bluuebunny/crossref_metadata_2025_split huggingface dataset:
Whole-genome phylogenomics of the tinamous (Aves: Tinamidae): comparing gene tree estimation error between BUSCOs and UCEs illuminates rapid divergence with introgression
Authors: Musher Lukas J. , Catanach Therese A. , Valqui Thomas , Brumfield Robb T. , Aleixo Alexandre , Johnson Kevin P. , Weckstein Jason D. 
Published: January 2024

AbstractIncomplete lineage sorting (ILS) and introgression increase genealogical discordance across the genome, which complicates phylogenetic inference. In such cases, identifying orthologs that result in gene trees with low estimation error is crucial because phylogenomic methods rely on accurate gene histories. We sequenced whole genomes of tinamous (Aves: Tinamidae) to reconstruct their interrelationships and dissect the sources of gene tree and species-tree discordance. We compared results based on five ortholog sets: (1) coding genes (BUSCOs), (2) ultraconserved elements (UCEs) with short flanking regions, (3) UCEs with intermediate flanks, (4) UCEs with long flanks, and (5) UCEs mapped to the Z-chromosome. We hypothesized that orthologs with more phylogenetically informative sites would result in more accurate species trees because the resulting gene trees contain lower stochastic error. Consistent with our hypothesis (and a large body of theory), we found that long UCEs had the most informative sites and lowest rates of error. Surprisingly, BUSCO gene trees contained high error compared to long UCEs, despite having many informative sites. Unlike UCEs, BUSCO gene sequences showed a positive association between the proportion of informative sites and gene tree error. Thus, the underlying properties of molecular evolution differ between BUSCO and UCE datasets, and these differences should be considered when selecting loci for phylogenomic analysis. Importantly, these results indicate stochastic error is not driving inaccurate gene tree estimation for BUSCO loci, instead suggesting a more problematic impact of systematic error in this data-type. Still, species trees from different datasets were mostly congruent. Only one clade, which has a history of ILS and introgression, exhibited substantial species-tree discordance across the different data sets. We suggest that agreement between the Z-chromosome dataset and that of long UCEs lends support to this topology because the Z-chromosome is expected to contain low rates of ILS and faster coalescent times due its relatively smaller effective population size. Overall, we present the most complete phylogeny for tinamous to date, identify an unrecognized species, and provide a case study for species-level phylogenomic analysis using whole-genomes.
Hybrid immunity to SARS-CoV-2 arises from serological recall of IgG antibodies distinctly imprinted by infection or vaccination
Authors: Voss William N. , Mallory Michael A. , Byrne Patrick O. , Marchioni Jeffrey M. , Knudson Sean A. , Powers John M. , Leist Sarah R. , Dadonaite Bernadeta , Townsend Douglas R. , Kain Jessica , Huang Yimin , Satterwhite Ed , Castillo Izabella N. , Mattocks Melissa , Paresi Chelsea , Munt Jennifer E. , Scobey Trevor , Seeger Allison , Premkumar Lakshmanane , Bloom Jesse D. , Georgiou George , McLellan Jason S. , Baric Ralph S. , Lavinder Jason J. , Ippolito Gregory C. 
Published: January 2024

SUMMARYWe used plasma IgG proteomics to study the molecular composition and temporal durability of polyclonal IgG antibodies triggered by ancestral SARS-CoV-2 infection, vaccination, or their combination ("hybrid immunity"). Infection, whether primary or post-vaccination, mainly triggered an anti-spike antibody response to the S2 domain, while vaccination predominantly induced anti-RBD antibodies. Immunological imprinting persisted after a secondary (hybrid) exposure, with >60% of the ensuing serological response originating from the initial antibodies generated during the first exposure. We highlight one instance where hybrid immunity arising from breakthrough infection resulted in a marked increase in the breadth and affinity of a highly abundant vaccination-elicited plasma IgG antibody, SC27. With an intrinsic binding affinity surpassing a theoretical maximum (KD< 5 pM), SC27 demonstrated potent neutralization of various SARS-CoV-2 variants and SARS-like zoonotic viruses (IC50∼0.1–1.75 nM) and provided robust protectionin vivo. Cryo-EM structural analysis unveiled that SC27 binds to the RBD class 1/4 epitope, with both VH and VL significantly contributing to the binding interface. These findings suggest that exceptionally broad and potent antibodies can be prevalent in plasma and can largely dictate the nature of serological neutralization.HIGHLIGHTS▪Infection and vaccination elicit unique IgG antibody profiles at the molecular level▪Immunological imprinting varies between infection (S2/NTD) and vaccination (RBD)▪Hybrid immunity maintains the imprint of first infection or first vaccination▪Hybrid immune IgG plasma mAbs have superior neutralization potency and breadth
Minimizing variability in the filament middle cerebral artery occlusion model in C57BL/6 mice by surgical optimization - the PURE-MCAo Model
Authors: Yoshimura Sodai , Dorok Maximilian , Mamrak Uta , Wehn Antonia , Krestel Eva , Khalin Igor , Plesnila Nikolaus 
Published: January 2024

