bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complete list of canonical post-transcriptional modifications in the Bacillus subtilis ribosome and their link to RbgA driven large subunit assembly
Authors: Popova Anna M , Jain Nikhil , Dong Xiyu , Abdollah-Nia Farshad , Britton Robert A , Williamson James R 
Published: July 2024

Abstract
Ribosomal RNA modifications in prokaryotes have been sporadically studied, but there is a lack of a comprehensive picture of modification sites across bacterial phylogeny. Bacillus subtilis is a preeminent model organism for gram-positive bacteria, with a well-annotated and editable genome, convenient for fundamental studies and industrial use. Yet remarkably, there has been no complete characterization of its rRNA modification inventory. By expanding modern MS tools for the discovery of RNA modifications, we found a total of 25 modification sites in 16S and 23S rRNA of B. subtilis, including the chemical identity of the modified nucleosides and their precise sequence location. Furthermore, by perturbing large subunit biogenesis using depletion of an essential factor RbgA and measuring the completion of 23S modifications in the accumulated intermediate, we provide a first look at the order of modification steps during the late stages of assembly in B. subtilis. While our work expands the knowledge of bacterial rRNA modification patterns, adding B. subtilis to the list of fully annotated species after Escherichia coli and Thermus thermophilus, in a broader context, it provides the experimental framework for discovery and functional profiling of rRNA modifications to ultimately elucidate their role in ribosome biogenesis and translation.
Clinical Utility of Plasma Microbial Cell-Free DNA Sequencing Among Immunocompromised Patients With Pneumonia
Authors: Madut Deng B , Chemaly Roy F , Dadwal Sanjeet S , Hill Joshua A , Lee Yeon Joo , Haidar Ghady , Luk Alfred , Drelick Alexander , Chin-Hong Peter V , Benamu Esther , Khawaja Fareed , Nanayakkara Deepa , Papanicolaou Genovefa A , Small Catherine Butkus , Fung Monica , Barron Michelle , Davis Thomas , McClain Micah T , Maziarz Eileen K , Bedoya Armando D , Gilstrap Daniel L , Todd Jamie L , Barkauskas Christina E , Heldman Madeleine R , Bigelow Robert , Leimberger Jeffrey D , Tsalik Ephraim L , Wolf Olivia , Mughar Mona , Lau Constance , Noll Nicholas , Hollemon Desiree , Duttagupta Radha , Lupu Daniel S , Bercovici Sivan , Perkins Bradley A , Blauwkamp Timothy A , Fowler Vance G , Holland Thomas L , Bergin Stephen P 
Published: July 2024

Abstract

Background
Plasma microbial cell-free DNA (mcfDNA) sequencing can establish the etiology of multiple infectious syndromes by identifying microbial DNA in plasma. However, data are needed to define the clinical scenarios where this tool offers the highest clinical benefit.

Methods
We conducted a prospective multicenter observational study that evaluated the impact of plasma mcfDNA sequencing compared with usual care testing among adults with hematologic malignancies. This is a secondary analysis of an expanded cohort that evaluated the clinical utility of plasma mcfDNA sequencing across prespecified and adjudicated outcomes. We examined the percentage of participants for whom plasma mcfDNA sequencing identified a probable cause of pneumonia or clinically relevant nonpneumonia infection. We then assessed potential changes in antimicrobial therapy based on plasma mcfDNA sequencing results and the potential for early mcfDNA testing to avoid bronchoscopy and its associated adverse events.

Results
Of 223 participants, at least 1 microbial detection by plasma mcfDNA sequencing was adjudicated as a probable cause of pneumonia in 57 (25.6%) and a clinically relevant nonpneumonia infection in 88 (39.5%). A probable cause of pneumonia was exclusively identified by plasma mcfDNA sequencing in 23 (10.3%) participants. Antimicrobial therapy would have changed for 41 (18.4%) participants had plasma mcfDNA results been available in real time. Among the 57 participants with a probable cause of pneumonia identified by plasma mcfDNA sequencing, bronchoscopy identified no additional probable cause of pneumonia in 52 (91.2%).

