bluuebunny/crossref_metadata_2025_split huggingface dataset:
#64 Common Admission Diagnoses for Children Hospitalized with Respiratory Syncytial Virus and Antibiotic Administration Practices in Amman, Jordan
Authors: Rankin Danielle A 
Published: June 2022

Abstract

Background
Determining the etiologic pathogen for acute respiratory infections is challenging, especially in low- and middle-income countries, where diagnostic testing is limited. These barriers may contribute to antibiotic overuse for viral infections. We aimed to evaluate the antibiotic administration patterns among hospitalized children with a research positive test for respiratory syncytial virus (RSV).

Method
Children admitted to a government-run hospital in Amman, Jordan with acute respiratory symptoms and/or fever from January 8 to March 17, 2020, were eligible for enrollment. Trained personnel conducted interviews and chart abstractions using a standardized data collection form. Nasal and/or throat swabs were collected and tested for RSV by PCR. Differences between the three most common admission diagnoses for RSV-positive children [bronchiolitis, bronchopneumonia (BP), and pneumonia] were evaluated.

Results
A total of 531 children were enrolled and tested and 401 (76%) were RSV-positive, of which 96% received an antibiotic and 25%, 26%, and 32% had an admission diagnosis of bronchiolitis, BP, or pneumonia, respectively. Compared to bronchiolitis and BP, RSV-positive children with a pneumonia were younger and more likely to require supplemental oxygen, receive an antibiotic during hospitalization, be admitted to the ICU; but were less likely to present with wheezing and to report antibiotic use prior to hospitalization (Table 1). RSV-positive children with BP were more likely to present with fever and have a higher C-reactive protein compared to the other diagnoses, whereas bronchiolitis was less likely to be administered antibiotics overall, but more likely to be given a macrolide.

Conclusion
Our results suggest that clinical presentation alone is insufficient in correctly determining causative pathogens that warrant empiric antibiotics. Thus, evaluating the role of point-of-care diagnostic testing in resource-limited settings is important and may help limit antibiotic use.
#71 Post-Exposure Prophylaxis for Varicella-Zoster Virus Exposure in High-Risk Children
Authors: Shteynberg Emily 
Published: June 2022

Abstract

Background
Despite universal childhood vaccination, Varicella-Zoster virus (VZV) remains a cause of severe infection following varicella exposure for immunocompromised children and high-risk infants. Post-exposure prophylaxis (PEP) is recommended to minimize this risk; however, providers may not consistently administer Varicella-specific immune globulin (VariZIG) as recommended in guidelines or may choose alternative regimens. The purpose of this study was to determine patterns of PEP for Varicella-Zoster Virus (VZV) at children’s hospitals.

Method
Using the Pediatric Health Information Systems database, clinical encounters with the ICD-9/10 codes for VZV exposure from 2009-2019 were reviewed. Only the first VZV exposure encounter for a given patient in the study period was included. Patients receiving prophylaxis or intravenous immunoglobulin (IVIG) within 30 days of the index encounter were also excluded. Presence of chronic illness or conditions at risk of progression to severe varicella disease was identified by reviewing ICD-9/10 codes for encounters in the prior 12 months. Choice and timing of PEP regimen exposure were identified, classified into the following categories: VZIG, intravenous immunoglobulin (IVIG), acyclovir, or combination prophylaxis. Clinical encounters for subsequent varicella disease within 30 days of exposure were recorded.

Results
There were 1770 children with first clinical encounters for VZV during the study period of which, 66 were excluded due to recent prior receipt of anti-viral therapy or IVIG. Of these 1704 children, 509 (29.9%) were prescribed PEP after VZV exposure, while 65 (3.8%) ultimately developed VZV disease. Of patients who received PEP, acyclovir was most frequently prescribed (n=195, 38.3%), divided between administration between1-4 days (n=132), 5-10 days (n=19), and both time periods (n=44), post-exposure. The proportion who received the other regimens was VariZIG (n=146, 28.7%), IVIG (n=115, 22.6%), and combination therapy (n=53, 10.4%). From 2009-2019, the proportion of children receiving acyclovir declined from 56% to 36%, VariZIG increased from 10 to 15%, IVIG decreased from 32 to 7%, while a similar percentage (8-9%) received a combination of Acyclovir and IG. The proportion of patients who subsequently had clinical encounters for varicella disease was highest for Acyclovir (30/195, 15.4%) followed by VariZIG (5/146, 3.4%), combination therapy (2/53, 3.8%), and IVIG alone (0/115). (p&lt;0.0001). Of the 65 patients that developed VZV disease, 24/65 (36.9%) had at least one high-risk condition.

