bluuebunny/crossref_metadata_2025 huggingface dataset:
GRAd-COV2 vaccine provides potent and durable immunity in randomised placebo-controlled phase 2 trial (COVITAR)
Authors: Capone Stefania , Fusco Francesco M. , Milleri Stefano , Borrè Silvio , Carbonara Sergio , Lo Caputo Sergio , Leone Sebastiano , Gori Giovanni , Maggi Paolo , Cascio Antonio , Lichtner Miriam , Cauda Roberto , Dal Zoppo Sarah , Cossu Maria V. , Gori Andrea , Roda Silvia , Confalonieri Paola , Bonora Stefano , Missale Gabriele , Codeluppi Mauro , Mezzaroma Ivano , Capici Serena , Pontali Emanuele , Libanore Marco , Diani Augusta , Lanini Simone , Battella Simone , Contino Alessandra M. , Piano Mortari Eva , Genova Francesco , Parente Gessica , Dragonetti Rosella , Colloca Stefano , Visani Luigi , Iannacone Claudio , Carsetti Rita , Folgori Antonella , Camerini Roberto ,   COVITAR study group
Published: October 2022

Background

SARS-CoV-2 ongoing pandemic and heterologous immunization approaches implemented worldwide for booster doses call for diversified vaccines portfolio. We report safety and immunogenicity of GRAd-COV2, a novel gorilla adenovirus-based COVID-19 vaccine, in a phase 2 trial aimed at identifying the appropriate dose and schedule.

Method

917 eligible adults aged 18 years or older, including participants with co-morbidities, were randomised to receive, 21 days apart, a single vaccine administration at 2×1011viral particles (vp) followed by placebo, or repeated vaccine administration at 1×1011vp, or two doses of placebo. Primary endpoints were the incidence of local and systemic solicited AEs for 7 days post each dose and the post-treatment (35 days after the first dose), geometric mean titers (GMTs) and geometric mean fold rise (GMFRs) of ELISA antibody responses to Spike protein. Additional humoral and cellular immune response parameters were monitored for up to six months.

Results

The safety profile of GRAd-COV2 was characterized by short-term, mild-to-moderate pain and tenderness at injection site, fatigue, headache, malaise, and myalgia. Neither related SAEs nor deaths were reported. Humoral (binding and neutralizing) Ab responses peaked at day 35 after a single administration, were boosted by a second vaccination, were sustained until day 57 to then decline at day 180. Potent, VOC cross-reactive T cell responses peaked already after first dose with high frequencies of long-lived CD8 T cells.

Conclusion

GRAd-COV2 was safe, and induced robust immune responses after a single immunization; the second administration increased humoral but not cellular immune responses.

Trial Registration

ClinicalTrials.govNCT04791423.

Funding

ReiThera Srl
Meta-Analysis of Clinical Phenotype and Patient Survival in Neurodevelopmental Disorder with Microcephaly, Arthrogryposis, and Structural Brain Anomalies Due to Bi-allelic Loss of Function Variants in SMPD4
Authors: Marchiori Dean
Published: October 2022

A recently described, rare genetic condition known as Neurodevelopmental Disorder with Microcephaly, Arthrogryposis, and Structural Brain Anomalies (NEDMABA) has been identified in children with bi-allelic loss-of-function variants inSMPD4. The progression of this condition is not well understood with the limited case reports described so far exhibiting a severe and clinically diverse phenotype. A gap exists in the understanding of associations present in the heterogenous features of the clinical phenotype, and the expected survival probabilities of affected individuals. This is driven in part to the paucity of analysis-ready data on reported cases. This analysis aims to collate and standardise available case reports into a common dataset, to analyse and identify meaningful clusters in the clinical phenotype, and to quantify the survival probability for children with NEDMABA. To overcome the challenge of multidimensional data on very few subjects, we employ Multiple Correspondence Analysis (MCA) as a dimension reduction technique, which is then subject to cluster analysis and interpretation. To account for censoring in the data, Kaplan-Meier estimation is formulated to calculate patient survival time. The analysis correctly detected the classic phenotype for this condition, as well as a new distinct feature-cluster relating to findings of vocal cord paralysis, feeding dysfunction and respiratory failure. The survival probability for those affected was found to decline sharply in early infancy with median survival of 150 days, but with some surviving as long as 12.5 years. This wide range of outcomes is provisionally associated with different variant types however this conclusion could not be validated based on very low sample sizes. AnRpackage calledSMPD4was developed to publish standardised analysis-ready datasets used in this study. This analysis represents the first of its kind to help describe associations and trajectories of individuals with this newly reported condition, despite challenges with sparse and inconsistent data. This analysis can provide clinicians and genetic counsellors with better information to aide in decision making and support for families with this rare condition.
COVID19 Diagnosis Using Chest X-rays and Transfer Learning
Authors: Stubblefield Jonathan , Causey Jason , Dale Dakota , Qualls Jake , Bellis Emily , Fowler Jennifer , Walker Karl , Huang Xiuzhen
Published: October 2022

