bluuebunny/crossref_metadata_2025 huggingface dataset:
A systematic review of the concept 'male involvement in maternal health' by natural language processing and descriptive analysis.
Authors: Galle Anna , Plaieser Gaelle , Van Steenstraeten Tessa , Griffin Sally , Osman Nafissa , Roelens Kristien , Degomme Olivier
Published: January 2021

Introduction
Experts agree that male involvement (MI) in maternal health (MH) is a multifaceted concept, but a universal definition is lacking, hampering comparison of findings and interpretation of the literature. This systematic review aims to examine the conceptualization of MI in MH globally and critically review commonly used indicators.
Methods
PubMed, Embase, Scopus, Web of Science and CINAHL databases were searched for quantitative literature (between the years 2000 and 2020) containing indicators or variables representing MI in MH, which was defined as the involvement, participation, engagement or support of men in all activities related to maternal health.

Results
After full text review, 282 studies were included in the review. Most studies were conducted in Africa (43%), followed by North America (23%), Asia (15%) and Europe (12%). Descriptive analysis and text mining analysis showed MI in MH has been conceptualised by focusing on two main aspects: psychosocial support and instrumental support for maternal health care utilisation. Differences in measurement and topics were noted according to continent with Africa focusing on HIV prevention, North America and Europe on psychosocial health and stress, and Asia on nutrition. One third of studies used one single indicator for assessing MI in MH and no common pattern of indicators could be identified. Antenatal care attendance was the most used indicator (40%) followed by financial support (17%), presence during childbirth (17%) and HIV testing (14%). Majority of studies did not collect data from men directly.

Discussion
Researchers often focus on a single aspect of MI in MH, resulting in the usage of a narrow and simplified set of indicators. Aspects such as communication between the couple, shared decision making, participation in household tasks and the subjective feeling of being supported have received little attention. We believe a more multidimensional approach can broaden the potential of MI programs. Further research, involving experts and pilot testing, is recommended to develop consensus regarding a more robust and comprehensive set of valid and feasible indicators for assessing MI in MH.
Machine learning approach for biopsy-based identification of eosinophilic esophagitis reveals importance of global features
Authors: Czyzewski Tomer , Daniel Nati , Rochman Mark , Caldwell Julie M. , Osswald Garrett A. , Collins Margaret H. , Rothenberg Marc E. , Savir Yonatan
Published: January 2021

Goal

Eosinophilic esophagitis (EoE) is an allergic inflammatory condition characterized by eosinophil accumulation in the esophageal mucosa. EoE diagnosis includes a manual assessment of eosinophil levels in mucosal biopsies—a time-consuming, laborious task that is difficult to standardize. One of the main challenges in automating this process, like many other biopsy-based diagnostics, is detecting features that are small relative to the size of the biopsy.

Results

In this work, we utilized hematoxylin- and eosin-stained slides from esophageal biopsies from patients with active EoE and control subjects to develop a platform based on a deep convolutional neural network (DCNN) that can classify esophageal biopsies with an accuracy of 85%, sensitivity of 82.5%, and specificity of 87%. Moreover, by combining several downscaling and cropping strategies, we show that some of the features contributing to the correct classification are global rather than specific, local features.

Conclusions

We report the ability of artificial intelligence to identify EoE using computer vision analysis of esophageal biopsy slides. Further, the DCNN features associated with EoE are based on not only local eosinophils but also global histologic changes. Our approach can be used for other conditions that rely on biopsy-based histologic diagnostics.

Impact Statement

Deep convolutional neural network (DCNN), together with a systematic downscaling approach, can classify esophageal biopsies with high accuracy and reveals a global nature of the histologic features of eosinophilic esophagitis. Our approach of systematic analysis of the image size versus downscaling tradeoff can be used to improve disease classification performance and insight gathering in digital pathology.
Rapid screening of pest resistance genes in maize using a sugarcane mosaic virus vector
Authors: Chung Seung Ho , Bigham Mahdiyeh , Lappe Ryan R. , Chan Barry , Nagalakshmi Ugrappa , Whitham Steven A. , Dinesh-Kumar Savithramma P. , Jander Georg
Published: January 2021

Spodoptera frugiperda(fall armyworm) is a notorious pest that threatens maize production world-wide. Current control measures involve the use of chemical insecticides and transgenic maize expressingBacillus thuringiensis(Bt) toxins. Although several additional transgenes have confirmed insecticidal activity in other plants, limited research has been conducted in maize, at least partially due to the technical difficulty of maize transformation. Here, we describe implementation of a sugarcane mosaic virus (SCMV) vector for rapidly testing the efficacy of transgenes for the control ofS. frugiperdain maize. Four categories of proteins were tested using the SCMV vector: (i) maize defense signaling proteins: peptide elicitors (Pep1 and Pep3) and jasmonate acid conjugating enzymes (JAR1a and JAR1b); (ii) maize defensive proteins: the previously identified ribosome-inactivating protein (RIP2) and maize proteinase inhibitor (MPI), and two proteins with predicted but unconfirmed anti-insect activities, an antimicrobial peptide (AMP) and a lectin (JAC1); (iii) lectins from other plant species:Allium cepaagglutinin (ACA) andGalanthus nivalisagglutinin (GNA); and (iv) spider and scorpion toxins: peptides fromUrodacus yaschenkoi(UyCT3 and UyCT5) andHadronyche versuta(Hvt). In most cases,S. frugiperdalarval growth on maize was reduced by transient SCMV-mediated overexpression of genes encoding these proteins. Additionally, experiments with some of the SCMV-expressed genes showed effectiveness against two aphid species,Rhopalosiphum maidis(corn leaf aphid) andMyzus persicae(green peach aphid). Together, these results demonstrate that SCMV vectors can be exploited as a rapid screening method for testing the efficacy and insecticidal activity of candidate genes in maize.
Ciliary chemosensitivity is enhanced by cilium geometry and motility
Authors: Hickey David , Vilfan Andrej , Golestanian Ramin
Published: January 2021

