bluuebunny/crossref_metadata_2025_split huggingface dataset:
Type 4 pili mediated natural competence inFusobacterium nucleatum
Authors: Sanders Blake E. , Umana Ariana , Nguyen Tam T.D. , Williams Kevin J. , Yoo Christopher C. , Casasanta Michael A. , Wozniak Bryce , Slade Daniel J. 
Published: June 2023

ABSTRACTMany bacterial species naturally take up DNA from their surroundings and recombine it into their chromosome through homologous gene transfer (HGT) to aid in survival and gain advantageous functions. Herein we present the first characterization of Type 4 pili mediated natural competence inFusobacterium nucleatum, which are Gram-negative, anaerobic bacteria that participate in a range of infections and diseases including periodontitis, preterm birth, and cancer. We bioinformatically identified components of the Type 4 conjugal pilus machinery and show this is a conserved system within theFusobacteriumgenus. We next validate Type 4 pili in natural competence inF. nucleatumstrain 23726 and show that gene deletions in key components of pilus deployment (pilQ)and cytoplasmic DNA import (comEC)abolish DNA uptake and chromosomal incorporation. We next show that natural competence may require nativeF. nucleatumDNA methylation to bypass restriction modification systems and allow subsequent genomic homologous recombination. In summary, this proof of principle study provides the first characterization of natural competence inFusobacterium nucleatumand highlights the potential to exploit this DNA import mechanism as a genetic tool to characterize virulence mechanisms of an opportunistic oral pathogen.
Host Gastric Corpus Microenvironment FacilitatesAscaris SuumLarval Hatching And Infection in a Murine Model
Authors: Wu Yifan , Adeniyi-Ipadeola Grace , Adkins-Threats Mahliya , Seasock Matthew , Suarez-Reyes Charlie , Fujiwara Ricardo , Bottazzi Maria Elena , Song Lizhen , Mills Jason C. , Weatherhead Jill E. 
Published: June 2023

AbstractAscariasis (roundworm) is the most common parasitic helminth infection globally and can lead to significant morbidity in children including chronic lung disease. Children become infected withAscarisspp. via oral ingestion of eggs. It has long been assumed thatAscarisegg hatching and larval translocation across the gastrointestinal mucosa to initiate infection occurs in the small intestine. Here, we show thatA. suumlarvae hatched in the host stomach in a murine model. Larvae utilize acidic mammalian chitinase (AMCase; acid chitinase;Chia) from chief cells and acid pumped by parietal cells to emerge from eggs on the surface of gastric epithelium. Furthermore, antagonizing AMCase and gastric acid in the stomach decreases parasitic burden in the liver and lungs and attenuates lung disease. GivenAscariseggs are chitin-coated, the gastric corpus would logically be the most likely organ for egg hatching, though this is the first study directly evincing the essential role of the host gastric corpus microenvironment. These findings point towards potential novel mechanisms for therapeutic targets to prevent ascariasis and identify a new biomedical significance of AMCase in mammals.
Elevated Expression ofsrpRiPPs Across Bacterial Phyla in Marine Sponges
Authors: Waterworth Samantha C. , Rees Evan R. , Clark Chase M. , Carlson Skylar , Miller Ian J. , Puglisi Melany , Kwan Jason C. 
Published: June 2023

