bluuebunny/crossref_metadata_2025_split huggingface dataset:
eRNA-IDO: A One-stop Platform for Identification, Interactome Discovery, and Functional Annotation of Enhancer RNAs
Authors: Zhang Yuwei , Gong Lihai , Ding Ruofan , Chen Wenyan , Rong Hao , Li Yanguo , Shameem Fawziya , Ali Korakkandan Arshad , Li Lei , Liao Qi 
Published: August 2024

Abstract
Growing evidence supports the transcription of enhancer RNAs (eRNAs) and their important roles in gene regulation. However, their interactions with other biomolecules and their corresponding functionality remain poorly understood. In an attempt to facilitate mechanistic research, this study presents eRNA-IDO, the first integrative computational platform for the identification, interactome discovery, and functional annotation of human eRNAs. eRNA-IDO comprises two modules: eRNA-ID and eRNA-Anno. Functionally, eRNA-ID can identify eRNAs from de novo assembled transcriptomes. eRNA-ID includes eight kinds of enhancer makers, enabling users to customize enhancer regions flexibly and conveniently. In addition, eRNA-Anno provides cell-/tissue-specific functional annotation for both new and known eRNAs by analyzing the eRNA interactome from prebuilt or user-defined networks between eRNAs and protein-coding genes. The prebuilt networks include the Genotype-Tissue Expression (GTEx)-based co-expression networks in normal tissues, The Cancer Genome Atlas (TCGA)-based co-expression networks in cancer tissues, and omics-based eRNA-centric regulatory networks. eRNA-IDO can facilitate research on the biogenesis and functions of eRNAs. The eRNA-IDO server is freely available at http://bioinfo.szbl.ac.cn/eRNA_IDO/.
Ethics in Patients’ Health Literacy: a scoping review and a critical discussion
Authors: Evripidou Melina , Efthymiou Areti , Velonaki Venetia , Kalokairinou Athina , Papastavrou Evridiki 
Published: August 2024

Abstract
A growing body of literature has acknowledged that a high number of populations with low Health Literacy (HL) is related to poor health outcomes, inequities in healthcare and high economic costs. Those findings have formulated the research questions of this review: (i) what ethical issues arise within the context of patients’ HL and (ii) What is the relationship between HL and quality of life? This review followed the guidelines of Joanna Briggs Institute (JBI) and the Preferred Reporting Items for Scoping Reviews (PRISMA-ScR) and it was conducted in five databases: PubMed, CINAHL, MEDLINE, Scopus and Science Direct between June 2022 and December 2023. Out of the 3164 titles retrieved, 285 abstracts were eligible to proceed. Following a thorough examination of the full text of 61 papers, 45 sources were identified that met the inclusion criteria. The data analysis process was guided by the research questions, employing a thematic approach. Four themes were identified: the use of language and patient understanding, human rights, the principlism approach (justice, beneficence, non-maleficence and autonomy) and quality of life. The first theme mainly focused on the relation of HL with the notion of consent forms and national action plans. Human rights in relation to HL were discussed as a minor issue. The bioethical framework by Beauchamp and Childress (Principles of Biomedical Ethics, 6th edn. Oxford University Press, New York, NY, 2009), was addressed by several studies, with a particular focus on justice and the loss of autonomy. Quality of life indicated a positive correlation with HL by most of the authors, while few studies revealed a moderate correlation.
Sarcopenia Is a Risk Factor for Postoperative Complications Among Older Adults With Inflammatory Bowel Disease
Authors: Minawala Ria , Kim Michelle , Delau Olivia , Ghiasian Ghoncheh , McKenney Anna Sophia , Da Luz Moreira Andre , Chodosh Joshua , McAdams-DeMarco Mara , Segev Dorry L , Adhikari Samrachana , Dodson John , Shaukat Aasma , Dane Bari , Faye Adam S 
Published: August 2024

Abstract

Background
Sarcopenia has been associated with adverse postoperative outcomes in older age cohorts, but has not been assessed in older adults with inflammatory bowel disease (IBD). Further, current assessments of sarcopenia among all aged individuals with IBD have used various measures of muscle mass as well as cutoffs to define its presence, leading to heterogeneous findings.