Conclusion
Varicella PEP in high-risk children was highly varied among children’s hospitals and often diverged from guideline recommendations. Use of acyclovir was associated with a higher rate of breakthrough infection. More consistent use of guideline-recommended agents like VariZIG may lead to less varicella disease and complications in high-risk children.
#77 Prevalence of Staphylococcus aureus bacteremia at Saint Damien Hospital, Nos Petits Frères et Sœurs January (HSD/NPFS) 2020-June 2021, Haiti
Authors: St Vil Ymeline Pateau 
Published: June 2022

Abstract

Background
Staphylococcus Aureus (SA) is one of the main agents implicated in healthcare-associated infections (HAI) [1]. These infections are associated with significant morbidity and mortality, particularly methicillin-resistant staphylococcal (MRSA) infections, and their costs are also a concern. Bacteremia is regularly monitored at Saint Damien Hospital (HSD), for the year 2020 an increase in Staphylococcus aureus (SA) bacteremia was observed in certain units of the hospital. In this context, all SA infections were reviewed during eighteen months to determine the prevalence of methicillin-resistant (MRSA) and methicillin-sensitive (MSSA) staphylococcus aureus infections, their origins: in healthcare-associated infections (HAI), community-acquired infections (CI) and the distribution of MRSA per unit

Method
A Descriptive retrospective study was carried out at Saint Damien Hospital from January 2020 to June 2021. It includes all hospitalized children under fourteen years old (14) who had a positive blood culture for SA per site, only the 1st blood culture was taken into account. According to NHSN/CDC, are defined as infections associated with healthcare-associated infections occurring at ≥ 72 hours of hospitalization (HAI) and as community-acquired infectious infections occurring at = &lt; 48 hours of hospitalization.. Data were collected from microbiology laboratory registers and patient records

Results
From January 2020 to June 2021, two thousand two hundred thirty five 2235 blood cultures were performed. The positivity rate was 21.43% (n=479/2235) distributed in different units. 16.49% SA strains were isolated (n=79/479), including fifty (50) strains of MRSA (63.29%) and twenty nine (29) strains of MSSA (36.70%) (n=29/79).From the strains of MRSA, 54% (n=27/50) were HAI and 46% community infections (CI) (n=23/50). The Origin of the infections (HAI/CI) was not significantly associated with MRSA and MSSA strains (p=0.6235), MRSA mainly came from emergency 48% (n=24/50) followed by neonatology 20% (n=10/50), intensive care 10% (5/50) and oncology at 10% (5/50). (n=19/79), the mortality rate attributable to MRSA and MSSA was 28% (n=14/50) and 17.24% (n=5/29), respectively. 46% of MRSA were resistant to more than 3 families of antibiotics (n = 23/50). SA strains were resistant to gentamycin at 30.37% (n=24/79) to 54.34% to sulfametoxazole (n=43/79) and 18.98% and to vancomycin (n=15/79

Conclusion
The frequency of SA infections, specifically MRSA, is of great concern. Its existence in the community and its multiresistance, in particular to vancomycin, is an alert making this bacteremia a priority at Saint Damien Hospital, the standard precautions measures, the proper use of antibiotics by clinicians and epidemiological surveillance local would be needed to help control its spread.
#26 Prognostic Value of High Sensitivity C-Reactive Protein in Neonatal Early Onset Sepsis
Authors: Allen Garrett 
Published: June 2022

Abstract

Background
Inflammatory markers have been used to evaluate sepsis development in early-onset sepsis (EOS)in newborns. In some infants, antibiotics are started prophylactically for suspected sepsis for 48 hours pending the results of blood cultures, the clinical course, and the results of serial C-reactive protein (CRP) levels. When collected serially at birth, at 12 hours, and at 24 hours of life, CRP levels persistently lower than 1mg/dL have been associated with &gt;90% negative predictive value (NPV) for the development of infection. Our practice has recently transitioned to using High sensitivity CRP (hs-CRP) which offers much lower detection limits. We thus hypothesized that in term infants, a single early hs-CRP level at a lower cutoff than 1 mg/dL would be highly predictive of normal clinical outcome defined as negative blood culture, clinically well-appearing infant, and 3 negative serial hs-CRPs.

Method
Retrospective chart review of infants born at ≥ 37 weeks gestational age (GA), started on antibiotics, and had serial hs-CRPs collected. The 12-hr hsCRP time point was chosen to evaluate the hypothesis. Infants were divided based on a cutoff level of 0.3 mg/dL.

