bluuebunny/crossref_metadata_2025_split huggingface dataset:
Themes and variations on piRNA-guided transposon control
Authors: Loubalova Zuzana , Konstantinidou Parthena , Haase Astrid D. 
Published: September 2023

AbstractPIWI-interacting RNAs (piRNAs) are responsible for preventing the movement of transposable elements in germ cells and protect the integrity of germline genomes. In this review, we examine the common elements of piRNA-guided silencing as well as the differences observed between species. We have categorized the mechanisms of piRNA biogenesis and function into modules. Individual PIWI proteins combine these modules in various ways to produce unique PIWI-piRNA pathways, which nevertheless possess the ability to perform conserved functions. This modular model incorporates conserved core mechanisms and accommodates variable co-factors. Adaptability is a hallmark of this RNA-based immune system. We believe that considering the differences in germ cell biology and resident transposons in different organisms is essential for placing the variations observed in piRNA biology into context, while still highlighting the conserved themes that underpin this process.
Evaluation of pediatric epigenetic clocks across multiple tissues
Authors: Fang Fang , Zhou Linran , Perng Wei , Marsit Carmen J. , Knight Anna K. , Cardenas Andres , Aung Max T. , Hivert Marie-France , Aris Izzuddin M. , Goodrich Jaclyn M. , Smith Alicia K. , Gaylord Abigail , Fry Rebecca C. , Oken Emily , O’Connor George , Ruden Douglas M. , Trasande Leonardo , Herbstman Julie B. , Camargo Carlos A. , Bush Nicole R. , Dunlop Anne L. , Dabelea Dana M. , Karagas Margaret R. , Breton Carrie V. , Ober Carole , Everson Todd M. , Page Grier P. , Ladd-Acosta Christine ,   on behalf of program collaborators for Environmental influences on Child Health Outcomes, Smith P. B. , Newby L. K. , Jacobson L. P. , Catellier D. J. , Gershon R. , Cella D. , Laham F. R. , Mansbach J. M. , Wu S. , Spergel J. M. , Celedón J. C. , Puls H. T. , Teach S. J. , Porter S. C. , Waynik I. Y. , Iyer S. S. , Samuels-Kalow M. E. , D.Thompson A. , Stevenson M. D. , Bauer C. S. , Inhofe N. R. , Boos M. , Macias C. G. , Gern J. , Jackson D. , Bacharier L. , Kattan M. , Wood R. , Rivera-Spoljaric K. , Bacharier L. , Bastain T. , Farzan S. , Habre R. , Karr C. , Tylavsky F. , Mason A. , Zhao Q. , Sathyanarayana S. , Bush N. , LeWinn K. Z. , Lester B. , Carter B. , Pastyrnak S. , Neal C. , Smith L. , Helderman J. , McEvoy C. , Tepper R. , Lyall K. , Volk H. , Schmidt R. , Croen L. , O’Shea M. , Vaidya R. , Obeid R. , Rollins C. , Bear K. , Pastyrnak S. , Lenski M. , Singh R. , Msall M. , Frazier J. , Gogcu S. , Montgomery A. , Kuban K. , Douglass L. , Jara H. , Joseph R. , Kerver J. M. , Perera F. 
Published: September 2023

Abstract
Background
Epigenetic clocks are promising tools for assessing biological age. We assessed the accuracy of pediatric epigenetic clocks in gestational and chronological age determination.

Results
Our study used data from seven tissue types on three DNA methylation profiling microarrays and found that the Knight and Bohlin clocks performed similarly for blood cells, while the Lee clock was superior for placental samples. The pediatric-buccal-epigenetic clock performed the best for pediatric buccal samples, while the Horvath clock is recommended for children's blood cell samples. The NeoAge clock stands out for its unique ability to predict post-menstrual age with high correlation with the observed age in infant buccal cell samples.

Conclusions
Our findings provide valuable guidance for future research and development of epigenetic clocks in pediatric samples, enabling more accurate assessments of biological age.
Lippes loop intrauterine device left in the uterus for 40 years as a rare cause of postmenopausal pelvic pain: a case report and review of the literature
Authors: Tilahun Temesgen , Tadesse Asfaw , Oljira Rut 
Published: September 2023

Abstract
Background
Intrauterine devices are a widely used method of contraception worldwide. These devices are reliable, cost-effective, long-acting, and reversible. Their placement in the uterus is usually simple and safe. Forgotten IUDs carry some complications and can adversely affect the health of women. Therefore, appropriate counseling during insertion and timely removal are crucial.

