bluuebunny/crossref_metadata_2025_split huggingface dataset:
Early Rehabilitation in Critically ill Children: A Two Center Implementation Study*
Authors: Choong Karen , Fraser Douglas D. , Al-Farsi Ahmed , Awlad Thani Saif , Cameron Saoirse , Clark Heather , Cuello Carlos , Debigaré Sylvie , Ewusie Joycelyne , Kennedy Kevin , Kho Michelle E. , Krasevich Kimberley , Martin Claudio M. , Thabane Lehana , Nanji Jasmine , Watts Catharine , Simpson Andrea , Todt Ashley , Wong Jonathan , Xie Feng , Vu Michael , Cupido Cynthia ,   on behalf of the Canadian Critical Care Trials Group
Published: January 2024

OBJECTIVES:To implement an early rehabilitation bundle in two Canadian PICUs.DESIGN AND SETTING:Implementation study in the PICUs at McMaster Children’s Hospital (site 1) and London Health Sciences (site 2).PATIENTS:All children under 18 years old admitted to the PICU were eligible for the intervention.INTERVENTIONS:A bundle consisting of: 1) analgesia-first sedation; 2) delirium monitoring and prevention; and 3) early mobilization.MEASUREMENTS AND MAIN RESULTS:Primary outcomes were the duration of implementation, bundle compliance, process of care, safety, and the factors influencing implementation. Secondary endpoints were the impact of the bundle on clinical outcomes such as pain, delirium, iatrogenic withdrawal, ventilator-free days, length of stay, and mortality. Implementation occurred over 26 months (August 2018 to October 2020). Data were collected on 1,036 patients representing 4,065 patient days. Bundle compliance was optimized within 6 months of roll-out. Goal setting for mobilization and level of arousal improved significantly (p< 0.01). Benzodiazepine, opioid, and dexmedetomidine use decreased in site 1 by 23.2% (95% CI, 30.8–15.5%), 26.1% (95% CI, 34.8–17.4%), and 9.2% (95% CI, 18.2–0.2%) patient exposure days, respectively, while at site 2, only dexmedetomidine exposure decreased significantly by 10.5% patient days (95% CI, 19.8–1.1%). Patient comfort, safety, and nursing workload were not adversely affected. There was no significant impact of the bundle on the rate of delirium, ventilator-free days, length of PICU stay, or mortality. Key facilitators to implementation included institutional support, unit-wide practice guidelines, dedicated PICU educators, easily accessible resources, and family engagement.CONCLUSIONS:A rehabilitation bundle can improve processes of care and reduce patient sedative exposure without increasing patient discomfort, nursing workload, or harm. We did not observe an impact on short-term clinical outcomes. The efficacy of a PICU-rehabilitation bundle requires ongoing study. Lessons learned in this study provide evidence to inform rehabilitation implementation in the PICU setting.
Stress Ulcer Prophylaxis Versus Placebo—A Blinded Pilot Randomized Controlled Trial to Evaluate the Safety of Two Strategies in Critically Ill Infants With Congenital Heart Disease
Authors: Mills Kimberly I. , Albert Ben D. , Bechard Lori J. , Chu Stephen , Duggan Christopher P. , Kaza Aditya , Rakoff-Nahoum Seth , Sleeper Lynn A. , Newburger Jane W. , Priebe Gregory P. , Mehta Nilesh M. 
Published: January 2024