ABSTRACTWe investigated transcriptional activity, at a genome-resolved level, of bacterial communities in twoS. officinalisand twoI. felixsponges, both of which are considered high microbial abundance (HMA) sponges that harbor similar bacterial communities. Overlap of metatranscriptional data on genome-resolved metagenomic data showed that genome bins classified within the Chloroflexota and Poribacteria phyla were the most abundant and transcriptionally active. However, abundant bins in general were not the most transcriptionally active, instead less abundant bins of the same phyla were most active indicating that numerical dominance does not imply transcriptional dominance. We found that although some primary metabolic functions appeared upregulated, they were not obviously attributable to any particular bacterial species. However, assessment of transcription levels of biosynthetic gene clusters (BGCs) encoding secondary metabolites revealed a high transcription of ribosomally synthesized and post-translationally modified peptides (RiPPs) in genome bins across diverse bacterial phyla, most of which were likelysrpRiPPs encoding brominated azol(in)e-containing compounds. However, the ecological role of these compounds remains elusive.IMPORTANCEMarine sponges and bacteria have formed close associations over several million years with many bacteria performing specialized functions within their sponge host. Previous studies have either assessed the genomes of a given sponge or the expression profile for a sponge holobiont as a whole. Here, we present the first genome-resolved transcriptomic study which gives us a snapshot of the transcriptional activity of individual bacteria in the context of four different sponge holobionts. Using this approach we found that the numerically dominant bacteria were not the most transcriptionally active and that relatively high expression of a ubiquitous biosynthetic gene cluster was evident in many different bacterial phyla in all four sponge samples.
Structured Ethical Review for Wastewater-Based Testing
Authors: Bowes Devin A. , Darling Amanda , Driver Erin M. , Kaya Devrim , Maal-Bared Rasha , Lee Lisa M. , Goodman Kenneth , Adhikari Sangeet , Aggarwal Srijan , Bivins Aaron , Bohrerova Zuzana , Cohen Alasdair , Duvallet Claire , Elnimeiry Rasha A. , Hutchison Justin M. , Kapoor Vikram , Keenum Ishi , Ling Fangqiong , Sills Deborah , Tiwari Ananda , Vikesland Peter , Ziels Ryan , Mansfeldt Cresten 
Published: June 2023

AbstractWastewater-based testing (WBT) for SARS-CoV-2 has rapidly expanded over the past three years due to its ability to provide a comprehensive measurement of disease prevalence independent of clinical testing. The development and simultaneous application of the field blurred the boundary between measuring biomarkers for research activities and for pursuit of public health goals, both areas with well-established ethical frameworks. Currently, WBT practitioners do not employ a standardized ethical review process (or associated data management safeguards), introducing the potential for adverse outcomes for WBT professionals and community members. To address this deficiency, an interdisciplinary group developed a framework for a structured ethical review of WBT. The workshop employed a consensus approach to create this framework as a set of 11-questions derived from primarily public health guidance because of the common exemption of wastewater samples to human subject research considerations. This study retrospectively applied the set of questions to peer- reviewed published reports on SARS-CoV-2 monitoring campaigns covering the emergent phase of the pandemic from March 2020 to February 2022 (n=53). Overall, 43% of the responses to the questions were unable to be assessed because of lack of reported information. It is therefore hypothesized that a systematic framework would at a minimum improve the communication of key ethical considerations for the application of WBT. Consistent application of a standardized ethical review will also assist in developing an engaged practice of critically applying and updating approaches and techniques to reflect the concerns held by both those practicing and being monitored by WBT supported campaigns.Abstract FigureSynopsisDevelopment of a structured ethical review facilitates retrospective analysis of published studies and drafted scenarios in the context of wastewater-based testing.
Exploring the Role of Chat GPT in patient care (diagnosis and Treatment) and medical research: A Systematic Review
Authors: Garg Ravindra Kumar , Urs Vijeth L , Agrawal Akshya Anand , Chaudhary Sarvesh Kumar , Paliwal Vimal , Kar Sujita Kumar 
Published: June 2023