AbstractBACKGROUNDIn the intraluminal filament middle cerebral artery occlusion (fMCAo) model, there is considerable variability in infarct volumes, especially in C57BL/6 mice, which often lack the P1 segment of the posterior cerebral artery (PCA) and therefore develop not only MCA but also PCA area infarcts after fMCAo. Another factor contributing to infarct volume variability is collateral flow to the MCA area. The aim of this study was to establish an optimal surgical method to reduce the infarct volume variability in C57BL/6 mice.METHODSC57BL/6 mice were subjected to 60 min of fMCAo with cerebral blood flow monitored by laser Doppler fluxmetry. The influence of the common carotid artery (CCA) ligation, filament morphology, and the pterygopalatine artery (PPA) ligation on lesion volume and neurological severity score 24 hours after reperfusion were assessed.RESULTThe use of filaments with appropriate length of coating and ligation of the PPA while maintaining perfusion of the CCA prevented the development of infarcts in the PCA area, resulted in pure MCA infarcts (68.3±14.5mm3, 26.1±3.6% of the hemisphere with Swanson’s correction) and reduced the variability of infarct volumes by more than half to 13.9% of the standard deviation divided by mean.CONCLUSIONSUsing improved surgical methods with suitable filaments to induce MCA occlusion in mice, we were able to producePCA area-unaffectedreproducible infarcts exclusively in the MCA area with reduced variability (PURE-MCAo). Our results may thus help to increase the reproducibility of the fMCAo model and reduce the number of animals required in preclinical stroke research.
Towards a Buruli Ulcer Rapid Diagnostic Test that Targets Mycolactone
Authors: Siirin Marina , Pedram Bijan , Gonzalez-Moa Maria J. , Warryn Louisa , Yotsu Rie , Saunders Jean M. , Saunders Aaron E. , Baldwin Richard K. , Porter Jessica L. , Stinear Timothy P. , Cruz-Mata Israel , de Souza Dziedzom Komi , Pluschke Gerd , Biamonte Marco A. 
Published: January 2024

AbstractWe report the development of a prototype rapid diagnostic test for Buruli ulcer, an ulcerative necrotizing skin disease caused byM. ulcerans. The test was designed to detect mycolactone, a metabolite unique toM. ulcerans. The chief technical challenge was to develop a simple workflow to extract trace amounts of mycolactone from wound exudates collected with a swab and, after a concentration step, to visualize the mycolactone by means of a lateral flow assay. This was achieved by utilizing a mouse monoclonal antibody specific for mycolactone and magnetic gold nanoshells. The latter are a novel class of reporter particles consisting of a ferrite core, a silica gel middle layer that serves to decrease the overall density of the nanoparticle and facilitate its resuspension in aqueous media, and an outer layer of gold, which provides a dark coloration through plasmon resonance effects. These nanoparticles, once conjugated to the anti-mycolactone antibody, enable the immunomagnetic concentration of the targeted analyte and its detection by lateral flow assay. The test procedure can be conducted within 2 hours with a magnetic rack and no powered instrumentation is required. The test can detect as little as 3.5–7 ng of mycolactone collected on a swab.Author summaryBuruli ulcer is a neglected tropical disease that affects the poorest of the poorest in Africa. Even young people can harbor large ulcers, with raw flesh directly exposed. While antibiotic treatments exist, there are no simple methods to diagnose the disease. Here, we attempted to detect mycolactone, a small molecule produced by the bacteria that causes Buruli ulcer. One difficulty was the sample type to be used, as the open wounds are sampled with a swab. The question was how to extract mycolactone from the swab and then detect it by means of a rapid diagnostic test, without using sophisticated equipment. We tried to answer this question by combining monoclonal antibodies specific for mycolactone and novel magnetic nanoparticles to concentrate and visualize mycolactone with a rapid test.
Hemoglobin-Albumin-Lymphocyte-Platelet (HALP) score as a predictive value of Incidental prostate cancer for patients going for Transurethral resection of the prostate (TURP): A Single Center Study
Authors: Bendari Ahmed 
Published: January 2024

