instances of Underbilling of CPT Codes
Authors: Greenburg Jack , Lu Yunrui , Lu Shuyang , Kamau Uhuru , Hamilton Robert , Pettus Jason , Preum Sarah , Vaickus Louis , Levy Joshua
Published: November 2022

Current Procedural Terminology Codes is a numerical coding system used to bill for medical procedures and services and crucially, represents a major reimbursement pathway. Given that Pathology services represent a consequential source of hospital revenue, understanding instances where codes may have been misassigned or underbilled is critical. Several algorithms have been proposed that can identify improperly billed CPT codes in existing datasets of pathology reports. Estimation of the fiscal impacts of these reports requires a coder (i.e., billing staff) to review the original reports and manually code them again. As the re-assignment of codes using machine learning algorithms can be done quickly, the bottleneck in validating these reassignments is in this manual re-coding process, which can prove cumbersome. This work documents the development of a rapidly deployable dashboard for examination of reports that the original coder may have misbilled. Our dashboard features the following main components: 1) a bar plot to show the predicted probabilities for each CPT code, 2) an interpretation plot showing how each word in the report combines to form the overall prediction, 3) a place for the user to input the CPT code they have chosen to assign. This dashboard utilizes the algorithms developed to accurately identify CPT codes to highlight the codes missed by the original coders. In order to demonstrate the function of this web application, we recruited pathologists to utilize it to highlight reports that had codes incorrectly assigned. We expect this application to accelerate the validation of reassigned codes through facilitating rapid review of false positive pathology reports. In the future, we will use this technology to review thousands of past cases in order to estimate the impact of underbilling has on departmental revenue.
Planetary Health, Indigenous Knowledge and Healthcare: a Scoping Review
Authors: Ela Jihae Abou El , Mudgway Mercedes , Harré Niki , Hamill James
Published: November 2022

Background

Planetary health is a movement to promote a healthy planet as the most important determinant of human health. Indigenous knowledge often encompasses a holistic view of nature and people in a way more akin to planetary health than to healthcare systems based on people alone. A change in healthcare’s worldview could help it become more environmentally sustainable. The aim of this review was to identify gaps in the literature and opportunities for further research at the nexus of Indigenous knowledge, environmental sustainability and healthcare.

Methods

We searched the databases Web of Science, Medline, and Google Scholar for peer-reviewed publications with terms pertaining to sustainability or planetary health, human healthcare, and indigenous or traditional knowledge. Papers were grouped by theme. Analysis was descriptive.

Results

The search process resulted in 10 eligible papers. Studies originated from 4 continents including one from Aotearoa New Zealand. Most (8/10) were published since 2020. Methodology included ethnography, discourse, imagery, descriptive, and quantitative analysis. One paper involved a particular healthcare system while all others considered general aspects of human health as related to the environment and Indigenous knowledge. Themes included 1) the importance of indigenous knowledge, 2) conceptual models that incorporate Indigenous approaches to health and the environment, and 3) the implementation of interventions. Within the limitations of the research available, it appears that Indigenous knowledge could make invaluable contributions to more environmentally responsible healthcare systems and can guide interventions to address planetary health problems.

Conclusion

Literature on Indigenous knowledge as related to planetary health and healthcare is limited and recent. There is scope for more research from many different Indigenous groups including Māori in Aotearoa, and scope for more collaborative research between healthcare systems and Indigenous peoples.
Tissue Forge: Interactive Biological and Biophysics Simulation Environment
Authors: Sego T.J. , Sluka James P. , Sauro Herbert M. , Glazier James A.
Published: November 2022

Tissue Forge is an open-source interactive environment for particle-based physics, chemistry and biology modeling and simulation. Tissue Forge allows users to create, simulate and explore models and virtual experiments based on soft condensed matter physics at multiple scales, from the molecular to the multicellular, using a simple, consistent interface. While Tissue Forge is designed to simplify solving problems in complex subcellular, cellular and tissue biophysics, it supports applications ranging from classic molecular dynamics to agent-based multicellular systems with dynamic populations. Tissue Forge users can build and interact with models and simulations in real-time and change simulation details during execution, or execute simulations off-screen and/or remotely in high-performance computing environments. Tissue Forge provides a growing library of built-in model components along with support for user-specified models during the development and application of custom, agent-based models. Tissue Forge includes an extensive Python API for model and simulation specification via Python scripts, an IPython console and a Jupyter Notebook, as well as C and C++ APIs for integrated applications with other software tools. Tissue Forge supports installations on 64-bit Windows, Linux and MacOS systems and is available for local installation via conda.