Conclusions
Plasma mcfDNA sequencing could improve management of both pneumonia and other concurrent infections in immunocompromised patients with suspected pneumonia.
‘Pirates’, Potentates, and Merchant Petitioning in the Early Nineteenth Century Straits Settlements
Authors: Connors Scott 
Published: July 2024

Abstract
In the nineteenth century Straits of Malacca, one of the globe’s most significant trading crossroads, merchants were integral to imperial stability and growth. Indeed, historians of the British empire have long sought to understand how colonial governments turned to merchants, both British and Asian, to extend commercial networks, establish local hierarchies and extend processes of state-building. Yet, merchants’ conceptions of their relationship to, and place within, colonial governance are less well understood. This article examines the emergence of colonial merchant politics in the British controlled Straits Settlements in the early nineteenth century. It concentrates on petitions produced by Asian merchants who demanded greater intervention by East India Company authorities in matters of maritime security and diplomacy. Petitions enabled the merchants of Singapore and Penang to inject their political and commercial visions into processes of colonial state-building. Moreover, these cases demonstrate that imperial margins — geographic, bureaucratic, linguistic and political — were productive spaces in which colonial power dynamics between state and society were contested and took on new meanings.
Healthy childhood development through outdoor risky play: Navigating the balance with injury prevention
Authors: Beaulieu Emilie , Beno Suzanne 
Published: July 2024

Abstract
Free play is essential for children’s development and for their physical, mental, and social health. Opportunities to engage in outdoor free play—and risky play in particular—have declined significantly in recent years, in part because safety measures have sought to prevent all play-related injuries rather than focusing on serious and fatal injuries. Risky play is defined by thrilling and exciting forms of free play that involve uncertainty of outcome and a possibility of physical injury. Proponents of risky play differentiate “risk” from “hazard” and seek to reframe perceived risk as an opportunity for situational evaluation and personal development. This statement weighs the burden of play-related injuries alongside the evidence in favour of risky play, including its benefits, risks, and nuances, which can vary depending on a child’s developmental stage, ability, and social and medical context. Approaches are offered to promote open, constructive discussions with families and organizations. Paediatricians are encouraged to think of outdoor risky play as one way to help prevent and manage common health problems such as obesity, anxiety, and behavioural issues.
Possible pathophysiologic roles of neurotransmitter systems in men with lifelong premature ejaculation: a scoping review
Authors: van Raaij Joost J , Serefoglu Ege Can , van Amelsvoort Thérèse A M J , Janssen Paddy K C 
Published: July 2024

Abstract

Introduction
Lifelong premature ejaculation (LPE) is a subtype of premature ejaculation. Genetic research on LPE has primarily focused on neurotransmitters such as serotonin, dopamine, and norepinephrine, whereas LPE treatment studies have focused on drugs such as selective serotonin reuptake inhibitors. However, findings from genetic association and pharmacotherapeutic studies have been inconsistent.

Objectives
To provide a quality overview of neurobiological targets that are potentially associated with LPE by investigating genetic association and pharmacotherapeutic studies.

Methods
This scoping review was conducted per the PRISMA-ScR tool (Preferred Reporting Items for Systematic Reviews and Meta-analyses Extension for Scoping Reviews). Five databases were searched in March 2023 without timeline- or language-related restrictions.

Results
After deduplication, 3949 records were obtained for review. Following screening and full-text review with citation tracking, 52 studies were included: 18 genetic and 34 pharmacotherapy studies. Serotonergic targets, such as the serotonin transporter and pre- and postsynaptic serotonergic receptors, were most often associated with LPE in genetic and pharmacotherapeutic studies. Mixed results were found among polymorphisms within genetic studies. This mechanism is in accordance with pharmacotherapeutic studies, as the highest efficacy was found for potent serotonergic antidepressants. Successful treatment was also observed with medication acting on phosphodiesterase-5 enzyme, such as tadalafil and vardenafil. Analyses of other genetic association studies did not yield any further evidence for associated targets.