Cilia are hairlike organelles involved in both sensory functions and motility. We discuss the question of whether the location of chemical receptors on cilia provides an advantage in terms of sensitivity. Using a simple advection-diffusion model, we compute the capture rates of diffusive molecules on a cilium. Because of its geometry, a non-motile cilium in a quiescent fluid has a capture rate equivalent to a circular absorbing region with ~ 4× its surface area. When the cilium is exposed to an external shear flow, the equivalent surface area increases to ~ 10×. Alternatively, if the cilium beats in a non-reciprocal way, its capture rate increases with the beating frequency to the power of 1/3. Altogether, our results show that the protruding geometry of a cilium could be one of the reasons why so many receptors are located on cilia. They also point to the advantage of combining motility with chemical reception.
A role for SHARPIN in platelet linear protein ubiquitination and function
Authors: Moore S. F. , Zhao X. , Mallah S. , Poole A.W. , Mundell S. J. , Hutchinson J. L. , Hers I.
Published: January 2021

SHARPIN (Src homology 3 and multiple ankyrin repeat domains protein (SHANK)- associated RH domain-interacting protein) as part of the linear ubiquitin chain assembly complex (LUBAC) catalyses the addition of linear (Met1-linked) ubiquitin chains to substrates. As part of this complex SHARPIN acts as a multi-functional modulator of immune/inflammatory responses through regulation of NfkB activation. In addition, SHARPIN can act as a negative regulator of integrin function. Despite platelets being anucleate cells several studies have determined potential roles for both ubiquitination and NfkB in regulating platelet function. However, little is known about either linear ubiquitination and/or SHARPIN in mouse platelets. In this study, we evaluated platelet function in mice with impaired SHARPIN expression. We confirmed that SHARPIN was expressed in platelets from wild-type mice but not in mice homozygous for SHARPINcpdmallele (cpdm/cpdm) and that this correlated with a reduction in linear ubiquitination. Platelet function in response to thrombin was unaffected. In contrast, CRP-XL-and U46619-mediated platelet responses and thrombus formation under flow on a collagen-coated surface were significantly reduced in the cpdm/cpdm mice. This was associated with impaired U46619-mediated intracellular signalling as well as a reduction in CRP-mediated ERK phosphorylation. Despite the reported role for NfκB in regulating platelet function, inhibiting IκBα phosphorylation did not recapitulate the cpdm/cpdm phenotype. Together, these data indicate that the lack of SHARPIN and linear ubiquitination results in impaired thrombosis and platelet functional responses to CRP and U46619. This phenotype is independent of NfκB pathway inhibition but may involve alternative signalling pathways regulated by linear ubiquitination.

Key Points

SHARPIN plays an essential role in platelet linear protein ubiquitination and CRP and U46619-mediated platelet function

In vitro thrombosis is significantly impaired in SHARPIN deficient mice
Optimisation and validation of a sensitive bioanalytical method for niclosamide
Authors: Arshad Usman , Pertinez Henry , Box Helen , Tatham Lee , Rajoli Rajith KR , Neary Megan , Sharp Joanne , Valentijn Anthony , Hobson James , Unsworth Catherine , Dwyer Andrew , Savage Alison , Mcdonald Tom O , Rannard Steve P , Curley Paul , Owen Andrew
Published: January 2021

The SARS-CoV-2 pandemic has spread at an unprecedented rate, and repurposing opportunities have been intensively studied with only limited success to date. If successful, repurposing will allow interventions to become more rapidly available than development of new chemical entities. Niclosamide has been proposed as a candidate for repurposing for SARS-CoV-2 based upon the observation that it is amongst the most potent antiviral molecules evaluatedin vitro. To investigate the pharmacokinetics of niclosamide, reliable, reproducible and sensitive bioanalytical assays are required. Here, a liquid chromatography tandem mass spectrometry assay is presented which was linear from 31.25-2000 ng/mL (high dynamic range) and 0.78-100 ng/mL (low dynamic range). Accuracy and precision ranged between 97.2% and 112.5%, 100.4% and 110.0%, respectively. The presented assay should have utility in preclinical evaluation of the exposure-response relationship and may be adapted for later evaluation of niclosamide in clinical trials.
Yolk platelets impede nuclear expansion inXenopusembryos
Authors: Shimogama Sora , Iwao Yasuhiro , Hara Yuki
Published: January 2021