AbstractAimsProstate cancer is a significant health concern worldwide, and early detection is crucial for effective treatment. This study aimed to investigate the role of the Hemoglobin-Albumin-Lymphocyte-Platelet (HALP) score in detecting prostate cancer in patients undergoing Transurethral Resection of the Prostate (TURP). Additionally, comprehensive analysis was performed to explore clinical parameters associated with incidentally diagnosed prostate cancer post-TURP.MethodsA total of 131 patients with symptomatic bladder outlet obstruction who underwent TURP were included in the study. The patients were divided into two groups: those with benign prostatic hyperplasia (BPH) and those with invasive prostatic carcinoma. The IPC group consisted of patients with both low-grade and high-grade IPC determined by Gleason score. Demographic data, including age, race, medical history, body mass index, smoking and alcohol status, and family history of prostate cancer, were evaluated. Postoperative measurement of specimen weight and prostate-specific antigen (PSA) levels were also analyzed.ResultResults revealed that approximately 50% of patients had BPH, while the remaining 50% had IPC. Patients with IPC, particularly high-grade IPC, had significantly higher PSA levels and lower resected specimen weight compared to those with BPH. The HALP score, which incorporates hemoglobin, albumin, lymphocyte, and platelet levels, showed promise as a discriminatory tool for distinguishing between BPH and IPC, as well as between high-grade IPC and BPH/low-grade IPC. Logistic regression analysis identified increased PSA levels, decreased HALP score, and smaller specimen weight as independent predictive factors for IPC after TURP. Notably, HALP score was the only significant independent predictive factor associated with high-grade IPC.ConclusionThese findings contribute to the understanding of risk factors and diagnostic tools for incidentally detected prostate cancer in patients with bladder outlet obstruction undergoing TURP. The HALP score, along with PSA levels and specimen weight, can aid in the early detection and management of prostate cancer. Further research is warranted to validate these findings and explore the clinical utility of the HALP score in predicting prostate cancer outcomes.
Comparison of the performance of multiple whole-genome sequence-based tools for the identification ofBacillus cereus sensu strictobiovar Thuringiensis
Authors: Chung Taejung , Salazar Abimel , Harm Grant , Johler Sophia , Carroll Laura M. , Kovac Jasna 
Published: January 2024

ABSTRACTTheBacillus cereus sensu stricto(s.s.) species comprises strains of biovarThuringiensis(Bt) known for their bioinsecticidal activity, as well as strains with foodborne pathogenic potential.Btstrains are identified (i) based on the production of insecticidal crystal proteins also known as Bt toxins or (ii) based on the presence ofcry,cyt, andvipgenes, which encode Bt toxins. Multiple bioinformatics tools have been developed for the detection of crystal protein-encoding genes based on whole-genome sequencing (WGS) data. However, the performance of these tools is yet to be evaluated using phenotypic data. Thus, the goal of this study was to assess the performance of four bioinformatics tools for the detection of crystal protein-encoding genes. The accuracy of sequence-based identification ofBtwas determined in reference to phenotypic microscope-based screening for production of crystal proteins. A total of 58 diverseB. cereus s.l.strains isolated from clinical, food, environmental, and commercial biopesticide products were underwent WGS. Isolates were examined for crystal protein production using phase contrast microscopy. Crystal protein-encoding genes were detected using BtToxin_Digger, BTyper3, IDOPS, and Cry_processor. Out of 58 isolates, the phenotypic production of crystal proteins was confirmed for 18 isolates. Specificity and sensitivity ofBtidentification based on sequences were 0.85 and 0.94 for BtToxin_Digger, 0.97 and 0.89 for BTyper3, 0.95 and 0.94 for IDOPS, and 0.88 and 1.00 for Cry_processor, respectively. Cry_processor predicted crystal protein production with highest specificity, and BtToxin_Digger and IDOPS predicted crystal protein production with the highest sensitivity. Three out of four tested bioinformatic tools performed well overall, with IDOPS achieving both high sensitivity and specificity (>0.90).IMPORTANCEBacillus cereus s.s.biovarThuringiensis(Bt) is used as an organic biopesticide. It is differentiated from the foodborne pathogenBacillus cereus s.s.by the production of insecticidal crystal proteins. Thus, reliable genomic identification of biovarThuringiensisis necessary to ensure food safety and facilitate risk assessment. This study assessed the accuracy of WGS-based identification ofBtcompared to phenotypic microscopy-based screening for crystal protein production. Multiple bioinformatics tools were compared to assess their performance in predicting crystal protein production. Among them, IDOPS performed best overall at WGS- basedBtidentification.
Stepwise Neofunctionalization of the NF-κB Family Member c-Rel during Vertebrate Evolution
Authors: Daly Allison E. , Chang Abraham B. , Purbey Prabhat , Williams Kevin J. , Yeh George , Li Shuxing , Pope Scott D. , Venkatesh Byrappa , Redelings Benjamin D. , Li Sibon , Nguyen Kaylin , Rodrigues Joseph , Jorgensen Kelsey , Siggers Trevor , Chen Lin , Smale Stephen T. 
Published: January 2024