OBJECTIVES:The routine use of stress ulcer prophylaxis (SUP) in infants with congenital heart disease (CHD) in the cardiac ICU (CICU) is controversial. We aimed to conduct a pilot study to explore the feasibility of performing a subsequent larger trial to assess the safety and efficacy of withholding SUP in this population (NCT03667703).DESIGN, SETTING, PATIENTS:Single-center, prospective, double-blinded, parallel group (SUP vs. placebo), pilot randomized controlled pilot trial (RCT) in infants with CHD admitted to the CICU and anticipated to require respiratory support for greater than 24 hours.INTERVENTIONS:Patients were randomized 1:1 (stratified by age and admission type) to receive a histamine-2 receptor antagonist or placebo until respiratory support was discontinued, up to 14 days, or transfer from the CICU, if earlier.MEASUREMENTS AND MAIN RESULTS:Feasibility was defined a priori by thresholds of screening rate, consent rate, timely drug allocation, and protocol adherence. The safety outcome was the rate of clinically significant upper gastrointestinal (UGI) bleeding. We screened 1,426 patients from February 2019 to March 2022; of 132 eligible patients, we gained informed consent in 70 (53%). Two patients did not require CICU admission after obtaining consent, and the remaining 68 patients were randomized to SUP (n= 34) or placebo (n= 34). Ten patients were withdrawn early, because of a change in eligibility (n= 3) or open-label SUP use (n= 7, 10%). Study procedures were completed in 58 patients (89% protocol adherence). All feasibility criteria were met. There were no clinically significant episodes of UGI bleeding during the pilot RCT. The percentage of patients with other nonserious adverse events did not differ between groups.CONCLUSIONS:Withholding of SUP in infants with CHD admitted to the CICU was feasible. A larger multicenter RCT designed to confirm the safety of this intervention and its impact on incidence of UGI bleeding, gastrointestinal microbiome, and other clinical outcomes is warranted.
Society for Simulation in Healthcare Guidelines for Simulation Training
Authors: Stefanidis Dimitrios , Cook David , Kalantar-Motamedi Seyed-Mohammad , Muret-Wagstaff Sharon , Calhoun Aaron W. , Lauridsen Kasper G. , Paige John T. , Lockey Andrew , Donoghue Aaron , Hall Andrew K. , Patocka Catherine , Palaganas Janice , Gross Isabel T. , Kessler David , Vermylen Julia , Lin Yiqun , Aebersold Michelle , Chang Todd P. , Duff Jonathan , Kolbe Michaela , Rutherford-Hemming Tonya , Decker Sharon , Collings Amelia , Toseef Ansari Mohammed 
Published: January 2024

BackgroundSimulation has become a staple in the training of healthcare professionals with accumulating evidence on its effectiveness. However, guidelines for optimal methods of simulation training do not currently exist.MethodsSystematic reviews of the literature on 16 identified key questions were conducted and expert panel consensus recommendations determined using the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) methodology.ObjectiveThese evidence-based guidelines from the Society for Simulation in Healthcare intend to support healthcare professionals in decisions on the most effective methods for simulation training in healthcareResultsTwenty recommendations on 16 questions were determined using GRADE. Four expert recommendations were also provided.ConclusionsThe first evidence-based guidelines for simulation training are provided to guide instructors and learners on the most effective use of simulation in healthcare.
Insights from comparative plastid genomics of colorless facultative pathogensPrototheca(Chlorophyta): Unveiling membrane transport and organelle division as key functions
Authors: Maciszewski Kacper , Wilga Gabriela , Jagielski Tomasz , Bakuła Zofia , Gawor Jan , Gromadka Robert , Karnkowska Anna 
Published: January 2024

AbstractPlastids are usually involved in photosynthesis, but the secondary loss of this function is a widespread phenomenon in various lineages of algae and plants. In addition to the loss of genes associated with photosynthesis, the plastid genomes of colorless algae are frequently reduced further. To understand the pathways of reductive evolution associated with the loss of photosynthesis, it is necessary to study a number of closely related strains.Prototheca, a chlorophytean genus of facultative pathogens, provides an excellent opportunity to study this process with its well-sampled array of diverse colorless strains.We have sequenced the plastid genomes of 13Protothecastrains and reconstructed a comprehensive phylogeny that reveals evolutionary patterns within the genus and among its closest relatives. Our robust phylogenomic analysis revealed three independent losses of photosynthesis among theProtothecastrains and considerable coding content variability in their ptDNA. Despite this diversity, allProtothecastrains retain the same key plastid functions. These include processes related to gene expression, as well as crucial roles in fatty acid and cysteine biosynthesis, membrane transport, and organelle division. While the retention of vestigial genomes in colorless plastids is typically associated with the biosynthesis of secondary metabolites, the remarkable conservation of plastid membrane transport and organellar division systems in the nonphotosynthetic generaProtothecaandHelicosporidiumprovides an additional constraint against the loss of ptDNA in this lineage. Furthermore, these genes can potentially serve as targets for therapeutic intervention, indicating their importance beyond the evolutionary context.
Colistin resistance genes inEscherichia coliisolated from patients with urinary tract infections
Authors: Al Momani Waleed M. , Ata Nour , Maslat Ahmed O. 
Published: January 2024