Conclusions
This review is the first comprehensive scoping review on LPE. We found that serotonergic targets are most often associated with LPE, suggesting that the serotonergic pathway is a predisposing factor in LPE. Furthermore, there is some evidence for phosphodiesterase 5 inhibitors, which should be investigated. Other previously investigated neurobiological targets appear less likely to contribute to LPE. Future studies should focus on multiple targets, ideally in a genome-wide association study design.
This review has been registered with the Open Science Framework (doi:10.17605/OSF.IO/JUQSD).
The brominated flame retardant hexabromocyclododecane causes systemic changes in polyunsaturated fatty acid incorporation in mouse lipids
Authors: Kramer Naomi E , Siracusa Jacob , Xu Hannah , Barnett Lillie M , Finnerty Morgan C , Guo Tai L , Wagner John J , Leach III Franklin E , Cummings Brian S 
Published: July 2024

Abstract
Brominated flame retardants are used in many household products to reduce flammability, but often leach into the surrounding environment over time. Hexabromocyclododecane (HBCD) is a brominated flame retardant detected in human blood across the world. HBCD exposure can result in neurological problems and altered lipid metabolism, but to date, the two remain unlinked. As lipids constitute ∼50% of brain dry weight, lipid metabolism plays a critical role in neuronal function and homeostasis. To determine the effect of HBCD exposure on brain lipid metabolism, young adult male C57BL/6 mice were exposed to 1 mg/kg HBCD every 3 d for 28 d. Major lipid classes were found to change across brain regions, including membrane glycerolipids such as phosphatidylcholine and phosphatidylethanolamine, and sphingolipids such as hexosylceramide. In addition, saturated, monounsaturated, and polyunsaturated fatty acids were enriched within brain lipid species. To understand the source of the brain lipidomic alterations, the blood and liver lipidomes and the cecal microbiome were evaluated. The liver and blood demonstrated changes amongst multiple lipid classes, including triacylglycerol suppression, as well as altered esterified fatty acid content. Significant alterations were also detected in the cecal microbiome, with decreases in the Firmicutes to Bacteriodetes ratio, changes in beta diversity, and pathway alterations associated with metabolic pathways and amino acid biosynthesis. These data demonstrate that HBCD can induce lipidomic alterations across brain regions and organs and support a potential role of the microbiome in these alterations.
Isotretinoin-Induced Hypersomnia: A Cross-sectional Study and Literature Review
Authors: Shawky Ahmed , Elsheikh Mohamed , Elrewiny Emad M. , Adwi Mohamed , Rageh Mahmoud A. 
Published: July 2024

ABSTRACT

BACKGROUND
Isotretinoin is an oral retinoic drug for severe resistant acne cases that has controversially been associated with multiple psychiatric adverse effects. Research has primarily focused on depression and suicidality; however, a few case studies reported hypersomnia and sleep changes after isotretinoin initiation.

OBJECTIVE
To assess sleep quality and measure rates of hypersomnia, depression, and anxiety in patients undergoing isotretinoin therapy.

METHODS
This cross-sectional study was conducted at outpatient clinics of the university hospital. The rate of self-reported oversleeping was measured. In addition, researchers used the Pittsburgh Sleep Quality Index to assess sleep quality and conducted semistructured clinical interviews to detect depression and anxiety.

RESULTS
Of 123 patients with acne on isotretinoin, 77 (62.6%) reported oversleeping. Nearly half (60 patients, 48.8%) were categorized as poor sleepers according to the Pittsburgh Sleep Quality Index. The interviews revealed anxiety and depression percentages among 9.8% and 4.9% of participants, respectively.

CONCLUSIONS
Hypersomnia was noticeably high in this study sample; thus, it may cautiously suggest a possible link between isotretinoin and hypersomnia. However, more research is needed to investigate this potential relationship.
Assessing Neural Synchrony in the Cochlear Nerve to Electrical Stimulation in Children With Auditory Neuropathy Spectrum Disorder
Authors: He Shuman , Chao Xiuhua , Yuan Yi , Skidmore Jeffrey , Uhler Kristin M. 
Published: July 2024

Objectives:
This study reported phase locking values (PLVs) that quantified the trial-to-trial phase coherence of electrically evoked compound action potentials in children with auditory neuropathy spectrum disorders (ANSD) and children with Gap Junction Beta 2 (GJB2) mutations, a patient population without noticeable cochlear nerve damage.