During metazoan early embryogenesis, the intracellular properties of proteins and organelles change dynamically through rapid cleavage. In particular, a change in the nucleus size is known to contribute to embryonic development-dependent cell cycle and gene expression regulation. Here, we compared the nuclear sizes of various blastomeres from developingXenopusembryos and analyzed the mechanisms that control the nuclear expansion dynamics by manipulating the amount of intracellular components in a cell-free system. There was slower nuclear expansion during longer interphase durations in blastomeres from vegetal hemispheres than those from animal hemispheres. Furthermore, upon recapitulating interphase events by manipulating the concentration of yolk platelets, which are originally rich in the vegetal blastomeres, in cell-free cytoplasmic extracts, there was slower nuclear expansion and DNA replication as compared to normal yolk-free conditions. Under these conditions, the supplemented yolk platelets accumulated around the nucleus in a microtubule-dependent manner and impeded organization of the endoplasmic reticulum network. Overall, we propose that yolk platelets around the nucleus reduce membrane supply from the endoplasmic reticulum to the nucleus, resulting in slower nuclear expansion in the yolk-rich vegetal blastomeres.
Reducing phenotypic instabilities of microbial population during continuous cultivation based on cell switching dynamics
Authors: Nguyen Thai Minh , Telek Samuel , Zicler Andrew , Martinez Juan Andres , Zacchetti Boris , Kopp Julian , Slouka Christoph , Herwig Christoph , Grünberger Alexander , Delvigne Frank
Published: January 2021

Predicting the fate of a microbial population (i.e., growth, gene expression…) remains a challenge, especially when this population is exposed to very dynamic environmental conditions, such as those encountered during continuous cultivation. Indeed, the dynamic nature of continuous cultivation process implies the potential deviation of the microbial population involving genotypic and phenotypic diversification. This work has been focused on the induction of the arabinose operon inEscherichia colias a model system. As a preliminary step, the GFP level triggered by an arabinose-inducible ParaBADpromoter has been tracked by flow cytometry in chemostat with glucose-arabinose co-feeding. For a large range of glucose-arabinose co-feeding, the simultaneous occurrence of GFP positive and negative subpopulation was observed. In a second set of experiments, continuous cultivation was performed by adding either glucose or arabinose, based on the ability of individual cells for switching from low GFP to high GFP states, according to a technology called segregostat. In segregostat mode of cultivation, on-line flow cytometry analysis was used for adjusting the arabinose/glucose transitions based on the phenotypic switching capabilities of the microbial population. This strategy allowed finding an appropriate arabinose pulsing frequency, leading to a prolonged maintenance of the induction level with limited impact on phenotypic diversity for more than 60 generations. This result suggests that constraining individual cells into a given phenotypic trajectory is maybe not the best strategy for directing cell population. Instead, allowing individual cells switching around a predefined threshold seems to be a robust strategy leading to oscillating, but predictable, cell population behavior.
A conserved uORF regulates APOBEC3G translation and is targeted by HIV-1 Vif protein to repress the antiviral factor
Authors: Libre Camille , Seissler Tanja , Guerrero Santiago , Batisse Julien , Verriez Cédric , Stupfler Benjamin , Gilmer Orian , Cabrera-Rodriguez Romina , Weber Melanie M. , Valenzuela-Fernandez Agustin , Cimarelli Andrea , Etienne Lucie , Marquet Roland , Paillart Jean-Christophe
Published: January 2021

The HIV-1 Vif protein is essential for viral fitness and pathogenicity. Vif decreases expression of cellular restriction factors APOBEC3G (A3G), A3F, A3D and A3H, which inhibit HIV-1 replication by inducing hypermutation during reverse transcription. Vif counteracts A3G at several levels (transcription, translation and protein degradation) that together reduce the levels of A3G in cells and prevent its incorporation into viral particles. How Vif affects A3G translation remains unclear. Here, we uncovered the importance of a short conserved uORF (upstream ORF) located within two critical stem-loop structures of the 5’ untranslated region (5’UTR) of A3G mRNA for this process. A3G translation occurs through a combination of leaky-scanning and translation re-initiation and the presence of an intact uORF decreases the extent of global A3G translation under normal conditions. Interestingly, the uORF is also absolutely required for Vif-mediated translation inhibition and redirection of A3G mRNA into stress granules. Overall, we discovered that A3G translation is regulated by a small uORF conserved in the human population and that Vif uses this specific feature to repress its translation.
Uneven declines between corals and cryptobenthic fish symbionts from multiple disturbances
Authors: Froehlich Catheline Y.M. , Klanten O. Selma , Hing Martin L. , Dowton Mark , Wong Marian Y.L.
Published: January 2021

With the onset and increasing frequency of multiple disturbances, the recovery potential of critical ecosystem-building species and their mutual symbionts is threatened. Similar effects to both hosts and their symbionts following disturbances have been assumed. However, we report unequal declines between hosts and symbionts throughout multiple climate-driven disturbances in reef-buildingAcroporacorals and cryptobenthic coral-dwellingGobiodongobies. Communities were surveyed before and after consecutive cyclones (2014, 2015) and heatwaves (2016, 2017). After cyclones, coral size and goby group size decreased similarly by 28-30%. After heatwave-induced bleaching, coral size decreased substantially (47%) and the few gobies recorded mostly inhabited corals singly. Despite several coral species still occurring after bleaching, all goby species declined, leaving 78% of corals uninhabited. These findings suggest that gobies, which are important mutual symbionts for corals, are unable to cope with consecutive disturbances. This disproportionate decline could lead to ecosystem-level disruptions through loss of key symbiotic services to corals.
Periplasm homeostatic regulation maintains spatial constraints essential for cell envelope processes and cell viability
Authors: Mandela Eric , Stubenrauch Christopher J. , Ryoo David , Hwang Hyea , Cohen Eli J. , Torres Von L. , Deo Pankaj , Webb Chaille T. , Huang Cheng , Schittenhelm Ralf B. , Beeby Morgan , Gumbart JC , Lithgow Trevor , Hay Iain D.
Published: January 2021