1

Author Summary

Tissue Forge is a physics-based modeling and simulation software environment for research problems in physics, chemistry and biology. Tissue Forge supports modeling at a wide range of scales, from as small as the sub-nanometer, to as large as hundreds of micrometers, using particle-based models. It provides rich features for simulation development and application at all stages of model-based research, like real-time simulation visualization and interactivity, and off-screen batch execution, rendering, and GPU acceleration. Users can employ built-in models to represent a wide variety of physical processes, like chemical reactions, fluid convection and intercellular adhesion, or define their own models for agentand rule-based modeling. Tissue Forge is open-source, free and easy to install, supports simulation development in C, C++ and Python programming languages, and can be used as integrated software or in an interactive IPython console and Jupyter Notebook. Tissue Forge also provides a dedicated space for application-specific and user-contributed modeling and simulation features, and developers are welcome to contribute their custom features for distribution in future releases.
The association between type of conception through medically assisted reproduction and childhood cognition: A Danish population-wide cohort study
Authors: Fallesen Peter
Published: November 2022

Previous research has found that children conceived through medically assisted reproduction (MAR) on average has cognitive outcomes on par with or above naturally conceived children. However, previous work has been unable to consider the relationship at a full population level nor consider heterogeneity across type of MAR. We use all Danish live births in the years 2006-2009 (n=259,608) with indicator for MAR conceptions (n=13,554). The dependent variable is the within-year-and-grade standardized test scores carried out in second and third grade in primary schools. We compare the test scores for spontaneously conceived (SC) children and conceived through intrauterine insemination (IUI) and assisted reproductive technologies (ART). We estimate ordinary least squares regressions with a baseline model only adjusted for birthyear and models adjusted for birth-related confounders and socio-demographic family characteristics. At baseline, ART and IUI conceived children performed better in tests than SC peers. After adjusting, ART conceived performed worse than SC peer, and IUI conceived performed as well as SC peers and better than ART conceived. Results likely reflect differences in selection of potential parents into type of MAR as well as consequences of differences in fecundability.
The Impact of War on HIV/AIDS Service Provision: in Rural Health Facilities of Tigray, Northern Ethiopia
Authors: Weledegebriel Migbnesh Gebremedhin , Abebe Haftom Temesgen , Gidey Kidu , Bisrat Haileselassie , Gebru Tekae , Tsegay Niguse , Abera Bisrat Tesfay , Gebremeskel Hailay , Asmerom Demoze , Gebreweld Angesom , Miruts Fikadu , Wasihun Araya Gebreyesus , Hagos Kiflom , Gebrehiwet Tesfay Gebregzabher
Published: November 2022

Back ground

HIV/AIDS remained among the common public health problems worldwide. Despite the extensive delivery of ART and improved coverage of the service access, still, man-made problems like war have negatively influenced the utilization of antiretroviral treatment services. The war in Tigray Region in the northern Ethiopia broke out in November 2020 and thereby has brought about an extreme damage on most of the infrastructure in Tigray, including the health institutions. The purpose of this study is, therefore, to assess and report the trend of HIV service provision across the war affected rural health facilities in Tigray.

Methods

The study was conducted in 33 rural health facilities during the active war in Tigray. A facility based retrospective cross-sectional study design was conducted among health facilities from July 03 to August 05, 2021.

Result

A total of 33 health facilities from 25 rural districts were included in the HIV service delivery assessment. A total of 3274 and 3298 HIV patients were seen during pre-war period in September and October 2020, respectively. The number of follow-up patients during the war period in January remained to be only 847(25%) which is significantly reduced with a P value<0.001. A similar trend was observed during the subsequent months until May. The trend of follow-up patients on ART significantly declined from 1940 in September (pre-war) to 331(16.6%) in May (during the war). This study also revealed a 95.5% reduction of laboratory service provision to HIV/AIDS patients during the war in January and with similar trends thereafter (P<0.001).

Conclusion

The war has led to a significant decline of HIV service provision in the rural health facilities and most part of the region during the first eight months of active war in Tigray.
A systematic review and meta-analysis comparing the diagnostic accuracy tests of COVID-19
Authors: Vilca-Alosilla Juan Jeferson , Candia-Puma Mayron Antonio , Coronel-Monje Katiusca , Goyzueta-Mamani Luis Daniel , Galdino Alexsandro Sobreira , Machado-de-Ávila Ricardo Andrez , Giunchetti Rodolfo Cordeiro , Ferraz Coelho Eduardo Antonio , Chávez-Fumagalli Miguel Angel
Published: November 2022

