bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA editing enzymes: structure, biological functions and applications
Authors: Zhang Dejiu , Zhu Lei , Gao Yanyan , Wang Yin , Li Peifeng 
Published: March 2024

AbstractWith the advancement of sequencing technologies and bioinformatics, over than 170 different RNA modifications have been identified. However, only a few of these modifications can lead to base pair changes, which are called RNA editing. RNA editing is a ubiquitous modification in mammalian transcriptomes and is an important co/posttranscriptional modification that plays a crucial role in various cellular processes. There are two main types of RNA editing events: adenosine to inosine (A-to-I) editing, catalyzed by ADARs on double-stranded RNA or ADATs on tRNA, and cytosine to uridine (C-to-U) editing catalyzed by APOBECs. This article provides an overview of the structure, function, and applications of RNA editing enzymes. We discuss the structural characteristics of three RNA editing enzyme families and their catalytic mechanisms in RNA editing. We also explain the biological role of RNA editing, particularly in innate immunity, cancer biogenesis, and antiviral activity. Additionally, this article describes RNA editing tools for manipulating RNA to correct disease-causing mutations, as well as the potential applications of RNA editing enzymes in the field of biotechnology and therapy.
Treatment setting and buprenorphine discontinuation: an analysis of multi-state insurance claims
Authors: Xu Kevin Y. , Gertner Alex K. , Greenfield Shelly F. , Williams Arthur Robin , Grucza Richard A. 
Published: March 2024

Abstract
Background
Potential differences in buprenorphine treatment outcomes across various treatment settings are poorly characterized in multi-state administrative data. We thus evaluated the association of opioid use disorder (OUD) treatment setting and insurance type with risk of buprenorphine discontinuation among commercial insurance and Medicaid enrollees initiated on buprenorphine.

Methods
In this observational, retrospective cohort study using the Merative MarketScan databases (2006–2016), we analyzed buprenorphine retention in 58,200 US adults with OUD. Predictor variables included insurance status (Medicaid vs commercial) and treatment setting, operationalized as substance use disorder (SUD) specialty treatment facility versus outpatient primary care physicians (PCPs) versus outpatient psychiatry, ascertained by linking physician visit codes to buprenorphine prescriptions. Treatment setting was inferred based on timing of prescriber visit claims preceding prescription fills. We estimated time to buprenorphine discontinuation using multivariable cox regression.

Results
Among enrollees with OUD receiving buprenorphine, 26,168 (45.0%) had prescriptions from SUD facilities without outpatient buprenorphine treatment, with the remaining treated by outpatient PCPs (n = 23,899, 41.1%) and psychiatrists (n = 8133, 13.9%). Overall, 50.6% and 73.3% discontinued treatment at 180 and 365 days respectively. Buprenorphine discontinuation was higher among enrollees receiving prescriptions from SUD facilities (aHR = 1.03[1.01–1.06]) and PCPs (aHR = 1.07[1.05–1.10]). Medicaid enrollees had lower buprenorphine retention than those with commercial insurance, particularly those receiving buprenorphine from SUD facilities and PCPs (aHR = 1.24[1.20–1.29] and aHR = 1.39[1.34–1.45] respectively, relative to comparator group of commercial insurance enrollees receiving buprenorphine from outpatient psychiatry).

Conclusion
Buprenorphine discontinuation is high across outpatient PCP, psychiatry, and SUD treatment facility settings, with potentially lower treatment retention among Medicaid enrollees receiving care from SUD facilities and PCPs.
Classification of soybeans from different habitats based on metabolomic–transcriptomic integration
Authors: Wang Jinghui , Zheng Qiyou , Wang Chenxu , Zhou Ao 
Published: March 2024