The cell envelope of Gram-negative bacteria consists of two membranes surrounding a periplasm and peptidoglycan layer. Molecular machines spanning the cell envelope depend on spatial constraints and load-bearing forces across the cell envelope and surface. The mechanisms dictating spatial constraints across the cell envelope remain incompletely defined. InEscherichia coli, the coiled-coil lipoprotein Lpp contributes the only covalent linkage between the outer membrane and the underlying peptidoglycan layer. Using proteomics, molecular dynamics and a synthetic lethal screen we show that lengthening Lpp to the upper limit does not change the spatial constraint, but rather impacts the load-bearing capacity across the outer membrane. Our findings demonstrateE. coliexpressing elongated Lpp homeostatically counteracts periplasmic enlargement with a combination of tilting Lpp and reducing Lpp abundance. By genetic screening we identified all of the genes inE. colithat become essential in order to enact this homeostasis, and by quantitative proteomics discovered that very few proteins need to be up- or down-regulated in steady-state levels in order to enact this homeostasis. We observed increased levels of factors determining cell stiffness, decrease membrane integrity, increase membrane vesiculation and a dependance on otherwise non-essential tethers to maintain lipid transport and peptidoglycan biosynthesis. Further this has implications for understanding how spatial constraint across the envelope controls processes such as flagellum-driven motility, cellular signaling and protein translocation
FOXO1 and FOXO3 cooperatively regulate innate lymphoid cell development
Authors: Luu Thuy T. , Søndergaard Jonas Nørskov , Peña-Pérez Lucía , Kharazi Shabnam , Krstic Aleksandra , Meinke Stephan , Schmied Laurent , Frengen Nicolai , Heshmati Yaser , Kierczak Marcin , Bouderlique Thibault , Wagner Arnika Kathleen , Gustafsson Charlotte , Chambers Benedict J. , Achour Adnane , Kutter Claudia , Höglund Petter , Månsson Robert , Kadri Nadir
Published: January 2021

The natural killer (NK) and non-cytotoxic innate lymphoid cells (ILC) lineages play vital role in the regulation of the immune system. Yet understanding of mechanisms controlling NK/ILC development remains incomplete. The evolutionary conserved FOXO family of forkhead transcription factors are critical regulators of cellular processes. We found that the loss of FOXO1 and FOXO3 together caused impaired activation of the NK gene expression program and reduced ETS binding already at the common lymphoid progenitor (CLP) level and a block at the ILC progenitor (ILCP) to NK progenitor transition. FOXO controlled NK cell maturation in organ specific manner and their ability to respond to IL-15. At the ILCP level, disruption of the ILC lineage specific gene programs was associated with broad perturbation of the generation of the non-cytotoxic ILC subsets. We concluded that FOXO1 and FOXO3 cooperatively regulate ILC lineage specification at the progenitor level as well as the generation of mature ILCs.
Correcting statistical bias in correlation-based kinship estimators
Authors: Jiang Wei , Zhang Xiangyu , Li Siting , Song Shuang , Zhao Hongyu
Published: January 2021

Accurate estimate of relatedness is important for genetic data analyses, such as association mapping and heritability estimation based on data collected from genome-wide association studies. Inaccurate relatedness estimates may lead to spurious associations and biased heritability estimations. Individual-level genotype data are often used to estimate kinship coefficient between individuals. The commonly used sample correlation-based genomic relationship matrix (scGRM) method estimates kinship coefficient by calculating the average sample correlation coefficient among all single nucleotide polymorphisms (SNPs), where the observed allele frequencies are used to calculate both the expectations and variances of genotypes. Although this method is widely used, a substantial proportion of estimated kinship coefficients are negative, which are difficult to interpret. In this paper, through mathematical derivation, we show that there indeed exists bias in the estimated kinship coefficient using the scGRM method when the observed allele frequencies are regarded as true frequencies. This leads to negative bias for the average estimate of kinship among all individuals, which explains the estimated negative kinship coefficients. Based on this observation, we propose an unbiased estimation method, UKin, which can reduce the bias. We justify our improved method with rigorous mathematical proof. We have conducted simulations as well as two real data analyses to demonstrate that both bias and root mean square error in kinship coefficient estimation can be reduced by using UKin. Further simulations indicate that the power in association mapping can also be improved by using our unbiased kinship estimates to adjust for cryptic relatedness.

Author summary

Inference of relatedness plays an important role in genetic data analysis. Many methods have been proposed to estimate kinship coefficients, including the commonly used genomic relationship matrix method. However, a substantial proportion of the kinship coefficients estimated by this method are negative, which is difficult to interpret. In this paper, through mathematical derivation, we show that there indeed exists a negative bias in this approach. To correct for this bias, we propose a new kinship coefficient estimation method, UKin, which is unbiased without requiring extra genetic information nor added computational complexity. The better performance of UKin in reducing bias and root mean squared error is demonstrated through theory, simulations and analysis of data from the young-onset breast cancer and familial intracranial aneurysm studies.
Development of loop-mediated isothermal amplification (LAMP) assay for detection of Pseudocercospora angolensis in sweet orange
Authors: Driciru Patricia , Claire Mugasa M , Acidri Robert , Adriko John
Published: January 2021

