bluuebunny/crossref_metadata_2025_split huggingface dataset:
Implementation of a coronavirus disease 2019 infection prevention and control training program in a low-middle income country
Authors: Perera Niranjala , Haldane Victoria , Ratnapalan Savithiri , Samaraweera Sudath , Karunathilake Mahesh , Gunarathna Chintha , Bandara Pavithri , Kawirathne Pandula , Wei Xiaolin 
Published: February 2022

ABSTRACT

Introduction and aims:
The COVID-19 pandemic poses an ongoing risk to health workers globally. This is particularly true in low- and middle-income countries (LMICs) where resource constraints, ongoing waves of infection, and limited access to vaccines disproportionately burden health systems. Thus, infection prevention and control (IPC) training for COVID-19 remains an important tool to safeguard health workers. We report on the implementation of evidence-based and role-specific COVID-19 IPC training for health workers in a hospital and public health field setting in Sri Lanka.

Methods:
We describe the development of training materials, which were contextualized to local needs and targeted to different staffing categories including support staff. We describe development of role- and context-specific IPC guidelines and accompanying training materials and videos during the first year of the COVID-19 pandemic. We describe in-person training activities and an overview of session leadership and participation.

Results:
Key to program implementation was the role of champions in facilitating the training, as well as delivery of training sessions featuring multi-media videos and role play to enhance the training experience. A total of 296 health workers participated in the training program sessions. Of these, 198 were hospital staff and 98 were from the public health workforce. Of the 296 health workers who participated in a training session, 277 completed a pre-test questionnaire and 256 completed post-test questionnaires. A significant increase in knowledge score was observed among all categories of staff who participated in training;however, support staff had the lowest pre-test knowledge on IPC practices at 71%, which improved to only 77% after the formal class.

Conclusion:
Implementing an IPC training program during a complex health emergency is a challenging, yet necessary task. Leveraging champions, offering training through multiple modalities including the use of videos and role play, as well as inclusion of all staff categories, is crucial to making training accessible.
Lysobacter antarcticus sp. nov., an SUF-system-containing bacterium from Antarctic coastal sediment
Authors: Liu Zuoyang , Jiang Peiqiang , Niu Guojiang , Wang Wenjing , Li Jing 
Published: February 2022

A Gram-stain-negative, heterotrophic, aerobic, non-motile, rod-shaped bacterial strain (GW1-59T) belonging to the genus

Lysobacter

was isolated from coastal sediment collected from the Chinese Great Wall Station, Antarctica. The strain was identified using a polyphasic taxonomic approach. The strain grew well on Reasoner's 2A media and could grow in the presence of 0–4 % (w/v) NaCl (optimum, 1 %), at pH 9.0–11.0 and at 15–37 °C (optimum, 30 °C). Strain GW1-59T possessed ubiquinone-8 as the sole respiratory quinone. The major phospholipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The major fatty acids were summed feature 9 (10-methyl C16 : 0 and/or iso-C17 : 1
ω9c), iso-C15 : 0, iso-C16 : 0, iso-C17 : 0, C16 : 0 and iso-C11 : 0 3-OH. DNA–DNA relatedness with

Lysobacter concretionis

Ko07T, the nearest phylogenetic relative (98.5 % 16S rRNA gene sequence similarity) was 23.4 % (21.1–25.9 %). The average nucleotide identity value between strain GW1-59T and

L. concretionis

Ko07T was 80.1 %. The physiological and biochemical results and low level of DNA–DNA relatedness suggested the phenotypic and genotypic differentiation of strain GW1-59T from other

Lysobacter

species. On the basis of phenotypic, phylogenetic and genotypic data, a novel species, Lysobacter antarcticus sp. nov., is proposed. The type strain is GW1-59T (=CCTCC AB 2019390T=KCTC 72831T).
Roseomonas rubea sp. nov., isolated from rice paddy soil
Authors: Lee Hyo-Jin , Whang Kyung-Sook 
Published: February 2022

Three pale-red-pigmented, Gram-stain-negative, coccobacilli-shaped, motile and strictly aerobic bacteria, strains MO17T, MO41 and NPKOSM1, were isolated from rice paddy soil. Colonies were circular with entire edges, convex and pale red. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains MO17T, MO41 and NPKOSM1 belonged to the genus