AbstractSoybeans are a significant agricultural product in China, with certain geographical locations often yielding higher quality, and thus more expensive, soybean crops. In this study, metabolomics and transcriptomics analyses were conducted on soybean samples from nine regions in Heilongjiang and Liaoning Provinces using untargeted liquid chromatography–mass spectrometry (LC–MS) and Illumina sequencing technologies. The primary objective was to devise an effective and unbiased method for determining the geographical origin of each soybean variety to mitigate potential fraudulent practices. Through multidimensional and unidimensional analyses, successful identification of differentially expressed metabolites (DEMs) and differentially expressed genes (DEGs) was achieved, yielding statistically significant outcomes. Integration of the metabolomics and transcriptomics datasets facilitated the construction of a correlation network model capable of distinguishing soybeans originating from different geographical locations, leading to the identification of significant biomarkers exemplifying noteworthy distinctions. To validate the feasibility of this method in practical applications, partial least squares discriminant analysis was employed to differentiate soybean samples from the nine regions. The results convincingly showcased the applicability and reliability of this approach in accurately pinpointing the geographical origin of soybeans. Distinguishing itself from prior research in soybean traceability, this study incorporates an integrated analysis of metabolomics and transcriptomics data, thereby unveiling biomarkers that offer a more precise differentiation of soybean traits across distinct regions, thereby bridging a critical research gap within the soybean traceability domain. This innovative dual-data integration analysis methodology is poised to enhance the accuracy of soybean traceability tools and lay a new foundation for future agricultural product identification research.
Global prevalence of organohalide-respiring bacteria dechlorinating polychlorinated biphenyls in sewage sludge
Authors: Xu Guofang , Zhao Siyan , Rogers Matthew J. , Chen Chen , He Jianzhong 
Published: March 2024

Abstract
Background
Massive amounts of sewage sludge are generated during biological sewage treatment and are commonly subjected to anaerobic digestion, land application, and landfill disposal. Concurrently, persistent organic pollutants (POPs) are frequently found in sludge treatment and disposal systems, posing significant risks to both human health and wildlife. Metabolically versatile microorganisms originating from sewage sludge are inevitably introduced to sludge treatment and disposal systems, potentially affecting the fate of POPs. However, there is currently a dearth of comprehensive assessments regarding the capability of sewage sludge microbiota from geographically disparate regions to attenuate POPs and the underpinning microbiomes.

Results
Here we report the global prevalence of organohalide-respiring bacteria (OHRB) known for their capacity to attenuate POPs in sewage sludge, with an occurrence frequency of ~50% in the investigated samples (605 of 1186). Subsequent laboratory tests revealed microbial reductive dechlorination of polychlorinated biphenyls (PCBs), one of the most notorious categories of POPs, in 80 out of 84 sludge microcosms via various pathways. Most chlorines were removed from the para- and meta-positions of PCBs; nevertheless, ortho-dechlorination of PCBs also occurred widely, although to lower extents. Abundances of several well-characterized OHRB genera (Dehalococcoides, Dehalogenimonas, and Dehalobacter) and uncultivated Dehalococcoidia lineages increased during incubation and were positively correlated with PCB dechlorination, suggesting their involvement in dechlorinating PCBs. The previously identified PCB reductive dehalogenase (RDase) genes pcbA4 and pcbA5 tended to coexist in most sludge microcosms, but the low ratios of these RDase genes to OHRB abundance also indicated the existence of currently undescribed RDases in sewage sludge. Microbial community analyses revealed a positive correlation between biodiversity and PCB dechlorination activity although there was an apparent threshold of community co-occurrence network complexity beyond which dechlorination activity decreased.

Conclusions
Our findings that sludge microbiota exhibited nearly ubiquitous dechlorination of PCBs indicate widespread and nonnegligible impacts of sludge microbiota on the fate of POPs in sludge treatment and disposal systems. The existence of diverse OHRB also suggests sewage sludge as an alternative source to obtain POP-attenuating consortia and calls for further exploration of OHRB populations in sewage sludge.
Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants
Authors: Hu Huifeng , Kristensen Jannie Munk , Herbold Craig William , Pjevac Petra , Kitzinger Katharina , Hausmann Bela , Dueholm Morten Kam Dahl , Nielsen Per Halkjaer , Wagner Michael 
Published: March 2024

Abstract
Background
Microorganisms are responsible for nutrient removal and resource recovery in wastewater treatment plants (WWTPs), and their diversity is often studied by 16S rRNA gene amplicon sequencing. However, this approach underestimates the abundance and diversity of Patescibacteria due to the low coverage of commonly used PCR primers for this highly divergent bacterial phylum. Therefore, our current understanding of the global diversity, distribution, and ecological role of Patescibacteria in WWTPs is very incomplete. This is particularly relevant as Patescibacteria are considered to be associated with microbial host cells and can therefore influence the abundance and temporal variability of other microbial groups that are important for WWTP functioning.