In this work, we report a systematic review and meta-analysis that seeks to analyze the accuracy of diagnostic tests for coronavirus disease 2019 (COVID-19). The objective of this article is to detail the scientific findings based on diagnostic tests of the last years when the pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) occurred. Searches for published studies were carried out in the PubMed database between the years 2020 and 2021 for the diagnosis of COVID-19. Ninety-nine scientific articles that met the criteria were examined and accepted in the meta-analysis, and the diagnostic accuracy was evaluated through specificity and sensitivity. Molecular tests [Reverse transcription polymerase chain reaction (RT-PCR), reverse transcription loop-mediated isothermal amplification (RT-LAMP), and clustered regularly interspaced short palindromic repeats (CRISPR)] showed better performance in terms of sensitivity and specificity when compared to serological tests [Enzyme-linked immunosorbent assay (ELISA), chemiluminescence immunoassay (CLIA), lateral flow immunoassay (LFIA), chemiluminescent microparticle immunoassays (CMIA), and Fluorescence immunoassay (FIA)], which showed higher specificity, mainly for the detection of IgG antibodies; however, they showed sensitivity <90%. In addition, the antiviral neutralization bioassay (ANB) diagnostic test demonstrated high potential for the diagnosis of COVID-19, since it obtained the highest area under the curve restricted to the false-positive rates (AUCFPR) of 0.984. It is settled that the different diagnostic tests have been efficiently adapted for the detection of SARS-CoV-2; however, their performance still needs to be optimized to control future outbreaks of COVID-19, which will also serve to help the control of future infectious agents.
Echocardiography-Based Deep Learning Model to Differentiate Constrictive Pericarditis and Restrictive Cardiomyopathy
Authors: Chao Chieh-Ju , Jeong Jiwoong , Arsanjani Reza , Kim Kihong , Ayoub Chadi , Grogan Martha , Kane Garvan , Banerjee Imon , Oh Jae K
Published: November 2022

Background

Constrictive pericarditis (CP) is an uncommon but reversible cause of diastolic heart failure if appropriately identified and treated. Although echocardiography can detect CP based on characteristic cardiac motion and Doppler findings, its diagnosis remains a challenge for clinicians. Artificial intelligence (AI) may enhance identification of CP. We proposed a deep learning approach based on transthoracic echocardiography (TTE) to differentiate CP from restrictive cardiomyopathy (RCM).

Methods

Patients with a confirmed diagnosis of CP and cardiac amyloidosis (CA, as the representative disease of RCM) at Mayo Clinic Rochester from 1/2003-12/2021 were identified to extract baseline demographics and the apical 4 chamber (A4C) view from TTE studies. The cases were split into a 60:20:20 ratio for training, validation, and held-out test sets of the ResNet50 deep learning model. The model performance (differentiating CP and CA) was evaluated in the test set with the area under the curve (AUC). GradCAM was used for model interpretation.

Results

A total of 381 patients were identified, including 184 (48.3%) CP, and 197 (51.7%) CA cases. The mean age was 68.7±11.4, and 72.8% were male. ResNet50 had a performance with an AUC to differentiate the 2-class classification task (CP vs. CA, AUC 0.97). The GradCAM heatmap showed activation around the ventricular septal area.

Conclusion

With a standard A4C view, our AI model provides a platform for the early and accurate detection of CP, allowing for improved workflow efficiency and prompt referral for more advanced evaluation and intervention of CP.
Structural and Computational Design of a SARS-2 Spike Antigen with Increased Receptor Binding Domain Exposure and Improved Immunogenicity
Authors: Williams James A. , Biancucci Marco , Lessen Laura , Tian Sai , Balsaraf Ankita , Chen Lynn , Chesterman Chelsy , Maruggi Giulietta , Vandepaer Sarah , Huang Ying , Mallett Corey P. , Steff Ann-Muriel , Bottomley Matthew James , Malito Enrico , Wahome Newton , Harshbarger Wayne D.
Published: November 2022

Emerging SARS-CoV-2 variants of concern challenge the efficacy of approved vaccines and emphasize the need for improved antigens. Using an evolutionary-based design approach starting from the widely used engineered Spike antigen, S-2P, we sought to increase antigen production levels and the exposure of highly conserved and neutralization sensitive receptor-binding domain (RBD) epitopes. Thirty-six prototypes were generatedin silico, of which fifteen were produced and tested in biochemical assays. Design S2D14, which contains 20 mutations within the Spike S2 domain, showed a 6-fold increase in expression while preserving similar thermal stability and antigenicity as S-2P. Cryo-EM structures indicate that the dominant populations of S2D14 particles have RBDs in exposed states, and analysis of these structures revealed how modifications within the S2 domain balance trimer stability and RBD accessibility through formation and removal of hydrogen bonds and surface charge alterations. Importantly, vaccination of mice with adjuvanted S2D14 resulted in higher levels of neutralizing antibodies than adjuvanted S-2P against SARS-CoV-2 Wuhan strain and four variants of concern. These results can guide the design of next generation vaccines to combat current, and future coronaviruses and the approaches used may be broadly applicable to streamline the successful design of vaccine antigens.
Claspin-dependent and -independent Chk1 activation by a panel of biological stresses
Authors: Hsiao Hao-Wen , Yang Chi-Chun , Masai Hisao
Published: November 2022