Methods
In this single-institution, multihospital retrospective study, we identified all patients aged 60 years and older with IBD who underwent disease-related intestinal resection between 2012 and 2022. Skeletal Muscle Index (SMI) and Total Psoas Index (TPI) were measured at the superior L3 endplate on preoperative computed tomography scans and compared through receiver operating characteristic curve. We then performed multivariable logistic regression to assess risk factors associated with an adverse 30-day postoperative outcome. Our primary outcome included a 30-day composite of postoperative mortality and complications, including infection, bleeding, cardiac event, cerebrovascular accident, acute kidney injury, venous thromboembolism, reoperation, all-cause rehospitalization, and need for intensive care unit-level care.

Results
A total of 120 individuals were included. Overall, 52% were female, 40% had ulcerative colitis, 60% had Crohn’s disease, and median age at time of surgery was 70 years (interquartile range: 65-75). Forty percent of older adults had an adverse 30-day postoperative outcome, including infection (23%), readmission (17%), acute kidney injury (13%), bleeding (13%), intensive care unit admission (10%), cardiac event (8%), venous thromboembolism (7%), reoperation (6%), mortality (5%), and cerebrovascular accident (2%). When evaluating the predictive performance of SMI vs TPI for an adverse 30-day postoperative event, SMI had a significantly higher area under the curve of 0.66 (95% CI, 0.56-0.76) as compared to 0.58 (95% CI, 0.48-0.69) for TPI (P = .02). On multivariable logistic regression, prior IBD-related surgery (adjusted odds ratio [adjOR] 6.46, 95% CI, 1.85-22.51) and preoperative sepsis (adjOR 5.74, 95% CI, 1.36-24.17) significantly increased the odds of adverse postoperative outcomes, whereas increasing SMI was associated with a decreased risk of an adverse postoperative outcome (adjOR 0.88, 95% CI, 0.82-0.94).

Conclusions
Sarcopenia, as measured by SMI, is associated with an increased risk of postoperative complications among older adults with IBD. Measurement of SMI from preoperative imaging can help risk stratify older adults with IBD undergoing intestinal resection.
Cerebrospinal Fluid Cytokines and Chemokines Involved in Cytotoxic Cell Function and Risk of Acute 14-Day Mortality in Persons with Advanced HIV and Cryptococcal Meningitis
Authors: Okafor Elizabeth C , Mukaremera Liliane , Hullsiek Kathy H , Engen Nicole , Tugume Lillian , Ssebambulidde Kenneth , Musubire Abdu K , Nuwagira Edwin , Mpoza Edward , Williams Darlisha A , Muzoora Conrad , Rhein Joshua , Meya David B , Nielsen Kirsten , Boulware David R 
Published: August 2024

Abstract

Background
The role of the immune response in acute mortality of cryptococcal meningitis remains unclear.

Methods
Cerebrospinal fluid (CSF) from 337 Ugandans with first-episode cryptococcal meningitis was collected. CSF cytokines and chemokines were quantified and compared by 14-day survival, stratification by quartiles, and logistical regression to determine association with acute mortality.

Results
Eighty-four (24.9%) participants died by day 14. Persons who survived to day 14 had higher levels of proinflammatory macrophage inflammatory protein (MIP)-3β and interferon (IFN)-β and cytotoxicity-associated granzyme B and inteferon gamma-induced protein (IP)-10 compared to those who died (P &lt; .05 for each). Logistic regression analysis revealed that per 2-fold increase in proinflammatory interleukin (IL)-6, IL-1α, MIP-1β, MIP-3β, and IFN-β and cytotoxicity-associated IL-12, tumor necrosis factor–α, granzyme-B, and IP-10 CSF concentrations, the risk of acute 14-day mortality decreased. Similar biomarkers were implicated when stratified by quartiles and further identified that lower concentrations of anti-inflammatory IL-10 and IL-13 were associated with 14-day mortality (P &lt; .05 for each).

Conclusions
Proinflammatory and cytotoxicity-associated cytokine and chemokine responses in the CSF decrease the risk of acute 14-day mortality. These data suggest that a cytotoxic immune environment in the CSF could potentially improve acute survival. Further research on cytotoxic cells is crucial to improve understanding of innate and adaptive immune responses in cryptococcal meningitis.
Fungal endophytes Fusarium solani SGGF14 and Alternaria tenuissima SGGF21 enhance the glycyrrhizin production by modulating its key biosynthetic genes in licorice (Glycyrrhiza glabra L.)
Authors: Majidi Mehdi , Mirjalili Mohammad Hossein , Farzaneh Mohsen , Rezadoost Hassan 
Published: August 2024

Abstract

Aims
To identify promising fungal endophytes that are able to produce glycyrrhizin and enhance it in licorice and the mechanisms involved.