Results
Here, we evaluated the in silico coverage of widely used 16S rRNA gene-targeted primer pairs and redesigned a primer pair targeting the V4 region of bacterial and archaeal 16S rRNA genes to expand its coverage for Patescibacteria. We then experimentally evaluated and compared the performance of the original and modified V4-targeted primers on 565 WWTP samples from the MiDAS global sample collection. Using the modified primer pair, the percentage of ASVs classified as Patescibacteria increased from 5.9 to 23.8%, and the number of detected patescibacterial genera increased from 560 to 1576, while the detected diversity of the remaining microbial community remained similar. Due to this significantly improved coverage of Patescibacteria, we identified 23 core genera of Patescibacteria in WWTPs and described the global distribution pattern of these unusual microbes in these systems. Finally, correlation network analysis revealed potential host organisms that might be associated with Patescibacteria in WWTPs. Interestingly, strong indications were found for an association between Patescibacteria of the Saccharimonadia and globally abundant polyphosphate-accumulating organisms of the genus Ca. Phosphoribacter.

Conclusions
Our study (i) provides an improved 16S rRNA gene V4 region-targeted amplicon primer pair inclusive of Patescibacteria with little impact on the detection of other taxa, (ii) reveals the diversity and distribution patterns of Patescibacteria in WWTPs on a global scale, and (iii) provides new insights into the ecological role and potential hosts of Patescibacteria in WWTPs﻿.
Exploring the roles of academic expectation stress, adaptive coping, and academic resilience on perceived English proficiency
Authors: Kao Po-Chi 
Published: March 2024

AbstractThis study aims to examine and analyze a research model comprising three latent variables (academic expectation stress, adaptive coping, and academic resilience) to gain insights into the perceived English proficiency of EFL (English as a foreign language) learners. These variables have been overlooked in previous literature despite their importance in understanding learning outcomes. A total of 395 undergraduate students from a Taiwanese university participated in this study. Through the use of structural equation modeling, the hypotheses in the research model were tested. The findings of this research are as follows: (1) Academic expectation stress has a significant and negative impact on EFL learners’ perceived English proficiency; (2) Academic resilience positively predicts EFL learners’ perceived English proficiency; (3) Academic resilience mediates the relationship between academic expectation stress and perceived English proficiency; (4) Adaptive coping mediates the relationship between academic expectation stress and academic resilience. These results add valuable insights to the existing literature in EFL teaching and learning, shedding light on the dynamics of these variables.
Recent advances in the biosynthesis and industrial biotechnology of Gamma-amino butyric acid
Authors: Milon Ripon Baroi , Hu Pengchen , Zhang Xueqiong , Hu Xuechao , Ren Lujing 
Published: March 2024

AbstractGABA (Gamma-aminobutyric acid), a crucial neurotransmitter in the central nervous system, has gained significant attention in recent years due to its extensive benefits for human health. The review focused on recent advances in the biosynthesis and production of GABA. To begin with, the investigation evaluates GABA-producing strains and metabolic pathways, focusing on microbial sources such as Lactic Acid Bacteria, Escherichia coli, and Corynebacterium glutamicum. The metabolic pathways of GABA are elaborated upon, including the GABA shunt and critical enzymes involved in its synthesis. Next, strategies to enhance microbial GABA production are discussed, including optimization of fermentation factors, different fermentation methods such as co-culture strategy and two-step fermentation, and modification of the GABA metabolic pathway. The review also explores methods for determining glutamate (Glu) and GABA levels, emphasizing the importance of accurate quantification. Furthermore, a comprehensive market analysis and prospects are provided, highlighting current trends, potential applications, and challenges in the GABA industry. Overall, this review serves as a valuable resource for researchers and industrialists working on GABA advancements, focusing on its efficient synthesis processes and various applications, and providing novel ideas and approaches to improve GABA yield and quality.
Graphical Abstract
Effects of latroeggtoxin-VI on dopamine and α-synuclein in PC12 cells and the implications for Parkinson’s disease
Authors: Yu Dianmei , Wang Haiyan , Zhai Yiwen , Lei Zhixiang , Sun Minglu , Chen Si , Yin Panfeng , Wang Xianchun 
Published: March 2024

Abstract
Background
Parkinson’s disease (PD) is characterized by death of dopaminergic neurons leading to dopamine deficiency, excessive α-synuclein facilitating Lewy body formation, etc. Latroeggtoxin-VI (LETX-VI), a proteinaceous neurotoxin discovered from the eggs of spider L. tredecimguttatus, was previously found to promote the synthesis and release of PC12 cells, showing a great potential as a drug candidate for PD. However, the relevant mechanisms have not been understood completely. The present study explored the mechanism underlying the effects of LETX-VI on dopamine and α-synuclein of PC12 cells and the implications for PD.