Replication stress has been suggested to be an ultimate trigger of carcinogenesis. Oncogenic signal, such as overexpression of CyclinE, has been shown to induce replication stress. Here, we show that various biological stresses, including heat, oxidative stress, osmotic stress, LPS, hypoxia, and arsenate induce activation of Chk1, a key effector kinase for replication checkpoint. Some of these stresses indeed reduce the fork rate, inhibiting DNA replication. Analyses of Chk1 activation in the cell population with western analyses showed that Chk1 activation by these stresses is largely dependent on Claspin. On the other hand, single cell analyses with Fucci cells indicated that while Chk1 activation during S phase is dependent on Claspin, that in G1 is mostly independent of Claspin. We propose that various biological stresses activate Chk1 either directly by stalling DNA replication fork or by some other mechanism that does not involve replication inhibition. The former pathway predominantly occurs in S phase and depends on Claspin, while the latter pathway, which may occur throughout the cell cycle, is largely independent of Claspin.

Our findings provide evidence for novel links between replication stress checkpoint and other biological stresses and points to the presence of unknown mechanisms of Chk1 activation in mammalian cells.
Spatio-temporal modelling of the effect of selected environmental and land-use factors on species-rich calcareous grasslands: overgrazing and nitrogen deposition
Authors: Damgaard Christian
Published: November 2022

The abundance of sensitive plant species in calcareous grasslands are threatened by agricultural intensification with nutrient addition and increased livestock densities as well as by land abandonment. In order to quantify the effect of selected environmental and land-use factors on the observed variation and changes in the vegetation of calcareous grasslands, large-scale spatial and temporal pin-point plant cover monitoring data are fitted in a structural equation model. The analyzed vegetation data come from 100 Danish sites monitored over an eight year period. The important sources of measurement- and sampling uncertainties have been included using a hierarchical model structure. Furthermore, the measurement- and sampling uncertainties are separated from the process uncertainty, which is important when generating ecological predictions that may feed into local conservation management decisions. There were significant negative effects of grazing and nitrogen deposition on the change in cover of sensitive plant species. Whereas the negative effect of nitrogen deposition on the cover of sensitive species was expected, it was surprising that the model results suggest that the class of sensitive species may be subjected to overgrazing by the grazing regimes that are currently applied at protected Danish calcareous grasslands. The standardized regression coefficients suggest that the effects of both grazing and nitrogen deposition are relatively benign compared to the effects of soil type, soil pH and precipitation. The relatively large effect of precipitation is interesting, since it is predicted that the amount of precipitation and distribution over the season will change due to climate change, and the results suggest that climate change may lead to important species compositional changes in calcareous grasslands. The fitted model may be used to quantify the uncertainties when generating ecological forecasting and local adaptive management plans.
Widespread, depth-dependent cortical microstructure alterations in paediatric focal epilepsy
Authors: Casella Chiara , Vecchiato Katy , Cromb Daniel , Guo Yourong , Winkler Anderson M. , Hughes Emer , Dillon Louise , Green Elaine , Colford Kathleen , Egloff Alexia , Siddiqui Ata , Price Anthony , Grande Lucilio Cordero , Wood Tobias C. , Malik Shaihan , Teixeira Rui Pedro A.G. , Carmichael David W. , O’Muircheartaigh Jonathan
Published: November 2022

Objective

Tissue abnormalities in focal epilepsy may extend beyond the presumed focus. The underlying pathophysiology of these broader changes is unclear, and it is not known whether they result from ongoing disease processes, treatment-related side-effects, or whether they emerge earlier. Few studies have focused on the period of onset for most focal epilepsies, childhood. Fewer still have utilised quantitative MRI, which may provide a more sensitive and interpretable measure of tissue microstructural change. Here, we aimed to determine common spatial modes of changes in cortical architecture in children with heterogeneous drug-resistant focal epilepsy and, secondarily, whether changes were related to disease severity.

Methods

To assess cortical microstructure, quantitative T1 and T2 relaxometry (qT1 and qT2) was measured in 43 children with drug-resistant focal epilepsy [age-range=4-18 years] and 46 typically-developing children [age-range=2-18 years]. We assessed depth-dependent qT1 and qT2 values across the neocortex, as well as their gradient of change across cortical depths. We also determined whether global changes seen in group analyses were driven by focal pathologies in individual patients. Finally, as a proof-of-concept, we trained a classifier using qT1 and qT2 gradient maps from patients with radiologically-defined abnormalities (MRI-positive) and healthy controls, and tested if this could classify patients without reported radiological abnormalities (MRI-negative).