Case summary
We present the case of retained Lippes loop IUD for 40 years in a 75-year-old postmenopausal patient from Western Ethiopia. The patient presented to the hospital with postmenopausal pelvic pain. The loop was removed with spongy forceps. The patient was discharged with analgesia and doxycycline twice a day for 3 days.

Conclusion
Different works of the literature showed that retained Lippes loop IUD carries some complications. Our case was also presented with postmenopausal pelvic pain. Therefore, we recommend the removal of IUDs at their expiry date or menopause.
Characteristics and outcomes of patients with acute myeloid leukemia admitted to intensive care unit with acute respiratory failure: a post-hoc analysis of a prospective multicenter study
Authors: Secreto Carolina , Chean Dara , van de Louw Andry , Kouatchet Achille , Bauer Philippe , Cerrano Marco , Lengliné Etienne , Saillard Colombe , Chow-Chine Laurent , Perner Anders , Pickkers Peter , Soares Marcio , Rello Jordi , Pène Frédéric , Lemiale Virginie , Darmon Michael , Fodil Sofiane , Martin-Loeches Ignacio , Mehta Sangeeta , Schellongowski Peter , Azoulay Elie , Mokart Djamel 
Published: September 2023

Abstract
Background
Acute respiratory failure (ARF) is the leading cause of intensive care unit (ICU) admission in patients with Acute Myeloid Leukemia (AML) and data on prognostic factors affecting short-term outcome are needed.

Methods
This is a post-hoc analysis of a multicenter, international prospective cohort study on immunocompromised patients with ARF admitted to ICU. We evaluated hospital mortality and associated risk factors in patients with AML and ARF; secondly, we aimed to define specific subgroups within our study population through a cluster analysis.

Results
Overall, 201 of 1611 immunocompromised patients with ARF had AML and were included in the analysis. Hospital mortality was 46.8%. Variables independently associated with mortality were ECOG performance status ≥ 2 (OR = 2.79, p = 0.04), cough (OR = 2.94, p = 0.034), use of vasopressors (OR = 2.79, p = 0.044), leukemia-specific pulmonary involvement [namely leukostasis, pulmonary infiltration by blasts or acute lysis pneumopathy (OR = 4.76, p = 0.011)] and liver SOFA score (OR = 1.85, p = 0.014). Focal alveolar chest X-ray pattern was associated with survival (OR = 0.13, p = 0.001). We identified 3 clusters, that we named on the basis of the most frequently clinical, biological and radiological features found in each cluster: a “leukemic cluster”, with high-risk AML patients with isolated, milder ARF; a “pulmonary cluster”, consisting of symptomatic, highly oxygen-requiring, severe ARF with diffuse radiological findings in heavily immunocompromised patients; a clinical “inflammatory cluster”, including patients with multi-organ failures in addition to ARF. When included in the multivariate analysis, cluster 2 and 3 were independently associated with hospital mortality.

Conclusions
Among AML patients with ARF, factors associated with a worse outcome are related to patient’s background (performance status, leukemic pulmonary involvement), symptoms, radiological findings, the need for vasopressors and the liver SOFA score.
We identified three specific ARF syndromes in AML patients, which showed a prognostic significance and could guide clinicians to optimize management strategies.
Chaos detection scheme for multiple variable-frequency signals with overlapping frequencies
Authors: Chen Dawei , Shi Shuo , Gu Xuemai 
Published: September 2023

AbstractAs one of the most critical technologies in signal detection, weak signal detection has received a great deal of attention in many areas. Traditional methods perform well when the number of signal is single and the form of signal is simple, which are quite different from the situation in some real applications (e.g., the marine communication scenario). In this paper, we consider the problem of high-precision frequency detection of multiple variable-frequency signals with overlapping frequencies (MVFS-O) in the low signal-to-noise ratio scenario, whose key point is how to detect the parameters (frequency range and frequency modulation rate) of each signal. To solve the problem, a novel chaos detection scheme based on Duffing difference oscillator is proposed. In this scheme, the wide frequency detection range of the critical state is used to determine the frequency range of the signals quickly, and the Lyapunov exponent is used to discriminate the output state of the system qualitatively. Furthermore, combining with the time points of the periodic state of the system, we can obtain the FMR of the corresponding signal by analyzing overlapping frequency ratio. Numerical results are provided to verify the practical effectiveness of the proposed scheme.
How to update a living systematic review and keep it alive during a pandemic: a practical guide
Authors: Heron Leonie , Buitrago-Garcia Diana , Ipekci Aziz Mert , Baumann Rico , Imeri Hira , Salanti Georgia , Counotte Michel Jacques , Low Nicola 
Published: September 2023

Abstract
Background
The covid-19 pandemic has highlighted the role of living systematic reviews. The speed of evidence generated during the covid-19 pandemic accentuated the challenges of managing high volumes of research literature.

