bluuebunny/crossref_metadata_2025_split huggingface dataset:
Viral communities in a pH>10 serpentinite-like environment: insight into diversity and potential roles in modulating the microbiomes by bioactive vitamin B
9
synthesis
Authors: He Yu , Zhuo Shiyan , Gao Donghao , Pan Yue , Li Meng , Pan Jie , Jiang Yongguang , Hu Yidan , Guo Jinzhi , Lin Qin , Sanford Robert A. , Sun Weimin , Shang Jianying , Wei Na , Peng Shuming , Jiang Zhou , Li Shuyi , Li Yongzhe , Dong Yiran , Shi Liang 
Published: July 2024

ABSTRACT

Viral communities exist in a variety of ecosystems and play significant roles in mediating biogeochemical processes, whereas viruses inhabiting strongly alkaline geochemical systems remain underexplored. In this study, the viral diversity, potential functionalities, and virus–host interactions in a strongly alkaline environment (pH = 10.4–12.4) exposed to the leachates derived from the serpentinization-like reactions of smelting slags were investigated. The viral populations (e.g., Herelleviridae, Queuovirinae, and Inoviridae) were closely associated with the dominating prokaryotic hosts (e.g.,
Meiothermus
, Trueperaceae, and
Serpentinomonas
) in this ultrabasic environment. Auxiliary metabolic genes (AMGs) suggested that viruses may enhance hosts’ fitness by facilitating cofactor biosynthesis, hydrogen metabolism, and carbon cycling. To evaluate the activity of synthesis of essential cofactor vitamin B
9
by the viruses, a viral
folA
(v
folA
) gene encoding dihydrofolate reductase (DHFR) was introduced into a thymidine-auxotrophic strain
Escherichia coli
MG1655 Δ
folA
mutant, which restored the growth of the latter in the absence of thymidine. Notably, the homologs of the validated vDHFR were globally distributed in the viromes across various ecosystems. The present study sheds new light on the unique viral communities in hyperalkaline ecosystems and their potential beneficial impacts on the coexisting microbial consortia by supplying essential cofactors.

IMPORTANCE

This study presents a comprehensive investigation into the diversity, potential functionalities, and virus–microbe interactions in an artificially induced strongly alkaline environment. Functional validation of the detected viral
folA
genes encoding dihydrofolate reductase substantiated the synthesis of essential cofactors by viruses, which may be ubiquitous, considering the broad distribution of the viral genes associated with folate cycling.
Immunization with an mRNA DTP vaccine protects against pertussis in rats
Authors: Bitzer Graham J. , Fitzgerald Nicholas A. , DeJong Megan A. , Cunningham Casey , Chapman Joshua A. , Boehm Dylan T. , Pyles Gage M. , Huckaby Annalisa B. , Miller Sarah J. , Dublin Spencer R. , Warden Matthew D. , Barbier Mariette , Damron F. Heath 
Published: July 2024

ABSTRACT

Bordetella pertussis
is a Gram-negative bacterium that is the causative agent of the respiratory disease known as pertussis. Since the switch to the acellular vaccines of DTaP and Tap, pertussis cases in the US have risen and cyclically fallen. We have observed that mRNA pertussis vaccines are immunogenic and protective in mice. Here, we further evaluated the pertussis toxoid mRNA antigen and refined the formulation based on optimal pertussis toxin neutralization
in vivo
. We next evaluated the mRNA pertussis vaccine in Sprague-Dawley rats using an aerosol
B. pertussis
challenge model paired with whole-body plethysmography to monitor coughing and respiratory function. Female Sprague-Dawley rats were primed and boosted with either commercially available vaccines (DTaP or wP-DTP), an mRNA-DTP vaccine, or mock-vaccinated. The mRNA-DTP vaccine was immunogenic in rats and induced antigen-specific IgG antibodies comparable to DTaP. Rats were then aerosol challenged with a streptomycin-resistant emerging clinical isolate D420Sm1. Bacterial burden was assessed at days 1 and 9 post-challenge, and the mRNA vaccine reduced burden equal to both DTaP and wP-DTP. Whole-body plethysmography revealed that mRNA-DTP vaccinated rats were well protected against coughing which was comparable to the non-challenged group. These data suggest that an mRNA-DTP vaccine is immunogenic in rats and provides protection against aerosolized
B. pertussis
challenge in Sprague-Dawley rats.
Evaluation of a BioFire multiplex PCR panel for detection of joint infections using retrospective and prospectively collected specimens
Authors: Moran Angelica , Arellano Jekzaly , Bregman Karen , McElvania Erin 
Published: July 2024