A pandemic of respiratory illnesses from a novel coronavirus known as Sars-CoV-2 has swept across the globe since December of 2019. This is calling upon the research community including medical imaging to provide effective tools for use in combating this virus. Research in biomedical imaging of viral patients is already very active with machine learning models being created for diagnosing Sars-CoV-2 infections in patients using CT scans and chest x-rays. We aim to build upon this research. Here we used a transfer-learning approach to develop models capable of diagnosing COVID19 from chest x-ray. For this work we compiled a dataset of 112120 negative images from the Chest X-Ray 14 and 2725 positive images from public repositories. We tested multiple models, including logistic regression and random forest and XGBoost with and without principal components analysis, using five-fold cross-validation to evaluate recall, precision, and f1-score. These models were compared to a pre-trained deep-learning model for evaluating chest x-rays called COVID-Net. Our best model was XGBoost with principal components with a recall, precision, and f1-score of 0.692, 0.960, 0.804 respectively. This model greatly outperformed COVID-Net which scored 0.987, 0.025, 0.048. This model, with its high precision and reasonable sensitivity, would be most useful as “rule-in” test for COVID19. Though it outperforms some chemical assays in sensitivity, this model should be studied in patients who would not ordinarily receive a chest x-ray before being used for screening.

CCS CONCEPTS

Life and Medical Sciences • Machine Learning • Artificial Intelligence

Reference format

Jonathan Stubblefield, Jason Causey, Dakota Dale, Jake Qualls, Emily Bellis, Jennifer Fowler, Karl Walker and Xiuzhen Huang. 2022. COVID19 Diagnosis Using Chest X-Rays and Transfer Learning.
Association Analysis ofLCORLGenetic Variant (rs657074013A>AT) with Body-Height and Skeletal Frame in Pakistani Goats
Authors: Khalid Areeb , Ashraf Hajra , Asim Hibba , Ayman Maleeka , Saif Rashid
Published: October 2022

Goat is one of the most valued and cost-effective household animals serving humanity by providing its meat, milk, fiber, skin and manure. Particularly, meat and milk production depends on the physical traits of the animals e.g., large body-size/skeletal frame. Previous studies has shown that theLCORLgene is associated with the subject traits in humans and many other animal species. So, the current study is aimed to investigate the genetic variability/association of rs657074013A>AT variant within diverse goats from Pakistan. By using ARMS-PCR, a total of 51 samples were genotyped with allele-specific primer-set, results of the current study depicted that, 27% population is homozygous wild-type (A/A), 24% homozygous-mutant (AT/AT) and 49% is heterozygous (A/AT). Hardy Weinberg Equilibrium (HWE) analysis revealed that our overall sampled population obeys this principle withχ2(2,N= 51) = 0.046,p= 0.9730. Similarly, a significant genetic association was also envisioned by Chi-square statisticsp= 9.60 × 10−5using the PLINK data analysis toolset. Furthermore, alternative allele frequencies of 0.68 and 0.28 were also calculated within cases (n=25) and control (n=26) cohorts respectively along with an odds ratio of 5.242. As a nutshell, this pilot study improved our genomic insight by observing the variability and association of the subjectLCORLgenetic variant (c.828_829insA) in the Pakistani goat population, which may be used to improve this economically important trait by adopting marker-assisted breeding strategies and further investigated within other livestock species as well.
TsTX-κ beta (Ts8), a neurotoxin from the venom of the scorpionTityus serrulatus: antimicrobial and hemolytic activity
Authors: Oliveira Thiago de Jesus , Pereira Nayrob , Riciluca Katie Cristina Takeuti , do Nascimento Soraia Maria , Castro de Oliveira Ursula , da Silva Junior Pedro Ismael
Published: October 2022

Increase of infections caused by microorganisms resistant to conventional antibiotics is a health problem in Brazil and worldwide. The search for new molecules capable of inhibiting the growth of pathogens is a challenge for researchers, who find in venoms a rich source of biomolecules, including antimicrobial peptides (AMPs). The Brazilian scorpion,Tityus serrulatus, is one of the species that cause serious accidents, its venom is rich in neurotoxins that have been well characterized, highlighting their activities on channels (especially sodium and potassium). So, this work aimed to identify and characterize AMPs inT. serrulatusvenom. After milking and purification steps, the venom fractions were analyzed by liquid growth inhibition assay, the minimum inhibitory concentration (MIC) for different microorganisms was also tested. The fraction with antimicrobial activity was analyzed by electrophoresis and mass spectrometry, this AMP (molecular mass 6.881 kDa) has a similar amino acid sequences to TsTX-κ beta, a neurotoxin that acts on ion channels. The fragments from TsTX-κ beta were obtained, separated by high-performance liquid chromatography and subjected to biological tests. At high concentrations, these fragments showed hemolytic activity against human erythrocytes. Taken together, these data suggest that antimicrobial and hemolytic activities are associated by different sites from TsTX-κ beta, in addition to the identification of antimicrobial activity in a neurotoxin already known.