Methods
In this article, we summarise the characteristics of ongoing living systematic reviews on covid-19, and we follow a life cycle approach to describe key steps in a living systematic review.

Results
We identified 97 living systematic reviews on covid-19, published up to 7th November 2022, which focused mostly on the effects of pharmacological interventions (n = 46, 47%) or the prevalence of associated conditions or risk factors (n = 30, 31%). The scopes of several reviews overlapped considerably. Most living systematic reviews included both observational and randomised study designs (n = 45, 46%). Only one-third of the reviews has been updated at least once (n = 34, 35%). We address practical aspects of living systematic reviews including how to judge whether to start a living systematic review, methods for study identification and selection, data extraction and evaluation, and give recommendations at each step, drawing from our own experience. We also discuss when it is time to stop and how to publish updates.

Conclusions
Methods to improve the efficiency of searching, study selection, and data extraction using machine learning technologies are being developed, their performance and applicability, particularly for reviews based on observational study designs should improve, and ways of publishing living systematic reviews and their updates will continue to evolve. Finally, knowing when to end a living systematic review is as important as knowing when to start.
Measuring time in buprenorphine treatment stages among people with HIV and opioid use disorder by retention definition and its association with cocaine and hazardous alcohol use
Authors: Pytell Jarratt D. , Fojo Anthony T. , Keruly Jeanne C. , Snow LaQuita N. , Falade-Nwulia Oluwaseun , Moore Richard D. , Chander Geetanjali , Lesko Catherine R. 
Published: September 2023

Abstract
Background
We use a novel, longitudinal approach to describe average time spent in opioid use disorder (OUD) cascade of care stages for people with HIV (PWH) and with OUD, incorporating four definitions of treatment retention. Using this approach, we describe the impact of cocaine or hazardous alcohol use on time spent retained on buprenorphine.

Methods
We followed PWH with OUD enrolled in the Johns Hopkins HIV Clinical Cohort from their first buprenorphine treatment episode between 2013 and 2020. We estimated 4-year restricted mean time spent on buprenorphine below buprenorphine retention threshold, on buprenorphine above retention threshold, off buprenorphine and in HIV care, loss to follow-up, and death. Retention definitions were based on retention threshold (180 vs 90 days) and allowable treatment gap (7 vs 30 days). Differences in 2-year restricted mean time spent retained on buprenorphine were estimated for patients with and without cocaine or hazardous alcohol use.

Results
The study sample (N = 179) was 63% male, 82% non-Hispanic Black, and mean age was 53 (SD 8) years. Patients spent on average 13.9 months (95% CI 11.4, 16.4) on buprenorphine over 4 years. There were differences in time spent retained on buprenorphine based on the retention definition, ranging from 6.5 months (95% CI 4.6, 8.5) to 9.6 months (95% CI 7.4, 11.8). Patients with cocaine use spent fewer months retained on buprenorphine. There were no differences for patients with hazardous alcohol use.

Conclusions
PWH with OUD spend relatively little time receiving buprenorphine in their HIV primary care clinic. Concurrent cocaine use at buprenorphine initiation negatively impact time on buprenorphine.
Resveratrol alleviates DSS-induced IBD in mice by regulating the intestinal microbiota-macrophage-arginine metabolism axis
Authors: Xu Xinwei , Ocansey Dickson Kofi Wiredu , Pei Bing , Zhang Yaqin , Wang Naijian , Wang Zengxu , Mao Fei 
Published: September 2023

Abstract
Background
Inflammatory bowel disease (IBD) is a global disease with a growing public health concern and is associated with a complex interplay of factors, including the microbiota and immune system. Resveratrol, a natural anti-inflammatory and antioxidant agent, is known to relieve IBD but the mechanism involved is largely unexplored.