ABSTRACT

The BioFire Joint Infection Panel (JI panel) is a newly FDA-approved multiplex PCR assay for detection of common bone and joint pathogens with 39 targets which include select Gram-positive and Gram-negative bacteria, yeast, and antimicrobial resistance genes. We evaluated the performance of the JI panel in detecting joint infections in our patient population. Sixty-three frozen, residual joint fluid specimens were retrospectively tested using the JI panel. An additional 104 residual joint fluid specimens were de-identified and prospectively tested within 1 week of collection. Results from routine bacterial cultures were used as the reference standard, which included inoculation to agar plates and blood culture bottles. For the frozen specimens, the JI panel showed a positive percent agreement (PPA) of 92.8% and a negative percent agreement (NPA) of 97.1%. PPA was 71.4% and NPA was 94.8% for fresh specimens. A total of 12 discrepancies were observed among the 167 specimens tested. The JI panel demonstrated good overall agreement with routine culture for the detection of joint infections and may improve timely diagnosis when used in conjunction with bacterial culture. However, potential false-positive and false-negative results were observed in both retrospective and prospective testing of specimens.

IMPORTANCE
The BioFire JI panel is a new commercially available multiplex PCR assay for detecting common pathogens causing bone and joint infections. The test is performed directly on joint fluids with a fast turnaround time of 1 hour. Our study shows that while the JI panel overall shows good agreement with routine culture, discrepancies were observed in 7% of cases and results should be interpreted with appropriate clinical context.
Vaccine strains of Rift Valley fever virus exhibit attenuation at the maternal–fetal placental interface
Authors: McMillen Cynthia M. , Megli Christina , Radisic Rebecca , Skvarca Lauren B. , Hoehl Ryan M. , Boyles Devin A. , McGaughey Jackson J. , Bird Brian H. , McElroy Anita K. , Hartman Amy L. 
Published: July 2024

ABSTRACT

Rift Valley fever virus (RVFV) infection causes abortions in ruminant livestock and is associated with an increased likelihood of miscarriages in women. Using sheep and human placenta explant cultures, we sought to identify tissues at the maternal–fetal interface targeted by RVFV. Sheep villi and fetal membranes were highly permissive to RVFV infection resulting in markedly higher virus titers than human cultures. Sheep cultures were most permissive to wild-type RVFV and ΔNSm infection, while live-attenuated RVFV vaccines (LAVs; MP-12, ΔNSs, and ΔNSs/ΔNSm) exhibited reduced replication. The human fetal membrane restricted wild-type and LAV replication, and when infection occurred, it was prominent on the maternal-facing side. Type I and type III interferons were induced in human villi exposed to LAVs lacking the NSs protein. This study supports the use of sheep and human placenta explants to understand vertical transmission of RVFV in mammals and whether LAVs are attenuated at the maternal–fetal interface.

IMPORTANCE
A direct comparison of replication of Rift Valley fever virus (RVFV) in sheep and human placental explants reveals comparative efficiencies and permissivity to infection and replication. Vaccine strains of RVFV demonstrated reduced infection and replication capacity in the mammalian placenta. This study represents the first direct cross-host comparison of the vertical transmission capacity of this high-priority emerging mosquito-transmitted virus.
In vitro
higher-order oligomeric assembly of the respiratory syncytial virus M2-1 protein with longer RNAs
Authors: Gao Yunrong , Raghavan Anirudh , Espinosa Garcia Sara Andrea , Deng Bowei , Hurtado de Mendoza Diego , Liang Bo 
Published: July 2024

ABSTRACT

The respiratory syncytial virus (RSV) M2-1 protein is a transcriptional antitermination factor crucial for efficiently synthesizing multiple full-length viral mRNAs. During RSV infection, M2-1 exists in a complex with mRNA within cytoplasmic compartments called inclusion body-associated granules (IBAGs). Prior studies showed that M2-1 can bind along the entire length of viral mRNAs instead of just gene-end (GE) sequences, suggesting that M2-1 has more sophisticated RNA recognition and binding characteristics. Here, we analyzed the higher oligomeric complexes formed by M2-1 and RNAs
in vitro
using size exclusion chromatography (SEC), electrophoretic mobility shift assays (EMSA), negative stain electron microscopy (EM), and mutagenesis. We observed that the minimal RNA length for such higher oligomeric assembly is about 14 nucleotides for polyadenine sequences, and longer RNAs exhibit distinct RNA-induced binding modality to M2-1, leading to enhanced particle formation frequency and particle homogeneity as the local RNA concentration increases. We showed that particular cysteine residues of the M2-1 cysteine-cysteine-cystine-histidine (CCCH) zinc-binding motif are essential for higher oligomeric assembly. Furthermore, complexes assembled with long polyadenine sequences remain unaffected when co-incubated with ribonucleases or a zinc chelation agent. Our study provided new insights into the higher oligomeric assembly of M2-1 with longer RNA.