Methods and results
Fifteen fungal endophytes were isolated from Glycyrrhiza glabra L. rhizomes among which SGGF14 and SGGF21 isolates were found to produce glycyrrhizin by 4.29 and 2.58 µg g−1 dry weight in the first generation of their culture. These isolates were identified as Fusarium solani and Alternaria tenuissima, respectively, based on morphological characteristics and sequence analysis of internal transcribed spacer, TEF1, ATPase, and CAL regions. Subsequently, G. glabra plants were inoculated with these fungal isolates to examine their effect on glycyrrhizin production, plant growth parameters and the expression of key genes involved in glycyrrhizin pathway: SQS1, SQS2, bAS, CAS, LUS, CYP88D6, and CYP72A154. Endophytes were able to enhance glycyrrhizin content by 133%–171% in the plants. Natural control (NC) plants, harboring all natural endophytes, had better growth compared to SGGF14- and SGGF21-inoculated and endophyte-free (EF) plants. Expression of SQS1, SQS2, CYP88D6, and CYP72A154 was upregulated by inoculation with endophytes. LUS and CAS were downregulated after endophyte inoculation. Expression of bAS was higher in SGGF21-inoculated plants when compared with NC, EF, and SGGF14-inoculated plants.

Conclusions
Two selected fungal endophytes of G. glabra can produce glycyrrhizin and enhance glycyrrhizin content in planta by modulating the expression of key genes in glycyrrhizin biosynthetic pathway.
Predicting physical functioning status in older adults: insights from wrist accelerometer sensors and derived digital biomarkers of physical activity
Authors: Fan Lingjie , Zhao Junhan , Hu Yao , Zhang Junjie , Wang Xiyue , Wang Fengyi , Wu Mengyi , Lin Tao 
Published: August 2024

Abstract

Objective
Conventional physical activity (PA) metrics derived from wearable sensors may not capture the cumulative, transitions from sedentary to active, and multidimensional patterns of PA, limiting the ability to predict physical function impairment (PFI) in older adults. This study aims to identify unique temporal patterns and develop novel digital biomarkers from wrist accelerometer data for predicting PFI and its subtypes using explainable artificial intelligence techniques.

Materials and Methods
Wrist accelerometer streaming data from 747 participants in the National Health and Aging Trends Study (NHATS) were used to calculate 231 PA features through time-series analysis techniques—Tsfresh. Predictive models for PFI and its subtypes (walking, balance, and extremity strength) were developed using 6 machine learning (ML) algorithms with hyperparameter optimization. The SHapley Additive exPlanations method was employed to interpret the ML models and rank the importance of input features.

Results
Temporal analysis revealed peak PA differences between PFI and healthy controls from 9:00 to 11:00 am. The best-performing model (Gradient boosting Tree) achieved an area under the curve score of 85.93%, accuracy of 81.52%, sensitivity of 77.03%, and specificity of 87.50% when combining wrist accelerometer streaming data (WAPAS) features with demographic data.

Discussion
The novel digital biomarkers, including change quantiles, Fourier transform (FFT) coefficients, and Aggregated (AGG) Linear Trend, outperformed traditional PA metrics in predicting PFI. These findings highlight the importance of capturing the multidimensional nature of PA patterns for PFI.

Conclusion
This study investigates the potential of wrist accelerometer digital biomarkers in predicting PFI and its subtypes in older adults. Integrated PFI monitoring systems with digital biomarkers would improve the current state of remote PFI surveillance.
A GIS software-based method to identify public health data belonging to address-defined communities
Authors: Lam Amanda M , Singletary Mariana C , Cullen Theresa 
Published: August 2024

Abstract

Objective
This communication presents the results of defining a tribal health jurisdiction by a combination of tribal affiliation (TA) and case address.