Results
Forty infants were identified: mean birth weight of 3.19 (±0.47) kg and GA of 38 (± 1) weeks. 23 infants had a 12-hour HsCRP ≤0.30 mg/dL. They all had a negative blood culture, remained clinically well appearing, and all their serial hs-CRPs at ≤ 1 mg/dL. 22/23 infants received ≤48 hours antibiotics. One infant had antibiotics extended to 4 days due to hyperglycemia. 17 infants had their 12-hour hs-CRP &gt;0.30 mg/dL. All had a negative blood culture and 6 infants received &gt; 48 hours of antibiotics. Eleven infants had their third hs-CRP&gt; 1mg/dl, figure. Using only a single HsCRP with a cutoff level ≤0.30 mg/dL led to a 96% NPV that infants would need antibiotics &gt;48 hours. Sensitivity, specificity, and the positive predictive values were 86%, 67%, and 3% respectively.

Conclusion
Conclusion: At single HsCRP ≤0.30 mg/dl at 12 hours of life was associated with 96% NPV for infants being on antibiotics ≥ 48 hours. If confirmed in larger studies, these findings may help decrease the length of antibiotic therapy in well appearing term infants with suspected infection to 12 hours. Future directions would evaluate the NPV of HsCRP &lt;0.3 mg/dL for holding off on starting antibiotics for cases with low index of suspected sepsis.
#28 Examining Adherence to World Health Organization (WHO) Latent Tuberculosis Pediatric Infection Guidelines Among 30 High Tuberculosis Burden Countries
Authors: Islam Sumaiya , Kiriella Dona , Oridota Olutobi , Dixit Avika 
Published: June 2022

Abstract

Background
Approximately 1.2 million children are estimated to be infected with tuberculosis (TB) worldwide. The World Health Organization (WHO) routinely updates guidelines for the treatment to lateen tuberculosis infection (LTBI) in children with the last update provided in 2020. The objective of our study was to assess the impact of these updates on national LTBI guidelines devised by 30 high burden countries.

Method
We collected National LTBI guidelines from health ministries of high burden countries. Eleven countries had guidelines that were in English and published in the last 6 years out of the 30 high burden countries. The guidelines from the respective countries were compared for concordance with the most recent WHO guidelines on LTBI management in the pediatric population.

Results
We identified four subsections of the WHO guidelines: at-risk groups for LTBI testing, algorithms to rule out active TB disease, testing for LTBI, and TB preventive treatment options. Guidelines from Nigeria and Pakistan had the highest concordance in identifying at-risk groups for LTBI at 83.3% each, whereas Namibia had the lowest concordance for this subcategory at 16.67% . Nigeria had 100% concordance in defining an algorithm to rule out active TB disease. Pakistan and Uganda had 80% concordance for algorithms to rule out disease. Philippines, Nigeria and Pakistan had 100% concordance with testing for LTBI, with Ethiopia, Kenya and Myanmar having the lowest concordance with 0%. Namibia and Myanmar had the highest concordance in regards to TB preventive treatment options, with 64% and 50% concordance respectively; all other included guidelines had low concordance for TB preventive treatment options.

Conclusion
Our study examined general concordance of national LTBI guidelines with the WHO guidelines and in the domains of identification, testing, algorithms, treatment, and prevention. Most guidelines among the high burden countries had high concordance in identifying at-risk groups for LTBI testing and algorithms to rule out active TB disease. Further research is needed to assess factors that lead to discordance between national and WHO guidelines.
#68 Prevalence of Staphylococcus aureus bacteremia at Saint Damien Hospital, Nos Petits Frères et Sœurs January 2020-June 2021, Haiti
Authors: St Vil Ymeline Pateau 
Published: June 2022

Abstract

Background
Nosocomial bacteremia is a healthcare-associated infection. It presents significant morbidity and mortality. Its prevention is based on the control of the risk factors, collection, and analysis of data to set up actions and measures aimed at educating staff, patients, and families to mitigate complications. Bacteremia is regularly monitored at Saint Damien Hospital (HSD);an increase in Staphylococcus aureus (SA) bacteremia was observed in January 2020. All SA infections were reviewed at St Damien during eighteen months to determine the prevalence of Methicillin-resistant Staphylococcus aureus (MRSA) and Methicillin-sensitive Staphylococcus aureus (MSSA) and the distribution by unit. Also, the frequency of nosocomial and community SA was determined. Nosocomial infections and those associated with SA remain a public health concern because of the antimicrobial resistance, the death rate, and the associated cost.

