bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential action modes of Neutrophil Extracellular Trap-targeted drugs define T cell responses in SARS-CoV-2 infection
Authors: Bonilha Caio Santos , Veras Flavio Protasio , Ramos Anderson dos Santos , Gomes Giovanni Freitas , Lemes Robertha Mariana Rodrigues , Arruda Eurico , Alves-Filho José Carlos , Cunha Thiago Mattar , Cunha Fernando Queiroz 
Published: July 2024

AbstractNeutrophil extracellular traps (NETs) play a dual role in SARS-CoV-2 infection, aiding early immune defense but also contributing to lung damage. While NET targeting may improve clinical outcomes in SARS-CoV-2 infection, its impact on adaptive immunity, crucial for fighting the virus, remains unclear. Our study demonstrates that both recombinant human DNase (rhDNase), degrading NET structure, and GSK484, inhibiting NET formation, reduce lung NET concentration and improve clinical outcomes in infected mice, yet they differ in their influence on T cell responses. We show that rhDNase does not impact T cell responses, whereas GSK484 diminishes virus-specific T cell responses.In vitro, GSK484 decreases dendritic cell antigen presentation by impairing antigen uptake and reduces IL-2 signaling by affecting its production by T cells. In a model of lung inflammation, GSK484 diminishes antigen-specific T cell activation and proliferation, while rhDNase shows a potential to boost T cell responses via the presence of NET fragments that reduce T cell activation threshold. Our findings suggest that NET targeting with rhDNase or GSK484 holds therapeutic potential for treating SARS-CoV-2 infection, while their distinct modes of action shape T cell responses during the infection.
β-1,6-glucan plays a central role in the structure and remodeling of the bilaminate fungal cell wall
Authors: Bekirian Clara , Valsecchi Isabel , Bachellier-Bassi Sophie , Scandola Cyril , Guijarro J. Iñaki , Chauvel Murielle , Mourer Thierry , Gow Neil A.R. , Aimanianda Vishukumar , d’Enfert Christophe , Fontaine Thierry 
Published: July 2024

AbstractThe cell wall of human fungal pathogens plays critical roles as an architectural scaffold and as a target and modulator of the host immune response. Although the cell wall of the pathogenic yeastCandida albicansis intensively studied, one of the major fibrillar components in its cell wall, β-1,6- glucan, has been largely neglected. Here, we show that β-1,6-glucan is essential for bilayered cell wall organization, cell wall integrity and filamentous growth. For the first time, we show that β-1,6- glucan production compensates the defect in mannan elongation in the outer layer of the cell wall. In addition, β-1,6-glucan dynamics are also coordinated by host environmental stimuli and stresses with wall remodeling, where the regulation of β-1,6-glucan structure and chain length is a crucial process. As we point out that β-1,6-glucan is exposed at the yeast surface and modulate immune response, β-1,6-glucan must be considered a key factor in host-pathogen interactions.
Efficient Generation ofSOCS2Knock-out Sheep by Electroporation of CRISPR-Cas9 Ribonucleoprotein Complex with Dual-sgRNAs
Authors: Mahdi Ahmed K. , Fitzpatrick Devon S. , Hagen Darren E. , McNabb Bret R. , Beach Tara Urbano , Muir William M. , Werry Nicholas , Van Eenennaam Alison L. , Medrano Juan F. , Ross Pablo J. 
Published: July 2024

AbstractKnock-out (KO) sheep were produced using CRISPR-Cas9 ribonucleoprotein complexes in zygotes targeting an 85 bp section of the first exon of the Suppressor of Cytokine Signalling-2 (SOCS2) gene. Electroporation was performed 6 hours post-fertilization with dual-guide CRISPR-Cas9 ribonucleoproteins (RNPs). Fifty-two blastocysts were transferred to 13 estrus-synchronized recipients, yielding five live lambs and one stillborn. These lambs were all compound heterozygotes with mutations predicted to result inSOCS2KO. Three lambs carried large deletion alleles (259 bp, 1694 bp, and 2127 bp) that evaded initial detection via initial PCR screening. Off-target analysis identified a small number of mutations which may have been the result of off-target activity in regions with some homology to the guides, but notably such mutations were also observed in unedited controls. Further, we observed several orders of magnitude more mutations outside of these regions of homology in both edited animals and controls. Western blot and RT-PCR analysis of cell lines from SOCS2 KO lambs showed trace levels ofSOCS2mRNA and SOCS2 protein. In conclusion, combining IVF and electroporation of dual-guide CRISPR-Cas9 RNPs was effective at generating KO sheep.
Inhibition of serine racemase prevents diabetic retinopathy
Authors: Jiang Haiyan , Zhou Piansi , Jiang Xue , Wu Xiong , Mao Yandie , Liu Shuyi , Tang Shiqi , Zhou Jing , Zhang Zhiwen , Ren Bingbing , Shan Ge , Qu Jia , Wu Shengzhou 
Published: July 2024