Pseudocercospora angolensisis the causative agent ofPseudocercosporaleaf and fruit spot disease in citrus which can result in up to 100% yield loss. Early diagnosis of this disease is vital for effective control. This study aimed at developing a loop-mediated amplification (LAMP) system for detectingP. angolensisin sweet oranges in comparison with Polymerase Chain Reaction (PCR) and using microscopy as a gold standard. Twelve non-target species were used to assess the analytical specificity of LAMP and PCR whereas the analytical sensitivity was determined using serial dilutions ofP. angolensisDNA. The diagnostic accuracies of the two assays were evaluated using DNA from 150 diseased and 50 non-diseased sweet orange leaf samples. The analytical sensitivity and detection time of LAMP were of 10−4ng/ μl and 40 minutes, respectively. The analytical sensitivity of PCR was 10ng/μl and it was specific toP. angolensiswhereas three relatives ofP. angolensiswere detectable by LAMP. The diagnostic sensitivities of LAMP (93%) and microscopy (100%) were significantly different (X2= 8.38,P= 0.0038) unlike the diagnostic specificities (90%) and (100%), respectively (X2= 3.37,P= 0.066). Microscopy was significantly more sensitive than PCR (32.6%) (X2= 149.26,P< 2.2e-16) and equally specific as PCR (P=NA). The positive predictive values of PCR and LAMP were 100% and 96.5% respectively whereas the negative predictive values were 33.1% and 81.8% respectively. The LAMP assay developed in this study offers a great tool for routine screening sweet orange samples forP. angolensis.
Surveillance of genetic diversity and evolution in locally transmitted SARS-CoV-2 in Pakistan during the first wave of the COVID-19 pandemic
Authors: Shakeel Muhammad , Irfan Muhammad , Zaibunnisa  , Rashid Muhammad , Ansari Sabeeta Kanwal , Khan Ishtiaq Ahmad
Published: January 2021

Surveillance of genetic diversity in the SARS-CoV-2 is extremely important to detect the emergence of more infectious and deadly strains of the virus. In this study, we monitored mutational events in the SARS-CoV-2 genome through whole genome sequencing. The samples (n=48) were collected from the hot spot regions of the metropolitan city Karachi, Pakistan during the four months (May 2020 to August 2020) of first wave of the COVID-19 pandemic. The data analysis highlighted 122 mutations, including 120 single nucleotide variations (SNV), and 2 deletions. Among the 122 mutations, there were 71 singletons, and 51 recurrent mutations. A total of 16 mutations, including 5 nonsynonymous mutations, were detected in spike protein. Notably, the spike protein missense mutation D614G was observed in 31 genomes. The phylogenetic analysis revealed majority of the genomes (36) classified as B lineage, where 2 genomes were from B.6 lineage, 5 genomes from B.1 ancestral lineage and remaining from B.1 sub-lineages. It was noteworthy that three clusters of B.1 sub-lineages were observed, including B.1.36 lineage (10 genomes), B.1.160 lineage (11 genomes), and B.1.255 lineage (5 genomes), which represent independent events of SARS-CoV-2 transmission within the city. The sub-lineage B.1.36 had higher representation from the Asian countries and the UK, B.1.160 correspond to the European countries with highest representation from the UK, Denmark, and lesser representation from India, Saudi Arabia, France and Switzerland, and the third sub-lineage (B.1.255) correspond to the USA. Collectively, our study provides meaningful insight into the evolution of SARS-CoV-2 lineages in spatio-temporal local transmission during the first wave of the pandemic.
Listeria monocytogenesfaecal carriage is common and driven by microbiota
Authors: Garcia-Garcera Marc , Hafner Lukas , Burucoa Christophe , Moura Alexandra , Pichon Maxime , Lecuit Marc
Published: January 2021

Listeriagenus comprises two opportunistic pathogenic species,L. monocytogenes(Lm) andL. ivanovii, and several non-pathogenic species. All can thrive as saprophytes, whereas only pathogenic species cause systemic infections in human and cattle. IdentifyingListeriaspecies’ respective biotopes is critical to understand the ecological contribution ofListeriapathogenic potential. Here, we aimed at detectingListeriain samples of diverse origins, to highlight ecological differences between pathogenic and non-pathogenic species. We retrieved 16S rDNA datasets from the metagenomics MG-RAST database and determined the prevalence and abundance ofListeriaspecies in various sources. Overall,Listeriawas detected in 14% of datasets.Lmwas the most prevalent species, most abundant both in soil and host-associated environments, including in 5% of human stools.Lmwas also detected in 10% of human stool samples from an independent cohort of 900 healthy asymptomatic donors. A specific microbiota signature was associated withLmfaecal carriage in human, as well as in experimentally inoculated mice, in which it precededLmlong-term gut colonization, indicating that gut microbiota composition influencesLmfaecal carriage. These results suggest that asymptomatic faecal carriage, rather than disease, exerts purifying selection onLm“virulence genes”.
Effects of forced cohesin eviction and retention on X-inactivation and autosomes
Authors: Kriz Andrea J. , Colognori David , Sunwoo Hongjae , Nabet Behnam , Lee Jeannie T.
Published: January 2021