Key Contribution

Multifunction: antimicrobial and hemolytic activity associated to TsTX-κ beta, a neurotoxin that acts on potassium channels.
Structural Genomics of the Human Dopamine Receptor System
Authors: Xu Peiyu , Huang Sijie , Krumm Brian E. , Zhuang Youwen , Mao Chunyou , Zhang Yumu , Wang Yue , Huang Xi-Ping , Liu Yong-Feng , He Xinheng , Li Huadong , Yin Wanchao , Jiang Yi , Zhang Yan , Roth Bryan L. , Xu H. Eric
Published: October 2022

The dopamine system, including five dopamine receptors (D1R to D5R), plays essential roles in the central nervous system (CNS) and ligands that activate dopamine receptors have been used to treat many neuropsychiatric disorders, including Parkinson’s Disease (PD) and schizophrenia. Here, we report five cryo-EM structures of all subtypes of human dopamine receptors in complex with G-protein and bound to the pan agonist, Rotigotine, which is used to treat PD and restless legs syndrome. The structures reveal the basis of Rotigotine binding modes to different dopamine receptors. Structural analysis together with functional assays illuminate determinants of ligand polypharmacology and selectivity. The structures also uncover the mechanisms of the dopamine receptor activation, unique structural features among the five receptor subtypes, and the basis of G-protein coupling specificity. Our works provide a comprehensive set of structural templates for the rational design of specific ligands to treat CNS diseases targeting the dopaminergic system.
Energy extraction from air: structural basis of atmospheric hydrogen oxidation
Authors: Grinter Rhys , Kropp Ashleigh , Venugopal Hari , Senger Moritz , Badley Jack , Cabotaje Princess , Stripp Sven T. , Barlow Christopher K. , Belousoff Matthew , Cook Gregory M. , Vincent Kylie A. , Schittenhelm Ralf B. , Khalid Syma , Berggren Gustav , Greening Chris
Published: October 2022

Diverse aerobic bacteria use atmospheric H2as an energy source for growth and survival. This recently discovered yet globally significant process regulates the composition of the atmosphere, enhances soil biodiversity, and drives primary production in certain extreme environments. Atmospheric H2oxidation has been attributed to still uncharacterised members of the [NiFe]-hydrogenase superfamily. However, it is unresolved how these enzymes overcome the extraordinary catalytic challenge of selectively oxidizing picomolar levels of H2amid ambient levels of the catalytic poison O2, and how the derived electrons are transferred to the respiratory chain. Here we determined the 1.52 Å resolution CryoEM structure of the mycobacterial hydrogenase Huc and investigated its mechanism by integrating kinetics, electrochemistry, spectroscopy, mass spectrometry, and molecular dynamics simulations. Purified Huc is an oxygen-insensitive enzyme that couples the oxidation of atmospheric H2at its large subunit to the hydrogenation of the respiratory electron carrier menaquinone at its small subunit. The enzyme uses a narrow hydrophobic gas channel to selectively bind atmospheric H2at the expense of O2, while three [3Fe-4S] clusters and their unusual ligation by a D-histidine modulate the electrochemical properties of the enzyme such that atmospheric H2oxidation is energetically feasible. Huc forms an 833 kDa complex composed of an octamer of catalytic subunits around a membrane-associated central stalk, which extracts and transports menaquinone a remarkable 94 Å from the membrane, enabling its reduction. These findings provide a mechanistic basis for the biogeochemically and ecologically critical process of atmospheric H2oxidation. Through the first characterisation of a group 2 [NiFe]-hydrogenase, we also uncover a novel mode of energy coupling dependent on long-range quinone transport and pave way for the development of biocatalysts that oxidize H2in ambient air.
The expected loss of feature diversity (versus phylogenetic diversity) following rapid extinction at the present
Authors: Overwater Marcus , Pelletier Daniel , Steel Mike
Published: October 2022

The current rapid extinction of species leads not only to their loss but also the disappearance of the unique features they harbour, which have evolved along the branches of the underlying evolutionary tree. One proxy for estimating the feature diversity (FD) of a setSof species at the tips of a tree is ‘phylogenetic diversity’ (PD): the sum of the branch lengths of the subtree connecting the species inS. For a phylogenetic tree that evolves under a standard birth–death process, and which is then subject to a sudden extinction event at the present (the simple ‘field of bullets’ model with a survival probability ofsper species) the proportion of the originalPDthat is retained after extinction at the present is known to converge quickly to a particular concave functionφPD(s) astgrows. To investigate how the loss ofFDmirrors the loss ofPDfor a birth–death tree, we modelFDby assuming that distinct discrete features arise randomly and independently along the branches of the tree at raterand are lost at a constant ratev. We derive an exact mathematical expression for the ratioφFD(s) of the two expected feature diversities (prior to and following an extinction event at the present) astbecomes large. We find that althoughφFDhas a similar behaviour toφPD(and coincides with it forv= 0), whenv >0,φFD(s) is described by a function that is different fromφPD(s). We also derive an exact expression for the expected number of features that are present in preciselyoneextant species. Our paper begins by establishing some generic properties of FD in a more general (non-phylogenetic) setting and applies this to fixed trees, before considering the setting of random (birth–death) trees.
Sensitivity of endemic behaviour of Covid-19 under a multi-dose vaccination regime, to various biological parameters and control variables
Authors: Dagpunar John , Wu Chenchen
Published: October 2022

For an infectious disease such as Covid-19, we present a new four-stage vaccination model (un-vaccinated, dose 1+2, booster, repeated boosters), which examines the impact of vaccination coverage, vaccination rate, generation interval, control reproduction number, vaccine efficacies, and rates of waning immunity, upon the dynamics of infection. We derive a single equation that allows computation of equilibrium prevalence and incidence of infection, given knowledge about these parameter and variable values. Based upon a 20 compartment model, we develop a numerical simulation of the associated differential equations. The model is not a forecasting or even predictive one, given the uncertainty about several biological parameter values. Rather, it is intended to aid qualitative understanding of how equilibrium levels of infection may be impacted upon, by the parameters of the system. We examine one at a time sensitivity analysis around a base case scenario. The key finding which should be of interest to policy makers, is that while factors such as improved vaccine efficacy, increased vaccination rates, lower waning rates, and more stringent non-pharmaceutical interventions might be thought to improve equilibrium levels of infection, this might only be done to good effect, if vaccination coverage on a recurrent basis, is sufficiently high.
Midlife “Deaths of Despair” Trends in the US, Canada, and UK, 2001-2019: Is the US an Anomaly?
Authors: Dowd Jennifer Beam , Angus Colin , Zajacova Anna , Tilstra Andrea M.
Published: October 2022

