bluuebunny/crossref_metadata_2025 huggingface dataset:
Coping under stress: Prefrontal control predicts stress burden during the COVID-19 crisis
Authors: Monninger Maximilian , Pollok Tania M. , Aggensteiner Pascal-M. , Kaiser Anna , Reinhard Iris , Hermann Andrea , Meyer-Lindenberg Andreas , Brandeis Daniel , Banaschewski Tobias , Holz Nathalie E.
Published: July 2021

Background

The coronavirus (COVID-19) pandemic has confronted millions of people around the world with an unprecedented stressor, affecting physical and mental health. Accumulating evidence suggests that emotional and cognitive self-regulation is particularly needed to effectively cope with stress. Therefore, we investigated the predictive value of affective and inhibitory prefrontal control for stress burden during the COVID-19 crisis.

Method

Physical and mental health burden were assessed using an online survey, which was administered to 104 participants of an ongoing German at-risk birth cohort during the first wave in April 2020. Two follow-ups were carried out during the pandemic, one capturing the relaxation during summer and the other the beginning of the second wave of the crisis. Prefrontal activity during emotion regulation and inhibitory control were assessed prior to the COVID-19 crisis.

Results

Increased inferior frontal gyrus activity during emotion regulation predicted lower stress burden at the beginning of the first and the second wave of the crisis. In contrast, inferior and medial frontal gyrus activity during inhibitory control predicted effective coping only during the summer, when infection rates decreased but stress burden remained unchanged. These findings remained significant when controlling for sociodemographic and clinical confounders such as stressful life events prior to the crisis or current psychopathology.

Conclusions

We demonstrate that differential stress-buffering effects are predicted by the neural underpinnings of emotion regulation and cognitive regulation at different stages during the pandemic. These findings may inform future prevention strategies to foster stress coping in unforeseen situations.

Highlights

Health threatening stressors, such as the COVID-19 pandemic, significantly worsen well-being.

Results reveal high levels of stress during the course of the pandemic with an increase of stress burden towards the second wave.

Self-regulation is an important coping strategy to restore allostasis.

Higher prefrontal activity during emotion regulation predicted less stress during the peaks of infection rates in the first and second wave

Higher prefrontal inhibitory control predicted less stress burden between both waves when infection rates were low.

Our findings highlight the importance of prefrontal regulation as effective coping mechanisms in the face of unprecedented stressors.
Validation of Data Acquisition and Phase Estimation for Quantitative Susceptibility Mapping with a Rotating-Tube Phantom
Authors: Keenan Kathryn E. , Berman Ben P. , Carnicka Slavka , Russek Stephen E. , Wang Wen-Tung , Butman John A. , Pham Dzung L. , Dagher Joseph
Published: July 2021

Purpose

Quantitative Susceptibility Mapping (QSM) is an MRI tool with the potential to reveal pathological changes from magnetic susceptibility measurements. Before phase data can be used to recover susceptibility (Δχ), the QSM process begins with two steps: data acquisition and phase estimation. We assess the performance of these steps, when applied without user intervention, on several variations of a phantom imaging task.

Approach

We used a rotating-tube phantom with five tubes ranging from Δχ=0.05 ppm to Δχ=0.336 ppm. MRI data was acquired at nine angles of rotation for four different pulse sequences. The images were processed by 10 phase estimation algorithms including Laplacian, region-growing, branch-cut, temporal unwrapping and maximum-likelihood methods. We analyzed errors between measured and expected phase using the probability mass function and Cumulative Distribution Function.

Results

Repeatable acquisition and estimation methods were identified based on the probability of relative phase errors. For single-echo GRE and segmented EPI sequences, a region-growing method was most reliable with Pr(relative error<0.1)=0.95 and 0.90 respectively. For multi-echo sequences, a Maximum-Likelihood method was most reliable with Pr(relative error<0.1)=0.97. The most repeatable multi-echo methods outperformed the most repeatable single-echo methods.

Conclusions

We found a wide range of repeatability and reproducibility for off-the-shelf MRI acquisition and phase estimation approaches. The error was dominated in many cases by spatially discontinuous phase unwrapping errors. Any post-processing applied on erroneous phase estimates, such as QSM’s background field removal and dipole inversion, would suffer from error propagation. Our paradigm identifies methods that yield consistent and accurate phase estimates that would ultimately yield consistent and accurate Δχ estimates.
A survey of optimal strategy for signature-based drug repositioning and an application to liver cancer
Authors: Yang Chen , Chen Mengnuo , Wang Siying , Qian Ruolan , Huang Xiaowen , Wang Jun , Liu Zhicheng , Qin Wenxin , Wang Cun , Hang Hualian , Wang Hui
Published: July 2021

