bluuebunny/crossref_metadata_2025_split huggingface dataset:
Refining the pool of RNA-binding domains advances the classification and prediction of RNA-binding proteins
Authors: Wassmer Elsa , Koppány Gergely , Hermes Malte , Diederichs Sven , Caudron-Herger Maïwen 
Published: June 2024

Abstract
From transcription to decay, RNA-binding proteins (RBPs) influence RNA metabolism. Using the RBP2GO database that combines proteome-wide RBP screens from 13 species, we investigated the RNA-binding features of 176 896 proteins. By compiling published lists of RNA-binding domains (RBDs) and RNA-related protein family (Rfam) IDs with lists from the InterPro database, we analyzed the distribution of the RBDs and Rfam IDs in RBPs and non-RBPs to select RBDs and Rfam IDs that were enriched in RBPs. We also explored proteins for their content in intrinsically disordered regions (IDRs) and low complexity regions (LCRs). We found a strong positive correlation between IDRs and RBDs and a co-occurrence of specific LCRs. Our bioinformatic analysis indicated that RBDs/Rfam IDs were strong indicators of the RNA-binding potential of proteins and helped predicting new RBP candidates, especially in less investigated species. By further analyzing RBPs without RBD, we predicted new RBDs that were validated by RNA-bound peptides. Finally, we created the RBP2GO composite score by combining the RBP2GO score with new quality factors linked to RBDs and Rfam IDs. Based on the RBP2GO composite score, we compiled a list of 2018 high-confidence human RBPs. The knowledge collected here was integrated into the RBP2GO database at https://RBP2GO-2-Beta.dkfz.de.
Comparative analysis of RNA 3D structure prediction methods: towards enhanced modeling of RNA–ligand interactions
Authors: Nithin Chandran , Kmiecik Sebastian , Błaszczyk Roman , Nowicka Julita , Tuszyńska Irina 
Published: June 2024

Abstract
Accurate RNA structure models are crucial for designing small molecule ligands that modulate their functions. This study assesses six standalone RNA 3D structure prediction methods—DeepFoldRNA, RhoFold, BRiQ, FARFAR2, SimRNA and Vfold2, excluding web-based tools due to intellectual property concerns. We focus on reproducing the RNA structure existing in RNA-small molecule complexes, particularly on the ability to model ligand binding sites. Using a comprehensive set of RNA structures from the PDB, which includes diverse structural elements, we found that machine learning (ML)-based methods effectively predict global RNA folds but are less accurate with local interactions. Conversely, non-ML-based methods demonstrate higher precision in modeling intramolecular interactions, particularly with secondary structure restraints. Importantly, ligand-binding site accuracy can remain sufficiently high for practical use, even if the overall model quality is not optimal. With the recent release of AlphaFold 3, we included this advanced method in our tests. Benchmark subsets containing new structures, not used in the training of the tested ML methods, show that AlphaFold 3′s performance was comparable to other ML-based methods, albeit with some challenges in accurately modeling ligand binding sites. This study underscores the importance of enhancing binding site prediction accuracy and the challenges in modeling RNA–ligand interactions accurately.
Methods of Assessment of Zinc Status in Humans: An Updated Review and Meta-analysis
Authors: Ceballos-Rasgado Marena , Brazier Anna K M , Gupta Swarnim , Moran Victoria H , Pierella Elisa , Fekete Katalin , Lowe Nicola M 
Published: June 2024

Abstract

Context
The assessment of zinc status is difficult but essential for the identification of zinc deficiency and evaluation of interventions to improve zinc status.

Objective
The purpose of this systematic review (SR) and meta-analysis was to update the previously published SR of biomarkers of zinc status, conducted by the European Micronutrient Recommendations Aligned (EURRECA) network in 2009, to answer the question: Which putative measures (biomarkers) of zinc status appropriately reflect a change in zinc intake of at least 2 weeks?

Data Sources
A structured search strategy was used to identify articles published between January 2007 and September 2022 from MEDLINE (Ovid), Embase (Ovid), Cochrane Database of Systematic Reviews, and Cochrane Central Register of Controlled Trials (CENTRAL). Relevant articles were identified using previously defined eligibility criteria.

Data Extraction
Data were extracted and combined with data from the previous SR.