Background

Over the past decade, “deaths of despair” were strongly implicated in rising mid-life mortality in the US. Whether despair deaths and mid-life mortality trends are also changing in the peer countries such as the UK and Canada is not well known.

Methods

We compared all-cause and “despair” mortality trends at mid-life in the US, the UK (constituent nations England & Wales, Northern Ireland, and Scotland) and Canada from 2000-2019, using publicly available mortality data, stratified by three age groups (35-44, 45-54 and 55-64) and by sex. We examined trends in all-cause mortality and mortality by causes categorized as 1) suicides 2) alcohol-specific deaths 3) drug-related deaths. We employ several descriptive approaches to visually inspect age, period, and cohort trends in these causes of death.

Results

The US and Scotland both saw large increases and high absolute levels of drug-related deaths. The rest of the UK and Canada saw relative increases but much lower absolute levels in by comparison. Alcohol-specific deaths showed less consistent trends that did not track other “despair” causes, with older groups in Scotland seeing steep declines over time. Suicide deaths trended slowly upward in most countries.

Conclusions

In the UK, Scotland has suffered increases in drug-related mortality comparable to the US, while Canada and other UK constituent nations did not see dramatic increases. Alcohol-specific and suicide mortality generally follow different patterns to drug-related deaths across countries and over time, questioning the utility of a cohesive “deaths of despair” narrative.
Proton Transfers to DNA in Native Electrospray Ionization Mass Spectrometry: A QM/MM Study
Authors: Paulikat Mirko , Aranda Juan , Ippoliti Emiliano , Orozco Modesto , Carloni Paolo
Published: October 2022

Native electrospray ionization - ion mobility mass spectrometry (N-ESI/IM-MS) is a powerful approach for low-resolution structural studies of DNAs in the free state and in complex with ligands. Solvent vaporization is coupled with proton transfers from ammonium ions to the DNA resulting in a reduction of the DNA charge. Here we provide insight on these processes by classical MD and QM/MM free energy calculations on the (GpCpGpApApGpC) heptamer, for which a wealth of experiments is available. Our multiscale simulations, consistent with experimental data, reveal a highly complex scenario: the proton either sits on one of the molecules or is fully delocalized on both, depending on the level of hydration of the analytes and on size of the droplets formed during the electrospray experiments. This work complements our previous study on theintramolecularproton transfer on the same heptamer occurring after the processes studied here, and, together, provide a first molecular view of proton transfer in N-ESI/IM-MS.

TOC GRAPHICS
Elucidating the molecular programming of a nonlinear nonribosomal peptide synthetase responsible for fungal siderophore biosynthesis
Authors: Jenner Matthew , Hai Yang , Nguyen Hong H. , Passmore Munro , Skyrud Will , Kim Junyong , Garg Neil K. , Zhang Wenjun , Ogorzalek Loo Rachel R. , Tang Yi
Published: October 2022

Siderophores belonging to the ferrichrome family are essential for the viability of fungal species and play a key role for virulence of numerous pathogenic fungi. Despite their biological significance, our understanding of how these iron-chelating cyclic hexapeptides are assembled by non-ribosomal peptide synthetase (NRPS) assembly lines remains poorly understood, primarily due to the nonlinearity exhibited by the domain architecture. Herein, we report the biochemical characterization of the SidC NRPS, responsible for construction of the intracellular siderophore ferricrocin.In vitroreconstitution of purified SidC revealed its ability to produce ferricrocin and its structural variant, ferrichrome. Application of intact protein mass spectrometry uncovered several non-canonical events during peptidyl siderophore biosynthesis, including inter-modular loading of amino acid substrates and an adenylation domain capable of poly-amide bond formation. This work expands the scope of NRPS programming, allows biosynthetic assignment of ferrichrome NRPSs, and sets the stage for reprogramming towards novel hydroxamate scaffolds.
TRIM 25 nuclear translocation is hampered by localization to influenza A virus non-structural protein 1 cytosolic aggregates
Authors: Weiß Anne , Haralampiev Ivan , Kummer Susann
Published: October 2022