ABSTRACTIntroductionAntimicrobial resistance is alarmingly high because it happens in humans, environment, and animal sectors from a “One Health” viewpoint. Due to the fact, thatEscherichia coli (E. coli)is broadly disseminated in all sectors, the food web and the environment may have a role in carrying colistin resistance genes from animals to humans. The rise of plasmid-mediated mobile colistin resistance (MCR) genes threatens colistin efficacy, which is the last line to remedy Gram-negative infections multidrug resistance (MDR).ObjectivesThe current study aimed to investigate development of colistin resistance (MCR1-5) genes betweenE. coliisolated from patients with urinary tract infections (UTI) in Jordan.MethodsE. coli(n=132) isolated were collected from urine specimens.E. coliisolated from human UTI patients were examined for genes resistance to colistinMCR(1-5). All isolates were investigated against 20 antimicrobials utilizing the standard disk diffusion method. For analysis of colistin resistance, the broth microdilution technique was employed. In addition, theMCR(1-5) genes were detected by multiplex PCR assay.ResultsOut of 132 isolates, one isolate was colistin-resistant, having a minimum inhibitory concentration of 8 μg/mL and possessing theMCR-1 gene. A total of 132E. coliisolates showed high resistance against penicillin, amoxicillin, cephalexin, nalidixic acid, tetracycline, and cefepime in the percentages of 100%, 79.55%, 75.76%, 62.88%, 58.33%, and 53.79%, respectively. However, resistance was lowest towards fosfomycin (6.06%), florfenicol (10.61%), and chloramphenicol (15.91%). Significant differences were observed betweenE. coliisolated from pediatrics and those isolated from adults.ConclusionThis is the first report on the presence of the plasmid-codedMCR-1 gene recovered fromE. colifrom a patient with UTIs in Jordan. That is threatening as colistin is the last line used for infections induced by MDR gram-negative bacteria. There is a crucial need for control and harsh utilization of antibiotics to control and prevent the emergence and prevalence of colistin resistance genes.SummaryE. coliisolated from human UTI patients were examined for genes resistance to colistinMCR(1-5). This is the first report on the presence of the plasmid-codedMCR-1 gene recovered fromE. colifrom a patient with UTIs in Jordan. That is threatening as colistin is the last line used for infections induced by MDR gram-negative bacteria. There is a crucial need for control and harsh utilization of antibiotics to control and prevent the emergence and prevalence of colistin resistance genes. A total of 132E. coliisolates showed high resistance against penicillin, amoxicillin, cephalexin, nalidixic acid, tetracycline, and cefepime in the percentages of 100%, 79.55%, 75.76%, 62.88%, 58.33%, and 53.79%, respectively
Sunpheno: a deep neural network for phenological classification of sunflower images
Authors: Bengoa Luoni Sofia A. , Ricci Riccardo , Corzo Melanie A. , Hoxha Genc , Melgani Farid , Fernandez Paula C. 
Published: January 2024

AbstractLeaf senescence is a complex mechanism governed by multiple genetic and environmental variables that affect crop yield. It is the last stage of leaf development and is characterized by an active decline in the photosynthetic rate, nutrient recycling, and cell death. Leaf senescence begins in the lower leaves, and photoassimilates are translocated to the younger tissues. During early anthesis, leaf senescence becomes crucial for grain filling, because photoassimilates are translocated to the seeds. Therefore, a correct sync between leaf senescence and phenological stages is necessary to obtain the required yields. Furthermore, genotypes with early senescence were correlated with poor yield and low seed quality. Like all the crops growing in the field, studying phenology and its correlation with the senescence process is a laborious task where most of the parameters depend on highly trained people who conduct sampling and measurements. Several high-throughput phenotyping techniques have been developed in recent years. In this study, we evaluated the performance of five deep machine-learning methods for the evaluation of the phenological stages of sunflowers using images taken with cell phones in the field. From the analysis, we found that the method based on the pre-trained network resnet50 outperformed the other methods, both in terms of accuracy and velocity. Finally, the model generated, Sunpheno, was used to evaluate the phenological stages of two contrasting lines, B481_6 and R453, during senescence. We observed clear differences in phenological stages, confirming the results obtained in previous studies.
Geographic, ecological, and temporal patterns of seabird mortality during the 2022 HPAI H5N1 outbreak on the island of Newfoundland
Authors: McPhail Gretchen M. , Collins Sydney M. , Burt Tori V. , Careen Noah G. , Doiron Parker B. , Avery-Gomm Stephanie , Barychka Tatsiana , English Matthew D. , Giacinti Jolene A. , Jones Megan E.B. , Provencher Jennifer F. , Soos Catherine , Ward Christopher R.E. , Duffy Steven , Wilhelm Sabina I. , Wight Jordan , Rahman Ishraq , Hargan Kathryn E. , Lang Andrew S. , Montevecchi William A. 
Published: January 2024