SUMMARYAdaptive immunity and the five vertebrate NF-κB/Rel family members first appeared in cartilaginous fish, suggesting that divergence and specialization within the NF-κB family helped facilitate the evolution of adaptive immunity. One specialized function of the NF-κB c-Rel protein in macrophages is the activation ofIl12b, which encodes a key regulator of T-cell development. We found that c-Rel is a far more potent regulator ofIl12bthan of any other inducible genes in macrophages, with c-Rel regulation ofIl12bdependent on its heightened intrinsic DNA-binding affinity. c-Rel homodimers regulateIl12btranscription in part via motifs with little resemblance to canonical NF-κB motifs. ChIP-seq experiments further defined distinct c-Rel DNA-binding preferences genome-wide, and X-ray crystallography of a c-Rel/RelA chimeric protein identified key amino acid changes that support the unique c-Rel properties. Unexpectedly, these changes, along with the c-Rel/RelA binding affinity differences, were largely restricted to mammalian species. Together, our findings reveal how a transcription factor family member can undergo a structural transition at a late stage of vertebrate evolution, resulting in an increased intrinsic DNA binding affinity and with clear functional consequences, presumably to support the increasing complexity of immune regulation.
Artemisinin-resistantPlasmodium falciparumKelch13 mutant proteins display reduced heme-binding affinity and decreased artemisinin activation
Authors: Rahman Abdur , Tamseel Sabahat , Coppée Romain , Dutta Smritikana , Khan Nawaal , Faaiz Mohammad , Rastogi Harshita , Nath Jyoti Rani , Chowdhury Pramit , Ashish  , Clain Jérôme , Bhattacharjee Souvik 
Published: January 2024

AbstractThe rapid emergence of artemisinin resistance (ART-R) poses a challenge to global malaria control efforts. ART potency is triggered by ferrous iron- and/or heme-mediated cleavage of the endoperoxide bond to generate reactive heme-ART alkoxy radicals and covalent heme-ART adducts that alkylate parasite targets or inhibit the detoxification of heme into β-hematin crystals; both of which lead to parasite death. Mutations in theP. falciparumKelch-containing protein Kelch13 (PfKekch13) confer clinical ART-R, in which the resistant parasites exhibit impaired hemoglobin uptake, reduced heme yield, and thus decreased ART activation. However, a more direct involvement of PfKelch13 in heme-mediated ART activation has not been reported. Here, we show that recombinant, purified PfKelch13 wild-type (WT) protein displays measurable binding affinity for both iron and heme, the main effectors for ART activation. Comparative biochemical analyses further indicate weaker heme-binding affinities in the two Southeast Asian ART-R PfKelch13 mutants C580Y and R539T compared to the ART-sensitive WT and A578S mutant proteins, which ultimately translates into reduced yield of heme-ART derivatives. In conclusion, this study provides the first evidence for regulated ART activationviathe heme-binding propensity of PfKelch13, which may contribute towards modulating the level of ART-R in malaria parasites with PfKelch13 mutations.
DecodingKlebsiella pneumoniaein Poultry Chain: Unveiling Genetic Landscape, Antibiotic Resistance, and Biocide Tolerance in Non-Clinical Reservoirs
Authors: Mourão Joana , Magalhães Mafalda , Ribeiro-Almeida Marisa , Rebelo Andreia , Novais Carla , Peixe Luísa , Novais Ângela , Antunes Patrícia 
Published: January 2024