Results

We uncovered depth-dependent qT1 and qT2 increases in widespread cortical areas in patients, likely representing microstructural alterations in myelin or gliosis. Changes did not correlate with disease severity measures, suggesting they may represent antecedent neurobiological alterations. Using a classifier trained with MRI-positive patients and controls, sensitivity was 62% at 100% specificity on held-out MRI-negative patients.

Significance

These findings suggest the presence of a potential imaging endophenotype of focal epilepsy, detectable irrespective of radiologically-identified abnormalities, and potentially evident pre-symptomatically.

Key Points

We assessed cortical microstructure in children with focal epilepsy

Quantitative T1 and T2 relaxometry (qT1 and qT2) was measured in the neocortex

Patients showed extensive qT1/qT2 increases and intracortical organization changes

Alterations may appear during cerebral development, prior to disease onset
Testing heterochrony: Connecting skull shape ontogeny and evolution of feeding adaptations in baleen whales
Authors: Lanzetti Agnese , Miguez Roberto Portela , Fernandez Vincent , Goswami Anjali
Published: November 2022

Ontogeny plays a key role in the evolution of organisms, as changes during the complex processes of development can allow for new traits to arise. Identifying changes in ontogenetic allometry – the relationship between skull shape and size during growth – can reveal the processes underlying major evolutionary transformations. Baleen whales (Mysticeti, Cetacea) underwent major morphological changes in transitioning from their ancestral raptorial feeding mode to the three specialised filter feeding modes observed in extant taxa. Heterochronic processes have been implicated in the evolution of these feeding modes, and their associated specialised cranial morphologies, but their role has never been tested with quantitative data. Here, we quantified skull shapes ontogeny and reconstructed ancestral allometric trajectories using 3D geometric morphometrics and phylogenetic comparative methods on sample representing modern mysticetes diversity. Our results demonstrate that Mysticeti, while having a common developmental trajectory, present distinct cranial shapes from early in their ontogeny corresponding to their different feeding ecologies. Size is the main driver of shape disparity across mysticetes. Disparate heterochronic processes are evident in the evolution of the group: skim feeders present accelerated growth relative to the ancestral nodes, while Balaenopteridae have overall slower growth, or paedomorphosis. The grey whale is the only taxon with a relatively faster rate of growth in this group, which might be connected to its unique benthic feeding strategy. Reconstructed ancestral allometries and related skull shapes indicate that extinct taxa used less specialized filter feeding modes, a finding broadly in line with the available fossil evidence.
Coupled mechanical mapping and interference contrast microscopy reveal viscoelastic and adhesion hallmarks of monocytes differentiation into macrophages
Authors: Eroles Mar , Lopez-Alonso Javier , Ortega Alexandre , Boudier Thomas , Gharzeddine Khaldoun , Lafont Frank , Franz Clemens M. , Millet Arnaud , Valoteau Claire , Rico Felix
Published: November 2022

Monocytes in the blood torrent, when activated by pro-inflammatory signals, adhere to the vascular endothelium and migrate into the tissue for ultimately differentiate into macrophages. Mechanics and adhesion play a crucial role in macrophage functions, such as migration and phagocytosis. However, how monocytes change their adhesion and mechanical properties upon differentiation into macrophages is still not well understood.

In this work, we combined atomic force microscopy (AFM) viscoelastic mapping with interference contrast microscopy (ICM) to simultaneously probe, at the single-cell level, viscoelasticity and adhesion during monocyte differentiation. THP-1 monocytic cells were differentiated into macrophages through phorbol 12-myristate 13-acetate (PMA). Morphological quantification was achieved using holographic tomography imaging and the expression of integrin subunit CD11b was tracked as a marker of differentiation.

Holographic tomography proved to be a quantitative in vivo technique, revealing a dramatic increase in macrophage volume and surface area and two subpopulations, spread and round macrophages. AFM viscoelastic mapping revealed an increased stiffness and more solid-like behavior of differentiated macrophages, especially in the lamellipodia and microvilli regions. Differentiated cells revealed an important increase of the apparent Young’s modulus (E0) and a decrease of cell fluidity (β) on differentiated cells, which correlated with an increase in adhesion area. Macrophages with a spreading phenotype enhanced these changes. Remarkably, when adhesion was eliminated, differentiated macrophages remained stiffer and more solid-like than monocytes, suggesting a permanent reorganization of the cytoskeleton. We speculate that the more solid-like microvilli and lamellipodia might help macrophages to minimize energy dissipation during mechanosensitive activity, such as phagocytosis, making it more efficient. Our proposed approach revealed viscoelastic and adhesion hallmarks of monocyte differentiation that may be important for biological function.
KARRIKIN INSENSITIVE2(KAI2)-dependent signaling pathway controls vegetative reproduction inMarchantia polymorpha
Authors: Komatsu Aino , Kodama Kyoichi , Mizuno Yohei , Fujibayashi Mizuki , Naramoto Satoshi , Kyozuka Junko
Published: November 2022