IMPORTANCE

Respiratory syncytial virus (RSV) causes significant respiratory infections in infants, the elderly, and immunocompromised individuals. The virus forms specialized compartments to produce genetic material, with the M2-1 protein playing a pivotal role. M2-1 acts as an anti-terminator in viral transcription, ensuring the creation of complete viral mRNA and associating with both viral and cellular mRNA. Our research focuses on understanding M2-1’s function in viral mRNA synthesis by modeling interactions in a controlled environment. This approach is crucial due to the challenges of studying these compartments
in vivo
. Reconstructing the system
in vitro
uncovers structural and biochemical aspects and reveals the potential functions of M2-1 and its homologs in related viruses. Our work may contribute to identifying targets for antiviral inhibitors and advancing RSV infection treatment.
Complete genome sequence of
Cereibacter sphaeroides
f. sp. denitrificans strain IL106
Authors: Stock Emma K. , Terrell Kaziah J. , Rayyan Amiera A. , Kyndt John A. 
Published: July 2024

ABSTRACT

Cereibacter sphaeroides
is a non-sulfur purple bacterium, one of the most versatile and thoroughly studied species of its kind, can grow on a variety of compounds photoheterotrophically, and is often used in bioremediation. We present the complete genome of
Cereibacter sphaeroides
f. sp. denitrificans underscoring its unique features.
Updating the Upper Cretaceous (Campanian) Two Medicine Formation of Montana: Lithostratigraphic revisions, new CA-ID-TIMS U-Pb ages, and a calibrated framework for dinosaur occurrences
Authors: Rogers Raymond R. , Horner John R. , Ramezani Jahandar , Roberts Eric M. , Varricchio David J. 
Published: July 2024

Abstract
The Campanian Two Medicine Formation of northwestern Montana, USA, is richly fossiliferous, and discoveries made within the unit over the past century have greatly advanced our appreciation of dinosaur paleobiology and evolution. Previously undifferentiated from a lithostratigraphic perspective, the formation is now subdivided into four new members that include (from base to top) (1) the Rock City Member, (2) the Shields Crossing Member, (3) the Hagans Crossing Member, and (4) the Flag Butte Member. These new formal units and their associated fossil occurrences are also now included in an age model founded on eight high-resolution chemical abrasion–isotope dilution–thermal ionization mass spectrometry (CA-ID-TIMS) U-Pb ages. New age data confirm that the Two Medicine Formation accumulated during much of the Campanian, with deposition spanning ca. 82.4 Ma to 74.4 Ma. New age data further indicate that a major reorganization of depositional systems, marked by a shift from predominantly lacustrine to alluvial facies and accompanied by a dramatic increase in accommodation, transpired near the base of the new Flag Butte Member at ca. 76.3 Ma. This change in depositional regime correlates in age with the Judith River–Belly River discontinuity, which marks the contact between the McClelland Ferry and Coal Ridge Members in the Judith River Formation and coincides with the onset of the Bearpaw transgression in north-central Montana. The new lithostratigraphic and chronostratigraphic framework for the Two Medicine Formation serves to contextualize and calibrate the formation’s rich dinosaur fossil record, which can now be interrogated with increased clarity and precision. These results also provide ground truth for numerical models that explore the structure of the fossil record in relation to alluvial architecture and terrestrial sequence stratigraphy.
Methotrexate versus conventional disease-modifying antirheumatic drugs in the treatment of non-anterior sarcoidosis-associated uveitis
Authors: Leclercq Mathilde , Sève Pascal , Biard Lucie , Vautier Mathieu , Maalouf Georgina , Leroux Gaëlle , Domont Fanny , Toutée Adélaïde , Fardeau Christine , Sales de Gauzy Thomas , Touhami Sara , Kodjikian Laurent , Cacoub Patrice , Bodaghi Bahram , Saadoun David , Desbois Anne-Claire 
Published: July 2024

Aims
To compare the safety and efficacy of methotrexate (MTX), mycophenolate mofetil (MMF) and azathioprine (AZA) in non-anterior sarcoidosis-associated uveitis.

Methods
Retrospective study including non-anterior sarcoidosis-associated uveitis according to the revised International Workshop on Ocular Sarcoidosis criteria. The primary outcome was defined as the median time to relapse or occurrence of serious adverse events leading to treatment discontinuation.