AbstractBackgroundChatGPT(Chat Generative Pre-trained Transformer) is an artificial intelligence (AI) based on a natural language processing tool developed by OpenAI (California, USA). This systematic review examines the potential of Chat GPT in diagnosing and treating patients and its contributions to medical research.MethodsIn order to locate articles on ChatGPT’s use in clinical practise and medical research, this systematic review used PRISMA standards and conducted database searches across several sources. Selected records were analysed using ChatGPT, which also produced a summary for each article. The resultant word document was transformed to a PDF and handled using ChatPDF. The review looked at topics pertaining to scholarly publishing, clinical practise, and medical research.ResultsWe reviewed 118 publications. There are difficulties and moral conundrums associated with using ChatGPT in therapeutic settings and medical research. Patient inquiries, note writing, decision-making, trial enrolment, data management, decision support, research support, and patient education are all things that ChatGPT can help with. However, the solutions it provides are frequently inadequate and inconsistent, presenting issues with its originality, privacy, accuracy, bias, and legality. When utilising ChatGPT for academic writings, there are issues with prejudice and plagiarism, and because it lacks human-like characteristics, its authority as an author is called into question.ConclusionsChatGPT has limitations when used in research and healthcare. Even while it aids in patient treatment, concerns regarding accuracy, authorship, and bias arise. Currently, ChatGPT can serve as a “clinical assistant” and be a huge assistance with research and scholarly writing.
Mapping factors that may influence attrition and retention of midwives: a scoping review protocol
Authors: Moncrieff Gill , Cheyne Helen , Downe Soo , Maxwell Margaret 
Published: June 2023

AbstractIntroductionAn appropriately staffed midwifery workforce is essential for the provision of safe and high-quality maternity care. However, there is a global and national shortage of midwives. Understaffed maternity services are frequently identified as contributing to unsafe care provision and adverse outcomes for mothers and babies. While there is a need to recruit midwives through pre-registration midwifery programmes, this is associated with cost and resource implications, and is counteracted to a large extent by the high number of midwives leaving the workforce. It is increasingly recognised that there is a critical need to attend to retention in midwifery in order to develop and maintain safe staffing levels. The objective of this review is to collate and map factors that have been found to influence attrition and retention in midwifery.Methods and analysisJoanna Briggs Institute guidance for scoping reviews and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews will be used to guide the review process and reporting of the review. CINAHL, MEDLINE, PsycINFO, and Scopus databases will be used to carry out the search for relevant literature. Results will be screened against inclusion criteria. Data will be extracted using a pre-formed data extraction tool and findings will be presented in narrative, tabular, and graphical formats.Ethics and disseminationThe review will collate data from existing research, therefore ethics approval is not required. Findings will be published in journals, presented at conferences, and will be translated into infographics and other formats for online dissemination.Strengths and limitations of this studyThis will be the first review to systematically map the factors found to influence midwives’ decision to stay in or leave their role as a midwifeScoping reviews provide a rigorous and structured method through which to collate and map evidence on a given topicThis protocol and the full review will follow Joanna Briggs Institute guidance for scoping reviews and will be reported in line with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping ReviewsThe review will be of relevance to other high income countries but is unlikely be relevant for low and middle income countries
Hormonal steroids bind theNeisseria gonorrhoeaemultidrug resistance regulator, MtrR, to induce a multidrug binding efflux pump and stress-response sigma factor
Authors: Hooks Grace M. , Ayala Julio C. , Beggs Grace A. , Perfect John R. , Schumacher Maria A. , Shafer William M. , Brennan Richard G. 
Published: June 2023

AbstractOverexpression of the multidrug efflux pump MtrCDE, a critical factor of multidrug-resistance inNeisseria gonorrhoeae, the causative agent of gonorrheae, is repressed by the transcriptional regulator, MtrR (multiple transferable resistance repressor). Here, we report the results from a series ofin vitroexperiments to identify innate, human inducers of MtrR and to understand the biochemical and structural mechanisms of the gene regulatory function of MtrR. Isothermal titration calorimetry experiments reveal that MtrR binds the hormonal steroids progesterone, β-estradiol, and testosterone, all of which are present at significant concentrations at urogenital infection sites as well as ethinyl estrogen, a component of some birth control pills. Binding of these steroids results in decreased affinity of MtrR for cognate DNA, as demonstrated by fluorescence polarization-based assays. The crystal structures of MtrR bound to each steroid provided insight into the flexibility of the binding pocket, elucidated specific residue-ligand interactions, and revealed the conformational consequences of the induction mechanism of MtrR. Three residues, D171, W136 and R176 are key to the specific binding of these gonadal steroids. These studies provide a molecular understanding of the transcriptional regulation by MtrR that promotesN. gonorrhoeaesurvival in its human host.
Taphonomic damage obfuscates interpretation of the retroarticular region of theAsteriornismandible
Authors: Crane Abi , Benito Juan , Chen Albert , Musser Grace , Torres Christopher R. , Clarke Julia A. , Lautenschlager Stephan , Ksepka Daniel T. , Field Daniel J. 
Published: June 2023