Materials and Methods
Through a county-tribal partnership, Geographic Information System (GIS) software and custom code were used to extract tribal data from county data by identifying reservation addresses in county extracts of COVID-19 case records from December 30, 2019, to December 31, 2022 (n = 374 653) and COVID-19 vaccination records from December 1, 2020, to April 18, 2023 (n = 2 355 058).

Results
The tool identified 1.91 times as many case records and 3.76 times as many vaccination records as filtering by TA alone.

Discussion and Conclusion
This method of identifying communities by patient address, in combination with TA and enrollment, can help tribal health jurisdictions attain equitable access to public health data, when done in partnership with a data sharing agreement. This methodology has potential applications for other populations underrepresented in public health and clinical research.
Determination of Total Aflatoxins in Polished Rice by Liquid Chromatography–Fluorescence Detection with Multifunctional Column Cleanup and Precolumn Derivatization: Single-Laboratory and Inter-Laboratory Validation Studies
Authors: Yoshinari Tomoya , Watanabe Takahiro , Takeuchi Toshihiko , Ohnishi Takahiro 
Published: August 2024

Abstract

Background
Aflatoxins (AFs) are toxic metabolites produced by Aspergillus spp. Because AFs are potent carcinogens in humans and animals, many countries have set regulatory limits for AFs in foods to prevent dietary exposure. From a global food safety perspective, in 2023, the Codex Alimentarius Commission established the maximum level (ML) of total AFs in certain cereals and cereal-based products, including polished rice. Therefore, validated analytical methods for AFs detection are necessary.

Objective
In this study, an HPLC–fluorescence method coupled with multifunctional column cleanup and trifluoroacetic acid derivatization was developed for the determination of AF levels in polished rice.

Methods
Our method was validated in a single-laboratory study using AF-spiked materials, followed by an inter-laboratory validation study. Twelve laboratories participated in the inter-laboratory validation study, and five polished rice test samples artificially contaminated with AFs were analyzed.

Results
In a single-laboratory study, the ranges of mean recoveries of AF B1, B2, G1, G2, and total AFs were 101, 100–103, 93–96, 95–98, and 97–99%, respectively. The RSDs for within-day and between-day variations were all ≤4.4%. In the inter-laboratory validation study, the RSDs for repeatability and reproducibility were from 0.7 to 2.7% and 3.3 to 8.9% for all analytes, respectively.

Conclusion
In response to the Codex ML and method performance criteria for AFs in polished rice, an analytical method based on HPLC–fluorescence detection was developed. All method performance parameters estimated from the test results of the single-laboratory and inter-laboratory validation studies met the criteria required by the Codex.

Highlights
Single- and inter-laboratory studies for the validation of an analytical method for AF level determination in polished rice were successfully performed. This analytical method will be suitable to determine AF levels around the Codex ML set for polished rice.
Muscle, season, sex, and carcass weight affected pork texture, collagen characteristics, and intramuscular fat content
Authors: Li Xiying , Ha Minh , Warner Robyn D , Lealiifano Amy , Hewitt Robert J E , D’Souza Darryl N , Trezona Megan , Dunshea Frank R 
Published: August 2024

Abstract
In this study, pigs from 3 supply chains were slaughtered in an Australian summer and winter (n = 20 for each supply chain). The pigs were from 2 sexes (female and castrated male) and 2 carcass weight groups (high: 95.0 to 100.0 kg and low: 75.0 to 80.0 kg). From each carcass, the Biceps femoris (BF), Longissimus thoracis et lumborum (LTL), and Triceps brachii (TB) were excised at 24 h postmortem, vacuum packed, frozen at 24-48 h and transported to the lab. Cooking loss, Warner–Bratzler shear force (WBSF) and texture profile analysis (adhesiveness, chewiness, cohesiveness, hardness, resilience, and springiness) were measured in LTL and BF. pH, collagen content, and solubility and intramuscular fat (IMF) content were determined for all muscles. Results showed that BF was tougher than LTL, and winter samples were tougher than summer ones (P &lt; 0.05). The TB had higher pH, collagen, and IMF content than BF and LTL (P &lt; 0.05). Collagen solubility was higher in castrated male and winter samples. pH, collagen solubility, and IMF content were significantly (P &lt; 0.05) related to chewiness and hardness in pork BF and LTL. pH and IMF were also related to cooking loss, while collagen solubility and IMF were related to WBSF (P &lt; 0.05). The relationships of pH and IMF with pork texture were predominantly driven by the LTL, while the relationships between collagen solubility and texture were predominantly driven by the BF. Collagen solubility and IMF of pork BF and TB were related to those of LTL, but the correlations were not strong enough for prediction. Pork texture and chemical components were affected by muscle, seasons, sex and carcass weight. pH, collagen solubility, and IMF-affected pork texture.
Outcomes of endoscopic retrograde cholangiopancreatography performed in the AM versus PM: does procedural timing matter?
Authors: Sabrie Nasruddin , Gimpaya Nikko , Khalaf Kareem , Deeb Maya , Mhalawi Wedad , Meleka Michael , Tham Daniel C , Mokhtar Ahmed H , Na Caleb , Abal Sophia P , Malipatil Sharan B , Gupta Sarang , Jugnundan Sechiv , Chopra Deiya , Khan Rishad , Calo Natalia C , Teshima Christopher W , May Gary R , Mosko Jeffrey D , Grover Samir C 
Published: August 2024