Data Analysis
A random-effects model was used to calculate pooled mean differences using STATA (StataCorp). The risk of bias and the certainty of evidence for all outcomes were assessed. Additional data on 7 of the 32 previously reported biomarkers were identified, along with data on an additional 40 putative biomarkers from studies published since 2007. Pooled data analysis confirmed that, in healthy participants, both plasma/serum zinc concentration and urinary zinc excretion responded to changes in zinc intake (plasma/serum: mean effect [95% CI], controlled studies: 2.17 µmol/L [1.73, 2.61]; P &lt; .005, I2 = 97.8; before-and-after studies: 2.87 µmol/L [2.45, 3.30]; P &lt; .005, I2 = 98.1%; urine zinc: 0.39 mmol/mol creatinine [0.17, 0.62]; P &lt; .005, I2 = 81.2; 3.09 µmol/day [0.16, 6.02]; P = .039, I2 = 94.3).

Conclusion
The updated analyses support the conclusion that plasma/serum and urinary zinc respond to changes in zinc intake in studies of healthy participants. Several additional putative biomarkers were identified, but more studies are needed to assess the sensitivity and reliability.

Systematic Review Registration
PROSPERO no. CRD42020219843.
Relationship of Curcumin with Aging and Alzheimer and Parkinson Disease, the Most Prevalent Age-Related Neurodegenerative Diseases: A Narrative Review
Authors: Turer Büşra Yurt , Sanlier Nevin 
Published: June 2024

Abstract
The elderly population is increasing worldwide every day. Age is a significant factor in the progression of neurological diseases, which can also cause cognitive decline and memory disorders. Inflammation and oxidative stress are primary drivers of senescence and disorders, particularly those associated with aging and neurodegenerative diseases. Bioactive phytochemicals are considered a promising therapeutic strategy in combating aging and age-related pathological conditions. One of the phytochemicals with diverse biological properties encompassing antioxidant, anti-inflammatory, antibacterial, antiviral, anticancer, antifungal, antidepressant, anti-allergic, and anti-aging properties is curcumin. Curcumin, a polyphenolic structure with a distinct orange hue and unique chemical properties, is derived from the roots of Curcuma longa, a member of the Zingiberaceae family, commonly known as turmeric. It has been noted that the incidence of neurodegenerative diseases is low in societies that consume curcumin widely. Therefore, this review investigates the effect of curcumin on aging and Alzheimer and Parkinson disease, which are the most prevalent age-related neurodegenerative diseases.
The Association of Oral Processing Factors and Nutrient Intake in Community-Dwelling Older Adults: A Systematic Review and Meta-Analysis
Authors: Nitsuwat Supatchayaporn , Webster James , Sarkar Anwesha , Cade Janet 
Published: June 2024

Abstract

Context
Oral health and food oral-processing issues emerge with functional decline in the older adult population, potentially increasing the risk of malnutrition. Impairment of oral health is associated with poorer nutrition status; however, the relationship between oral factors and the intake of each nutrient remains poorly understood.

Objective
The associations between different oral factors and nutrient intakes among community-dwelling older adults were investigated.

Data Sources
A literature search from 5 databases (Web of Science, Scopus, Cochrane Library, Ovid [MEDLINE and Embase], and CINAHL) was completed on February 1, 2022. The search was limited to peer-reviewed articles published between the years 2012 and 2022.

Data Extraction
Six cross-sectional studies were included in the meta-analysis. Two authors independently completed the data extraction and summarized the study characteristics, factors adjusted for in the statistical analysis, the outcome, and summary statistics of the results.

Data Analysis
Meta-analyses showed evidence of a significant association between compromised oral factors (namely, denture status, chewing ability, and the number of teeth) with lower energy (weighted mean difference [WMD], –107 kcal d–1 (95% CI, –132 to –81), protein (WMD, –5.2 g d–1; 95% CI, –6.6 to –3.8), fat (WMD, –4.6 g d–1; 95% CI, –6.7 to –2.6), carbohydrate (WMD, –8.8 g d–1; 95% CI, –13.9 to –3.7), and vitamin C intakes (WMD, –12.9 mg d–1; 95% CI, –16.6 to –9.2) in older adults.

Conclusion
Oral health can be an indicator of compromised daily energy, protein, fat, carbohydrate, and vitamin C intakes in older adults. However, the small sample size of the studies included in this review and the heterogeneity among macronutrient studies should be considered. Because of the lack of studies covering all aspects of food oral processing (eg, salivary flow rate, tongue pressure), the associations between oral processing and nutrient intake were not thoroughly explored.