AbstractAsteriornis maastrichtensis, from the latest Cretaceous of Belgium, is among the oldest known crown bird fossils, and its three-dimensionally preserved skull provides the most substantial insights into the cranial morphology of early crown birds to date. Phylogenetic analyses recoveredAsteriornisas a total-group member of Galloanserae (the clade uniting Galliformes and Anseriformes. One important feature supporting this placement was enlargement of the retroarticular processes, which form elongate caudal extensions of the mandible in extant Galloanserae. Here, we reinterpret the jaw ofAsteriornisand illustrate that the caudalmost portion of the mandibles are in fact not preserved. Instead, the caudal extremities of both the left and right mandibular rami extend to the surface of the fossil block containing the holotype skull, where they have eroded away. The originally identified retroarticular process of the right mandible—which exhibits a morphology and orientation strikingly similar to the retroarticular processes of certain extant and fossil galloanserans, including the early Palaeogene total-clade anseriformsConflictoandNettapterornis—instead represents a twisted and caudally displaced medial process. Nonetheless, anatomical comparisons with extant taxa reveal that we are unable to exclude the possibility thatAsteriornisexhibited robust retroarticular processes comparable to those of extant Galloanserae. In light of the reinterpreted morphology of theAsteriornismandible, we update the original anatomical character matrix used to investigate its phylogenetic relationships, and our revised phylogenetic analyses continue to support its position as a total-group galloanseran, as initially interpreted. We demonstrate additional morphological traits of the mandible supporting this phylogenetic position and provide new data on the nature and distribution of retroarticular processes among early crown birds.
Including the Invisible Fraction in Whole Population Studies: a Guide to the Genetic Sampling of Unhatched Bird Eggs
Authors: Morland Fay , Patel Selina , Santure Anna W. , Brekke Patricia , Hemmings Nicola 
Published: June 2023

AbstractEarly embryo mortality has recently been proven to be a significant component of avian reproductive failure. Due to the difficulty in distinguishing eggs which have suffered early embryo mortality from unfertilised eggs, this cause of reproductive failure has historically been underestimated and overlooked. We describe methods for recognising and collecting undeveloped, unhatched eggs from wild bird populations, identifying and isolating embryonic material in unhatched eggs, and efficiently extracting DNA from those samples. We test these methods on unhatched eggs collected from the field which have undergone post-mortem incubation. We obtained DNA yields from early-stage embryos that are sufficient for a wide range of molecular techniques, including microsatellite genotyping for parentage analysis and sex-typing. The type of tissue sample taken from the egg affected downstream DNA yields and microsatellite amplification rates. Species-specific microsatellite markers had higher amplification success rates than cross-species markers. We make key recommendations for each stage of the sampling and extraction process and suggest improvements potential and protocol modifications. Genetic and possibly genomic analysis of embryos that die early in development has the potential to advance many fields. The methods described here will allow a more in-depth exploration of the previously overlooked causes of early embryo mortality in wild populations of birds, including threatened species.
ALS-causing SOD1 mutations H46R and G85R form similar novel amyloid fibril structures and promote ferroptosis in cells
Authors: Wang Li-Qiang , Ma Yeyang , Zhang Mu-Ya , Yuan Han-Ye , Li Xiang-Ning , Xia Wencheng , Zhao Kun , Huang Xi , Chen Jie , Zou Liangyu , Li Dan , Wang Zhengzhi , Le Weidong , Liu Cong , Liang Yi 
Published: June 2023