Roseomonas

and were closely related to

Roseomonas sediminicola

FW-3T (98.2 %),

Roseomonas oryzicola

YC6724T (98.0 %),

Roseomonas soli

5N26T (98.0 %),

Roseomonas eburnea

BUT-5T (97.8 %),

Roseomonas alkaliterrae

YIM 78007T (97.7 %),

Roseomonas lacus

TH-G33T (97.6 %) and

Roseomonas terrae

DS-48T (96.8 %). The DNA–DNA hybridization values between strains MO17T, MO41 and NPKOSM1 were 84–92 %, and the values between the three strains and their close phylogenetic relatives were also below 70 %. The major cellular fatty acids were C18 : 1
ω7c, C16 : 0 and summed feature 3 (C16 : 1
ω7c and/or iso-C15 : 0 2OH). The predominant respiratory quinone was identified as Q-10. The polar lipids detected were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, one unidentified aminophospholipid and two unknown phospholipids. Based on their distinctive phenotypic, phylogenetic and chemotaxonomic characteristics, the three strains are considered to represent novel species of the genus

Roseomonas

for which the name Roseomonas rubea sp. nov. is proposed. The type strain is MO17T (=KACC 19933T=NBRC 114495T).
Spike-dependent dynamic partitioning of the Locus coeruleus network through noradrenergic volume release in a simulation of nucleus core
Authors: Baral Shristi , Hosseini Hassan , More Kaushik , Fabrin Thomaz M.C. , Braun Jochen , Prigge Matthias 
Published: February 2022

AbstractThe Locus coeruleus (LC) modulates various neuronal circuits throughout the brain. Its unique architectural organization encompasses a net of axonal innervation that spans the entire brain; while its somatic core is highly compact. Recent research revealed an unexpected cellular input specificity within the nucleus that can give rise to various network states that either broadcast norepinephrine signals throughout the brain or pointedly modulate specific brain areas. Such adaptive input-output functions likely surpass our existing network models that build upon a given synaptic wiring configuration between neurons. As the distances between noradrenergic neurons in the core of the LC are unusually small, neighboring neurons could theoretically impact each other via volume transmission of NE. We therefore set out to investigate if such interaction could be mediated through noradrenergic alpha2-receptors in a spiking neuron model of the LC. We validate our model of LC neurons through comparison with experimental patch-clamp data and identify key variables that impact alpha2-mediated inhibition of neighboring LC neurons. Our simulation confirms a reliable autoinhibition of LC neurons after episodes of high neuronal activity that continue even after neuronal activity subsided. Also, dendro-somatic synapses inhibit spontaneous spiking in the somatic compartment of connected neurons in our model. We determined the exact position of hundreds of LC neurons in the mouse brain stem via a tissue clearing approach and, based on this, further determined that 25 percent of noradrenergic neurons have a neighboring LC neuron within less than a 25-micrometer radius. By modeling NE diffusion, we estimate that more than 15 percent of alpha2-adrenergic receptors fraction can bind NE within such diffusion radius. Our spiking neuron model of LC neurons predicts that repeated or long-lasting episodes of high neuronal activity induce partitioning of the gross LC network, and reduces the spike rate in neighboring neurons at distances smaller than 25 micrometers.As these volume-mediate neighboring effects are challenging to test with the current methodology, our findings can guide future experimental approaches to test this phenomenon and its physiological consequences.
RNA targeting with CRISPR-Cas13a facilitates bacteriophage genome engineering
Authors: Guan Jingwen , Oromí-Bosch Agnès , Mendoza Senén D. , Karambelkar Shweta , Berry Joel , Bondy-Denomy Joseph 
Published: February 2022