Methods
This study examines the modulatory effect of resveratrol on intestinal immunity, microbiota, metabolites, and related functions and pathways in the BALB/c mice model of IBD. Mouse RAW264.7 macrophage cell line was used to further explore the involvement of the macrophage-arginine metabolism axis. The treatment outcome was assessed through qRT-PCR, western blot, immunofluorescence, immunohistochemistry, and fecal 16S rDNA sequencing and UHPLC/Q-TOF–MS.

Results
Results showed that resveratrol treatment significantly reduced disease activity index (DAI), retained mice weight, repaired colon and spleen tissues, upregulated IL-10 and the tight junction proteins Occludin and Claudin 1, and decreased pro-inflammatory cytokines IL-1β, IL-6, and TNF-α. Resveratrol reduced the number of dysregulated metabolites and improved the gut microbial community structure and diversity, including reversing changes in the phyla Bacteroidetes, Proteobacteria, and Firmicutes, increasing ‘beneficial’ genera, and decreasing potential pathogens such as Lachnoclostridium, Acinobacter, and Serratia. Arginine–proline metabolism was significantly different between the colitis-treated and untreated groups. In the colon mucosa and RAW264.7 macrophage, resveratrol regulated arginine metabolism towards colon protection by increasing Arg1 and Slc6a8 and decreasing iNOS.

Conclusion
This uncovers a previously unknown mechanism of resveratrol treatment in IBD and provides the microbiota-macrophage-arginine metabolism axis as a potential therapeutic target for intestinal inflammation.
Rapid point-of-care detection of SARS-CoV-2 infection in exhaled breath using ion mobility spectrometry: a pilot study
Authors: Voit Florian , Erber J. , Feuerherd M. , Fries H. , Bitterlich N. , Diehl-Wiesenecker E. , Gladis S. , Lieb J. , Protzer U. , Schneider J. , Geisler F. , Somasundaram R. , Schmid R. M. , Bauer W. , Spinner C. D. 
Published: September 2023

Abstract
Background
An effective testing strategy is essential for pandemic control of the novel Coronavirus disease 2019 (COVID-19) caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Breath gas analysis can expand the available toolbox for diagnostic tests by using a rapid, cost-beneficial, high-throughput point-of-care test. We conducted a bi-center clinical pilot study in Germany to evaluate breath gas analysis using multi-capillary column ion mobility spectrometry (MCC-IMS) to detect SARS-CoV-2 infection.

Methods
Between September 23, 2020, and June 11, 2021, breath gas measurements were performed on 380 patients (SARS-CoV-2 real-time polymerase chain reaction (PCR) positive: 186; PCR negative: 194) presenting to the emergency department (ED) with respiratory symptoms.

Results
Breath gas analysis using MCC-IMS identified 110 peaks; 54 showed statistically significant differences in peak intensity between the SARS-CoV-2 PCR-negative and PCR-positive groups. A decision tree analysis classification resulted in a sensitivity of 83% and specificity of 86%, but limited robustness to dataset changes. Modest values for the sensitivity (74%) and specificity (52%) were obtained using linear discriminant analysis. A systematic search for peaks led to a sensitivity of 77% and specificity of 67%; however, validation by transferability to other data is questionable.

Conclusions
Despite identifying several peaks by MCC-IMS with significant differences in peak intensity between PCR-negative and PCR-positive samples, finding a classification system that allows reliable differentiation between the two groups proved to be difficult. However, with some modifications to the setup, breath gas analysis using MCC-IMS may be a useful diagnostic toolbox for SARS-CoV-2 infection.
Trial registration: This study was registered at ClinicalTrials.gov on September 21, 2020 (NCT04556318; Study-ID: HC-N-H-2004).
Evaluation of Acinetobacter baumannii, Klebsiella pneumoniae, and Staphylococcus aureus respiratory tract superinfections among patients with COVID-19 at a tertiary-care hospital in Tehran, Iran
Authors: Mobarak-Qamsari Maryam , Jenaghi Bita , Sahebi Leyla , Norouzi-Shadehi Mahsa , Salehi Mohammad-Reza , Shakoori-Farahani Abbas , Khoshnevis Hoda , Abdollahi Alireza , Feizabadi Mohammad-Mehdi 
Published: September 2023

Abstract
Background
The emergence of healthcare-associated infections (HAIs) or superinfections in COVID-19 patients has resulted in poor prognosis and increased mortality.

Methods
In a cross-sectional study, 101 respiratory samples were collected from ICU-admitted COVID-19 patients. The HAI rate, demographics, and antibiotic resistance were assessed.