Pharmacologic perturbation projects, such as Connectivity Map (CMap) and Library of Integrated Network-based Cellular Signatures (LINCS), have produced many perturbed expression data, providing enormous opportunities for computational therapeutic discovery. However, currently there is no consensus on which methodologies and parameters are the most optimal to conduct such analysis. Aiming to fill this gap, we developed new benchmarking standards for quantitatively estimating drug retrieval performance. Investigations of potential factors influencing drug retrieval were conducted based on these standards. As a result, we determined an optimal strategy for LINCS data-based therapeutic discovery. With this approach, we further identified new therapeutics for liver cancer of which the current treatment modalities remain imperfect. Both computational and experimental results demonstrated homoharringtonine (HHT) could be a promising anti-liver cancer agent. In summary, our findings will not only impact the future applications of LINCS data but also offer new opportunities for therapeutic intervention for liver cancer.
Small Vessel Diseases: 3D Characteristics of the Vasculature and White Matter
Authors: Saito Rie , Tainaka Kazuki , Nozaki Hiroaki , Uemura Masahiro , Toyoshima Yasuko , Suzuki Masahiro , Tanaka Masaharu , Hasegawa Arika , Abe Takashi , Sato Aki , Hashidate Hideki , Igarashi Shuichi , Koike Ryoko , Ueda Akihiko , Ueda Mitsuharu , Ando Yukio , Akazawa Kohei , Onodera Osamu , Kakita Akiyoshi
Published: July 2021

Cerebral small vessel disease (SVD) is associated with white matter hyperintensities (WMHs), thereby contributing to vascular dementia and movement disorder. However, the pathomechanisms responsible for WMH-related small vessel degeneration remain poorly understood due to the technical limitations of current methods. The aim of this study was to clarify the 2- and 3-dimensional (2D and 3D) pathological features of small vessels and white matter (WM) in the brains of patients with cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL), HTRA1-autosomal dominant disease (HTRA1-AD) and sporadic SVD (sSVD). From a cohort of 86 consecutive autopsied patients with SVDs, we retrieved those with genetically confirmed CADASIL and HTRA1-AD (three and three, respectively), and four with sSVD. We quantitatively evaluated WM and vascular changes in the frontal portion of the centrum semiovale and temporal lobe using conventional 2D and chemically cleared 3D analytical methods with light-sheet fluorescence microscopy. Quantitatively, the WM pathology, including the density of myelin, axons and gliosis, was most severe in CADASIL, but unexpectedly sSVD was second in order of severity, followed by HTRA1-AD. The density of clasmatodendrocytes, known to be irreversibly injured astrocytes, was considerably highest in HTRA1-AD. The vascular pathology, including arteriole and capillary sclerosis and the extent of the perivascular space, was most severe in CADASIL, whereas the density of smooth muscle actin (SMA) positivity was most decreased in HTRA1-AD. 3D immunohistochemistry for SMA demonstrated two distinct patterns of SMA loss within the vessels: (1) CADASIL and sSVD: diffuse loss, being prominent in small branches, (2) HTRA1-AD: selective loss in main branches. Overall, the extent of WM and vascular degeneration is most severe in CADASIL, whereas SMA loss is most evident in HTRA1-AD. These differences in the size and distribution of affected vessels may be related to the heterogeneous WM pathology and underlying pathomechanisms of SVD.
Antimicrobial activity of a repurposed harmine-derived compound on extensively drug-resistantAcinetobacter baumanniiclinical isolates
Authors: Breine Anke , Van Gysel Mégane , Elsocht Mathias , Whiteway Clémence , Philippe Chantal , Quinet Théo , Valcek Adam , Wouters Johan , Ballet Steven , Van der Henst Charles
Published: July 2021

Synopsis

Objectives

The spread of antibiotic resistant bacteria is an important threat for human healthcare.Acinetobacter baumanniibacteria impose one of the major issues, as multidrug- to pandrug-resistant strains have been found, rendering some infections untreatable. In addition,A. baumanniiis a champion in surviving in harsh environments, being capable of resisting to disinfectants and to persist prolonged periods of desiccation. Due to the high degree of variability found inA. baumanniiisolates, the search for new antibacterials is challenging. Here, we screened a compound library to identify compounds active against recent isolates ofA. baumanniibacteria.

Methods

A repurposing drug screen was undertaken to identifyA. baumanniigrowth inhibitors. One hit was further characterized by determining its IC50and testing its activity on 43 recent clinicalA. baumanniiisolates, amongst which 40 are extensively drug- and carbapenem-resistant strains.

Results

The repurposing screen led to the identification of a harmine-derived compound, called HDC1, which proved to have bactericidal activity on the multidrug-resistant AB5075-VUB reference strain with an IC50of 48.23 µM. In addition, HDC1 impairs growth of all 43 recent clinicalA. baumanniiisolates.

Conclusions

We identified a compound with inhibitory activity on all tested, extensively drug-resistant clinicalA. baumanniiisolates.
Deciphering the tumor-specific immunopeptidome in vivo with genetically engineered mouse models
Authors: Jaeger Alex M. , Stopfer Lauren E. , Sanders Emma A. , Sandel Demi A. , Freed-Pastor William A. , Rideout William M. , Naranjo Santiago , Fessenden Tim , Winter Peter S. , Kohn Ryan E. , Schenkel Jason , Shanahan Sean-Luc , Shalek Alex K. , Spranger Stefani , White Forest M. , Jacks Tyler
Published: July 2021