AbstractThe viruses that infect bacteria, bacteriophages (or phages), possess numerous genes of unknown function. Genetic tools are required to understand their biology and enhance their efficacy as antimicrobials. Pseudomonas aeruginosa jumbo phage ΦKZ and its relatives are a broad host range phage family that assemble a proteinaceous “phage nucleus” structure during infection. Due to the phage nucleus, DNA-targeting CRISPR-Cas is ineffective against this phage and thus there are currently no reverse genetic tools for this family. Here, we develop a DNA phage genome editing technology using the RNA-targeting CRISPR-Cas13a enzyme as a selection tool, an anti-CRISPR gene (acrVIA1) as a selectable marker, and homologous recombination. Precise insertion of foreign genes, gene deletions, and the addition of chromosomal fluorescent tags into the ΦKZ genome were achieved. Deletion of phuZ, which encodes a tubulin-like protein that centers the phage nucleus during infection, led to the mispositioning of the phage nucleus but surprisingly had no impact on phage replication, despite a proposed role in capsid trafficking. A chromosomal fluorescent tag placed on gp93, a proposed “inner body” protein in the phage head revealed a protein that is injected with the phage genome, localizes with the maturing phage nucleus, and is massively synthesized around the phage nucleus late in infection. Successful editing of two other phages that resist DNA-targeting CRISPR-Cas systems [OMKO1 (ΦKZ-like) and PaMx41] demonstrates the flexibility of this method. RNA-targeting Cas13a system holds great promise for becoming a universal genetic editing tool for intractable phages. This phage genetic engineering platform enables the systematic study of phage genes of unknown function and the precise modification of phages for use in a variety of applications.Graphical abstract
A randomized clinical trial of a booster dose with low versus standard dose of AZD1222 in adult after 2 doses of inactivated vaccines
Authors: Nanthapisal Sira , Puthanakit Thanyawee , Jaru-Ampornpan Peera , Nantanee Rapisa , Sodsai Pimpayao , Himananto Orawan , Sophonphan Jiratchaya , Suchartlikitwong Pintip , Hiransuthikul Narin , Angkasekwinai Pornpimon , Tangsathapornpong Auchara , Hirankarn Nattiya 
Published: February 2022

AbstractBackgroundImmunogenicity of inactivated SARS-CoV-2 vaccine has waning antibody over time. With the emergence of the SARS-CoV-2 delta variant, which requires higher neutralizing antibody to prevent infection, a booster dose is needed.ObjectiveTo evaluate immunogenicity and reactogenicity of standard- versus low-dose ChAdOx1 nCoV-19 vaccine booster after CoronaVac in healthy adults.MethodsA double-blinded, randomized, controlled trial of adult, aged 18-59 years, with completion of 2-dose CoronaVac at 21-28 days apart for more than 2 months was conducted. Participants were randomized to receive AZD1222 (Oxford/AstraZeneca) intramuscularly; standard dose (SD, 5×1010 viral particles) or low dose (LD, 2.5×1010 viral particles). Surrogate virus neutralization test (sVNT) against wild type and delta variant, and anti-spike-receptor-binding-domain IgG (anti-S-RBD IgG) were compared as geometric mean ratio (GMR) at day 14 and 90 between LD and SD arms.ResultsFrom July-August 2021, 422 adults with median age of 44 (IQR 36–51) years were enrolled. The median interval from CoronaVac to AZD1222 booster was 77 (IQR 64–95) days. At baseline, geometric means (GMs) of sVNT against delta variant and anti-S-RBD IgG were 18.1%inhibition (95%CI 16.4-20.0) and 111.5 (105.1-118.3) BAU/ml. GMs of sVNT against delta variant and anti-S-RBD IgG in SD were 95.6%inhibition (95%CI 94.3-97.0) and 1975.1 (1841.7-2118.2) BAU/ml at day 14, and 89.4%inhibition (86.4-92.4) and 938.6 (859.9-1024.4) BAU/ml at day 90, respectively. GMRs of sVNT against delta variant and anti-S-RBD IgG in LD compared to SD were 1.00 (95%CI 0.98-1.02) and 0.84 (0.76–0.93) at day 14, and 0.98 (0.94-1.03) and 0.89 (0.79-1.00) at day 90, respectively. LD recipients had significantly lower rate of fever (6.8%vs25.0%) and myalgia (51.9%vs70.7%) compared to SD.ConclusionHalf-dose AZD1222 booster after 2-dose inactivated SARS-CoV-2 vaccination had non-inferior immunogenicity, yet lower systemic reactogenicity. Fractional low-dose AZD1222 booster should be considered especially in resource-constrained settings.Highlights-Low dose AZD1222 could boost comparable immunity to standard dose in healthy adult who completed 2 doses of inactivated SARS-CoV-2 vaccines.-Less reactogenicity occurred in low-dose AZD1222 booster than standard-dose recipients.Thai Clinical Trials Registry (thaiclinicaltrials.org): TCTR20210722003
Predicting patient-reported outcomes following lumbar spine surgery: development and external validation of multivariable prediction models
Authors: Halicka Monika , Wilby Martin , Duarte Rui , Brown Christopher 
Published: February 2022