Non-structural protein 1 (NS1) of influenza A virus (IAV) is involved in multiple blocking processes of cellular antiviral action. One of these includes the binding of cytosolic tripartite motif-containing protein 25 (TRIM25) to impede nuclear translocation and, thus, counteracting the block of viral RNA elongation taking place inside the nucleus. In addition, TRIM25 is part of the RIG-I signaling pathway and is an important component regarding the activation of interferon-induced genes and triggering cellular antiviral responses. In this study, we focus on the spatial localization of TRIM25 with respect to cytosolic NS1 aggregates found in IAV infected cells. Besides strain specific characteristics, we confirmed co-localization of TRIM25 to NS1 cytosolic aggregates at 16 hours post infection for all investigated IAV strains based on image analysis on single cell level. Immunoprecipitation further confirmed the interaction between NS1 and TRIM25 when comparing wt IAV and recombinant IAV devoid of NS1 expression. Of note, we combined fluorescencein situhybridization targeting viral RNA with immunolabeling of TRIM25 suitable for nanoscopy and the diffraction limited detection of NS1 in one imaging approach. Our study reveals strain dependent differences in the block of IRF3 activation in respect to the accumulation of TRIM25 in cytosolic NS1 aggregates.
Absence of estrogen leads to defects in spermatogenesis and increased semen abnormalities in male rabbits
Authors: Dewaele Aurélie , Dujardin Emilie , André Marjolaine , Albina Audrey , Jammes Hélène , Giton Frank , Sellem Eli , Jolivet Geneviève , Pailhoux Eric , Pannetier Maëlle
Published: October 2022

Estrogens are steroid hormones produced by the aromatization of androgens by the aromatase enzyme, encoded by theCYP19A1gene. Although generally referred to as “female sex hormones”, estrogen is also produced in the adult testes of many mammals, including humans. To better understand the function of estrogens in the male, we used the rabbit model which is an important biomedical model. First, the expression ofCYP19A1was localized, demonstrating that testicular estrogens are produced by meiotic germ cells inside the seminiferous tubules. Next, the cells expressing ESR1 and ESR2 were identified, showing that estrogens could exert their function on post-meiotic germ cells in the tubules and play a role during sperm maturation, since ESR1 and ESR2 were detected in thecaudaepididymis. Then, CRISPR/Cas9CYP19A1−/−genetically modified rabbits were analyzed.CYP19A1−/−males showed decreased fertility with lower sperm count associated with hypo-spermatogenesis and lower spermatid number. Germ/sperm cell DNA methylation was unchanged, while sperm parameters were affected asCYP19A1−/−males exhibited reduced sperm motility associated with increased flagellar defects. In conclusion, testicular estrogens could be involved in the spermatocyte-spermatid transition in the testis, and in the acquisition of sperm motility in the epididymis.
Maternal patterns of inheritance alter transcript expression in eggs
Authors: Harry Nathan D. , Zakas Christina
Published: October 2022

Modifications to early development can lead to evolutionary diversification. The early stages of development are under maternal control, as mothers produce eggs loaded with nutrients, proteins and mRNAs that direct early embryogenesis. Maternally provided mRNAs are the only expressed genes in initial stages of development and are known to be tightly regulated. Differences in maternal mRNA provisioning could lead to phenotypic changes in embryogenesis and ultimately evolutionary changes in development. However, the extent to which variation in maternal mRNA provisioning impacts ontogeny or life-history is unknown. Here, we use a species with dimorphic development— where females make eggs and larvae of different sizes and life-history modes—to investigate the extent of variation in maternal mRNA provisioning to the egg. We examine the effect of gene expression differences on subsequent generations of egg provisioning and determine the regulatory architecture underlying mRNA provisioning differences. We find that there is significant variation in gene expression across eggs of different development modes, and that both parent-of-origin and allele-specific effects contribute to mRNA expression differences. We also find that offspring of intraspecific crosses differentially provision their eggs based on their parents’ cross direction. This effect of allelic expression based on parent-of-origin has not been previously demonstrated in reproductive traits like oogenesis.

AUTHOR SUMMARY

Variation in early developmental programs can provide the basis for evolutionary diversification. In the early embryo, cellular functions are carried out by proteins and transcripts contributed by the mother to the egg until the embryo’s own genome can take over. Since these maternal factors are responsible for setting up all of the subsequent development of the offspring, they tend to be tightly regulated. However, variation exists in the amount and types of transcripts mothers provide. Here we examine how the variation in maternal transcripts that occurs in eggs of the speciesStreblospio benedicti, leads to developmental differences.S. benedictioffspring follow one of two distinct developmental programs that originate with egg size differences. We find significant variation in maternally provided transcripts correlated with the two life-histories, and that some of this variation in egg transcripts is directly related to the developmental type of the mother’s own parents. This parental effect on how mothers provide transcripts to their eggs has not previously been described and indicates the possibility for an offspring’s grandparents to affect their early developmental program by modulating the transcripts their mother provides.
A Multiparametric and High-Throughput Platform for Host-Virus Binding Screens
Authors: Schlegel Jan , Porebski Bartlomiej , Andronico Luca , Hanke Leo , Edwards Steven , Brismar Hjalmar , Murrell Benjamin , McInerney Gerald , Fernandez-Capetillo Oscar , Sezgin Erdinc
Published: October 2022

Speed is key during infectious disease outbreaks. It is essential, for example, to identify critical host binding factors to the pathogens as fast as possible. The complexity of host plasma membrane is often a limiting factor hindering fast and accurate determination of host binding factors as well as high-throughput screening for neutralizing antimicrobial drug targets. Here we describe a multi-parametric and high-throughput platform tackling this bottleneck and enabling fast screens for host binding factors as well as new antiviral drug targets. The sensitivity and robustness of our platform was validated by blocking SARS-CoV-2 spike particles with nanobodies and IgGs from human serum samples.