Design:
PLVs were measured at three electrode locations in 11 children with ANSD and 11 children with GJB2 mutations. Smaller PLVs indicated poorer neural synchrony. A linear mixed-effects model was used to compare PLVs measured at different electrode locations between participant groups.

Results:
After controlling for the stimulation level effect, children with ANSD had smaller PLVs than children with GJB2 mutations at all three electrode locations.

Conclusions:
Cochlear-implanted children with ANSD show poorer peripheral neural synchrony than children with GJB2 mutations.
Medication burden and anticholinergic use are associated with overt HE in individuals with cirrhosis
Authors: Montrose Jonathan A. , Desai Archita , Nephew Lauren , Patidar Kavish R. , Ghabril Marwan S. , Campbell Noll L. , Chalasani Naga , Qiu Yingjie , Hays Matthew E. , Orman Eric S. 
Published: July 2024

Background:
Polypharmacy and anticholinergic medications are associated with cognitive decline in elderly populations. Although several medications have been associated with HE, associations between medication burden, anticholinergics, and HE have not been explored. We examined medication burden and anticholinergics in patients with cirrhosis and their associations with HE-related hospitalization.

Methods:
We conducted a retrospective cohort study of patients aged 18–80 with cirrhosis seen in hepatology clinics during 2019. The number of chronic medications (medication burden) and anticholinergic use were recorded. The primary outcome was HE-related hospitalization.

Results:
A total of 1039 patients were followed for a median of 840 days. Thirty-seven percent had a history of HE, and 9.8% had an HE-related hospitalization during follow-up. The mean number of chronic medications was 6.1 ± 4.3. Increasing medication burden was associated with HE-related hospitalizations in univariable (HR: 1.09, 95% CI: 1.05–1.12) and multivariable (HR: 1.07, 95% CI: 1.03–1.11) models. This relationship was maintained in those with baseline HE but not in those without baseline HE. Twenty-one percent were taking an anticholinergic medication. Anticholinergic exposure was associated with increased HE-related hospitalizations in both univariable (HR: 1.68, 95% CI: 1.09–2.57) and multivariable (HR: 1.71, 95% CI: 1.11–2.63) models. This relationship was maintained in those with baseline HE but not in those without baseline HE.

Conclusions:
Anticholinergic use and medication burden are both associated with HE-related hospitalizations, particularly in those with a history of HE. Special considerations to limit anticholinergics and minimize overall medication burden should be tested for potential benefit in this population.
Design, implementation, and impact of a cirrhosis-specific remote patient monitoring program
Authors: Penrice Daniel D. , Hara Kamalpreet S. , Sordi-Chara Beatriz , Kezer Camille , Schmidt Kathryn , Kassmeyer Blake , Lennon Ryan , Rosedahl Jordan , Roellinger Daniel , Rattan Puru , Williams Katherine , Kloft-Nelson Sara , Leuenberger Angela , Kamath Patrick S. , Shah Vijay H. , Simonetto Douglas A. 
Published: July 2024

Background:
Remote patient monitoring (RPM) is an emerging focus in health care, and specialized programs may reduce medical costs, supplement in-office visits, and improve patient satisfaction. In this study, we describe the development, feasibility, and early outcomes of an RPM program for patients with decompensated cirrhosis.

Methods:
Forty-six patients were offered enrollment at the time of hospital discharge in the cirrhosis RPM program (CiRPM), of which 41 completed at least 30 days of monitoring. Participants were mailed remote monitoring equipment and a tablet to be used for patient-reported outcomes. Alerts were continuously monitored by virtual nursing staff who could perform targeted interventions. A cohort of historical controls (n = 74) was created for comparison using inverse probability of treatment weighting.