AbstractBackgroundThis study aimed to develop and externally validate prediction models of spinal surgery outcomes based on a retrospective review of a prospective clinical database, uniquely comparing multivariate regression and machine learning approaches, and identifying the most important predictors.MethodsOutcomes were change in back and leg pain intensity and Core Outcome Measures Index (COMI) from baseline to the last available postoperative follow-up (3-24 months), defined as minimal clinically important change (MCID) and continuous change score. Eligible patients underwent lumbar spine surgery for degenerative pathology between 2011 and 2021. Data were split by surgery date into development (N=2691) and validation (N=1616) sets. Multivariate logistic and linear regression, and random forest classification and regression models, were fit to the development data and validated on the external data.ResultsAll models demonstrated good calibration in the validation data. Discrimination ability (area under the curve) for MCID ranged from 0.63 (COMI) to 0.72 (back pain) in regression, and from 0.62 (COMI) to 0.68 (back pain) in random forests. The explained variation in continuous change scores spanned 16%-28% in linear, and 15%-25% in random forests regression. The most important predictors included age, baseline scores on the respective outcome measures, type of degenerative pathology, previous spinal surgeries, smoking status, morbidity, and duration of hospital stay.ConclusionsThe developed models appear robust and generalisable across different outcomes and modelling approaches but produced only borderline acceptable discrimination ability, suggesting the need to assess further prognostic factors. External validation showed no advantage of the machine learning approach.
Strain-dependent induction of primary bile acid 7-dehydroxylation by cholic acid
Authors: Vico-Oton Eduard , Volet Colin , Jacquemin Nicolas , Dong Yuan , Hapfelmeier Siegfried , Meibom Karin Lederballe , Bernier-Latmani Rizlan 
Published: February 2022

AbstractBile acids (BAs) are steroid-derived molecules with important roles in digestion, the maintenance of host metabolism and immunomodulation. Primary BAs are synthesised by the host, while secondary BAs are produced by the gut microbiome through transformation of the former. Regulation of microbial production of secondary BAs is not well understood, particularly the production of 7-dehydroxylated BAs, which are the most potent agonists for host BA receptors. The 7-dehydroxylation of cholic acid (CA) is well established and is linked to the expression of a bile acid-inducible (bai) operon responsible for this process. However, little to no 7-dehydroxylation has been reported for other host-derived BAs (e.g., chenodeoxycholic acid, CDCA or ursodeoxycholic acid, UDCA). Here, we demonstrate that the 7-dehydroxylation of CDCA and UDCA byClostridium scindensis induced by CA suggesting that CA-dependent transcriptional regulation of 7-dehydroxylation is generalisable to CDCA and UDCA. In contrast, the murine isolateExtibacter murisdid not respond to CA exposurein vitro, suggesting thatbaigenes are regulated differently in this strain. However, it could 7-dehydroxylatein vivoand itsin vitroactivity was promoted by the addition of cecal content. The accessory genebaiJwas only upregulated in theClostridium scindensATCC 35704 strain, implying mechanistic differences amongst isolates. Interestingly, the human-derivedC. scindensstrains were also capable of 7-dehydroxylating murine bile acids (muricholic acids) to a limited extent. This study shows novel 7-dehydroxylation activityin vitroas a result of CA-driven induction and suggests distinctbaigene induction mechanisms across bacterial species.
MicroRNAs are deeply linked to the emergence of the complex octopus brain
Authors: Zolotarov Grygoriy , Fromm Bastian , Legnini Ivano , Ayoub Salah , Polese Gianluca , Maselli Valeria , Chabot Peter J. , Vinther Jakob , Styfhals Ruth , Seuntjens Eve , Di Cosmo Anna , Peterson Kevin J. , Rajewsky Nikolaus 
Published: February 2022