Results
58 patients with non-anterior sarcoidosis-associated uveitis (MTX (n=33), MMF (n=16) and AZA (n=9)) were included. The time to treatment failure (ie, primary outcome) after adjustment for corticosteroids dose and the presence of vasculitis was significantly higher with MTX (median time of 34.5 months with MTX (IQR: 11.8 –not reached) vs 8.4 months (3.1–22.9) with MMF and 16.8 months (8.0–90.1) with AZA (p=0.020)). The risk of relapse at 12 months was more than twice lower in MTX as compared with MMF (p=0.046). Low visual acuity at the last visit was significantly lower with MTX (4% vs 9% in MMF vs 57% in AZA group (p=0.008)). Regarding all 75 lines of treatment (MTX (n=39), MMF (n=24) and AZA (n=12)), MTX was more effective than MMF and AZA to obtain treatment response at 3 months (OR 10.85; 95% CI 1.13 to 104.6; p=0.039). Significant corticosteroid-sparing effect at 12 months (p=0.035) was only observed under MTX. Serious adverse events were observed in 6/39 (15%), 5/24 (21%) and 2/12 (17%) with MTX, MMF and AZA, respectively.

Conclusion
In non-anterior sarcoidosis-associated uveitis, MTX seems to be more efficient compared with AZA and MMF and with an acceptable safety profile.
Topical glyceryl trinitrate (GTN) and eccentric exercises in the treatment of mid-portion achilles tendinopathy (the NEAT trial): a randomised double-blind placebo-controlled trial
Authors: Kirwan Paul D , Duffy Trevor , French Helen P 
Published: July 2024

ObjectivesTo investigate if daily treatment with glyceryl trinitrate (GTN) ointment, over 24 weeks combined with a 12-week eccentric exercise programme is more effective for chronic mid-portion Achilles tendinopathy than placebo ointment and eccentric exercise.MethodsThis was a single-site randomised double-blind placebo-controlled trial at an acute hospital, Dublin, Ireland. Patients with chronic mid-portion Achilles tendinopathy were randomised to either 24 weeks of daily GTN ointment or placebo ointment. Both groups received an identical 12-week eccentric exercise programme. The primary outcome measure was the Victorian Institute of Sport Assessment–Achilles (VISA-A) questionnaire at 24 weeks, which measures pain, function and activity. Secondary outcomes included pain severity, self-reported physical function, calf muscle function, pressure pain thresholds and ultrasound changes. Statistical analyses were performed according to intention-to-treat principles.Results76 patients (30 women; 46 men, mean age±SD, 45.6±8.2 years) were recruited for the trial. Significant improvements in VISA-A scores occurred in both groups at 6-week, 12-week and 24-week follow-up. The increase was not significantly different between groups, adjusted mean between-group difference from baseline to week 6, –1.33 (95% CI –6.96 to 4.31); week 12, −1.25 (95% CI −8.0 to 5.49) and week 24, –3.8 (95% CI –10.6 to 3.0); negative values favour GTN. There was no significant between-group difference in any of the secondary outcome measures at 6, 12 and 24 weeks.ConclusionsAdding daily GTN ointment over 24 weeks to a 12-week eccentric exercise programme did not improve pain, function and activity level in patients with chronic mid-portion Achilles tendinopathy when compared with placebo ointment.
Where is the research on sport-related concussion in Olympic athletes? A descriptive report and assessment of the impact of access to multidisciplinary care on recovery
Authors: Romeas Thomas , Croteau Félix , Leclerc Suzanne 
Published: July 2024

ObjectivesThis cohort study reported descriptive statistics in athletes engaged in Summer and Winter Olympic sports who sustained a sport-related concussion (SRC) and assessed the impact of access to multidisciplinary care and injury modifiers on recovery.Methods133 athletes formed two subgroups treated in a Canadian sport institute medical clinic: earlier (≤7 days) and late (≥8 days) access. Descriptive sample characteristics were reported and unrestricted return to sport (RTS) was evaluated based on access groups as well as injury modifiers. Correlations were assessed between time to RTS, history of concussions, the number of specialist consults and initial symptoms.Results160 SRC (median age 19.1 years; female=86 (54%); male=74 (46%)) were observed with a median (IQR) RTS duration of 34.0 (21.0–63.0) days. Median days to care access was different in the early (1; nSRC=77) and late (20; nSRC=83) groups, resulting in median (IQR) RTS duration of 26.0 (17.0–38.5) and 45.0 (27.5–84.5) days, respectively (p<0.001). Initial symptoms displayed a meaningful correlation with prognosis in this study (p<0.05), and female athletes (52 days (95% CI 42 to 101)) had longer recovery trajectories than male athletes (39 days (95% CI 31 to 65)) in the late access group (p<0.05).ConclusionsOlympic athletes in this cohort experienced an RTS time frame of about a month, partly due to limited access to multidisciplinary care and resources. Earlier access to care shortened the RTS delay. Greater initial symptoms and female sex in the late access group were meaningful modifiers of a longer RTS.
Potentially inappropriate medication as a predictor of poor prognosis of COVID-19 in older adults: a South Korean nationwide cohort study
Authors: Kim Hyungmin , Hong Song Hee 
Published: July 2024

