bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Plagiarism Paperdemic - Plagiarism in infection journals in the era of COVID-19
Authors: Menshawey Rahma , Menshawey Esraa , Mitkees Ahmed , Mahamud Bilal A. 
Published: August 2022

AbstractBackgroundThe COVID-19 pandemic has caused drastic changes in the publishing framework in order to quickly review and publish vital information during this public health emergency. The quality of the academic work being published may have been compromised. One area of concern is plagiarism, where the work of others is directly copied and represented as one’s own. The purpose of this study is to determine the presence of plagiarism in infection journals in papers relating to the COVID-19 pandemic.MethodsConsecutively occurring original research or reviews relating to the COVID-19 pandemic, published in infection journals as ranked by SCOPUS Journal finder were collected. Each manuscript was optimized and uploaded to the Turnitin program. Similarity reports were then manually checked for true plagiarism within the text, where any sentence with more than 80% copying was deemed plagiarised.ResultsA total of 310 papers were analyzed in this cross-sectional study. Papers from a total of 23 journals among 4 quartiles were examined. Of the papers we examined, 41.6% were deemed plagiarised (n=129). Among the plagiarised papers, the average number of copied sentences was 5.42±9.18. The highest recorded similarity report was 60%, and the highest number of copied sentences was 85. Plagiarism was higher in papers published in the year 2020. The most problematic area in the manuscripts was the discussion section. Self plagiarism was identified in 31 papers. Average time to judge all manuscripts was 2.45±3.09. Among all the plagiarized papers 72% belonged to papers where the similarity report was ≤15% (n=93). Papers published from core anglosphere speaking countries were not associated with higher rates of plagiarism. No significant differences were found with regards to plagiarism events among the quartiles.ConclusionPlagiarism is prevalent in COVID19 related publications in infection journals among various quartiles. It is not enough to rely only on similarity reports. Such reports must be accompanied by manual curation of the results with an appropriate threshold to be able to appropriately determine if plagiarism is occurring. The majority of plagiarism is occurring in reports of less than 15% similarity, and this is a blind spot. Incorporating a manual judge could save future time in avoiding retractions and improving the quality of papers in these journals.“A poor original is better than a good imitation.”— Ella Wheeler Wilcox
Broad immunity to SARS-CoV-2 variants of concern mediated by a SARS-CoV-2 receptor-binding domain protein vaccine
Authors: Deliyannis Georgia , Gherardin Nicholas A. , Wong Chinn Yi , Grimley Samantha L. , Cooney James P. , Redmond Samuel , Ellenberg Paula , Davidson Kathryn , Mordant Francesca L. , Smith Tim , Gillard Marianne , Lopez Ester , McAuley Julie , Tan Chee Wah , Wang Jing , Zeng Weiguang , Littlejohn Mason , Zhou Runhong , Chan Jasper Fuk-Woo , Chen Zhi-wei , Hartwig Airn E. , Bowen Richard , Mackenzie Jason M. , Vincan Elizabeth , Torresi Joseph , Kedzierska Katherine , Pouton Colin W. , Gordon Tom , Wang Lin-fa , Kent Stephen J. , Wheatley Adam K. , Lewin Sharon R. , Subbarao Kanta , Chung Amy , Pellegrini Marc , Munro Trent , Nolan Terry , Rockman Steven , Jackson David C. , Purcell Damian F.J. , Godfrey Dale I. 
Published: August 2022