AbstractMore than two hundred genetic mutations of Cu, Zn-superoxide dismutase (SOD1) have been identified in amyotrophic lateral sclerosis (ALS), a neurodegenerative disease characterized by the selective death of motor neurons through ferroptosis. Two ALS-causing SOD1 mutations, H46R and G85R, are metal-binding region mutants with reduced affinity for metal ions. Here, we generated amyloid fibrils from the apo forms of H46R and G85R under reducing conditions and determined their structures using cryo-EM. We built models for the fibril cores, comprising residues 85−153 for H46R and 82−153 for G85R. These mutations disrupt crucial interactions in the wild-type SOD1 fibril, resulting in amyloid fibrils with distinct structures compared to the wild-type fibril. Remarkably, H46R and G85R form similar novel amyloid fibril structures. The fibril cores display a serpentine fold containing seven or eight β-strands, which are stabilized by a hydrophobic cavity. In the G85R fibril core, Arg85 and Asp101 form a salt bridge for stabilization. We demonstrate that fibril seeds from H46R and G85R cause more severe mitochondrial impairment and significantly promote ferroptosis in neuronal cells, compared with those from wild-type SOD1. Our findings reveal how different SOD1 mutations can result in similar amyloid fibril structures and contribute to ALS pathology.
Tools for Quantitative Analysis of Calcium Signaling Data Using Jupyter-Lab Notebooks
Authors: Rugis John , Chaffer James , Sneyd James , Yule David 
Published: June 2023

AbstractCalcium signaling data analysis has become increasing complex as the size of acquired datasets increases. In this paper we present a Ca2+signaling data analysis method that employs custom written software scripts deployed in a collection of Jupyter-Lab “notebooks” which were designed to cope with this complexity. The notebook contents are organized to optimize data analysis workflow and efficiency. The method is demonstrated through application to several different Ca2+signaling experiment types.
SnakeFace: a transfer learning based app for snake classification
Authors: Pires Jorge Guerra , Dias Braga Luiz Henrique 
Published: June 2023

AbstractIntroductiondeep learning emerged in 2012 as one of the most important machine learning technologies, reducing image identification error from 25% to 5%. This article has two goals: 1) to demonstrate to the general public the ease of building state-of-the-art machine learning models without coding expertise; 2) to present a basic model adaptable to any biological image identification, such as species identification. Method: We present three test-of-concept models that showcase distinct perspectives of the app. The models aim at separating images into classes such as genus, species, and subspecies, and the input images can be easily adapted for different cases. We have applied deep learning and transfer learning using Teachable Machine. Results: Our basic models demonstrate high accuracy in identifying different species based on images, highlighting the potential for this method to be applied in biology. Discussions: the presented models showcase the ease of using machine learning nowadays for image identification. Furthermore, the adaptability of this method to various species and genuses emphasizes its importance in the biological fields, as root for inspiring collaborations with computer science. On our, future collaborations could lead to increasingly accurate and efficient models in this arena using well-curated datasets.
Optimal Filters for ERP Research II: Recommended Settings for Seven Common ERP Components
Authors: Zhang Guanghui , Garrett David R. , Luck Steven J. 
Published: June 2023

AbstractIn research with event-related potentials (ERPs), aggressive filters can substantially improve the signal-to-noise ratio and maximize statistical power, but they can also produce significant waveform distortion. Although this tradeoff has been well documented, the field lacks recommendations for filter cutoffs that quantitatively address both of these competing considerations. To fill this gap, we quantified the effects of a broad range of low-pass filter and high-pass filter cutoffs for seven common ERP components (P3b, N400, N170, N2pc, mismatch negativity, error-related negativity, and lateralized readiness potential) recorded from a set of neurotypical young adults. We also examined four common scoring methods (mean amplitude, peak amplitude, peak latency, and 50% area latency). For each combination of component and scoring method, we quantified the effects of filtering on data quality (noise level and signal-to-noise ratio) and waveform distortion. This led to recommendations for optimal low-pass and high-pass filter cutoffs. We repeated the analyses after adding artificial noise to provide recommendations for datasets with moderately greater noise levels. For researchers who are analyzing data with similar ERP components, noise levels, and participant populations, using the recommended filter settings should lead to improved data quality and statistical power without creating problematic waveform distortion.