Results:
Patients were enrolled in the program for a mean of 83.9 days, with 28 (68%) completing the full 90-day program. Participants uploaded vital signs and responded to symptom-based questionnaires on 93% of the monitored days. On end-of-program surveys, over 75% of patients expressed satisfaction with the program. Gender, age, and MELD-Na were similar between CiRPM and weighted control groups. The 90-day readmission rate was 34% in CiRPM and 47% in weighted controls. In the CiRPM group, 12% of subjects had 2 or more admissions, compared to 37% in the weighted control group.

Conclusion:
This study demonstrates the feasibility of a cirrhosis-specific RPM program. Overall, patient satisfaction and utilization of the CiRPM was high. Future studies are needed to confirm the impact of RPM on the reduction of hospital readmissions in decompensated cirrhosis.
Validating perceptions with clinical measures: A latent growth curve on the associations between patient experience and hospital-associated infections in Norway over time
Authors: Addo Seth Ayisi 
Published: July 2024

Objective
The aim of the study was to examine the parallel relationships between the growth rates of patient-reported experiences and hospital-associated infections (HAIs) over time.

Data Sources/Study Setting
The study employed five waves (years) of data among hospitals across Norway from the Norwegian Health Directorate website for both patient experience and HAIs.

Study Design
The study employed a longitudinal design, testing and comparing different models. A latent growth curve model with autoregressions emerged as the best fit for the data.

Data Collection/Extraction Methods
The data extracted from the website included 102 hospitals. However, the study used 61 hospitals after data cleaning, each with 400 patient respondents for each year.

Principal Findings
The results showed that for both patient experiences and HAIs, hospitals that recorded higher scores at the starting point experienced a lower growth rate over time compared to hospitals that recorded lower infections at the starting point. Second, it was found that the starting point for patient experience significantly related to the starting point for HAIs, such that the higher the score for patient experience, the lower the score on infections across hospitals. The results also indicated that almost all lagged effects on either patient-reported experience or HAIs were significant.

Conclusions
This study shows the significance of patient experience, not only for patient-reported outcomes but also for clinical outcomes. This thus ascertains the relevance of the patient experience pillar for the other pillars of quality health care, namely, clinical effectiveness and safety.
Abdominal Hartmann reversal versus combined transanal/abdominal approach: Outcomes and technical notes
Authors: Barugola Giuliano , Bertocchi Elisa , Gentile Irene , Masini Gaia , Secci Federica , Mazzi Cristina , Ruffo Giacomo 
Published: July 2024

Background:
Hartmann’s reversal (HR) is one of the most technically challenging operations in colorectal surgery. A small percentage of HR operations are performed laparoscopically. The pelvic dissection is the key point of the procedure and can be demanding when the rectal stump is extraperitoneal and if the pelvic condition is complex.

Methods:
A retrospective observational single-center study was designed to analyze the outcomes of patients with an extraperitoneal rectal stump who underwent HR from January 2015 to December 2020 at IRCCS Sacro Cuore Don Calabria Hospital in Negrar of Valpolicella. The patients were divided into two groups: group 1 underwent a purely abdominal Hartmann’s reversal (A-HR) and group 2 underwent a combined transanal and abdominal Hartmann’s reversal (TA-HR).

Results:
Forty-two patients were divided into the groups as follows: 22 (52.3%) patients in the A-HR group versus 20 (47.62%) patients in the TA-HR. The transanal approach did not significantly affect the operative time. The rate of rectovaginal fistula was higher in the TA-HR group (65% vs. 4.5%). The anastomosis was performed mechanically in all A-HR cases and 50% of TA-HR patients (P < 0.01). No difference in temporary stoma creation was found. The rate of complications was lower in the TA-HR group (P = 0.05). The A-HR group was statistically significantly associated with redo surgery (P = 0.04). Stoma failure rate at the end of the follow-up did not differ between the two groups.

Conclusions:
Transanal Hartmann reversal seems to be a safe approach in patients with a complex pelvis and extraperitoneal rectal stump.