Teaser

A fast screening platform tackling host-pathogen interactions.
Single-cell phenotypic plasticity modulates social behaviour inDictyostelium discoideum
Authors: Forget Mathieu , Adiba Sandrine , De Monte Silvia
Published: October 2022

InDictyosteliumchimeras, strains social behaviour is defined based on their relative representation in the spores – the reproductive cells resulting from development – referred to as spore bias. Some strains, called ‘cheaters’, display systematically positive spore bias in chimeras and are considered a threat to the evolutionary stability of multicellular organization. The selective advantage gained by cheaters is indeed predicted to undermine collective functions whenever social behaviours are genetically determined. However, genotypes are not the only determinant of spore bias, and the relative role of genetic and plastic phenotypic differences in strains evolutionary success is unclear.

Here, we control phenotypic heterogeneity by harvesting cells in different growth phases, and study the effects of plastic variation on spore bias in chimeras composed of isogenic or genetically different populations. Spore bias is shown to depend both on growth phase and on population composition, and to be negatively correlated to the fraction of ‘loners’,i.e. cells that do not join aggregates. We examined several single-cell mechanical properties that are expected to affect aggregation efficiency, and found that variations in the fraction of slowly moving cells with growth phase may explain why earlier cultures appear to be underrepresented in the spores. The involvement of a go-or-grow mechanism during cell aggregation is also consistent with known variations of cell-cycle phase distribution during population growth. We confirm the expected ubiquity of growth-phase induced spore bias variation by showing that it is not negligible in genetic chimeras, and can even reverse the classification of a strain’s social behaviour. These results suggest that aggregation can provide an efficient ‘lottery’ system to harness the evolutionary spread of cheaters.
The heat shock protein LarA activates the Lon protease at the onset of proteotoxic stress
Authors: Omnus Deike J. , Fink Matthias J. , Kallazhi Aswathy , Zaragoza Maria Xandri , Jonas Kristina
Published: October 2022

The Lon protease is a highly conserved protein degradation machine that has critical regulatory and protein quality control functions in cells from the three domains of life. Here, we report the discovery of a α-proteobacterial heat shock protein, LarA, that functions as a dedicated Lon regulator. We show that LarA accumulates at the onset of proteotoxic stress and allosterically activates Lon-catalysed degradation of a large group of substrates through a five amino acid sequence at its C-terminus. Further, we find that LarA is regulated by Lon itself, which is critical to prevent toxic overactivation of Lon. We suggest that the temporal LarA-dependent activation of Lon helps to meet an increased proteolysis demand at the onset of protein unfolding stress. Our study defines a regulatory interaction of a conserved protease with a heat shock protein, serving as a paradigm of how protease activity can be tuned under changing environmental conditions.
Allelic compatibility in plant immune receptors facilitates engineering of new effector recognition specificities
Authors: Bentham Adam R. , De la Concepcion Juan Carlos , Benjumea Javier Vega , Jones Sally , Mendel Melanie , Stubbs Jack , Stevenson Clare E. M. , Maidment Josephine H.R. , Youles Mark , Kourelis Jiorgos , Zdrzałek Rafał , Kamoun Sophien , Banfield Mark J.
Published: October 2022

Engineering expanded effector recognition in plant immune receptors is a promising prospect for generating new disease resistant crop varieties. However, modification of plant NLR receptors has proven challenging due to the lack of understanding of their context as part of complex immune systems. Here, we demonstrate a new avenue for NLR-mediated engineering that exploits the allelic diversity in the Pik NLR pair to allow for the generation of receptors with expanded recognition specificities, which would otherwise result in constitutive cell death. This work lays the foundation for the incorporation of new effector recognition motifs into the Pik system and advances the development of designer NLRs that can be tailored to specific secreted pathogen signatures.

Engineering the plant immune system offers genetic solutions to mitigate crop diseases caused by diverse agriculturally significant pathogens and pests. Modification of intracellular plant immune receptors of the nucleotide-binding leucine rich repeat (NLRs) superfamily for expanded recognition of pathogen virulence proteins (effectors) is a promising approach for engineering novel disease resistance. However, engineering can cause NLR autoactivation, resulting in constitutive defence responses that are deleterious to the plant. This may be due to plant NLRs associating in highly complex signalling networks that co-evolve together, and changes through breeding or genetic modification can generate incompatible combinations, resulting in autoimmune phenotypes. We have previously shown how alleles of the rice NLR pair Pik have differentially co-evolved, and how sensor/helper mismatching between non-co-evolved alleles triggers constitutive activation and cell death (De la Concepcion et al., 2021b). Here, we dissect incompatibility determinants in the Pik pair and found that HMA domains integrated in Pik-1 not only evolved to bind pathogen effectors but also likely co-evolved with other NLR domains to maintain immune homeostasis. This explains why changes in integrated domains can lead to autoactivation. We then used this knowledge to facilitate engineering of new effector recognition specificities overcoming initial autoimmune penalties. We show that by mismatching alleles of the rice sensor and helper NLRs Pik-1 and Pik-2, we can enable the integration of synthetic HMA domains with novel and enhanced recognition of an effector from the rice blast fungus. Taken together, our results reveal a new strategy for engineering NLRs, which has the potential to allow an expanded set of integrations and therefore new disease resistance specificities in plants.
Anterograde Trafficking of Toll-Like Receptors Requires the Cargo Sorting Adaptors TMED-2 and 7 and specific N-glycans
Authors: Holm Julia E.J. , Soares Sandro G. , Symmons Martyn F. , Moncrieffe Martin C. , Gay Nicholas J.
Published: October 2022