Effective immunosurveillance of cancer requires the presentation of peptide antigens on major histocompatibility complex Class I (MHC-I). Recent developments in proteomics have improved the identification of peptides that are naturally presented by MHC-I, collectively known as the “immunopeptidome”. Current approaches to profile tumor immunopeptidomes have been limited to in vitro investigation, which fails to capture the in vivo repertoire of MHC-I peptides, or bulk tumor lysates, which are obscured by the lack of tumor-specific MHC-I isolation. To overcome these limitations, we report here the engineering of a Cre recombinase-inducible affinity tag into the endogenous mouse MHC-I gene and targeting of this allele to the KrasLSL-G12D/+; p53fl/fl (KP) mouse model (KP; KbStrep). This novel approach has allowed us to isolate tumor-specific MHC-I peptides from autochthonous pancreatic ductal adenocarcinoma (PDAC) and lung adenocarcinoma (LUAD) in vivo. With this powerful analytical tool, we were able to profile the evolution of the LUAD immunopeptidome through tumor progression and show that in vivo MHC-I presentation is shaped by post-translational mechanisms. We also uncovered novel, putative LUAD tumor associated antigens (TAAs). Many peptides that were recurrently presented in vivo exhibited very low expression of the cognate mRNA, provoking reconsideration of antigen prediction pipelines that triage peptides according to transcript abundance. Beyond cancer, the KbStrep allele is compatible with a broad range of Cre-driver lines to explore antigen presentation in vivo in the pursuit of understanding basic immunology, infectious disease, and autoimmunity.
Sleep deprivation reduces the density of individual spine subtypes in a branch-specific fashion in CA1 neurons
Authors: Bolsius Youri G , Meerlo Peter , Kas Martien J , Abel Ted , Havekes Robbert
Published: July 2021

Sleep deprivation has a negative impact on hippocampus-dependent memory, which are thought to depend on cellular plasticity. We previously found that five hours of sleep deprivation robustly decreases dendritic spine density in the CA1 area of the hippocampus in adult male mice. However, recent work by others suggests that sleep deprivation increases the density of certain spine types on specific dendritic branches. Based on these recent findings and our previous work, we conducted a more in-depth analysis of different spine types on branches 1, 2 and 5 of both apical and basal dendrites to assess whether five hours of sleep deprivation may have previously unrecognized spine-type and branch-specific effects. This analysis shows no spine-type specific changes on branch 1 and 2 of apical dendrites after sleep deprivation. In contrast, sleep deprivation decreases the number of mushroom and branched spines on branch 5. Likewise, sleep deprivation reduces thin, mushroom, and filopodia spine density on branch 5 of the basal dendrites, without affecting spines on branch 1 and 2. Our findings indicate that sleep deprivation leads to local branch-specific reduction in the density of individual spine types, and that local effects might not reflect the overall impact of sleep deprivation on CA1 structural plasticity. Moreover, our analysis underscores that focusing on a subset of dendritic branches may lead to potential misinterpretation of the overall impact of in this case sleep deprivation on structural plasticity.
The MpsB protein contributes to both the toxicity and immune evasion capacity of Staphylococcus aureus
Authors: Douglas Edward J.A. , Duggan Seána , Brignoli Tarcisio , Massey Ruth C.
Published: July 2021

Understanding the role specific bacterial factors play in the development of severe disease in humans is critical if new approaches to tackle such infections are to be developed. In this study we focus on genes we have found to be associated with patient outcome following bacteraemia caused by the major human pathogen Staphylococcus aureus. By examining the contribution these genes make to the ability of the bacteria to survive exposure to the antibacterial factors found in serum, we identify three novel serum resistance associated genes, mdeA, mpsB and yycH. Detailed analysis of an MpsB mutant supports its previous association with the slow growing SCV phenotype of S. aureus, and we demonstrate that the effect this mutation has on membrane potential prevents the activation of the Agr quorum sensing system, and as a consequence the mutant bacteria do not produce cytolytic toxins. Given the importance of both toxin production and immune evasion to the ability of S. aureus to cause disease, we believe these findings explain the role of the mpsB gene as a mortality-associate locus during human disease.
A Comprehensive Overview of the Physical Health of the Adolescent Brain Cognitive Development Study (ABCD) Cohort at Baseline
Authors: Palmer Clare E. , Sheth Chandni , Marshall Andrew T. , Adise Shana , Baker Fiona C. , Chang Linda , Clark Duncan B. , Dagher Rada K. , Dowling Gayathri J. , Gonzalez Marybel R. , Haist Frank , Herting Megan M. , Huber Rebekah S. , Jernigan Terry L. , LeBlanc Kimberly , Lee Karen , Lisdahl Krista M. , Neigh Gretchen , Patterson Megan W. , Renshaw Perry , Rhee Kyung E. , Tapert Susan , Thompson Wesley K. , Uban Kristina , Sowell Elizabeth R. , Yurgelun-Todd Deborah
Published: July 2021

Physical health in childhood is crucial for neurobiological as well as overall development, and can shape long-term outcomes into adulthood. The landmark, longitudinal Adolescent Brain Cognitive Development StudySM (ABCD study®), was designed to investigate brain development and health in almost 12,000 youth who were recruited when they were 9-10 years old and will be followed through adolescence and early adulthood. The overall goal of this paper is to provide descriptive analyses of physical health measures in the ABCD study at baseline, including but not limited to sleep, physical activity and sports involvement, and body mass index, and how these measures vary across demographic groups. This paper outlines how the physical health of the ABCD sample corresponds with that of the US population and highlights important avenues for health disparity research. This manuscript will provide important information for ABCD users and help guide analyses investigating physical health as it pertains to adolescent and young adult development.
Functional profiling of long intergenic non-coding RNAs in fission yeast
Authors: Rodriguez-Lopez Maria , Anver Shajahan , Cotobal Cristina , Kamrad Stephan , Malecki Michal , Correia-Melo Clara , Hoti Mimoza , Townsend StJohn , Marguerat Samuel Blaise , Pong Sheng , Wu Mary , Montemayor Luis , Howell Michael , Ralser Markus , Bahler Jurg
Published: July 2021