In vegetative reproduction ofMarchantia polymorpha, propagules, called gemmae, are formed in gemma cups. Despite its significance for survival, control of gemma and gemma cup formation by environmental cues is not well understood. We show here that the number of gemmae formed in a gemma cup is a genetic trait. Gemma formation starts from the central region of the floor of the gemma cup, proceeds to the periphery, and terminates when the appropriate number of gemmae are initiated. The MpKARRIKIN INSENSITIVE2 (MpKAI2)-dependent signaling pathway promotes gemma cup formation and gemma initiation. The number of gemmae in a cup is controlled by modulating the ON/OFF switch of the KAI2-dependent signaling. Termination of the signaling results in the accumulation of MpSMXL, a suppressor protein. In the Mpsmxlmutants, gemma initiation continues, leading to the formation of a highly increased number of gemmae in a cup. Consistent with its function, the MpKAI2-dependent signaling pathway is active in gemma cups where gemmae initiate, as well as in the notch region of the mature gemma and midrib of the ventral side of the thallus. In this work, we also show thatGEMMA CUP-ASSOCIATED MYB1works downstream of this signaling pathway to promote gemma cup formation and gemma initiation. We also found that the availability of potassium affects gemma cup formation independently from the KAI2-dependent signaling pathway inM. polymorpha. We propose that the ancestral function of the KAI2-dependent signaling pathway may be to optimize vegetative reproduction by adapting to the environment.
Individual Decision-Making Underlying the Tragedy of the Commons
Authors: Chawla Megha , Piva Matthew , Ahmed Shamma , Jia Ruonan , Levy Ifat , Chang Steve W. C.
Published: November 2022

Group decision-making is common in everyday life, whether a family is sharing a meal or a corporation is dividing profits. Research in economics on group decision-making has coalesced into a theory known as the tragedy of the commons, which states that resources are inevitably overused when shared by a group. However, even while multiple approaches to mitigating overuse of common resources have been put forward, notable counterexamples to the tragedy of the commons exist such that groups are ultimately able to avoid resource overuse. Development of a computerized paradigm amenable to behavioral modeling and simulation analyses could allow for exploration of whether resources will be overused in a given group of individuals and allow for the rapid testing of behavioral interventions designed to reduce instances of resource overuse. Using a newly developed group decision-making task, we studied how participants made decisions to utilize shared resources for the potential to receive a larger amount of money or conserve resources for a smaller amount of money. Using behavioral modeling, we found that valuation of resource overuse is most impacted only when an exceptionally small amount of resources are remaining. Using computational analyses, we were able to differentiate individual participants by both group earnings and self-reported social attitudes in ways that correlated with their willingness to utilize resources. These results signify the importance of individual differences in group composition regarding the tragedy of the commons, emphasizing the impact of the attitudes and behaviors of individual group members in predicting shared resource use.
Localization of the pioneer factor GAF to subnuclear foci is driven by DNA binding and required to silence satellite repeat expression
Authors: Gaskill Marissa. M. , Soluri Isabella V. , Branks Annemarie E. , Boka Alan P. , Stadler Michael R. , Vietor Katherine , Huang Hao-Yu S. , Gibson Tyler J. , Mir Mustafa , Blythe Shelby A. , Harrison Melissa M.
Published: November 2022

Abstract/Summary

The eukaryotic genome is organized to enable the precise regulation of gene expression required for development. This organization is established during early development when the embryo transitions from a fertilized germ cell to the totipotent zygote. To understand the factors and processes that drive genomic organization, we focused on the pioneer factor GAGA factor (GAF) that is required for early embryonic development inDrosophila.GAF transcriptionally activates the zygotic genome and is localized to subnuclear foci. We show that this non-uniform distribution is driven by binding to the highly abundant GA-satellite repeats. At GA-repeats, GAF is necessary to form heterochromatin and silence transcription. Thus, GAF is required to establish both active and silent regions. We propose that foci formation enables GAF to have opposing transcriptional roles within a single nucleus. Our data support a model in which modulation of the subnuclear concentration of transcription factors acts to organize the nucleus into functionally distinct domains that are essential for the robust regulation of gene expression.
Electrostatic regulation of thecis- andtrans-membrane interactions of synaptotagmin-1
Authors: Ali Moussa Houda Yasmine , Park Yongsoo
Published: November 2022