Toll-Like Receptors (TLRs) play a pivotal role in immunity by recognizing conserved structural features of pathogens and initiating the innate immune response. TLR signaling is subject to complex regulation that remains poorly understood. Here we show that two small type I transmembrane receptors, TMED2 and 7, that function as cargo sorting adaptors in the early secretory pathway are required for transport of TLRs from the ER to Golgi. Protein interaction studies reveal that TMED7 interacts with TLR2, TLR4, and TLR5 but not with TLR3 and TLR9. On the other hand, TMED2 interacts with TLR2, TLR4 and TLR3. Dominant negative forms of TMED7 suppress the export of cell surface TLRs from the ER to the Golgi. By contrast TMED2 is required for the ER-export of both plasma membrane and endosomal TLRs. We also find that a specific N-linked glycan of TLR2 is required for anterograde trafficking and may be directly recognised by TMEDs. Together, these findings suggest that association of TMED2 and TMED7 with TLRs facilitates anterograde transport from the ER to the Golgi.
E3-specific degrader discovery by dynamic tracing of substrate receptor abundance
Authors: Hanzl Alexander , Barone Eleonora , Bauer Sophie , Yue Hong , Nowak Radosław P. , Hahn Elisa , Pankevich Eugenia V. , Koren Anna , Kubicek Stefan , Fischer Eric S. , Winter Georg E.
Published: October 2022

Targeted protein degradation (TPD) is a new pharmacology based on small-molecule degraders that induce proximity between a protein of interest (POI) and an E3 ubiquitin ligase. Of the approximately 600 E3s encoded in the human genome, only around two percent can be co-opted with degraders. This underrepresentation is caused by a paucity of discovery approaches to identify degraders for defined E3s. This hampers a rational expansion of the druggable proteome, and stymies critical advancements in the field, such as tissue- and cell-specific degradation. Here, we focus on dynamic NEDD8 conjugation, a posttranslational, regulatory circuit that controls the activity of 250 cullin RING E3 ligases (CRLs). Leveraging this regulatory layer enabled us to develop a scalable assay to identify compounds that alter the interactome of an E3 of interest by tracing their abundance after pharmacologically induced auto-degradation. Initial validation studies are performed for CRBN and VHL, but proteomics studies indicate broad applicability for many CRLs. Among amenable ligases, we select CRLDCAF15for a proof-of-concept screen, leading to the identification of a novel DCAF15-dependent molecular glue degrader inducing the degradation of RBM23 and RBM39. Together, this strategy empowers the scalable identification of degraders specific to a ligase of interest.
Financial toxicity among cancer patients, survivors, and their families in the United Kingdom: a scoping review
Authors: Ngan Tran Thu , Tien Tran Hoang , Donnelly Michael , O’Neill Ciaran
Published: October 2022

Background

The aim of this scoping review was to identify key research gaps and priorities in order to advance policy and practice for people living with cancer in the UK.

Methods

The review adhered to PRISMA guidelines for scoping review. We searched MEDLINE, EMBASE, Scopus, Web of Science, and Google Scholar on July 16, 2022. There were no restrictions in terms of study design and publication time; grey literature was included. The key words, ‘financial’ or ‘economic’, were combined with each of the following words ‘hardship/stress/burden/distress/strain/toxicity/catastrophe/consequence/impact.’

Results

29/629 studies/reports published during 1982-2022 were eligible to be included in the review. No study conducted a comprehensive inquiry and reported all aspects of FT or used a validated measure of FT. The most three commonly reported outcomes related to financial hardship were financial well-being (24/29), benefit/welfare (17/29), and mental health status (16/29).

Conclusions

It is evident that FT is experienced by UK cancer patients/survivors and that the issue is under-researched. There is an urgent need for further research including rigorous studies which contribute to a comprehensive understanding about the nature and extent of FT, disparities in experience, the impacts of FT on outcomes, and potential solutions to alleviate FT and related problems.
Prediction and location of malignant nodules and microcalcifications in mammography via Deep Learning
Authors: Coronado-Gutiérrez David , Franco Pablo , López Carlos
Published: October 2022

Objectives

To propose a tool to detect and locate malignant nodules and microcalcifications in mammography and judge its potential as a screening tool.

Methods

In this institutional review board approved retrospective study we presented a new tool based on deep learning techniques to predict and locate lesions in mammograms, called quantusMM. 3,114 mammograms from 976 patients were collected from Onkologikoa (Instituto Oncológico de Kutxa) databases for this purpose: 1,248 images with malignant nodules, 736 with malignant microcalcifications and 1,131 without any suspicious findings. The proposed methods split the images in patches to be able to locate the lesions in the image. Then, these methods select the patches most likely to have a lesion based on the brightness values of the pixels. 80% of the selected patches (with the corresponding outcome) were used to train deep learning algorithms and the remaining 20% were used to test the performance to classify into malignant parts or control parts.

Results

The proposed methods obtain an area under the ROC curve (AUC) of 95.5% to predict malignant nodules using the patches, and 90.4% to predict malignant nodules into the whole images. To predict malignant microcalcifications the method obtains an AUC of 99.0% into patches and 90.0% into the whole images.