Eukaryotic genomes express numerous long intergenic non-coding RNAs (lincRNAs) that do not overlap any coding genes. Some lincRNAs function in various aspects of gene regulation, but it is not clear in general to what extent lincRNAs contribute to the information flow from genotype to phenotype. To explore this question, we systematically analyzed cellular roles of lincRNAs in Schizosaccharomyces pombe. Using seamless CRISPR/Cas9-based genome editing, we deleted 141 lincRNA genes to broadly phenotype these mutants, together with 238 diverse coding-gene mutants for functional context. We applied high-throughput colony-based assays to determine mutant growth and viability in benign conditions and in response to 145 different nutrient, drug and stress conditions. These analyses uncovered phenotypes for 47.5% of the lincRNAs and 96% of the protein-coding genes. For 110 lincRNA mutants, we also performed high-throughput microscopy and flow-cytometry assays, linking 37% of these lincRNAs with cell-size and/or cell-cycle control. With all assays combined, we detected phenotypes for 84 (59.6%) of all lincRNA deletion mutants tested. For complementary functional inference, we analyzed colony growth of strains ectopically overexpressing 113 lincRNA genes under 47 different conditions. Of these overexpression strains, 102 (90.3%) showed altered growth under certain conditions. Clustering analyses provided further functional clues and relationships for some of the lincRNAs. These rich phenomics datasets associate lincRNA mutants with hundreds of phenotypes, indicating that most of the lincRNAs analyzed exert cellular functions in specific environmental or physiological contexts. This study provides groundwork to further dissect the roles of these lincRNAs in the relevant conditions.
Long Term Study of Motivational and Cognitive Effects of Low-intensity Focused Ultrasound Neuromodulation in the Dorsal Striatum of Nonhuman Primates
Authors: Munoz F , Meaney A , Gross A , Liu K , Pouliopoulos AN , Liu D , Konofagou EE , Ferrera VP
Published: July 2021

Noninvasive brain stimulation using focused ultrasound (FUS) has many potential applications as a research and clinical tool, including incorporation into neural prosthetics for cognitive rehabilitation. To develop this technology, it is necessary to evaluate the safety and efficacy of FUS neuromodulation for specific brain targets and cognitive functions. It is also important to test whether repeated long-term application of FUS to deep brain targets improves or degrades behavioral and cognitive function. To this end, we investigated the effects of FUS in the dorsal striatum of nonhuman primates (NHP) performing a visual-motor decision-making task for small or large rewards. Over the course of 2 years, we performed 129 and 147 FUS applications, respectively, in two NHP. FUS (0.5 MHz @ 0.2 – 0.8 MPa) was applied to the putamen and caudate in both hemispheres to evaluate the effects on movement accuracy, motivation, decision accuracy, and response time. Sonicating the caudate or the putamen unilaterally resulted in modest but statistically significant improvements in motivation and decision accuracy, but at the cost of slower reaction times. The effects were dose (i.e., FUS pressure) and reward dependent. There was no effect on reaching accuracy, nor was there long-term behavioral impairment or neurological trauma evident on T1-weighted, T2-weighted, or susceptibility-weighted MRI scans. Sonication also resulted in significant changes in resting state functional connectivity between the caudate and multiple cortical regions. The results indicate that applying FUS to the dorsal striatum can positively impact the motivational and cognitive aspects of decision making. The capability of FUS to improve motivation and cognition in NHPs points to its therapeutic potential in treating a wide variety of human neural diseases, and warrants further development as a novel technique for non-invasive deep brain stimulation.
Classic genome-wide association methods are unlikely to identify causal variants in strongly clonal microbial populations
Authors: Chen Peter E. , Shapiro B. Jesse
Published: July 2021

Since the advent of genome-wide association studies (GWAS) in human genomes, an increasing sophistication of methods has been developed for more robust association detection. Currently, the backbone of human GWAS approaches is allele-counting-based methods where the signal of association is derived from alleles that are identical-by-state. Borrowing this approach from human GWAS, allele-counting-based methods have been popularized in microbial GWAS, notably the generalized linear model using either dimension reduction for fixed covariates and/or a genetic relationship matrix as a random effect in a mixed model to control for population stratification. In this work, we show how the effects of linkage disequilibrium (LD) can potentially obscure true-positive genotype-phenotype associations (i.e., genetic variants causally associated with the phenotype of interest) and also lead to unacceptably high rates of false-positive associations when applying these classical approaches to GWAS in weakly recombining microbial genomes. We developed a GWAS method called POUTINE (https://github.com/Peter-Two-Point-O/POUTINE), which relies on homoplastic mutation to both clarify the source of putative causal variants and reduce likely false-positive associations compared to traditional allele counting methods. Using datasets of M. tuberculosis genomes and antibiotic-resistance phenotypes, we show that LD can in fact render all association signals from allele counting methods to be fully indistinguishable from hundreds to thousands of sites scattered across an entire genome. These classic GWAS methods thus fail to pinpoint likely causal genotype-phenotype associations and separate them from background noise, even after applying methods to correct for population structure. We therefore urge caution when utilizing classical approaches, particularly in populations that are strongly clonal.
Antimicrobial activity of flavonoids glycosides and pyrrolizidine alkaloids from propolis of Scaptotrigona aff. postica
Authors: Cantero TM , da Silva Junior PI , Negri Giuseppina , Nascimento RM , Mendonça RZ
Published: July 2021