AbstractThe SARS-CoV-2 global pandemic has fuelled the generation of vaccines at an unprecedented pace and scale. However, many challenges remain, including: the emergence of vaccine-resistant mutant viruses, vaccine stability during storage and transport, waning vaccine-induced immunity, and concerns about infrequent adverse events associated with existing vaccines. Here, we report on a protein subunit vaccine comprising the receptor-binding domain (RBD) of the ancestral SARS-CoV-2 spike protein, dimerised with an immunoglobulin IgG1 Fc domain. These were tested in conjunction with three different adjuvants: a TLR2 agonist R4-Pam2Cys, an NKT cell agonist glycolipid α-Galactosylceramide, or MF59® squalene oil-in-water adjuvant. Each formulation drove strong neutralising antibody (nAb) responses and provided durable and highly protective immunity against lower and upper airway infection in mouse models of COVID-19. We have also developed an RBD-human IgG1 Fc vaccine with an RBD sequence of the highly immuno-evasive beta variant (N501Y, E484K, K417N). This ‘beta variant’ RBD vaccine, combined with MF59® adjuvant, induced strong protection in mice against the beta strain as well as the ancestral strain. Furthermore, when used as a third dose booster vaccine following priming with whole spike vaccine, anti-sera from beta-RBD-Fc immunised mice increased titres of nAb against other variants including alpha, delta, delta+, gamma, lambda, mu, and omicron BA.1 and BA.2. These results demonstrated that an RBD-Fc protein subunit/MF59® adjuvanted vaccine can induce high levels of broad nAbs, including when used as a booster following prior immunisation of mice with whole ancestral-strain Spike vaccines. This vaccine platform offers a potential approach to augment some of the currently approved vaccines in the face of emerging variants of concern, and it has now entered a phase I clinical trial.
Predictors of post-stroke cognitive impairment at three-month following first episode of stroke among patients attended at tertiary hospitals in Dodoma, central Tanzania: a protocol of a prospective longitudinal observational study
Authors: Alphonce Baraka , Meda John , Nyundo Azan 
Published: August 2022

AbstractIntroductionNeurocognitive deficits after stroke are a common manifestation and pose a significant impact on the quality of life for patients and families; however, little attention is given to the burden and associated impact of cognitive impairment following stroke. The study aims to determine the prevalence and predictors of post-stroke cognitive impairment (PSCI) among adult stroke patients admitted to tertiary hospitals in Dodoma, TanzaniaMethodologyA prospective longitudinal study is conducted at tertiary hospitals in the Dodoma region, central Tanzania. Participants with the first stroke confirmed by CT/MRI brain aged ≥ 18 years who meet the inclusion criteria are enrolled and followed up. Baseline socio-demographic and clinical factors are identified during admission, while other clinical variables are determined during the three-month follow-up period. Descriptive statistics are used to summarize data; continuous data will be reported as Mean (SD) or Median (IQR), and categorical data will be summarized using proportions and frequencies. Univariate and multivariate logistic regression analysis will be used to determine predictors of PSCI
A light sheet fluorescence microscopy protocol for Caenorhabditis elegans larvae and adults
Authors: Smith Jayson J. , Kenny Isabel W. , Wolff Carsten , Cray Rachel , Kumar Abhishek , Sherwood David R. , Matus David Q. 
Published: August 2022

AbstractLight sheet fluorescence microscopy (LSFM) has become a method of choice for live imaging because of its fast acquisition and reduced photobleaching and phototoxicity. Despite the strengths and growing availability of LSFM systems, no generalized LSFM mounting protocol has been adapted for live imaging of post-embryonic stages of C. elegans. A major challenge has been to develop methods to limit animal movement using a mounting media that matches the refractive index of the optical system. Here, we describe a simple mounting and immobilization protocol using a refractive-index matched UV-curable hydrogel within fluorinated ethylene propylene (FEP) tubes for efficient and reliable imaging of larval and adult C. elegans stages.
Risk and Outcome of Second primary malignancy in patients with classical Hodgkin lymphoma
Authors: Wang Fan 
Published: August 2022

AbstractBACKGROUNDHodgkin lymphoma survivors demonstrated increased risk of secondary primary malignancies (SPMs), but comprehensive analysis of the risk and outcome of SPMs in classical Hodgkin lymphoma (cHL) patients has not yet been reported.METHODSPatients with classical Hodgkin Lymphoma from 1975 to 2017 were identified from the Surveillance, Epidemiology and End Results (SEER) database. Standardized incidence ratios (SIRs) were calculated for the risk of solid and hematologic SPMs in cHL patients compared to the general population. The outcome of cHL patients developing SPMs were assessed by performing survival, competing risks regression and cox proportional regression analyses.RESULTSIn a follow-up of 26,493 cHL survivors for 365,156 person years, 3,866 (14.59%) secondary cancers were identified, with an SIR of 2.09 (95% CI: 2.02 - 2.15). The increased risk was still notable after follow-up of 10 years or more, and the risk is more pronounced for patients with female gender, younger age, advanced stage, chemotherapy and radiation therapy. The overall survival is worse for cHL patients with SPMs after 5 years of follow-up (P < 0.0001). The main cause of death for cHL patients with SPMs is not cHL but other causes including SPMs. Multivariate Cox regression analysis confirmed SPMs as an independently adverse prognostic factor for cHL survivors (hazard ratio, 1.08; 95% CI, 1.03-1.14, P□=□0.002).CONCLUSIONSThere is a significantly increased risk of developing SPMs for cHL survivors. The overall survival is worse for cHL patients and SPMs is an independent prognostic factor for cHL.
Prosociality in a despotic society
Authors: Bhattacharjee Debottam , Cousin Eythan , Pflüger Lena S. , Massen Jorg J.M. 
Published: August 2022