Method
A descriptive retrospective study was carried out over a period from January 2020 to June 2021 for all patients hospitalized in pediatrics who underwent a blood culture and whose results reported SA. Data were collected from microbiology laboratory registers and patient records.

Results
From January 2020 to June 2021, two thousand two hundred thirty-five (n = 2235) blood cultures were performed for a total of four thousand two hundred eighty-seven (n=4287) admissions. From these blood cultures performed, 11% of microorganisms (n=479) were isolated, of which 18.37% are SA (n=88). From these SA 68% were resistant to methicillin/MRSA (n=60), 32% sensitive to methicillin/MSSA (n=28).51% (n= 45) were associated with nosocomial infections (NI), 49% (n= 43) related to community infections. From the MRSA strains, 57% (n=34) are of nosocomial (NI) and 43% (n=26) are of community infection. These strains mainly came from emergency services 40% (n=24) followed by neonatology 22% (13) and intensive care 17% (10 ). The mortality rate for MRSA and MSSA were 32% (n=19) and 18% (n=5), respectively. 40% of MRSA isolates were multi-drug resistant (n=24). The resistance rate was 76% for penicillin (n=67) 65% for oxacillin (n=57) 35% for cefoxitin (n=31).

Conclusion
The frequency of isolation of Staphylococcus Aureus (SA) as well as the prevalence of SA and MRSA infections, was relatively high during this period. Its existence in a community setting and multidrug resistance to antibiotics is an alert making this bacteremia a public health priority to be monitored and brought under control.
Anomalous phenomena in cyclopropenylidene (c-C3H2) with accurate collisional rate coefficients
Authors: Sharma Mohit K , Chandra Suresh 
Published: June 2022

ABSTRACT
Collisional rate coefficients are important parameters, but their calculation is a tedious task. Accurate collisional rate coefficients for collisional transitions between pure rotational levels of cyclopropenylidene (c-C3H2), colliding with He atom, are now available. Strong anomalous absorption line 220–211 at 21.587 GHz of cyclopropenylidene is found ubiquitous in interstellar medium. It is therefore worth to analyse the line spectrum of c-C3H2 using accurate collisional rate coefficients. After performing the Sobolev analysis of c-C3H2, we have found four anomalous absorption lines namely 22,0–21,1, 44,0–43,1, 33,0–32,1, and 43,2–50,5. We have also found two weak MASER lines, 40,4–33,1 and 51,4–44,1, which may make the detection of c-C3H2 in a cosmic object more convenient. Even for low kinetic temperature and low column density of cyclopropenylidene, the detection of 22,0–21,1 transition is possible, and it may be the reason for its detection in a large number of cosmic objects. The stability of results is tested.
A panchromatic view of star cluster formation in a simulated dwarf galaxy starburst
Authors: Lahén Natalia , Naab Thorsten , Kauffmann Guinevere 
Published: June 2022

ABSTRACT
We present a photometric analysis of star and star cluster (SC) formation in a high-resolution simulation of a dwarf galaxy starburst that allows the formation of individual stars to be followed. Previous work demonstrated that the properties of the SCs formed in the simulation are in good agreement with observations. In this paper, we create mock spectral energy distributions and broad-band photometric images using the radiative transfer code skirt 9. We test several observational star formation rate (SFR) tracers and find that 24 $\mu$m, total infrared and Hα trace the underlying SFR during the (post)starburst phase, while UV tracers yield a more accurate picture of star formation during quiescent phases prior to and after the merger. We then place the simulated galaxy at distances of 10 and 50 Mpc and use aperture photometry at Hubble Space Telescope resolution to analyse the simulated SC population. During the starburst phase, a hierarchically forming set of SCs leads inaccurate source separation because of crowding. This results in estimated SC mass function slopes that are up to ∼0.3 shallower than the true slope of ∼−1.9 to −2 found for the bound clusters identified from the particle data in the simulation. The masses of the largest clusters are overestimated by a factor of up to 2.9 due to unresolved clusters within the apertures. The aperture-based analysis also produces a relation between cluster formation efficiency and SFR surface density that is slightly flatter than that recovered from bound clusters. The differences are strongest in quiescent SF environments.
Hot-mode accretion and the physics of thin-disc galaxy formation
Authors: Hafen Zachary , Stern Jonathan , Bullock James , Gurvich Alexander B , Yu Sijie , Faucher-Giguère Claude-André , Fielding Drummond B , Anglés-Alcázar Daniel , Quataert Eliot , Wetzel Andrew , Starkenburg Tjitske , Boylan-Kolchin Michael , Moreno Jorge , Feldmann Robert , El-Badry Kareem , Chan T K , Trapp Cameron , Kereš Dušan , Hopkins Philip F 
Published: June 2022