Stingless bees belonging to the Meliponinae subfamily, are known as meliponines. Scaptotrigona affinis postica Latreille, 1807 from northeast of Brazil is popularly known as ‘tubi’ in Maranhão State. Scaptotrigona, which is widely distributed in neotropical regions, includes species that build their hives in pre-existing cavities. Flavones di-C-glycosides, and the pyrrolizidine alkaloid 7-(3-methoxy-2-methylbutyryl)-9-echimidinylretronecine were reported previously in propolis from S. postica. Fractions 40 AEP and 40 MEP from ethanolic extract were analyzed by LC-MS. The chromatographic profile of fractions 40 AEP and 40 MEP revealed the presence of many pyrrolizidine alkaloids, among them, lithosenine (14), lithosenine arabinoside (19), 7-angeloyl-9-(2,3- dihydroxybutyryl) retronecine (1), 7-(2-methylbutyryl) retronecine (3), 9-sarracinoylretronecine (13) and viridinatine (8),besides the flavonoids schaftoside (15), aromadendrin-7-O-methyl ether (12), 7-methoxy-5,6,3’,4’,5’,6’-hexahydroxy-flavone-3-O-glucuronide (11), mangiferin (10) and 3-O-methyl mangiferin (17). Fractions 40 AEP and 40 MEP showed antimicrobial activity against Gram negative bacteria, including Escherichia coli D31-streptomycin resistant. Cell viability was expressed in terms of the relative absorbance of treated and untreated cells (control). There was no statistical difference between treated and untreated cells.
A novel α/β T-cell subpopulation defined by recognition of EPCR
Authors: Erausquin Elena , Morán-Garrido María , Saiz Jorge , Barbas Coral , Dichiara-Rodríguez Gilda , Ramírez Natalia , López-Sagaseta Jacinto
Published: July 2021

T-cell self-recognition of antigen presenting molecules is led by antigen-dependent or independent mechanisms. The endothelial protein C receptor (EPCR) shares remarkable similarity with CD1d, including a lipid binding cavity. We have identified EPCR-specific α/β T-cells in the peripheral blood of healthy donors. The average frequency in the CD3+ leukocyte pool is comparable to other autoreactive T-cell subsets that specifically bind MHC-like receptors. Alteration of the EPCR lipid cargo, revealed by X-ray diffraction studies, points to a prevalent, yet not exclusive, lipid-independent self-recognition. In addition, we solve the EPCR lipidome, and detect species not yet described as EPCR ligands. These studies report, for the first time, novel recognition by circulating α/β T-cells and provide grounds for EPCR and lipid mediated T-cell restriction.
Acquired resistance to PD-L1 inhibition is associated with an enhanced type I IFN-stimulated secretory program in tumor cells
Authors: Shi Yuhao , Dolan Melissa , Mastri Michalis , Mckenery Amber , Hill James W. , Dommer Adam , Benzekry Sebastien , Long Mark , Abrams Scott , Puzanov Igor , Ebos John M.L.
Published: July 2021

Background

Interferon (IFN) pathway activation in tumors can have dual, sometimes opposing, influences on immune responses. Therapeutic inhibition of programmed cell death ligand (PD-L1) – a treatment that reverses PD-1-mediated suppression of tumor-killing T-cells - is linked to alterations in IFN signaling; however, less is known about the role of IFNs after treatment resistance. Since IFN-regulated intracellular signaling can control extracellular secretory programs in tumors to modulate immunity, we examined the consequences of PD-L1 blockade on IFN-related secretory changes in preclinical models of acquired resistance.

Methods

Therapy-resistant cell variants were derived from orthotopically grown mouse tumors initially sensitive or insensitive to PD-L1 antibody treatment. Cells representing acquired resistance were analyzed for changes to IFN-regulated secretory machinery that could impact tumor progression.

Results

We identified a PD-L1 treatment-induced secretome (PTIS) that was enriched for several IFN-stimulated genes (ISGs) and significantly enhanced when stimulated by type I IFNs (IFNα or IFNβ). Secretory changes were specific to treatment-sensitive tumor models and found to suppress activation of T cellsex vivowhile diminishing tumor cell cytotoxicity, revealing a tumor-intrinsic treatment adaptation with potentially broad tumor-extrinsic effects. When reimplantedin vivo, resistant tumor growth was slowed by the blockade of individual secreted PTIS components (such as IL6) and stopped altogether by a more generalized disruption of type I IFN signaling.In vitro, genetic or therapeutic methods to target PD-L1 could only partially recapitulate the IFN-enhanced PTIS phenotype, showing thatin vivo-based systems with intact tumor:immune cell interactions are needed to faithfully mimic acquired resistance as it occurs in patients.