Results
After PC12 cells were treated with LETX-VI, the level of dopamine was significantly increased in a dose-dependent way within a certain range of concentrations. Further mechanism analysis showed that LETX-VI upregulated the expression of tyrosine hydroxylase (TH) and L-dopa decarboxylase to enhance the biosynthesis of dopamine, and downregulated that of monoamine oxidase B to reduce the degradation of dopamine. At the same time, LETX-VI promoted the transport and release of dopamine through modulating the abundance and/or posttranslational modification of vesicular monoamine transporter 2 (VMAT2) and dopamine transporter (DAT). While the level of dopamine was increased by LETX-VI treatment, α-synuclein content was reduced by the spider toxin. α-Synuclein overexpression significantly decreased the dopamine level and LETX-VI efficiently alleviated the inhibitory action of excessive α-synuclein on dopamine. In the MPTP-induced mouse model of PD, application of LETX-VI ameliorated parkinsonian behaviors of the mice, and reduced the magnitude of MPTP-induced α-synuclein upregulation and TH downregulation. In addition, LETX-VI displayed neuroprotective effects by inhibiting MPTP-induced decrease in the numbers of TH-positive and Nissl-stained neurons in mouse brain tissues.

Conclusions
All the results demonstrate that LETX-VI promotes the synthesis and release of dopamine in PC12 cells via multiple mechanisms including preventing abnormal α-synuclein accumulation, showing implications in the prevention and treatment of PD.
Evaluation of psychometric properties of sleep quality questionnaire among medical students of Guilan University of Medical Sciences
Authors: Pourramzani Ali , Ghafari Samane , Shafiee Arman , Fili Jafar , Sattari Mohammad Amin , Borna Nahid , Hajishah Hamed 
Published: March 2024

Abstract
Background
Since evaluating sleep quality among students is of great importance and is one of the challenges facing the health field regarding this group, we were determined to conduct this study to evaluate the psychometric properties of the Sleep Quality Questionnaire (SQQ) among the medical students at the Guilan University of Medical Sciences.

Methods
This research was conducted as a cross-sectional study. In the procedure, a random group of medical students at Guilan University of Medical Sciences were provided with questionnaires and the study’s pre-prepared checklist and were asked to answer them accurately. The questionnaires used in this study include the Sleep Quality Questionnaire (SQQ), and the Pittsburgh Sleep Quality Index (PSQI). After collecting the entries, all the data were subjected to a statistical analysis using the SPSS software.

Results
In this study, 249 medical students with an average age of 23.88 ± 2.46 were evaluated, of which 140 (56.2%) were female and the rest were male. According to the results, the average sleep quality for SQQ was 19.31 ± 8.06, and the Pittsburgh Sleep Quality Index (PSQI) was 7.95 ± 3.76. Based on the results obtained from the exploratory analysis, it was determined that no high overlap exists between the two evaluated factors in the sleep quality questionnaires, confirming their divergent validity. In evaluating the convergent validity, the correlation between the SQQ and PSQI questionnaires was reported as 0.642, which was significant (p < 0.001). Cronbach’s alpha for the SQQ questionnaire was equivalent to 0.882, which is verified since the minimum value is 0.70. Also, utilizing the test-retest method, the reliability was found to be 0.74, which is acceptable according to the minimum value of 0.70. SQQ scores had a direct and meaningful relationship with age (r = 0.185, p = 0.003). Based on the pairwise comparison, there was a significant difference in SQQ scores between the students in different stages and the duration of sleep.