AbstractRetinal diabetic neuropathy (RDN) precedes retinal microvascular pathology in diabetic retinopathy (DR), but the therapy by antagonizing RDN to stall DR is rare. Emerging evidence including ours suggest that serine racemase (SRR) drives DR at least by promoting RDN. Thus, we explore the therapy by antagonizing SRR to stall and treat DR. We herein indicate that inhibition of SRR by oral gavage of l-aspartic acid β-hydroxymate (L-ABH), a competitive inhibitor of SRR, mitigated photoreceptor dysfunction, loss of retinal ganglion cells (RGC) and retinal endothelial cell and pericyte in db/db mice, a type II diabetes model. To dissect the mechanism, intravitreal injection of L-ABH mitigates glutamate-induced neurotoxicity in the retina. In the whole body, gastrointestinal-based delivery of L-ABH maintained euglycemia and improved glucose tolerance either in db/db mice or in diet-induced obesity mice. In conclusion, inhibition of SRR prevented retinal neurovascular abnormalities in diabetic animals through executing neuroprotection in the retina and maintaining glucose homeostasis in the system. Our study reveals a novel strategy to prevent DR.
Treatment recommendations based on Network Meta-Analysis: rules for risk-averse decision-makers
Authors: Ades A E , Pedder Hugo , Davies Annabel L , Thom H , Phillippo David M , Downing Beatrice , Caldwell Deborah M , Welton Nicky J 
Published: July 2024

ABSTRACTBackgroundThe treatment recommendation based on a Network Meta-analysis (NMA) is usually the single treatment with the highest Expected Value (EV) on an evaluative function. We explore approaches which recommend multiple treatments and which penalize uncertainty, making them suitable for risk-averse decision makers.MethodsWe introduce Loss-adjusted EV (LaEV) and compare it to GRADE and three probability-based rankings. We define the properties of a valid ranking under uncertainty and other desirable properties of ranking systems. A two-stage process is proposed: the first selects treatments superior to the reference treatment; the second identifies those that are also within a Minimal Clinically Important Difference (MCID) of the best treatment. Decision rules and ranking systems are compared on stylized examples and 10 NMAs used in NICE Guidelines.ResultsOnly LaEV reliably delivers valid rankings under uncertainty and has all the desirable properties. In 10 NMAs comparing between 4 and 40 treatments, an EV decision maker would recommend 4-14 treatments, and LaEV 0-3 (median 2) fewer. GRADE rules give rise to anomalies, and, like the probability-based rankings, the number of treatments recommended depends on arbitrary probability cutoffs. Among treatments that are superior to the reference, GRADE privileges the more uncertain ones, and in 3/10 cases GRADE failed to recommend the treatment with the highest EV and LaEV.ConclusionsA two-stage approach based on MCID ensures that EV- and LaEV-based rules recommend a clinically appropriate number of treatments. For a risk-averse decision maker, LaEV is conservative, simple to implement, and has an independent theoretical foundation.HighlightsWhat is already known?A risk-neutral decision-maker should make treatment decisions based on Expected Value (EV), meaning that the single treatment with the highest expected efficacy from a network meta-analysis should be recommended, regardless of uncertainty. In practice, decision makers may recommend several treatments, and take uncertainty into account on anad hocbasis.What is new?We introduce Loss-adjusted EV (LaEV) as a mechanism for risk-averse decision making, and set out desirable properties of ranking systems. We define a ranking as valid under uncertainty if a higher EV is ranked above a lower one at the same uncertainty and a lower uncertainty above a higher one at the same EV. We compare LaEV to GRADE and probabilistic rankings. Of the methods examined, only LaEV provides a valid ranking under uncertainty and has all the desirable properties.ImplicationsFor a risk-averse decision maker, LaEV is a reliable, conservative, and easy-to-implement decision metric, with an independent theoretical foundation. Adoption of a risk-averse stance might focus attention on more accurate quantification of uncertainty, and encourage generation of better quality evidence.
Using Family History Data to Improve the Power of Association Studies: Application to Cancer in UK Biobank
Authors: Wilcox Naomi , Tyrer Jonathan P. , Dennis Joe , Yang Xin , Perry John R. B. , Gardner Eugene J. , Easton Douglas F. 
Published: July 2024