Conclusions

These results suggest that prolongedin vivoPD-L1 inhibition can ‘rewire’ type I IFN signaling to drive secretory programs that help protect tumors from immune cell attack and represent a targetable vulnerability to overcome acquired resistance in patients.
TGFβ2 regulates human trabecular meshwork cell contractility via ERK and ROCK pathways with distinct signaling crosstalk dependent on the culture substrate
Authors: Li Haiyan , Henty-Ridilla Jessica L. , Ganapathy Preethi S. , Herberg Samuel
Published: July 2021

Transforming growth factor beta 2 (TGFβ2) is a major contributor to the pathologic changes occurring in human trabecular meshwork (HTM) cells in primary open-angle glaucoma. Receptor binding of TGFβ2 activates non-canonical extracellular-signal-regulated kinase (ERK) and Rho-associated kinase (ROCK) signaling pathways, both broadly affecting HTM cell behavior. However, exactly how these signaling pathways converge to regulate pathologic HTM cell contractility associated with glaucomatous dysfunction is unclear. Here, we investigated the molecular mechanism underlying TGFβ2-induced pathologic HTM cell contractility, and the crosstalk between ERK and ROCK signaling pathways. We compared soft biomimetic hydrogels composed of collagen type I, elastin-like polypeptide, and hyaluronic acid with conventional stiff glass coverslips. Results show that HTM cell morphology and filamentous (F)-actin organization was affected by the underlying culture substrate: TGFβ2 increased HTM cell contractility via ERK and ROCK signaling pathways by differentially regulating F-actin, α-smooth muscle actin, fibronectin, and phospho-myosin light chain in cells grown on hydrogels compared to glass. Importantly, we showed that ERK inhibition further increased TGFβ2-induced phospho-myosin light chain levels in HTM cells on hydrogels, but not on glass, which translated into hypercontractility of three-dimensional (3D) HTM cell-laden hydrogels. ROCK inhibition had precisely the opposite effects and potently relaxed the TGFβ2-induced hydrogels. This suggests that ERK signaling negatively regulates ROCK-mediated HTM cell contractility, and that impairment of this crosstalk balance contributes to the pathologic contraction associated with the glaucomatous stressor TGFβ2. These findings emphasize the critical importance of using 3D tissue-mimetic extracellular matrix substrates for investigating HTM cell physiology and glaucomatous pathophysiologyin vitro.
The effects of introgression across thousands of quantitative traits revealed by gene expression in wild tomatoes
Authors: Hibbins Mark S. , Hahn Matthew W.
Published: July 2021

It is now understood that introgression can serve as powerful evolutionary force, providing genetic variation that can shape the course of trait evolution. Introgression also induces a shared evolutionary history that is not captured by the species phylogeny, potentially complicating evolutionary analyses that use a species tree. Such analyses are often carried out on gene expression data across species, where the measurement of thousands of trait values allows for powerful inferences while controlling for shared phylogeny. Here, we present a Brownian motion model for quantitative trait evolution under the multispecies network coalescent framework, demonstrating that introgression can generate apparently convergent patterns of evolution when averaged across thousands of quantitative traits. We test our theoretical predictions using whole-transcriptome expression data from ovules in the wild tomato genus Solanum. Examining two sub-clades that both have evidence for post-speciation introgression, but that differ substantially in its magnitude, we find patterns of evolution that are consistent with histories of introgression in both the sign and magnitude of ovule gene expression. Additionally, in the sub-clade with a higher rate of introgression, we observe a correlation between local gene tree topology and expression similarity, implicating a role for introgressed cis-regulatory variation in generating these broad-scale patterns. Our results have important implications for the study of gene expression evolution—and quantitative trait evolution more broadly—in systems with evidence of introgression.
CRISPR/Cas9 deletions induce adverse on-target genomic effects leading to functional DNA in human cells
Authors: Geng Keyi , Merino Lara G. , Wedemann Linda , Martens Aniek , Sobota Małgorzata , Sanchez Yerma P. , Søndergaard Jonas Nørskov , White Robert J. , Kutter Claudia
Published: July 2021

The CRISPR/Cas9 system is widely used to permanently delete genomic regions by inducing double-strand breaks via dual guide RNAs. However, on-target consequences of Cas9 deletion events have yet to be fully investigated. To characterize Cas9-induced genotypic abnormalities in human cells, we utilized an innovative droplet-based target enrichment approach followed by long-read sequencing and coupled it to a customized de novo sequence assembly. This approach enabled us to dissect the sequence content at kilobase scale within an on-target genomic locus. We here describe extensive genomic disruptions by Cas9, involving a genomic duplication and inversion of the target region as well as integrations of exogenous DNA and interchromosomal DNA fragment rearrangements at the double-strand break sites often at the same time. Although these events altered the genomic composition of the on-target region, we found that the aberrant DNA fragments are still functional, marked by active histones and bound by RNA polymerase III. In HAP1 cells, the integration of the target-derived fragments accelerated cell proliferation in deletion clones. Our findings broaden the consequential spectrum of the Cas9 deletion system, reinforce the necessity of meticulous genomic validations and rationalize extra caution when interpreting results from a deletion event.
Goldilocks and RNA: Where Mg2+ concentration is just right
Authors: Guth-Metzler Rebecca , Mohamed Ahmad Mohyeldin , Cowan Elizabeth T. , Henning Ashleigh , Ito Chieri , Frenkel-Pinter Moran , Wartell Roger M. , Glass Jennifer B. , Williams Loren Dean
Published: July 2021