AbstractHumans possess remarkable prosocial tendencies beyond the confinement of kinship, which may be instrumental in promoting cooperative interactions and sociality at large. Yet, prosociality is an evolutionary conundrum as it does not provide immediate benefits to the actor. The ‘domestication’ and ‘cooperative-breeding’ hypotheses postulated that enhanced social tolerance and inter-individual dependence could nonetheless facilitate the evolution of prosociality. However, inconsistent results due to varying experimental paradigms, and restricted focus of research on tolerant and cooperatively breeding species, have impeded our understanding so far. Albeit counterintuitively, despotic societies with relatively low social tolerance levels represent an excellent opportunity to investigate prosociality due to their kin favoritism and potential interdependence among individuals in terms of social support. Japanese macaques (Macaca fuscata) live in strictly hierarchical matrilineal societies, where kin members have strong social bonds. Additionally, support from non-kins can be crucial to form coalitions and rank up in the hierarchy. Using a group-service paradigm, we tested prosociality in a semi-free-ranging group of Japanese macaques. In contrast to currently existing evidence, we found that individuals (n=25) can act prosocially and at comparably high rates as cooperative breeding- or self-domesticated species. The macaques benefitted not only their kin members but other individuals to whom they showed relatively high social tolerance. We emphasize the roles of complex socio-ecological conditions in facilitating individual prosocial tendencies. Furthermore, these results call for a novel evolutionary framework regarding prosociality that focuses on different forms of interdependence and expands beyond cooperative breeding- and (self-)domesticated species.Significance statementWhat made humans so incredibly prosocial? Examining the evolutionary trajectory of prosocial acts led comparative psychologists to explore various taxa. Empirical evidence so far suggests that enhanced social tolerance and interdependence among individuals facilitate prosociality. Conventionally, despotism is characterized by low group-level tolerance, yet kin favoritism, nepotism, and high interdependence (in support and coalition formation) are also fundamental properties of despotic societies. Under such complex socio-ecological conditions, individual prosocial acts could thus be vital. We found, for the first time, high levels of prosociality in the very despotic Japanese macaques. Individuals benefitted both kin-relatives and others to whom they showed relatively high dyadic social tolerance. This study signifies that prosociality can be favored even in a highly despotic society.
Protein-protein complexes can undermine ultrasensitivity-dependent biological adaptation
Authors: Jeynes-Smith C. , Araujo R. P. 
Published: August 2022

AbstractRobust Perfect Adaptation (RPA) is a ubiquitously-observed signalling response across all scales of biological organisation. A major class of network architectures that drive RPA in complex networks is the Opposer module – a feedback-regulated network into which specialised integral-computing ‘opposer node(s)’ are embedded. Although ultrasensitivity-generating chemical reactions have long been considered a possible mechanism for such adaptation-conferring opposer nodes, this hypothesis has relied on simplified Michaelian models, which neglect the presence of protein-protein complexes, and which are now widely acknowledged to make inaccurate predictions of signalling responses. Here we develop complex-complete models of interlinked covalent-modification cycles with embedded ultrasensitivity: explicitly capturing all molecular interactions and protein complexes. Strikingly, we demonstrate that the presence of protein-protein complexes thwarts the network’s capacity for RPA in any ‘free’ active protein form, conferring RPA capacity instead on the concentration of a larger protein pool consisting of two distinct forms of a single protein. Furthermore, compared to predictions by simplified models, the parametric requirements for RPA in this protein pool are much more severe, and RPA generally obtains over a narrower range of input stimuli. These surprising results raise fundamental new questions as to the biochemical requirements for adaptation-conferring Opposer modules within complex cellular networks.
A multiomics analysis of direct interkingdom dynamics between influenza A virus and Streptococcus pneumoniae uncovers host-independent changes to bacterial virulence fitness
Authors: Platt Maryann P. , Lin Yi-Han , Penix Trevor , Wiscovitch-Russo Rosana , Vashee Isha , Mares Chris A. , Rosch Jason W. , Yu Yanbao , Gonzalez-Juarbe Norberto 
Published: August 2022