AbstractThe rise of antibiotic resistance in the food chain is influenced by the use of antimicrobial agents, such as antibiotics, metals, and biocides, throughout the entire farm-to-fork continuum. Besides, non-clinical reservoirs potentially contribute to the transmission of critical pathogens such as multidrug-resistant (MDR)Klebsiella pneumoniae. However, limited knowledge exists about the population structure and genomic diversity ofK. pneumoniaecirculating in conventional poultry production. We conducted a comprehensive characterization ofK. pneumoniaeacross the whole chicken production chain (flocks/environment/meat, 2019-2022), exploring factors beyond antibiotics, like copper and quaternary ammonium compounds (QACs). Clonal diversity and adaptive features ofK. pneumoniaewere characterized through cultural, molecular (FT-IR), and whole-genome-sequencing (WGS) approaches. All except one flock were positive forK. pneumoniaewith a significant increase (p < 0.05) from early to pre-slaughter stages, most persisting in chicken meat batches. Colistin-resistantK. pneumoniaerates were low (4%), while most samples carried MDR strains (67%) and copper-tolerant isolates (63%;sil+pcoclusters; MICCuSO4≥16mM), particularly at pre-slaughter. Benzalkonium chloride consistently exhibited activity inK. pneumoniae(MIC/MBC range=4-64mg/L) from diverse and representative strains independently of the presence/absence of genes linked to QACs tolerance. A polyclonalK. pneumoniaepopulation, discriminated by FT-IR and WGS, included various lineages dispersed throughout the chicken’s lifecycle at the farm (ST29-KL124, ST11-KL106, ST15-KL19, ST1228-KL38), until the meat (ST1-KL19, ST11-KL111, ST6405-KL109, and ST6406-CG147-KL111), or over years (ST631-49 KL109, ST6651-KL107, ST6406-CG147-KL111). Notably, some lineages were identical to those from human clinical isolates. WGS also revealed F-type multireplicon plasmids carryingsil+pco(copper) co-located withqacEΔ1±qacF(QACs) and antibiotic resistance genes like those disseminated in humans. In conclusion, chicken farms and their derived meat are significant reservoirs for diverseK. pneumoniaeclones enriched in antibiotic resistance and metal tolerance genes, some exhibiting genetic similarities with human clinical strains. Further research is imperative to unravel the factors influencingK. pneumoniaepersistence and dissemination within poultry production, contributing to improved food safety risk management. This study underscores the significance of understanding the interplay between antimicrobial control strategies and non-clinical sources to effectively address the spread of antimicrobial resistance.
Retinoic acid generates a beneficial microenvironment for liver progenitor cell activation in acute liver failure
Authors: Wang Sai , Link Frederik , Munker Stefan , Wang Wenjing , Feng Rilu , Liebe Roman , Li Yujia , Yao Ye , Liu Hui , Shao Chen , Ebert Matthias P. A. , Ding Huiguo , Dooley Steven , Weng Hong-Lei , Wang Shan-Shan 
Published: January 2024

AbstractObjectiveWhen massive necrosis occurs in acute liver failure (ALF), rapid expansion of hepatic stem cells called liver progenitor cells (LPC) in a process called ductular reaction (DR) is required for survival. The exact underlying mechanisms of this process are not known to date. In ALF, high levels of retinoic acid (RA), a molecule known for its pleiotropic roles in embryonic development, are secreted by activated hepatic stellate cells (HSCs). We hypothesized that RA plays a key role during DR in ALF.MethodsRNA-Seq was performed to identify molecular signaling pathways affected by all-trans retinoid acid (atRA) treatment in HepaRG LPC cells. Functional assays for RA were performed in HepaRG cells with atRA treatment as well as co-culture with LX-2 cellsin vitro, and liver tissue of patients suffering from ALFin vivo.ResultsUnder ALF conditions, activated HSCs secreted RA, inducing RARα nuclear translocation in LPCs. RNA-seq data and investigations in HepaRG cells revealed that atRA treatment activated the WNT-β-Catenin pathway, enhanced stemness genes (SOX9, AFP, et.al), promoted energy storage, and elevated the expression of ATP-binding cassette (ABC) transporters depending on RARα nuclear translocation. Further, atRA treatment-induced pathways were confirmed in a co-culture system of HepaRG with LX-2 cells. Patients with ALF who displayed RARα nuclear translocation in LPC had significantly better MELD scores than those without.ConclusionIn ALF, RA secreted by activated hepatic stellate cells promotes LPC activation, a prerequisite for subsequent LPC-mediated liver regeneration.
CryoCycle your grids: Plunge vitrifying and reusing clipped grids to advance cryoEM democratization
Authors: Serbynovskyi Viacheslav , Wang Jing , Chua Eugene YD , Ishemgulova Aygul , Alink Lambertus M. , Budell William C. , Johnston Jake D. , Dubbeldam Charlie , Gonzalez Fabio A. , Rozovsky Sharon , Eng Edward T. , de Marco Alex , Noble Alex J. 
Published: January 2024

ABSTRACTCryoEM democratization is hampered by access to costly plunge-freezing supplies. We introduce methods, called CryoCycle, for reliably blotting, vitrifying, and reusing clipped cryoEM grids. We demonstrate that vitreous ice may be produced by plunging clipped grids with purified proteins into liquid ethane and that clipped grids may be reused several times for different protein samples. Furthermore, we demonstrate the vitrification of thin areas of cells prepared on gold-coated, pre-clipped grids.