Depletion of architectural factors globally alters chromatin structure, but only modestly affects gene expression. We revisit the structure-function relationship using the inactive X chromosome (Xi) as a model. We investigate cohesin imbalances by forcing its depletion or retention using degron-tagged RAD21 (cohesin subunit) or WAPL (cohesin release factor). Interestingly, cohesin loss disrupts Xi superstructure, unveiling superloops between escapee genes, with minimal effect on gene repression. By contrast, forced cohesin retention markedly affects Xi superstructure and compromises spreading of Xist RNA-Polycomb complexes, attenuating Xi silencing. Effects are greatest at distal chromosomal ends, where looping contacts with theXistlocus are weakened. Surprisingly, cohesin loss created an “Xi superloop” and cohesin retention created “Xi megadomains” on the active X. Across the genome, a proper cohesin balance protects against aberrant inter-chromosomal interactions and tempers Polycomb-mediated repression. We conclude that a balance of cohesin eviction and retention regulates X-inactivation and inter-chromosomal interactions across the genome.
Constitutive high expression of NOXA sensitizes human embryonic stem cells for rapid cell death
Authors: Basundra Richa , Kapoor Sahil , Hollville Emilie , Kiapour Nazanin , Lopez Adriana Beltran , Melchiorre Nicole Marie , Deshmukh Mohanish
Published: January 2021

Human embryonic stem (hES) cells are highly sensitive to apoptotic stimuli such as DNA damage, which allows for rapid elimination of mutated cells during development. However, the mechanisms that maintain hES cells in the primed apoptotic state are not completely known. Key activators of apoptosis, the BH3-only proteins, are present at low levels in most cell types. In contrast, hES cells have constitutive high levels of the BH3-only protein, NOXA. We examined the importance of NOXA for enabling apoptosis in hES cells. hES cells deleted forNOXAshowed remarkable protection against multiple apoptotic stimuli. NOXA was constitutively localized to the mitochondria, where it interacted with MCL1. Strikingly, inhibition of MCL1 inNOXAknockout cells was sufficient to sensitize these cells to DNA damage, and subsequently, cell death. Our study demonstrates, an essential function of constitutive high levels of NOXA in hES cells is to effectively antagonize MCL1 to permit rapid apoptosis.

Significance statement

Human embryonic stem (hES) cells give rise to the entire organism, hence understanding how these cells regulate their survival and death is important. These cells undergo rapid death in response to DNA damage thereby removing mutated cells from the developing embryo. We focused on identifying the mechanism underlying the sensitivity of these cells to DNA damage. We discovered that the protein NOXA is essential for cell death in hES cells. Further, the crucial function of NOXA is to neutralize high levels of antiapototic protein, MCL1, thus enabling hES cells to respond rapidly to DNA damage.
Structural mechanism of CARD8 regulation by DPP9
Authors: Sharif Humayun , Hollingsworth L. Robert , Griswold Andrew R. , Hsiao Jeffrey C. , Wang Qinghui , Bachovchin Daniel A. , Wu Hao
Published: January 2021

CARD8 is a germline-encoded pattern recognition receptor that detects intracellular danger signals. Like the related inflammasome sensor NLRP1, CARD8 undergoes constitutive autoprocessing within its function-to-find domain (FIIND), generating two polypeptides that stay associated and autoinhibited. Certain pathogen- and danger-associated activities, including the inhibition of the serine dipeptidases DPP8 and DPP9 (DPP8/9), induce the proteasome-mediated degradation of the N-terminal (NT) fragment, releasing the C-terminal (CT) fragment to form a caspase-1 activating inflammasome. DPP8/9 also bind directly to the CARD8 FIIND, but the role that this interaction plays in CARD8 inflammasome regulation is not yet understood. Here, we solved several cryo-EM structures of CARD8 bound to DPP9, with or without the DPP inhibitor Val-boroPro (VbP), which revealed a ternary complex composed of one DPP9, the full-length CARD8, and one CARD8-CT. Through structure-guided biochemical and cellular experiments, we demonstrated that DPP9’s structure restrains CARD8-CT after proteasomal degradation. Moreover, although DPP inhibitors do not directly displace CARD8 from DPP9in vitro, we show that they can nevertheless destabilize this complex in cells. Overall, these results demonstrate that DPP8/9 inhibitors cause CARD8 inflammasome activation via at least two distinct mechanisms, one upstream and one downstream of the proteasome.
Age-related demethylation of the TDP-43 autoregulatory region in the human motor cortex
Authors: Koike Yuka , Sugai Akihiro , Hara Norikazu , Ito Junko , Yokoseki Akio , Ishihara Tomohiko , Yamagishi Takuma , Tsuboguchi Shintaro , Tada Mari , Ikeuchi Takeshi , Kakita Akiyoshi , Onodera Osamu
Published: January 2021

In amyotrophic lateral sclerosis (ALS), TAR DNA-binding protein 43 (TDP-43), which is encoded byTARDBP, forms aggregates in the motor cortex. This aggregate formation may be triggered by an increase in the TDP-43 level with aging. However, the amount of TDP-43 is autoregulated by alternative splicing of theTARDBP3’UTR, and how this autoregulation is affected by aging remains to be elucidated. We found that DNA demethylation in the autoregulatory region in the TARDBP 3′UTR reduced alternative splicing and increasedTARDBPmRNA expression. Furthermore, in the human motor cortex, we found that this region was demethylated with aging, resulting in increased expression ofTARDBPmRNA. The acceleration of DNA demethylation in the motor cortex was associated with the age of ALS onset. In summary, the dysregulation of TDP-43 autoregulation by age-related DNA demethylation in the motor cortex may explain the contribution of aging and motor system selectivity in ALS.
The termite fungal cultivarTermitomycescombines diverse enzymes and oxidative reactions for plant biomass conversion
Authors: Schalk Felix , Gostinčar Cene , Kreuzenbeck Nina B. , Conlon Benjamin H. , Sommerwerk Elisabeth , Rabe Patrick , Burkhardt Immo , Krüger Thomas , Kniemeyer Olaf , Brakhage Axel A. , Gunde-Cimerman Nina , de Beer Z. Wilhelm , Dickschat Jeroen S. , Poulsen Michael , Beemelmanns Christine
Published: January 2021