AbstractIn large cohort studies the number of unaffected individuals outnumbers the number of affected individuals, and the power can be low to detect associations for outcomes with low prevalence. We consider how including recorded family history in regression models increases the power to detect associations between genetic variants and disease risk. We show theoretically and using Monte-Carlo simulations that including family history of the disease, with a weighting of 0.5 compared to true cases, increases the power to detect associations. This is a powerful approach for detecting variants with moderate effects, but for larger effect sizes a weighting of >0.5 can be more powerful. We illustrate this both for common variants and for exome sequencing data for over 400,000 individuals in UK Biobank to evaluate the association between the burden of protein-truncating variants in genes and risk for 4 cancer types.
Simulating 500 million years of evolution with a language model
Authors: Hayes Thomas , Rao Roshan , Akin Halil , Sofroniew Nicholas J. , Oktay Deniz , Lin Zeming , Verkuil Robert , Tran Vincent Q. , Deaton Jonathan , Wiggert Marius , Badkundri Rohil , Shafkat Irhum , Gong Jun , Derry Alexander , Molina Raul S. , Thomas Neil , Khan Yousuf , Mishra Chetan , Kim Carolyn , Bartie Liam J. , Nemeth Matthew , Hsu Patrick D. , Sercu Tom , Candido Salvatore , Rives Alexander 
Published: July 2024

AbstractMore than three billion years of evolution have produced an image of biology encoded into the space of natural proteins. Here we show that language models trained on tokens generated by evolution can act as evolutionary simulators to generate functional proteins that are far away from known proteins. We present ESM3, a frontier multimodal generative language model that reasons over the sequence, structure, and function of proteins. ESM3 can follow complex prompts combining its modalities and is highly responsive to biological alignment. We have prompted ESM3 to generate fluorescent proteins with a chain of thought. Among the generations that we synthesized, we found a bright fluorescent protein at far distance (58% identity) from known fluorescent proteins. Similarly distant natural fluorescent proteins are separated by over five hundred million years of evolution.
A stabilized MERS-CoV spike ferritin nanoparticle vaccine elicits robust and protective neutralizing antibody responses
Authors: Powell Abigail E. , Caruso Hannah , Park Soyoon , Chen Jui-Lin , O’Rear Jessica , Ferrer Brian J. , Belnap David M. , Walker Audrey , Bruening Anneliese , Hartwig Airn , Ahyong Vida , Dougherty Cristy S. , Bowen Richard , Ledgerwood Julie E. , Kay Michael S. , Weidenbacher Payton A.-B. , Palanski Brad A. 
Published: July 2024

SummaryMiddle East respiratory syndrome coronavirus (MERS-CoV) was first identified as a human pathogen in 2012 and causes ongoing sporadic infections and outbreak clusters. Despite case fatality rates (CFRs) of over 30% and the pandemic potential associated with betacoronaviruses, a safe and efficacious vaccine has not been developed for prevention of MERS in at-risk individuals. Here we report the design, in vitro characterization, and preclinical evaluation of MERS-CoV antigens. Our lead candidate comprises a stabilized spike ectodomain displayed on a self-assembling ferritin nanoparticle that can be produced from a high-expressing, stable cell pool. This vaccine elicits robust antibody titers in BALB/c mice as measured by MERS- CoV pseudovirus and live-virus neutralization assays. Immunization of non-human primates (NHPs) with a single dose of Alhydrogel-adjuvanted vaccine elicits >103geometric mean titer (GMT) of pseudovirus neutralizing antibodies that can be boosted with a second dose. These antibody levels are durable, with GMTs that surpass the post-prime levels for more than 5 months post-boost. Importantly, sera from these NHPs exhibit broad cross-reactivity against lentiviruses pseudotyped with spike proteins from MERS-CoV clades A, B, and C as well as a more distant pangolin merbecovirus. In transgenic mice expressing human DPP4, immunization provided dose-dependent protection against MERS-CoV lethal challenge, and in an established alpaca challenge model, immunization fully protected against MERS-CoV infection. This protein-based MERS-CoV nanoparticle vaccine is a promising candidate for advancement to clinical development to protect at-risk individuals and for future use in a potential outbreak setting.
Essential Roles of RodA Peptidoglycan Polymerase and PBP2 Transpeptidase in Expression of Cell Wall-Spanning Supramolecular Organelles and ModulatingSalmonellaVirulence
Authors: Doble Anne C. , Gollan Bethany C , Clark-Corrigall John , Bulmer David M. , Daniel Richard A , Mastroeni Pietro , Khan C. M. Anjam 
Published: July 2024