Conclusion
The current study’s findings indicate that the SQQ questionnaire possesses adequate validity and reliability, which could be utilized to evaluate sleep quality in domestic studies.
A national study of clinical discussions about cannabis use among Veteran patients prescribed opioids
Authors: Zaman Tauheed , Bravata Dawn M. , Byers Amy , Krebs Erin , Leonard Samuel , Austin Charles , Sandbrink Friedhelm , Hasin Deborah S. , Keyhani Salomeh 
Published: March 2024

Abstract
Background
The Veterans Health Administration tracks urine drug tests (UDTs) among patients on long-term opioid therapy (LTOT) and recommends discussing the health effects of cannabis use.

Objective
To determine the occurrence of cannabis-related discussions between providers and patients on LTOT during six months following UDT positive for cannabis, and examine factors associated with documenting cannabis use.

Design
We identified patients prescribed LTOT with a UDT positive for cannabis in 2019. We developed a text-processing tool to extract discussions around cannabis use from their charts.

Subjects
Twelve thousand seventy patients were included. Chart review was conducted on a random sample of 1,946 patients.

Main measures
The presence of a cannabis term in the chart suggesting documented cannabis use or cannabis-related discussions. Content of those discussions was extracted in a subset of patients. Logistic regression was used to examine the association between patient factors, including state of residence legal status, with documentation of cannabis use.

Key Results
Among the 12,070 patients, 65.8% (N = 7,948) had a cannabis term, whereas 34.1% (N = 4,122) of patients lacked a cannabis term, suggesting that no documentation of cannabis use or discussion between provider and patient took place. Among the subset of patients who had a discussion documented, 47% related to cannabis use for medical reasons, 35% related to a discussion of VA policy or legal issues, and 17% related to a discussion specific to medical risks or harm reduction strategies. In adjusted analyses, residents of states with legalized recreational cannabis were less likely to have any cannabis-related discussion compared to patients in non-legal states [OR 0.73, 95% CI 0.64–0.82].

Conclusions
One-third of LTOT patients did not have documentation of cannabis use in the chart in the 6 months following a positive UDT for cannabis. Discussions related to the medical risks of cannabis use or harm reduction strategies were uncommon.
A Case of Maturity-Onset Diabetes of the Young With Complex Mutations
Authors: Bulchandani Sheetal , Kundra Priya 
Published: March 2024

Abstract
Maturity-onset diabetes of the young (MODY) encompasses a group of rare monogenic forms of diabetes, with 14 subtypes described in the literature, each with a distinct underlying genetic mutation. We present a case with mutations in 2 different genes that are known to be responsible for MODY. A 33-year-old male individual presented to the endocrinology clinic for evaluation. He was diagnosed with type 2 diabetes mellitus at 13 years of age and was initially treated with insulin, which was subsequently switched to repaglinide and metformin. The patient reported a history of hypoglycemia at birth and in his daughter. His biological father was diagnosed with diabetes mellitus at 16 years of age. Genetic testing for monogenic diabetes revealed a pathogenic variant in hepatocyte nuclear factor 4 alpha and a variant of unknown significance in Paired Box Gene 4. The treatment was switched to glipizide 2.5 mg orally, which resulted in adequate glycemic control. Genetic testing was recommended for his daughter. MODY can be missed because of its broad clinical presentation. Heightened vigilance and a low threshold for genetic testing for MODY are required in patients with a high likelihood of having MODY, as the treatment can be tailored to individual patient needs.
An Unlikely Source of Iodine Uptake: A Bronchogenic Cyst Masquerading as Metastatic Thyroid Cancer
Authors: Dillon Martha , Zielinski Rachel , Worth Jennifer , Sanders Melinda , Ibrahim Omar , Vedere Tarunya 
Published: March 2024

Abstract
Radioactive iodine therapy and posttreatment scanning are essential components of differentiated thyroid carcinoma treatment and detection of metastatic disease. False-positive results can be seen on an I-131 scan and are important for clinicians to be aware of. Here, we present a case of a 33-year-old female with follicular thyroid carcinoma who was noted to have an area of moderate uptake in the chest on a whole-body scan following remnant ablation with 30 mCi of I-131 (1.11GBq) concerning for a metastatic hilar lymph node. This was determined to be a mediastinal bronchogenic cyst on surgical pathology. It has been previously proposed that the expression of sodium iodide symporters in some bronchogenic cysts could be the mechanism by which iodine uptake is seen within them. We were able to demonstrate positive immunohistochemical staining for both sodium iodide symporter and the associated paired box gene 8 transcription factor in the cyst sample, which supports the proposed theory.