Macrotermitine termites have domesticated fungi in the genusTermitomycesas their primary food source using pre-digested plant biomass. To access the full nutritional value of lignin-enriched plant biomass, the termite-fungus symbiosis requires the depolymerization of this complex phenolic polymer. While most previous work suggests that lignocellulose degradation is accomplished predominantly by the fungal cultivar, our current understanding of the underlying biomolecular mechanisms remains rudimentary. Here, we provide conclusive OMICs and activity-based evidence thatTermitomycespartially depolymerizes lignocellulose through the combined actions of high-redox potential oxidizing enzymes (laccases, aryl-alcohol oxidases and a manganese peroxidase), the production of extracellular H2O2and Fenton-based oxidative degradation, which is catalyzed by a newly described 2-methoxybenzoquinone/hydroquinone redox shuttle system and mediated by secreted chelating dicarboxylic acids. In combination, our approaches reveal a comprehensive depiction of how the efficient biomass degradation mechanism in this ancient insect agricultural symbiosis is accomplished through a combination of white- and brown-rot mechanisms.

Importance

Fungus-growing termites have perfected the decomposition of recalcitrant plant biomass to access valuable nutrients by engaging in a tripartite symbiosis with complementary contributions from a fungal mutualist and a co-diversified gut microbiome. This complex symbiotic interplay makes them one of the most successful and important decomposers for carbon cycling in Old World ecosystems. To date, most research has focused on the enzymatic contributions of microbial partners to carbohydrate decomposition. Here we provide genomic, transcriptomic and enzymatic evidence thatTermitomycesalso employs redox mechanisms, including diverse ligninolytic enzymes and a Fenton-based hydroquinone-catalyzed lignin-degradation mechanism, to break down lignin-rich plant material. Insights into these efficient decomposition mechanisms open new sources of efficient ligninolytic agents applicable for energy generation from renewable sources.
Modelling the Spreading of the SARS-CoV-2 in Presence of the Lockdown and Quarantine Measures by a "Kinetic-Type Reactions" Approach
Authors: SONNINO Giorgio , PEETERS Philippe , NARDONE Pasquale
Published: January 2021

We propose a realistic model for the evolution of the COVID-19 pandemic subject to the lockdown and quarantine measures, which takes into account the time-delay for recovery or death processes. The dynamic equations for the entire process are derived by adopting a "kinetic-type reactions" approach. More specifically, the lockdown and the quarantine measures are modelled by some kind of inhibitor reactions where susceptible and infected individuals can be "trapped" into inactive states. The dynamics for the recovered people is obtained by accounting people who are only traced back to hospitalised infected people. To get the evolution equation we take inspiration from the Michaelis- Menten enzyme-substrate reaction model (the so-called "MM reaction") where the "enzyme" is associated to the "available hospital beds", the "substrate" to the "infected people", and the "product" to the "recovered people", respectively. In other words, everything happens as if the hospitals beds act as a "catalyser" in the hospital recovery process. Of course, in our case the reverse "MM reactions" has no sense in our case and, consequently, the kinetic constant is equal to zero. Finally, the O.D.E.s for people tested positive to COVID-19 is simply modelled by the following kinetic scheme S+I=>2I with I=>R or I=>D, with "S", "I", "R", and "D" denoting the compartments Susceptible, Infected, Recovered, and Deceased people, respectively. The resulting "kinetic-type equations" provide the O.D.E.s, for elementary "reaction steps", describing the number of the infected people, the total number of the recovered people previously hospitalised, subject to the lockdown and the quarantine measure, and the total number of deaths. The model foresees also the second wave of Infection by Coronavirus. The tests carried out on real data for Belgium, France and Germany confirmed the correctness of our model.
Knowledge of and Attitudes on Artificial Intelligence in Healthcare: A Provincial Survey Study of Medical Students
Authors: Mehta Nishila , Harish Vinyas , Bilimoria Krish , Morgado Felipe , Ginsburg Shiphra , Law Marcus , Das Sunit
Published: January 2021

Background

There has been growing acknowledgement that undergraduate medical education (UME) must play a formal role in instructing future physicians on the promises and limitations of artificial intelligence (AI), as these tools are integrated into medical practice.

Methods

We conducted an exploratory survey of medical students’ knowledge of AI, perceptions on the role of AI in medicine, and preferences surrounding the integration of AI competencies into medical education. The survey was completed by 321 medical students (13.4% response rate) at four medical schools in Ontario.

Results

Medical students are generally optimistic regarding AI’s capabilities to carry out a variety of healthcare functions, from clinical to administrative, with reservations about specific task types such as personal counselling and empathetic care. They believe AI will raise novel ethical and social challenges. Students are concerned about how AI will affect the medical job market, with 25% responding that it was actively impacting their choice of specialty. Students agree that medical education must do more to prepare them for the impact of AI in medicine (79%), and the majority (68%) believe that this training should begin at the UME level.