AbstractHighly pathogenic avian influenza (HPAI) H5N1 caused mass seabird mortality across the North Atlantic in 2022. Following outbreaks in Europe, the first case in North America was detected on the island of Newfoundland (NFLD), Canada in November 2021, before spreading through all North American flyways. During the following breeding season, NFLD experienced the second-highest number of seabird mortalities in Canadian provinces. Surveys and citizen reports identified 13543 seabird mortalities from April to September 2022. Many carcasses occurred on the west coast of NFLD in May and June 2022. Reported mortalities peaked in July along the southeastern coast. In August and September, mortalities were concentrated along the northeastern coast. With the exception of two colony surveys, reported mortalities decreased in September. Most mortality was found among Northern Gannet (6622), Common Murre (5992), Atlantic Puffin (282), and Black-legged Kittiwake (217). Using comprehensive knowledge of seabird ecology, we formulated exploratory hypotheses regarding traits that could contribute to mortality. Species differences in mortality were most strongly associated with nesting density, timing of breeding, and at-sea overlap with allospecifics from other colonies. Unprecedented seabird mortality and ongoing transmission within the circulating avian influenza viruses highlight the need for continued monitoring and development of conservation strategies.
Mobile-CRISPRi as a powerful tool for modulatingVibriogene expression
Authors: Geyman Logan , Tanner Madeline , Rosario-Melendez Natalia , Peters Jason , Mandel Mark J. , van Kessel Julia C. 
Published: January 2024

AbstractCRISPRi (Clustered Regularly Interspaced Palindromic Repeats interference) is a gene knockdown method that uses a deactivated Cas9 protein (dCas9) that binds a specific gene target locus dictated by an encoded guide RNA (sgRNA) to block transcription. Mobile-CRISPRi is a suite of modular vectors that enable CRISPRi knockdowns in diverse bacteria by integrating IPTG-inducibledcas9andsgRNAgenes into the genome using Tn7transposition. Here, we show that the Mobile-CRISPRi system functions robustly and specifically in multipleVibriospecies:Vibrio cholerae, Vibrio fischeri, Vibrio vulnificus, Vibrio parahaemolyticus, andVibrio campbellii. We demonstrate efficacy by targeting both essential and non-essential genes that function to produce defined, measurable phenotypes: bioluminescence, quorum sensing, cell division, and growth arrest. We anticipate that Mobile-CRISPRi will be used inVibriospecies to systematically probe gene function and essentiality in various behaviors and native environments.
Multiomics analysis revealsB.MO1 as a distinctBabesiaspecies and provides insights into its evolution and virulence
Authors: Singh Pallavi , Vydyam Pratap , Fang Tiffany , Estrada Karel , Gonzalez Luis Miguel , Grande Ricardo , Kumar Madelyn , Chakravarty Sakshar , Berry Vincent , Ranwez Vincent , Carcy Bernard , Depoix Delphine , Sánchez Sergio , Cornillot Emmanuel , Abel Steven , Ciampossin Loic , Lenz Todd , Harb Omar , Sanchez-Flores Alejandro , Montero Estrella , Le Roch Karine G. , Lonardi Stefano , Ben Mamoun Choukri 
Published: January 2024