AbstractThe increased spread of multidrug-resistant bacteria no longer sensitive to commonly used antibiotics poses a major threat to human health. The search for potential new drug targets is critical in disease control and prevention. Whilst several components of the cell wall synthesis machinery are already targeted by beta-lactam antibiotics, other elements of this machinery present opportunities for novel drug targets. Landmark studies revealed RodA exhibits peptidoglycan polymerase activity inBacillus subtilisandEscherichia coli,highlighting RodA as a prime for the next generation of antimicrobial drugs. However, the role of RodA in virulence remains unexplored. Through targeted mutagenesis, virulence gene reporter assays, and phenotypic screening, we demonstrate that the presence of RodA or PBP2, is intrinsically linked to the regulation of virulence gene expression inSalmonella. Specifically, deletion of either of these components causes both disruption in cell morphology and a complete downregulation in major cell invasion-associated virulence factorsin vitro,and attenuated virulencein vivo. Significantly, this study highlights the importance of RodA and PBP2 in both the biology and virulence of an important bacterial pathogen, identifying them as promising targets for developing new antibiotics.
Porphyromonas gingivalisactivates Heat-Shock-Protein 27 to drive a LC3C-specific probacterial form of select autophagy that is redox sensitive for intracellular bacterial survival in human gingival mucosa
Authors: Wellslager Bridgette , Roberts JoAnn , Chowdhury Nityananda , Madan Lalima , Orellana Elsy , Yilmaz Özlem 
Published: July 2024

ABSTRACTPorphyromonas gingivalis, a major oral pathobiont, evades canonical host pathogen clearance in human primary gingival epithelial cells (GECs) by initiating a non-canonical variant of autophagy consisting of Microtubule-associated protein 1A/1B-light chain 3 (LC3)-rich autophagosomes, which then act as replicative niches. Simultaneously,P. gingivalisinhibits apoptosis and oxidative-stress, including extracellular-ATP (eATP)-mediated reactive-oxygen-species (ROS) production via phosphorylating Heat Shock Protein 27 (HSp27) with the bacterial nucleoside-diphosphate-kinase (Ndk). Here, we have mechanistically identified thatP. gingivalis-mediated induction of HSp27 is crucial for the recruitment of the LC3 isoform, LC3C, to drive the formation of liveP. gingivalis-containing Beclin1-ATG14-rich autophagosomes that are redox sensitive and non-degrading. HSp27 depletions of both infected GECs and gingiva-mimicking organotypic-culture systems resulted in the collapse ofP. gingivalis-mediated autophagosomes, and abolishedP. gingivalis-induced LC3C-specific autophagic-flux in a HSp27-dependent manner. Concurrently, HSp27 depletion accompanied by eATP treatment abrogated protracted Beclin 1-ATG14 partnering and decreased live intracellularP. gingivalislevels. These events were only partially restored via treatments with the antioxidant N-acetyl cysteine (NAC), which rescued the cellular redox environment independent of HSp27. Moreover, the temporal phosphorylation of HSp27 by the bacterial Ndk results in HSp27 tightly partnering with LC3C, hindering LC3C canonical cleavage, extending Beclin 1-ATG14 association, and halting canonical maturation. These findings pinpoint how HSp27 pleiotropically serves as a major platform-molecule, redox regulator, and stepwise modulator of LC3C duringP. gingivalis-mediated non-canonical autophagy. Thus, our findings can determine specific molecular strategies for interfering with the host-adaptedP. gingivalis’ successful mucosal colonization and oral dysbiosis.
Identification of mCMQ069, a novel antimalarial with potential for a single-dose cure and/or 28-day chemoprevention
Authors: Gupta Anil K. , Pedroarena James , Nazarian Armen , Antonova-Koch Jenya , Weiss Frank , Kumpornsin Krittikorn , Chi Victor , Woods Ashley K. , Lee Kyoung-Jin , Joseph Sean B. , Li Shuangwei , Brittain Jason , De Hostos Eugenio , Duffy James , Cooper Anne , Schultz Peter G. , McNamara Case W. , Chatterjee Arnab K. 
Published: July 2024