Conclusions

Medical students expect AI will be widely integrated into healthcare and are enthusiastic to obtain AI competencies in undergraduate medical education.
Increased peripheral blood neutrophil activation phenotypes and NETosis in critically ill COVID-19 patients
Authors: Masso-Silva Jorge A. , Moshensky Alexander , Lam Michael T. Y. , Odish Mazen , Patel Arjun , Xu Le , Hansen Emily , Trescott Samantha , Nguyen Celina , Kim Roy , Perofsky Katherine , Perera Samantha , Ma Lauren , Pham Josephine , Rolfsen Mark , Olay Jarod , Shin John , Dan Jennifer M. , Abbott Robert , Ramirez Sydney , Alexander Thomas H. , Lin Grace Y. , Fuentes Ana Lucia , Advani Ira , Gunge Deepti , Pretorius Victor , Malhotra Atul , Sun Xin , Duran Jason , Crotty Shane , Coufal Nicole G. , Meier Angela , Alexander Laura E. Crotty
Published: January 2021

Background

Increased inflammation is a hallmark of COVID-19, with pulmonary and systemic inflammation identified in multiple cohorts of patients. Definitive cellular and molecular pathways driving severe forms of this disease remain uncertain. Neutrophils, the most numerous leukocytes in blood circulation, can contribute to immunopathology in infections, inflammatory diseases and acute respiratory distress syndrome (ARDS), a primary cause of morbidity and mortality in COVID-19. Changes in multiple neutrophil functions and circulating cytokine levels over time during COVID-19 may help define disease severity and guide care and decision making.

Methods

Blood was obtained serially from critically ill COVID-19 patients for 11 days. Neutrophil oxidative burst, neutrophil extracellular trap formation (NETosis), phagocytosis and cytokine levels were assessed ex vivo. Lung tissue was obtained immediately post-mortem for immunostaining.

Results

Elevations in neutrophil-associated cytokines IL-8 and IL-6, and general inflammatory cytokines IP-10, GM-CSF, IL-1b, IL-10 and TNF, were identified in COVID-19 plasma both at the first measurement and at multiple timepoints across hospitalization (p < 0.0001). Neutrophils had exaggerated oxidative burst (p < 0.0001), NETosis (p < 0.0001) and phagocytosis (p < 0.0001) relative to controls. Increased NETosis correlated with both leukocytosis and neutrophilia. Neutrophils and NETs were identified within airways and alveoli in the lung parenchyma of 40% of SARS-CoV-2 infected lungs. While elevations in IL-8 and ANC correlated to COVID-19 disease severity, plasma IL-8 levels alone correlated with death.

Conclusions

Circulating neutrophils in COVID-19 exhibit an activated phenotype with increased oxidative burst, NETosis and phagocytosis. Readily accessible and dynamic, plasma IL-8 and circulating neutrophil function may be potential COVID-19 disease biomarkers.
Combinatorial clinically driven blood biomarker functional genomics significantly enhances genotype-phenotype resolution and diagnostics in neuromuscular disease
Authors: Chakravorty Samya , Berger Kiera , Rufibach Laura , Gloster Logan , Emmons Sarah , Shenoy Sreekala , Hegde Madhuri , Dinasarapu Ashok Reddy , Gibson Greg
Published: January 2021

Purpose

50-60% of neuromuscular-disease patients remain undiagnosed even after extensive genetic testing that hinders precision-medicine/clinical-trial-enrollment. Importantly, those with DNA-based molecular diagnosis often remain without known molecular mechanism driving different degrees of disease severity that hinders patient stratification and trial-readiness. These are due to: a) clinical-genetic-heterogeneity (eg: limb-girdle-muscular-dystrophies(LGMDs)>30-subtypes); b) high-prevalence of variants-of-uncertain-significance (VUSs); (c) unresolved genotype-phenotype-correlations for patient stratification, and (d) lack of minimally-invasive biomarker-driven-assays. We therefore implemented a combinatorial phenotype-driven blood-biomarker functional-genomics approach to enhance diagnostics and trial-readiness by elucidating disease mechanisms of a neuromuscular-disease patient-cohort clinically-suspected of Dysferlinopathy/related-LGMD, the second-most-prevalent LGMD in the US.

Methods

We used CD14+monocyte protein-expression-assay on 364 Dysferlinopathy/related-LGMD-suspected patient-cohort without complete molecular-diagnosis or genotype-phenotype correlation; and then combined with blood-based targeted-transcriptome-sequencing (RNA-Seq) with tiered-analytical-algorithm correlating with clinical-measurements for a subset of patients.

Results

Our combinatorial-approach significantly increased the diagnostic-yield from 25% (N=326; 18%-27%; 95%CI) to 82% (N=38; 69.08% to 84.92%; 95% CI) by combining monocyte-assay with enhanced-RNA-Seq-analysis and clinical-correlation, following ACMG-AMP-guidelines. The tiered-analytical-approach detected aberrant-splicing, allele-expression-imbalance, nonsense-mediated-decay, and compound-heterozygosity without parental/offspring-DNA-testing, leading to VUS-reclassifications, identification of variant-pathomechanisms, and enhanced genotype-phenotype resolution including those with carrier-range Dysferlin-protein-expression and milder-symptoms, allowing patient-stratification for better trial-readiness. We identified uniform-distribution of pathogenic-variants acrossDYSF-gene-domains without any hotspot suggesting the relevance of upcoming gene-(full-DYSF-cDNA)-therapy trials.

Conclusion

Our results show the relevance of using a clinically-driven multi-tiered-approach utilizing a minimally-invasive biomarker-functional-genomic platform for precision-medicine-diagnostics, trial-recruitment/monitoring, elucidating pathogenic-mechanisms for patient stratification to enhance better trial outcomes, which in turn, will guide more rational use of current-therapeutics and development of novel-interventions for neuromuscular-disorders, and applicable to other genetic-disorders.