Synaptotagmin-1 is a vesicular protein and Ca2+sensor for Ca2+-dependent exocytosis. Ca2+induces synaptotagmin-1 binding to its own vesicle membrane, called thecis-interaction, thus preventing thetrans-interaction of synaptotagmin-1 to the plasma membrane. However, the electrostatic regulation of thecis- andtrans-membrane interaction of synaptotagmin-1 was poorly understood in different Ca2+-buffering conditions. Here we provide an assay to monitor thecis- andtrans-membrane interactions of synaptotagmin-1 by using native purified vesicles and the plasma membrane-mimicking liposomes (PM-liposomes). Both ATP and EGTA similarly reverse thecis-membrane interaction of synaptotagmin-1 in free [Ca2+] of 10 to 100 μM. High PIP2concentrations in the PM-liposomes reduce the Hill coefficient of vesicle fusion and synaptotagmin-1 membrane binding; this observation suggests that local PIP2concentrations control the Ca2+-cooperativity of synaptotagmin-1. Our data provide evidence that Ca2+chelators, including EGTA and polyphosphate anions such as ATP, ADP, and AMP, electrostatically reverse thecis-interaction of synaptotagmin-1.
Two-step GISAXS characterization of NiSi2 nanoplates and Ni nanocrystals embedded in a silicon wafer covered with a silica thin film
Authors: da Silva Costa Daniel , Kellermann Guinther , Craievich Aldo F.
Published: November 2022

Here, an experimental grazing-incidence small-angle X-ray scattering (GISAXS) study of the nanostructure of a sample composed of a Si(001) wafer covered by a Ni-doped SiO2 thin film and thermally treated at high temperature is described. Previous studies indicated that this type of composite contains Ni nanocrystals mainly inside the thin film and NiSi2 nanoplates buried in the Si wafer. To achieve accurate determinations of low-resolution structural parameters of the nanoparticles derived from the experimental results (shape, volume and size), two GISAXS patterns were recorded. The first pattern was produced by the Si wafer covered by a nanoporous Ni-doped SiO2 thin film and the second pattern was recorded after removal of the SiO2 thin film by chemical etching. By using the procedure of best fitting of a modeled isotropic GISAXS intensity to a set of 1D GISAXS patterns recorded before thin-film removal, the average radius and radius dispersion of a size polydisperse set of spherical Ni nanocrystals were determined. The GISAXS pattern recorded after removal of the SiO2 thin film was almost completely due to the scattering intensity produced by oriented NiSi2 nanoplates located inside the Si wafer. By fitting a theoretical function for the X-ray scattering intensity produced by oriented nanoplates to a set of experimental 1D GISAXS patterns, the maximum diameters and average thickness of the hexagonal NiSi2 nanoplates were determined. The GISAXS intensity pattern produced by the sample after thin-film removal is essentially anisotropic (with only a weak isotropic contribution from Ni nanocrystals), thus allowing for precise quantitative determinations of the relevant sizes of the NiSi2 nanoplates.
Crystallization, structural study and analysis of intermolecular interactions of a 2-aminobenzoxazole–fumaric acid molecular salt
Authors: Razzoqova Surayyo , Torambetov Batirbay , Amanova Matluba , Kadirova Shakhnoza , Ibragimov Aziz , Ashurov Jamshid
Published: November 2022

The new organic salt, 2-aminobenzoxazol-3-ium 3-carboxyprop-2-enoate, C7H7N2O+·C4H3O4
−, of the two bioactive compounds 2-aminobenzoxazole and fumaric acid, crystallizes in the orthorhombic space group Pbca using classical evaporation of their solution in water. The usual topological analysis revealed four classical (N—H...O and O—H...O) and two non-classical (C—H...O) hydrogen bonds in the structure. Stacking was found as well for a pair of 2-aminobenzoxazolium cations. A Hirshfeld surface analysis including the two-dimensional fingerprint plots was performed to define the residual π–π interactions and to quantify the influences of different types of interactions by means of topological analysis. Analysis of the pairwise interaction energies was used to prove the formation of the corrugated paired layers of cation–anion dimers parallel to the plane (001) as a basic structural motif in the topological, as well as in the energetic structure of the crystal. It showed that the layers are connected by the hydrogen bonds inside and by stacking and π–π interactions and general dispersion between them.
Being a product consumer during the COVID-19 pandemic: profile of the Polish consumer in the organic dairy market
Authors: Wojciechowska-Solis Julia , Śmiglak-Krajewska Magdalena
Published: November 2022

Purpose

The purpose of this paper was to determine the profile of dairy product consumers in the organic market.

Design/methodology/approach

The study was based on a survey questionnaire developed by the author and administered to a total of 1,108 respondents. The statistical analysis (including descriptive statistics, the analysis of the discriminative function and the Chi2 test was performed with the use of Statistica 13.1 PL. The respondents’ gender was the factor behind the differences in how they behaved.