Abstract

Background
ERCP is a technically demanding procedure that carries a high cumulative adverse event (AE) rate of &gt;10%. Identifying risk factors for adverse events is paramount. Procedure timing, as a surrogate for endoscopist fatigue, has been shown to influence key quality metrics in colonoscopy, but data on this relationship in ERCP is sparse.

Methods
We conducted a retrospective cohort study of ERCP procedures performed by 5 experienced staff endoscopists, with or without advanced endoscopy fellow (AEF) involvement, from January 1, 2010 to December 1, 2020 at St Michael’s Hospital, Toronto, Ontario, a regional referral center for therapeutic endoscopy. The primary outcome was the difference in rate of selective deep, duct canulation between AM and PM procedures.

Results
A total of 5672 ERCP procedures were eligible for inclusion. 2793 (49.2%) procedures were performed in the AM and 2879 procedures (50.8%) were performed in the PM. We found no significant difference in the rate of selective ductal cannulation between AM and PM procedures in the unadjusted (82.8% AM vs. 83.1% P-value = .79) or adjusted (OR = 0.98, 95% CI, 0.85-1.12, P-value = .72) analyses. We found no significant difference in the mean procedural duration or rate of perforation between AM and PM procedures. The rate of immediate bleeding was slightly higher in the AM cohort.

Conclusion
In our single-center retrospective study, ERCP quality, including selective cannulation rates and immediate adverse events were not significantly different in procedures performed in the morning compared to those performed in the afternoon.
Sexually divergent selection, allometric constraints, and the evolution of sexual dimorphism in cichlids from Lake Tanganyika
Authors: Tsuboi Masahito , Takahashi Tetsumi 
Published: August 2024

Abstract
The evolution of sexual dimorphism is widely acknowledged as a manifestation of sex-specific genetic architecture. Although empirical studies suggested that sexual dimorphism evolves as a joint consequence of constraints arising from genetic architecture and sexually divergent selection, it remains unclear whether and how these established microevolutionary processes scale up to the macroevolutionary patterns of sexual dimorphism among taxa. Here, we studied how sexual selection and parental care drive sexual dimorphism in cichlid fishes from Lake Tanganyika. We found that male–male competition, female choice, and maternal mouthbrooding are associated with sexual dimorphism in body length, body colour, and head length, respectively, despite strong allometric relationships between body length and head length. Within-species (static) allometry of head length on body length evolved as sex-specific responses to mouthbrooding, where females evolved higher intercepts while males evolved steeper slopes. Thus, selection to increase mouth size in mouthbrooders may have broken down and reorganized the pattern of allometric constraints that are inherently strong and concordant between sexes. Furthermore, sex-specific responses to mouthbrooding left a remarkably clear signature on the macroevolutionary pattern, resulting in a decoupling of co-evolution in parameters of static allometries between sexes observed exclusively within maternal mouthbrooders. Our study provides multiple lines of evidence that are consistent with the idea that macroevolutionary patterns of sexual dimorphism in Lake Tanganyika cichlids result from sexually divergent selection. Our approach illustrates that an examination of within-population phenotypic variance in the phylogenetic comparative framework may facilitate nuanced understandings of how macroevolutionary patterns are generated by underlying microevolutionary processes.