AbstractBackgroundFor almost a century, it has been recognized that influenza A virus (IAV) infection can promote the development of secondary bacterial infections (SBI) mainly caused by Streptococcus pneumoniae (Spn). Recent observations have shown that IAV is able to directly bind to the surface of Spn. To gain a foundational understanding of how direct IAV-Spn interaction alters bacterial biological fitness we employed combinatorial multi-omic and molecular approaches.ResultsHere we show IAV significantly remodels the global transcriptome, proteome and phosphoproteome profiles of Spn independently of host effectors. We identified Spn surface proteins that interact with IAV proteins (hemagglutinin, nucleoprotein, and neuraminidase). In addition, IAV was found to directly modulate expression of Spn virulence determinants such as pneumococcal surface protein A, pneumolysin, and factors associated with antimicrobial resistance among many others. Metabolic pathways were significantly altered leading to changes in Spn growth rate. IAV was also found to drive Spn capsule shedding and the release of pneumococcal surface proteins. Released proteins were found to be involved in evasion of innate immune responses and actively reduced human complement hemolytic and opsonizing activity. IAV also led to phosphorylation changes in Spn proteins associated with metabolism and bacterial virulence. Validation of proteomic data showed significant changes in Spn galactose and glucose metabolism. Furthermore, supplementation with galactose rescued bacterial growth and promoted bacterial invasion, while glucose supplementation led to enhanced pneumolysin production and lung cell apoptosis.ConclusionsHere we demonstrate that IAV can directly modulate Spn biology without the requirement of host effectors and support the notion that inter-kingdom interactions between human viruses and commensal pathobionts can promote bacterial pathogenesis and microbiome dysbiosis.
Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes
Authors: Tan Asako , Murugapiran Senthil , Mikalauskas Alaya , Koble Jeff , Kennedy Drew , Hyde Fred , Ruotti Victor , Law Emily , Jensen Jordan , Schroth Gary P. , Macklaim Jean M. , Kuersten Scott , Le François Brice , Gohl Daryl M. 
Published: August 2022

AbstractBackgroundThe microbiota that colonize the human gut and other tissues are dynamic, varying both in composition and functional state between individuals and over time. In studying the function of the human microbiome and the mechanisms of microbiota-mediated phenotypes, gene expression measurements provide additional insights to DNA-based measurements of microbiome composition. However, efficient and unbiased removal of microbial ribosomal RNA (rRNA) presents a barrier to acquiring metatranscriptomic data, as rRNA typically accounts >90% of total RNA in microbial cells.ResultsHere we describe a probe set that achieves efficient enzymatic rRNA removal of complex human-associated microbial communities. We demonstrate that the custom probe set can be further refined through an iterative design process to efficiently deplete rRNA from a range of human microbiome samples, including adult and infant gut, as well as oral and vaginal communities. Using synthetic nucleic acid spike-ins, we show that the rRNA depletion process does not introduce substantial quantitative error in the resulting gene expression profiles. Successful rRNA depletion allows for efficient characterization of taxonomic and functional profiles, including during the development of the human gut microbiome.ConclusionsThe pan-human microbiome enzymatic rRNA depletion probes described here provide a powerful tool for studying the transcriptional dynamics and function of the human microbiome.
Prion propagation is dependent on key amino acids in Charge cluster 2 within the prion protein
Authors: Bhamra Savroop , Arora Parineeta , Manka Szymon W. , Schmidt Christian , Brown Craig , Rayner Melissa L. D. , Klöhn Peter-Christian , Clarke Anthony R. , Collinge John , Jat Parmjit S. 
Published: August 2022