Results
The HAI rate was 83.16% (76.62% bacterial and 6.54% fungal). The prevalence of 3 major HAI-causing organisms included Klebsiella pneumoniae (41.5%), Acinetobacter baumannii (20.8%), and Staphylococcus aureus (4.9%). Mortality and intubation ventilation proportions of 90% (p = 0.027) and 92.2% (p = 0.02) were significant among patients with superinfection, respectively. Multiple logistic regression analysis showed SpO2 pressure (odds ratio 0.842; 95% CI 0.750–0.945; p = 0.004) as a predictive factor in the association between antibiotic usage and mortality. More than 50% of patients received carbapenems. The resistance rates to at least one antibiotic of third-generation cephalosporins, aminoglycosides, quinolones/fluoroquinolones, tetracyclines, and β-lactam inhibitors were 95.2%, 95.2%, 90%, 57.1%, and 100% among A. baumannii isolates and 71.4%, 55%, 69%, 61.9%, and 59.5% among K. pneumoniae isolates, respectively. A proportion of 60% was recorded for methicillin-resistant S. aureus isolates.

Conclusion
As a result, antibiotic treatment should be administered following the microbial resistance profile. Contact isolation and infection control measures should be implemented as needed.
The association between post-term births and autism spectrum disorders: an updated systematic review and meta-analysis
Authors: Jenabi Ensiyeh , Farashi Sajjad , Salehi Amir Mohammad , Parsapoor Hamideh 
Published: September 2023

Abstract
Background
This study aimed to conduct a meta-analysis to determine whether post-term birth has an increased risk of ASD.

Materials and methods
To retrieve eligible studies regarding the effect of post-term and ASD in children, major databases including PubMed, Scopus, and Web of Science were searched. A random effect model was used for meta-analysis. For assessing the quality of included studies, the GRADE checklist was used.

Results
In total, 18 records were included with 1,412,667 sample populations from 12 countries. The pooled estimates of RR and OR showed a significant association between post-term birth and ASD among children, respectively (RR = 1.34, 95% CI 1.10 to 1.58) and (OR = 1.47, 95% CI 1.03 to 1.91). There was no heterogeneity among the studies that reported the risk of ASD among children based on RR (I2 = 6.6%, P = 0.301). There was high heterogeneity in the studies reported risk of ASD based on OR (I2 = 94.1%, P = 0.000).

Conclusion
Post-term births still occur relatively frequently (up to 5–10%) even in developed countries. Our results showed that post-term birth is an increased risk of ASD, although high heterogeneity was found among the studies reported based on adjusted and crude forms, however, after subgroup analysis by gender, this heterogeneity disappeared among males.
Respiratory co-infections in COVID-19-positive patients
Authors: M Abd El-Halim Rania , Hafez Hala , Albahet Ibrahim , Sherif Basma 
Published: September 2023

Abstract
Background
Opportunistic respiratory infections may complicate critically ill patients with COVID-19. Early detection of co-infections helps to administrate the appropriate antimicrobial agent, to guard against patient deterioration. This study aimed at estimating co-infections in COVID-19-positive patients.

Methods
Eighty-nine COVID-19-positive patients confirmed by SARS-COV-2 PCR were tested for post-COVID-19 lower respiratory tract co-infections through bacterial culture, fungal culture and galactomannan (GM) testing.

Results
Fourteen patients showed positive coinfection with Klebsiella, nine with Acinetobacter, six with Pseudomonas and three with E. coli. As for fungal infections, nine showed coinfection with Aspergillus, two with Zygomycetes and four with Candida. Galactomannan was positive among one patient with Aspergillus coinfection, one with Zygomycetes coinfection and three with Candida, 13 samples with negative fungal culture were positive for GM. Ten samples showed positive fungal growth, however, GM test was negative.

Conclusion
In our study, SARS-COV-2 respiratory coinfections were mainly implicated by bacterial pathogens; most commonly Klebsiella species (spp.), Aspergillus spp. were the most common cause of fungal coinfections, GM test showed low positive predictive value for fungal infection. Respiratory coinfections may complicate SARS-COV-2 probably due to the prolonged intensive care units (ICU) hospitalization, extensive empiric antimicrobial therapy, steroid therapy, mechanical ventilation during the COVID-19 outbreak. Antimicrobial stewardship programs are required so that antibiotics are prescribed judiciously according to the culture results.