Conclusions

The proposed tool shows potential to predict and locate malignant nodules and microcalcification lesions in mammography. This new approach could help in the first screening of patients and also could greatly benefit radiologists to support decision making.
Synthesis, crystal structure and Hirshfeld surface analysis of aqua(3-methoxycinnamato-κO)bis(1,10-phenanthroline-κ2
N,N′)cobalt(II) nitrate
Authors: Lehleh Asma , Boutebdja Mehdi , Beghidja Chahrazed , Beghidja Adel
Published: October 2022

The title compound, [Co(C10H9O3)(C12H8N2)2(H2O)]NO3 (I), crystallizes in the triclinic space group P\overline{1} with a monomeric [Co(3-meo-cin)(phen)2(H2O)]+ cation and a nitrate anion (3-meo-cin = 3-methoxy cinnamic acid) in the asymmetric unit. The CoII ion is coordinated by four N atoms from two 1,10-phenanthroline ligands and two O atoms, the first from a methoxy cinnamate ligand and the second from a coordinated water molecule, forming a distorted octahedral geometry. Discrete entities of the cation and nitrate anion are formed by water–nitrate O—H...O and phen–nitrate C—H...O hydrogen bonds. The components are further assembled into chains along the c-axis direction. Layers are than formed by slipped π–π stacking interactions parallel to the bc plane. The intermolecular interactions in the crystal structure were quantified and analysed using Hirshfeld surface analysis.
Interrelationships among enabling factors for BIM adoption in construction enterprises
Authors: Nguyen Thi-Thao-Nguyen , Do Sy Tien , Nguyen Viet Thanh , Nguyen Thu Anh
Published: October 2022

Purpose

This study aims to identify the enabling factors for Building Information Modeling (BIM) adoption in Vietnamese construction enterprises and uncover their interrelationships. This will help stakeholders focus on controlling and allocating resources (time, personnel, and costs) appropriately to adopt BIM and differentiate themselves from fierce competition in the architectural, engineering, construction and operations (AECO) industry.

Design/methodology/approach

This study first identifies and evaluates 32 enabling factors for applying BIM in the Vietnamese construction industry according to the TOE extended framework. Afterwards, a hybrid questionnaire survey using a convenient sampling method is conducted to capture stakeholders' views. The exploratory factor analysis (EFA) and the partial least squares structural equation modelling (PLS-SEM) technique are then applied to identify the constructs of the enabling factors and their interrelationships.

Findings

The study extracts six constructs that could have a significant impact on the adoption of BIM in construction enterprises, namely: technical feasibility (TF), human resources and management (HRM), company business vision (CBV), political environment (PE), economic viability (EV), and legal aspects (LA). Based on eleven proposed hypotheses, the analysis results confirm nine hypotheses and show that the HRM, TF, and CBV have the strongest effects on managers in evaluating the factors for BIM.

Originality/value

The results of the study fill the gap in knowledge by discovering the interrelationships among the enabling factors for BIM adoption in construction enterprises. The results might support the construction enterprises and their stakeholders in increasing the application of BIM, and digital transformation in construction industry.
Research on improving YOLOv5s algorithm for fabric defect detection
Authors: Zhou Shi , Zhao Jia , Shi Yi Shan , Wang Yi Fan , Mei Shun Qi
Published: October 2022

Purpose

In the fabric manufacturing industry, various unfavorable factors, including machine fault and yarn breakage, can easily cause fabric defects and affect product quality, begetting huge economic losses to enterprises. Thus, automatic fabric defect detection systems have become an important development direction. Herein, the most common defects in the fabric production process, like ribbon yarn, broken yarn, cotton ball, holes, yarn shedding and stains, are detected. Current fabric defect detection systems afford low detection accuracy and a high missed detection rate for small target fabric defects. Therefore, this study proposes deep learning technology for automatically detecting fabric defects by improving the YOLOv5s target detection algorithm. The improved algorithm is termed YOLOv5s-4SCK, which can effectively detect fabric defects. This study aims to discuss the aforementioned issues.

Design/methodology/approach

Specifically, based on the YOLOv5s algorithm, first, the structure of YOLOv5s is modified to add a small target detection layer, fully utilize deep and shallow features and reduce the missed detection rate of small target fabric defects. Second, the integration of CARAFE upsampling enables the effective retention of feature information and maintenance of a certain computational efficiency, thereby improving the detection accuracy. Finally, the K-Means++ clustering algorithm is used to analyze the position of the center point of the prior box to better obtain the anchor box and improve the average accuracy and evaluation index of detection.

Findings

The research results show that the YOLOv5s-4SCK algorithm increases the accuracy by 4.1% and the detection speed by 2 f.s-1 compared to the original YOLOv5s algorithm, and it effectively improves the original YOLOv5s problem of high missed detection rate of small targets.

Research limitations/implications

The YOLOv5s-4SCK proposed in this paper can effectively reduce the missed detection rate of fabric defects, improve the detection efficiency and has certain industrial value.

Practical implications

The proposed algorithm can quickly identify fabric defects, effectively improving the detection rate. In the future, the proposed algorithm will be applied in the actual industry.

Social implications

Automatic fabric defect detection reduces the manpower of inspectors, and the proposed YOLOv5s-4SCK algorithm is also suitable for other recognition fields.

Originality/value

The proposed YOLOv5s-4SCK algorithm has been tested using real cloth to ensure its accuracy, and its performance is better than the original YOLOv5s algorithm.