ABSTRACT
We use FIRE simulations to study disc formation in z ∼ 0, Milky Way-mass galaxies, and conclude that a key ingredient for the formation of thin stellar discs is the ability for accreting gas to develop an aligned angular momentum distribution via internal cancellation prior to joining the galaxy. Among galaxies with a high fraction ($\gt 70{{\ \rm per\ cent}}$) of their young stars in a thin disc (h/R ∼ 0.1), we find that: (i) hot, virial-temperature gas dominates the inflowing gas mass on halo scales (≳20 kpc), with radiative losses offset by compression heating; (ii) this hot accretion proceeds until angular momentum support slows inward motion, at which point the gas cools to $\lesssim 10^4\, {\rm K}$; (iii) prior to cooling, the accreting gas develops an angular momentum distribution that is aligned with the galaxy disc, and while cooling transitions from a quasi-spherical spatial configuration to a more-flattened, disc-like configuration. We show that the existence of this ‘rotating cooling flow’ accretion mode is strongly correlated with the fraction of stars forming in a thin disc, using a sample of 17 z ∼ 0 galaxies spanning a halo mass range of 1010.5 M⊙ ≲ Mh ≲ 1012 M⊙ and stellar mass range of 108 M⊙ ≲ M⋆ ≲ 1011 M⊙. Notably, galaxies with a thick disc or irregular morphology do not undergo significant angular momentum alignment of gas prior to accretion and show no correspondence between halo gas cooling and flattening. Our results suggest that rotating cooling flows (or, more generally, rotating subsonic flows) that become coherent and angular momentum-supported prior to accretion on to the galaxy are likely a necessary condition for the formation of thin, star-forming disc galaxies in a ΛCDM universe.
Tree House Explorer: A Novel Genome Browser for Phylogenomics
Authors: Harris Andrew J , Foley Nicole M , Williams Tiffani L , Murphy William J 
Published: June 2022

Abstract
Tree House Explorer (THEx) is a genome browser that integrates phylogenomic data and genomic annotations into a single interactive platform for combined analysis. THEx allows users to visualize genome-wide variation in evolutionary histories and genetic divergence on a chromosome-by-chromosome basis, with continuous sliding window comparisons to gene annotations, recombination rates, and other user-specified, highly customizable feature annotations. THEx provides a new platform for interactive phylogenomic data visualization to analyze and interpret the diverse evolutionary histories woven throughout genomes. Hosted on Conda, THEx integrates seamlessly into new or pre-existing workflows.
A Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy ofKlebsiella pneumoniaeStrains
Authors: Hennart Melanie , Guglielmini Julien , Bridel Sébastien , Maiden Martin C J , Jolley Keith A. , Criscuolo Alexis , Brisse Sylvain 
Published: June 2022

AbstractSublineages (SLs) within microbial species can differ widely in their ecology and pathogenicity, and their precise definition is important in basic research and for industrial or public health applications. Widely accepted strategies to define SLs are currently missing, which confuses communication in population biology and epidemiological surveillance. Here, we propose a broadly applicable genomic classification and nomenclature approach for bacterial strains, using the prominent public health threat Klebsiella pneumoniae as a model. Based on a 629-gene core genome multilocus sequence typing (cgMLST) scheme, we devised a dual barcoding system that combines multilevel single linkage (MLSL) clustering and life identification numbers (LINs). Phylogenetic and clustering analyses of &gt;7,000 genome sequences captured population structure discontinuities, which were used to guide the definition of 10 infraspecific genetic dissimilarity thresholds. The widely used 7-gene multilocus sequence typing (MLST) nomenclature was mapped onto MLSL SLs (threshold: 190 allelic mismatches) and clonal group (threshold: 43) identifiers for backwards nomenclature compatibility. The taxonomy is publicly accessible through a community-curated platform (https://bigsdb.pasteur.fr/klebsiella), which also enables external users’ genomic sequences identification. The proposed strain taxonomy combines two phylogenetically informative barcode systems that provide full stability (LIN codes) and nomenclatural continuity with previous nomenclature (MLSL). This species-specific dual barcoding strategy for the genomic taxonomy of microbial strains is broadly applicable and should contribute to unify global and cross-sector collaborative knowledge on the emergence and microevolution of bacterial pathogens.