ABSTRACTIn efforts towards eliminating malaria, a discovery program was initiated to identify a novel antimalarial using KAF156 as a starting point. Following the most recent TCP/TPP guidelines, we have identified mCMQ069 with a predicted single oral dose for treatment (∼40-106 mg) and one-month chemoprevention (∼96-216 mg). We have improved unbound MPC and predicted human clearance by 18-fold and 10-fold respectively when compared to KAF156.
Differential expression ofCCD4(4B)drives natural variation in fruit carotenoid content in strawberry (Fragariaspp.)
Authors: Amaya Iraida , Roldán-Guerra F. Javier , Ordóñez-Díaz José L. , Torreblanca Rocío , Wagner Henning , Veronika Waurich , Olbricht Klaus , Moreno-Rojas José M. , Sánchez-Sevilla José F. , Castillejo Cristina 
Published: July 2024

AbstractPigments, mainly anthocyanins and carotenoids, are important contributors to fruits’ visual appearance and nutritional properties. In strawberry (Fragariaspp.), the genetic and molecular mechanisms regulating fruit carotenoid biosynthesis and its natural variation remain largely unexplored. In this study, we sought to identify genomic loci contributing to variation in yellow flesh pigmentation. A major QTL,qYellow Flesh-4B, accounting for 82% of the total phenotypic variation was identified onF. ×ananassachromosome 4B. Following a candidate gene approach, we determined thatCCD4(4B),a carotenoid cleavage dioxygenase (CCD), was the underlying gene. Specific polymorphisms onCCD4(4B)promoter region were associated with the yellow flesh phenotype and with differential regulation ofCCD4(4B)expression during fruit ripening. Furthermore,CCD4(4B)expression levels were negatively correlated with violaxanthin, lutein, zeaxanthin, β-carotene and total carotenoid content. The role of CCD4(4B) in carotenoid turnover was confirmed by transient overexpression inF.×ananassafruits, which led to a decrease in carotenoid accumulation. Notably, a −35 C>T SNP identified inCCD4(4B)promoter was found to be predictive forCCD4(4B)expression, and carotenoid content in fruits of a diverse germplasm collection, which included different octoploidFragariaspecies. Taken together, these results provide important genetic insights into the natural variation of carotenoid content in strawberry. The High-Resolution Melting (HRM) DNA test here developed offers a fast and reliable method to predict high fruit carotenoid content, representing a useful tool for breeding projects aiming to enhance the nutritional value of this crop.
Implementing total quality management in a virtual organisation: thoughts and lessons from an interventionist approach
Authors: Norberto Carneiro Welington , Mendonça Neto Octavio Ribeiro de , Afonso Paulo , Oyadomari Jose Carlos Tiomatsu , Dultra-de-Lima Ronaldo Gomes 
Published: July 2024

PurposeThis article aims to understand the challenges and key takeaways of implementing total quality management (TQM) in a virtual organisation.Design/methodology/approachAn interventionist research (IVR) methodology combined with a qualitative critical event analysis was used to evaluate the challenges and concerns faced during the company’s adoption of TQM and understand the roles of the key players involved.FindingsStandard process tools such as desktop procedures (DTP), focused teams, and service-level agreements (SLAs) were fundamental to implementing TQM in the company. These processes require the right leaders, but external agents may also be influential, acting as accelerators of change in adopting and using management practices in small companies. Indeed, the researcher acted as a problem solver, bringing innovative solutions to the firm using a hands-on iterative approach.Practical implicationsThis research underscores the importance of critical success factors (CSF), such as employee engagement, training, and project management tools. These factors are not just important but crucial for the success of TQM in organisations seeking to adopt the industry’s best practices.Originality/valueThis study, conducted as a virtual IVR for TQM implementation, provides novel insights for practitioners and academics. It elucidates the pivotal role of some quality management tools in the journey towards TQM and the role of both internal and external critical players in the process, particularly in small virtual organisations based on innovative business models.