Findings

The consumers indicated the channels they rely upon to find information on organic dairy products; in addition to trusting the opinions of their family members and experts, they also use web platforms. Further, they specified their preferred locations for buying favorite products during the pandemic: specialized organic food shops, large distribution chains and online stores.

Practical implications

These outcomes will help in identifying target consumer segments and information channels for specific information and advertising messages. They also form an important resource for developing some potential strategies which the supply chain stakeholders could implement to promote organic consumption of dairy products.

Originality/value

This study identifies consumers’ preferred dairy products; motives for purchasing organic dairy products; barriers that consumers believe exist in the market; sources of knowledge about products purchased by consumers; and consumers’ preferred channels for purchasing organic dairy products. To the best of the author’s knowledge, this is the first study of dairy product consumers in the organic market in Poland.
From personal resources to proactive work strategies and performance: testing the antecedents and outcomes of strengths use in a three-wave study
Authors: Pap Zselyke , Tisu Luca , Vîrgă Delia
Published: November 2022

Purpose

Based on the Job Demands-Resources (JD-R) theory, this study aims to identify person-contingent antecedents and consequences of proactive strength-oriented behaviors at work. Thus, the authors propose and test a model in which psychological capital (PsyCap), as a personal resource, represents a precursor of strengths use, which in turn is a facilitator of employees' self-rated performance.

Design/methodology/approach

The authors tested the hypothesized mediation process through a cross-lagged study with three waves, using data collected from a sample of Romanian employees. The authors analyzed the data through structural equation modeling.

Findings

The results provided support for our model. The data showed significant, positive cross-lagged relationships between PsyCap, strengths use and performance across waves. Also, the authors identified a significant and positive indirect effect between PsyCap at T1 and performance at T3 through increased strengths use at T2.

Originality/value

This research brings new evidence for strengths use's placement as a proactive individual strategy within the JD-R theory. Practical implications are related to career self-management and work from home.
Race talk tensions: practicing racial literacy in a fourth-grade classroom
Authors: Daly Annie
Published: November 2022

Purpose

There is a pressing need to teach students how to talk critically about race to understand the personal and political implications of racism in the contemporary US society. Classroom race talk, however, often includes moments of discomfort or confusion as teachers and students navigate new norms for making sense of race and racism. The purpose of this paper is to examine how one white teacher and her multiracial class of fourth-grade students navigated race talk tensions while reading and discussing shared texts.

Design/methodology/approach

Data for this paper were collected as part of a larger, year-long qualitative study on antiracist pedagogy. In this paper, the author analyzes video data of classroom race talk recorded during whole-class and small-group literacy lessons. Using inductive coding and reconstructive critical discourse analysis, the author examines how the teacher and students co-constructed meaning during tense or confusing conversational moments.

Findings

The findings demonstrate that the teacher and students jointly mediated tensions by using the practices of racial literacy, which included learning about the history of racial inequality in the USA, considering racism as structural and systemic rather than individual and asking and answering questions for continued inquiry and critical self-reflection. While previous research studies have characterized race talk tensions as problems or obstacles to student learning, the findings from this study suggest that tensions can be generative to developing and enacting racial literacy.

Originality/value

In the current political climate, alarmist rhetoric issued by conservative politicians and media outlets has discredited race talk as harmful or damaging to children. This study offers a positive reframing of tensions, which may provide teachers encouragement to pursue literacy instruction that equips students with knowledge and skills to better understand and confront racism.
Inspiring guests’ imagination of “home away from home” to choose Airbnb through brand storytelling
Authors: Zheng Chunhui , Zhang Jia
Published: November 2022

Purpose

Airbnb attempts to stimulate consumer imagination and expectations of home through storytelling before their stay. The purpose of this study is to gain a holistic understanding of the psychological mechanisms by which brand storytelling can evoke consumer imagination of home away from home and their choice of peer-to-peer (P2P) accommodations.

Design/methodology/approach

By collecting 864 valid questionnaires through two rounds of surveys with Chinese consumers, this study examined the structural relations between narrative elements in the brand story (home characteristics, social interactions in advertising, advertising features), brand perception, self-image congruence and consumption intentions.

Findings

The results demonstrate that home characteristics, social interactions in advertising, and advertising features positively influence people’s brand perceptions, self-image congruence and consumption intentions through mental imagery processing.

Practical implications

This study offers helpful implications on how to create a home feeling in P2P accommodations and provides recommendations to promote the connection between consumers and the brand for P2P accommodation providers and hoteliers.

Originality/value

This study reveals the underlying mechanism of how various narrative elements in brand stories inspire the imagination and feeling of home in consumers during the prestay phase. By analysing the impact of specific trust systems and emotional needs on the construction of a feeling of home, this study is an important complement to existing studies on the study of home in P2P accommodation.