ObjectivesTo investigate the association between exposure to potentially inappropriate medication (PIM) and poor prognosis of COVID-19 in older adults, controlling for comorbidity and sociodemographic factors.Design and settingNationwide retrospective cohort study based on the national registry of COVID-19 patients, established through the linkage of South Korea’s national insurance claims database with the Korea Disease Control and Prevention Agency registry of patients with COVID-19, up to 31 July 2020.ParticipantsA total of 2217 COVID-19 patients over 60 years of age who tested positive between 20 January 2020 and 4 June 2020. Exposure to PIM was defined based on any prescription record of PIM during the 30 days prior to the date of testing positive for COVID-19.Primary outcome measuresMortality and utilisation of critical care from the date of testing positive until the end of isolation.ResultsAmong the 2217 COVID-19 patients over 60 years of age, 604 were exposed to PIM prior to infection. In the matched cohort of 583 pairs, PIM-exposed individuals exhibited higher rates of mortality (19.7% vs 9.8%, p<0.0001) and critical care utilisation (13.4% vs 8.9%, p=0.0156) compared with non-exposed individuals. The temporal association of PIM exposure with mortality was significant across all age groups (RR=1.68, 95% CI: 1.23~2.24), and a similar trend was observed for critical care utilisation (RR: 1.75, 95% CI: 1.26~2.39). The risk of mortality and critical care utilisation increased with exposure to a higher number of PIMs in terms of active pharmaceutical ingredients and drug categories.ConclusionExposure to PIM exacerbates the poor outcomes of older patients with COVID-19 who are already at high risk. Effective interventions are urgently needed to address PIM exposure and improve health outcomes in this vulnerable population.
How do different navigation systems affect emergency response time? A prospective simulation study
Authors: van Mark Anke , Hallstein Tim , Holzgreve Fabian , Groneberg David A. , Ohlendorf Daniela 
Published: July 2024

ObjectiveThere has not been a theoretical test run in Germany that compares different navigation systems with an industry solution (MapTrip112). The aim of this study was to compare navigation systems to elucidate whether the emergency response time (ERT) was reduced and, consequently, whether the adherence to the travel time improved.DesignProspective, simulation study, cross-sectional study.SettingOffices of the Institute of Occupational Medicine, Social Medicine and Environmental Medicine, Goethe University Frankfurt (60 590 Frankfurt am Main, Germany). The situation-adaptable industry navigation solution MapTrip112 was tested in its ‘Lights and Siren(s) (L&S)’ mode in comparison to the TomTom and Google Maps navigation systems. MapTrip112 was set to calculate a route that takes special emergency rights of way into account.Outcome measuresAll three navigation systems simultaneously calculated the distances and durations of fictitious routes. Three scenarios were tested: the University Hospital Frankfurt (60 596 Frankfurt am Main, Germany) and the Central Fire Station 1 (60435 Frankfurt am Main, Germany) served as the starting points for the urban routes, while the Odenwald Health Centre (64 711 Erbach, Germany) served as the starting point for rural routes. The routes’ endpoints were arbitrarily chosen locations inside the customary operational radius. The routes were selected for short and long distances as well as for different periods, including weekdays, weekends and evening rush hour (4–7 pm), in the German cities of Frankfurt am Main and Odenwaldkreis (Southern Hesse).ResultsThe time and distance were calculated for a total of 4650 trips. When comparing travel times and distances between rural and urban areas as well as between weekdays and weekends, statistically significant results were obtained (p<0.001). With time advantages ranging from 23.5 s to 300.5 s (4.75% to 50% of the travel time) on weekdays and weekends, MapTrip112 consistently outperformed both TomTom and Google Maps. For city missions, MapTrip112 achieved time gains of up to 50% over its competitors, with significant advantages during the rush hours and around specific locations such as the University Hospital Frankfurt and Fire Station 1.ConclusionMapTrip112 always achieved the fastest routes although these were not always accompanied by a shortened distance. These findings underscore MapTrip112’s superiority in providing efficient routing solutions across various scenarios. For this reason, the use of this software should be considered in practice and investigated in real-world conditions in further studies.