Magnesium, the most abundant divalent cation in cells, catalyzes RNA cleavage but also promotes RNA folding. Because folding can protect RNA from cleavage, we predicted a “Goldilocks peak”, which is a local maximum in RNA lifetime at the Mg2+ concentration required for folding. Here we use simulation and experiment to discover an innate yet sophisticated mechanism of control of RNA lifetime. By simulation we characterized the RNA Goldilocks peak and its dependence on cleavage parameters and extent of folding. Supporting experiments with yeast tRNAPhe and Tetrahymena ribozyme P4-P6 domains show that structured RNA can inhabit a Goldilocks peak in vitro. The Goldilocks peaks are tunable by differences in cleavage rate constants, Mg2+ binding cooperativity, and Mg2+ affinity. Broad ranges of those folding and cleavage parameters produce Goldilocks peaks of different intensities. Goldilocks behavior allows ultrafine control of RNA chemical lifetime, whereas non-folding RNAs do not display a Goldilocks peak. In sum, the effects of Mg2+ on RNA persistence are expected to be pleomorphic, both protecting and degrading RNA. In evolutionary context, Goldilocks behavior may have shaped RNA in an early Earth environment containing Mg2+ and other metals.
High throughput measurement of Arabidopsis thaliana fitness traits using deep learning
Authors: Wang Peipei , Meng Fanrui , Donaldson Paityn , Horan Sarah , Panchy Nicholas L. , Vischulis Elyse , Winship Eamon , Conner Jeffrey K. , Krysan Patrick J. , Shiu Shin-Han , Lehti-Shiu Melissa D.
Published: July 2021

Revealing the contributions of genes to plant phenotype is frequently challenging because the effects of loss of gene function may be subtle or be masked by genetic redundancy. Such effects can potentially be detected by measuring plant fitness, which reflects the cumulative effects of genetic changes over the lifetime of a plant. However, fitness is challenging to measure accurately, particularly in species with high fecundity and relatively small propagule sizes such as Arabidopsis thaliana.

An image segmentation-based (ImageJ) and a Faster Region Based Convolutional Neural Network (R-CNN) approach were used for measuring two Arabidopsis fitness traits: seed and fruit counts.

Although straightforward to use, ImageJ was error-prone (correlation between true and predicted seed counts, r2=0.849) because seeds touching each other were undercounted. In contrast, Faster R-CNN yielded near perfect seed counts (r2=0.9996) and highly accurate fruit counts (r2=0.980).

By examining seed counts, we were able to reveal fitness effects for genes that were previously reported to have no or condition-specific loss-of-function phenotypes.

Our study provides models to facilitate the investigation of Arabidopsis fitness traits and demonstrates the importance of examining fitness traits in the study of gene functions.
CHROMOMETHYLTRANSFERASE3/ KRYPTONITE maintain the sulfurea paramutation in Solanum lycopersicum
Authors: Martinho Cláudia , Wang Zhengming , Ghigi Andrea , Buddle Sarah , Barbour Felix , Yarur Antonia , Gouil Quentin , Müller Sebastian , Stam Maike , Liu Chang , Baulcombe David C.
Published: July 2021

Paramutation involves the transfer of a repressive epigenetic mark from a silent allele to an active homologue and, consequently, non-Mendelian inheritance. In tomato the sulfurea (sulf) paramutation is associated with a high level of CHG hypermethylation in a region overlapping the transcription start site of the SlTAB2 gene that affects chlorophyll synthesis. The CCG sub-context hypermethylation is under-represented at this region relative to CTG or CAG implicating the CHROMOMETHYLTRANSFERASE3 (CMT3) in paramutation at this locus. Consistent with this interpretation, loss of CMT3 function leads to loss of the sulf chlorosis, the associated CHG hypermethylation and paramutation. Loss of KRYPTONITE (KYP) histone methyl transferase function has a similar effect linked to reduced H3K9me2 at the promoter region of SlTAB2 and a shift in higher order chromatin structure at this locus. Mutation of the largest subunit of RNA polymerase V (PolV) in contrast does not affect sulf paramutation. These findings indicate the involvement of a CMT3/KYP dependent feedback rather than the PolV-dependent pathway leading to RNA directed DNA methylation (RdDM) in the maintenance of paramutation.
Qualification of ELISA and neutralization methodologies to measure SARS-CoV-2 humoral immunity using human clinical samples
Authors: Larsen Sasha E. , Berube Bryan J. , Pecor Tiffany , Cross Evan , Brown Bryan P. , Williams Brittany , Johnson Emma , Qu Pingping , Carter Lauren , Wrenn Samuel , Kepl Elizabeth , Sydeman Claire , King Neil P. , Baldwin Susan L. , Coler Rhea N.
Published: July 2021