AbstractPrions consist of assemblies of aberrantly folded cellular prion protein (PrPC) upon template-assisted conversion and propagation of disease-associated PrP. To dissect the N-terminal residues critical for efficient prion propagation, we generated a library of point, double, or triple alanine replacements within residues 23-111 of PrP, stably expressed them in cells silenced for endogenous mouse PrPC and challenged the reconstituted cells with four mouse prion strains. Amino acids (aa) 105-111 of Charge Cluster 2 (CC2), which is disordered in PrPC, were required for propagation of all four prion strains; other residues had no effect or exhibited strain-specific effects. Replacements in CC2, including aa105-111, dominantly inhibited prion propagation in the presence of endogenous wild type PrPC whilst other changes were not inhibitory. Single alanine replacements within aa105-111 identified leucine 108 and valine 111 or the cluster of lysine 105, threonine 106 and asparagine 107 as critical for prion propagation. These residues mediate specific ordering of CC2 in the prion fibrils from Rocky Mountain Laboratory (RML) and ME7 mouse prion strains.
Implementation of the β-hydroxyaspartate cycle increases growth performance of Pseudomonas putida on the PET monomer ethylene glycol
Authors: von Borzyskowski Lennart Schada , Schulz-Mirbach Helena , Castellanos Mauricio Troncoso , Severi Francesca , Gomez Coronado Paul A. , Glatter Timo , Bar-Even Arren , Lindner Steffen N. , Erb Tobias J. 
Published: August 2022

AbstractEthylene glycol (EG) is a promising next generation feedstock for bioprocesses. It is a key component of the ubiquitous plastic polyethylene terephthalate (PET) and other polyester fibers and plastics, used in antifreeze formulations, and can also be generated by electrochemical conversion of syngas, which makes EG a key compound in a circular bioeconomy. The majority of biotechnologically relevant bacteria assimilate EG via the glycerate pathway, a wasteful metabolic route that releases CO2 and requires reducing equivalents as well as ATP. In contrast, the recently characterized β-hydroxyaspartate cycle (BHAC) provides a more efficient, carbon-conserving route for C2 assimilation. Here we aimed at overcoming the natural limitations of EG metabolism in the industrially relevant strain Pseudomonas putida KT2440 by replacing the native glycerate pathway with the BHAC. We first prototyped the core reaction sequence of the BHAC in Escherichia coli before establishing the complete four-enzyme BHAC in Pseudomonas putida. Directed evolution on EG resulted in an improved strain that exhibits 35% faster growth and 20% increased biomass yield compared to a recently reported P. putida strain that was evolved to grow on EG via the glycerate pathway. Genome sequencing and proteomics highlight plastic adaptations of the genetic and metabolic networks in response to the introduction of the BHAC into P. putida and identify key mutations for its further integration during evolution. Taken together, our study shows that the BHAC can be utilized as ‘plug-and-play’ module for the metabolic engineering of two important microbial platform organisms, paving the way for multiple applications for a more efficient and carbon-conserving upcycling of EG in the future.
Harmonin homology domain-mediated interaction of RTEL1 helicase with RPA and DNA provides mechanistic insight into its role in DNA repair
Authors: Kumar Niranjan , Taneja Arushi , Ghosh Meenakshi , Rothweiler Ulli , Sundaresan Nagalingam Ravi , Singh Mahavir 
Published: August 2022

ABSTRACTThe regulator of telomere elongation helicase 1 (RTEL1) is an Fe-S cluster containing helicase that plays important roles in telomere DNA maintenance, DNA repair, and genome stability. It is a modular protein comprising a helicase domain, two tandem harmonin homology domains 1 & 2 (HHD1 and HHD2), and a Zn2+binding RING domain. In this study, we have unravelled a novel interaction between RTEL1 and replication protein A (RPA) and shown their co-localization upon DNA damage in the cells. Using NMR spectroscopy, we show that 32C domain of RPA and DNA competitively bind with HHD2 of RTEL1. To understand the structural basis of HHD2 – 32C and HHD2 - DNA interactions, we have determined a 1.6 Å resolution crystal structure of HHD2. NMR chemical shift perturbations-based mapping revealed the 32C and DNA binding surface on HHD2 of RTEL1. Together, these results establish an interplay among RTEL1, RPA, and DNA that provide mechanistic insights into the RTEL1 recruitment at DNA during the processes of replication, repair, and recombination.