AbstractSoft-bodied cephalopods such as the octopus are exceptionally intelligent invertebrates with a highly complex nervous system that evolved independently from vertebrates. Because of elevated RNA editing in their nervous tissues, we hypothesized that RNA regulation may play a major role in the cognitive success of this group. We thus profiled mRNAs and small RNAs in 18 tissues of the common octopus. We show that the major RNA innovation of soft-bodied cephalopods is a massive expansion of the miRNA gene repertoire. These novel miRNAs were primarily expressed in neuronal tissues, during development, and had conserved and thus likely functional target sites. The only comparable miRNA expansions happened, strikingly, in vertebrates. Thus, we propose that miRNAs are intimately linked to the evolution of complex animal brains.One-Sentence SummarymiRNAs are deeply linked to the emergence of complex brains.
Probing local chromatin dynamics by tracking telomeres
Authors: Benelli Rebecca , Weiss Matthias 
Published: February 2022

AbstractChromatin dynamics is key for cell viability and replication. In interphase, chromatin is decondensed, allowing the transcription machinery to access a plethora of DNA loci. Yet, decondensed chromatin occupies almost the entire nucleus, suggesting that DNA molecules can hardly move. Recent reports have even indicated that interphase chromatin behaves like a solid body on mesoscopic scales. To explore the local chromatin dynamics, we have performed single-particle tracking on telomeres under varying conditions. We find that mobile telomeres feature in all conditions a strongly subdiffusive, anti-persistent motion that is consistent with the monomer motion of a Rouse polymer in viscoelastic media. In addition, telomere trajectories show intermittent accumulations in local niches at physiological conditions, suggesting the surrounding chromatin to reorganize on these time scales. Reducing the temperature or exposing cells to osmotic stress resulted in a significant reduction of mobile telomeres and the number of visited niches. Altogether, our data indicate a vivid local chromatin dynamics, akin to a semi-dilute polymer solution, unless perturbations enforce a more rigid state of chromatin.Statement of SignificanceIn interphase cells, chromatin is decondensed and occupies almost the entire nucleus, suggesting DNA molecules to be fairly immobile. Recent reports even indicated chromatin to behave like a solid body on mesoscopic scales. Tracking individual telomeres, we have explored local chromatin dynamics under varying conditions. Our data reveal that telomeres show an antipersistent subdiffusion (fractional Brownian motion) at physiological conditions and at lower temperatures, indicating chromatin to be a viscoelastic fluid on submicron length scales. Telomeres also appear to visit local niches, supposedly provided by the constantly reorganizing chromatin. Applying osmotic stress significantly reduced the fraction of mobile telomeres and the number of visited niches, indicating that chromatin eventually assumes an elastic, solid-like behavior under these conditions.
Impaired dendritic spine development in a zebrafish model of Fragile X
Authors: DeMarco Elisabeth C. , Stoner George , Robles Estuardo 
Published: February 2022

AbstractDendritic spines are the principal site of excitatory synapse formation in the human brain. Impaired formation of spines during development has been observed in several autism spectrum disorders (ASDs), including Fragile X syndrome. Fragile X is caused by transcriptional silencing of the Fmr1 gene encoding the RNA-binding protein FMRP (Fragile X mental retardation protein). While spine development has been well characterized in the mammalian CNS, spines are not unique to mammals. Pyramidal neurons (PyrNs) of the zebrafish optic tectum form an apical dendrite containing a dense array of dendritic spines. We employed a genetic labeling system to monitor PyrN dendritic spine development in larval zebrafish. Our findings identify a developmental window when PyrN dendrite growth is concurrent with spine formation. Throughout this period, motile, transient filopodia gradually transform into stable spines containing postsynaptic specializations. fmr1 mutant zebrafish larvae exhibit pronounced defects in both PyrN dendrite growth and the formation of morphologically mature spines. Live imaging of PyrN dendrites suggests these defects are caused by an inability to stabilize nascent contacts. These findings indicate spine stabilization is essential for PyrN dendritic arborization and establish zebrafish larvae as a model system to study spine development in vivo.