In response to the SARS-CoV-2 pandemic many vaccines have been developed and evaluated in human clinical trials. The humoral immune response magnitude, composition and efficacy of neutralizing SARS-CoV-2 are essential endpoints for these trials. Robust assays that are reproducibly precise, linear, and specific for SARS-CoV-2 antigens would be beneficial for the vaccine pipeline. In this work we describe the methodologies and clinical qualification of three SARS-CoV-2 endpoint assays. We developed and qualified Endpoint titer ELISAs for total IgG, IgG1, IgG3, IgG4, IgM and IgA to evaluate the magnitude of specific responses to the trimeric spike (S) antigen and total IgG specific to the spike receptor binding domain (RBD) of SARS-CoV-2. We also qualified a pseudovirus neutralization assay which evaluates functional antibody titers capable of inhibiting the entry and replication of a lentivirus containing the Spike antigen of SARS-CoV-2. To complete the suite of assays we qualified a plaque reduction neutralization test (PRNT) methodology using the 2019-nCoV/USA-WA1/2020 isolate of SARS-CoV-2 to assess neutralizing titers of antibodies in plasma from normal healthy donors and convalescent COVID-19 individuals.
Prioritizing the economic indicators of SSC: an integrative QFD approach of performance prism and BSC
Authors: Goharshenasan Ali , Sheikh Aboumasoudi Abbas , Shahin Arash , Ansari Azarnoush
Published: July 2021

Purpose

This paper aims to propose an integrative economic model of the GRI (Global Reporting Initiative) and performance prism based on concurrent engineering and developed balanced scorecard (BSC).

Design/methodology/approach

In this paper, the supplier aspect added to the basic BSC framework, a quality function deployment (QFD) developed in four phases and the economic GRI priorities were determined. Finally, the outcomes of QFD were used in Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) for ranking the economic indicators.

Findings

The indicators of financial interpretation, risks and opportunities had the first rank in learning and growth, internal processes, customer and financial BSC aspects, and they had the second rank only in the suppliers' BSC aspect.

Research limitations/implications

In this paper, merely the economic indicators of the GRI standard was studied, and no comparison was made between the variables of the other standards and the GRI standard.

Originality/value

The most important contribution of this study is merging the supplier aspect and BSC based on the concept of suppliers, inputs, process, outputs and customers (SIPOC) in supply chain analysis. Achieving economic sustainability by a concurrent engineering approach is another novelty of this paper. The proposed model was examined in the tile and ceramic industry for the first time.
External sources of finance and value creation of Chinese mergers and acquisitions: does ownership type matter?
Authors: Bi Xiaogang , Boateng Agyenim
Published: July 2021

Purpose

This paper aims to investigate the effects of external sources of finance and ownership type on the value creation of Chinese acquiring firms.

Design/methodology/approach

The data set consists of domestic-listed mainland Chinese firms engaged in domestic mergers and acquisitions during the period 2004–2012. Standard event study methodology and cross-sectional regression analysis are used to examine the relationship between external finance, ownership type and value creation of the acquiring firms.

Findings

This paper finds that whereas bank financing is positively related to the firm value of privately-owned enterprises (POEs), bank financing has a negative but insignificant influence on the firm value of state-owned enterprises (SOEs). Moreover, equity financing has a negative and significant effect on the value creation of SOE acquirers, however, this appears not to be the case of POEs.

Research limitations/implications

The results suggest that the capital markets in China take into consideration the discriminatory and cheap access to bank loans available to SOEs as negative signals to stock markets, which cause capital markets to punish SOEs through price depreciation. Conversely, capital markets reward POEs in respect of Chinese banks’ discrimination against POEs in bank financing.

Practical implications

The results suggest that the capital markets in China take into account the discriminatory and cheap access to bank loans available to SOEs as negative signals to stock markets, which cause capital markets to punish SOEs through price depreciation. Conversely, capital markets reward POEs in respect of Chinese banks’ discrimination against POEs in bank financing.

Originality/value

The results of this study show that external sources of finance and ownership type influence acquiring firm value in an environment where the corporate governance system is weak and the banking sector is dominated by state banks. Further reforms in the financial sector, particularly, in the corporate governance system appear warranted.
Social and ethical practices and firm value: the moderating effect of green innovation: evidence from international ESG data
Authors: Chouaibi Salim , Chouaibi Jamel
Published: July 2021

Purpose

This study aims to examine the potential effect of integrating social and ethical practices into strategy on the market valuation of environmental, social and governance (ESG) businesses using the moderating effect of green innovation.

Design/methodology/approach

The sample used consisted of 523 international firms listed on the ESG index and headquartered in North America and Western Europe, forming an unbalanced panel of 7,845 observations spanning the period 2005–2019. The authors run a fixed-effects panel regression model using the Thomson Reuters ASSET4 to test the relationship between societal and ethical practices and the stock market value creation. Similarly, as an extension of the research, this paper exploits two robustness analyzes. The authors tested the dynamic dimension of the data set through the generalized moment method and the effect of the legal system.

Findings

Evidence reveals a significant positive relationship between societal and ethical practices and businesses’ market valuation. The empirical results indicate that societal and ethical strengths increase firm value with the moderating effect of green innovation and weaknesses reduce it. The results found with the dynamic dimension of the data set indicate the existence of continuity between firm values over time.

Research limitations/implications

Given the long study period, many firms with missing data were eliminated. To avoid the small sample size, countries with few observations were included, which led to an uneven distribution between observations per country.

Practical implications

Findings from this paper can help ESG firms to consider their future growth opportunities in a context where the approach of business ethics occupies a central position in business valuation.

Originality/value

This study is the only study that provides ESG companies with seven different nationalities with evidence for the effect of social and ethical practices regarding market valuation. This paper is also relevant as it addresses the relationship between social effectiveness and financial efficiency, as well as the dynamic effect of this relationship.