AbstractBabesiosis, caused by protozoan parasites of the genusBabesia, is an emerging tick-borne disease of significance for both human and animal health.Babesiaparasites infect erythrocytes of vertebrate hosts where they develop and multiply rapidly to cause the pathological symptoms associated with the disease. The identification of variousBabesiaspecies underscores the ongoing risk of new zoonotic pathogens capable of infecting humans, a concern amplified by anthropogenic activities and environmental shifts impacting the distribution and transmission dynamics of parasites, their vectors, and reservoir hosts. One such species,BabesiaMO1, previously implicated in severe cases of human babesiosis in the midwestern United States, was initially considered closely related toB. divergens, the predominant agent of human babesiosis in Europe. Yet, uncertainties persist regarding whether these pathogens represent distinct variants of the same species or are entirely separate species. We show that although bothB.MO1 andB. divergensshare similar genome sizes, comprising three nuclear chromosomes, one linear mitochondrial chromosome, and one circular apicoplast chromosome, major differences exist in terms of genomic sequence divergence, gene functions, transcription profiles, replication rates and susceptibility to antiparasitic drugs. Furthermore, both pathogens have evolved distinct classes of multigene families, crucial for their pathogenicity and adaptation to specific mammalian hosts. Leveraging genomic information forB.MO1,B. divergens, and other members of the Babesiidae family within Apicomplexa provides valuable insights into the evolution, diversity, and virulence of these parasites. This knowledge serves as a critical tool in preemptively addressing the emergence and rapid transmission of more virulent strains.
Catabolic pathway acquisition by soil pseudomonads readily enables growth with salicyl alcohol but does not affect colonization ofPopulusroots
Authors: Christel Stephan , Carrell Alyssa A. , Burdick Leah H. , Villalobos Solis Manuel I. , Abraham Paul E. , Jawdy Sara S. , Chaves Julie E. , Engle Nancy L. , Berhane Timkhite-Kulu , Yao Tao , Chen Jin-Gui , Muchero Wellington , Tschaplinski Timothy J. , Cregger Melissa A. , Michener Joshua K. 
Published: January 2024

ABSTRACTHorizontal gene transfer (HGT) is a fundamental evolutionary process that plays a key role in bacterial evolution. The likelihood of a successful transfer event is expected to depend on the precise balance of costs and benefits resulting from pathway acquisition. Most experimental analyses of HGT have focused on phenotypes that have large fitness benefits under appropriate selective conditions, such as antibiotic resistance. However, many examples of HGT involve phenotypes that are predicted to provide smaller benefits, such as the ability to catabolize additional carbon sources. We have experimentally reproduced one such HGT event in the laboratory, studying the effects of transferring a pathway for catabolism of the plant-derived aromatic compound salicyl alcohol into soil isolates from thePseudomonasgenus. We find that pathway acquisition enables rapid catabolism of salicyl alcohol with only minor disruptions to existing metabolic and regulatory networks of the new host. However, this new catabolic potential does not confer a measurable fitness advantage during competitive growth in the rhizosphere. We conclude that the phenotype of salicyl alcohol catabolism is readily transferred by HGT but is selectively neutral under environmentally-relevant conditions. We propose that this condition is common and that HGT of many pathways will be self-limiting, because the selective benefits are small and negative frequency-dependent.
EvoAug-TF: Extending evolution-inspired data augmentations for genomic deep learning to TensorFlow
Authors: Yu Yiyang , Muthukumar Shivani , Koo Peter K 
Published: January 2024

ABSTRACTDeep neural networks (DNNs) have been widely applied to predict the molecular functions of regulatory regions in the non-coding genome. DNNs are data hungry and thus require many training examples to fit data well. However, functional genomics experiments typically generate limited amounts of data, constrained by the activity levels of the molecular function under study inside the cell. Recently, EvoAug was introduced to train a genomic DNN with evolution-inspired augmentations. EvoAug-trained DNNs have demonstrated improved generalization and interpretability with attribution analysis. However, EvoAug only supports PyTorch-based models, which limits its applications to a broad class of genomic DNNs based in TensorFlow. Here, we extend EvoAug’s functionality to TensorFlow in a new package we call EvoAug-TF. Through a systematic benchmark, we find that EvoAug-TF yields comparable performance with the original EvoAug package.AvailabilityEvoAug-TF is freely available for users and is distributed under an open-source MIT license. Researchers can access the open-source code on GitHub (https://github.com/p-koo/evoaug-tf). The pre-compiled package is provided via PyPI (https://pypi.org/project/evoaug-tf) with in-depth documentation on ReadTheDocs (https://evoaug-tf.readthedocs.io). The scripts for reproducing the results are available at (https://github.com/p-koo/evoaug-tf_analysis).