Systematic Review Registration
PROSPERO registration no. CRD42022308823.
Cryptococcosis Associated With Biologic Therapy: A Narrative Review
Authors: Li Xin , Paccoud Olivier , Chan Koon-Ho , Yuen Kwok-Yung , Manchon Romain , Lanternier Fanny , Slavin Monica A , van de Veerdonk Frank L , Bicanic Tihana , Lortholary Olivier 
Published: June 2024

Abstract
Cryptococcus is an opportunistic fungal pathogen that can cause disseminated infection with predominant central nervous system involvement in patients with compromised immunity. Biologics are increasingly used in the treatment of neoplasms and autoimmune/inflammatory conditions and the prevention of transplant rejection, which may affect human defense mechanisms against cryptococcosis. In this review, we comprehensively investigate the association between cryptococcosis and various biologics, highlighting their risks of infection, clinical manifestations, and clinical outcomes. Clinicians should remain vigilant for the risk of cryptococcosis in patients receiving biologics that affect the Th1/macrophage activation pathways, such as tumor necrosis factor α antagonists, Bruton tyrosine kinase inhibitors, fingolimod, JAK/STAT inhibitors (Janus kinase/signal transducer and activator of transcription), and monoclonal antibody against CD52. Other risk factors—such as age, underlying condition, and concurrent immunosuppressants, especially corticosteroids—should also be taken into account during risk stratification.
Genetic factors of grain cadmium concentration in Polish wheat (Triticum polonicum L.)
Authors: Cheng Yiran , Liu Rui , Yang Tian , Yang Shan , Chen Jia , Huang Yiwen , Long Dan , Zeng Jian , Wu Dandan , Kang Houyang , Fan Xing , Sha Lina , Zhang Haiqin , Zhou Yonghong , Wang Yi 
Published: June 2024

Abstract
Wheat (Triticum aestivum L.) is one of the most important crops worldwide and a major source of human cadmium (Cd) intake. Limiting grain Cd concentration (Gr_Cd_Conc) in wheat is necessary to ensure food safety. However, the genetic factors associated with Cd uptake, translocation and distribution and Gr_Cd_Conc in wheat are poorly understood. Here, we mapped quantitative trait loci (QTLs) for Gr_Cd_Conc and its related transport pathway using a recombinant inbred line (RIL) population derived from 2 Polish wheat varieties (RIL_DT; dwarf Polish wheat [DPW] and tall Polish wheat [TPW]). We identified 29 novel major QTLs for grain and tissue Cd concentration; 14 novel major QTLs for Cd uptake, translocation, and distribution; and 27 major QTLs for agronomic traits. We also analyzed the pleiotropy of these QTLs. Six novel QTLs (QGr_Cd_Conc-1A, QGr_Cd_Conc-3A, QGr_Cd_Conc-4B, QGr_Cd_Conc-5B, QGr_Cd_Conc-6A, and QGr_Cd_Conc-7A) for Gr_Cd_Conc explained 8.16% to 17.02% of the phenotypic variation. QGr_Cd_Conc-3A, QGr_Cd_Conc-6A, and QGr_Cd_Conc-7A pleiotropically regulated Cd transport; 3 other QTLs were organ-specific for Gr_Cd_Conc. We fine-mapped the locus of QGr_Cd_Conc-4B and identified the candidate gene as Cation/Ca exchanger 2 (TpCCX2-4B), which was differentially expressed in DPW and TPW. It encodes an endoplasmic reticulum membrane/plasma membrane–localized Cd efflux transporter in yeast. Overexpression of TpCCX2-4B reduced Gr_Cd_Conc in rice. The average Gr_Cd_Conc was significantly lower in TpCCX2-4BDPW genotypes than in TpCCX2-4BTPW genotypes of the RIL_DT population and 2 other natural populations, based on a Kompetitive allele-specific PCR marker derived from the different promoter sequences between TpCCX2-4BDPW and TpCCX2-4BTPW. Our study reveals the genetic mechanism of Cd accumulation in wheat and provides valuable resources for genetic improvement of low–Cd-accumulating wheat cultivars.
How does pornography change desires? A pragmatic account
Authors: Lee Junhyo , Neufeld Eleonore 
Published: June 2024

AbstractRae Langton and Caroline West famously argue that pornography operates like a language game, in that it introduces certain views about women into the common ground via presupposition accommodation. While this pragmatic model explains how pornography has the potential to change its viewers’ beliefs, it leaves open how pornography changes people's desires. Our aim in this paper is to show how Langton and West's discourse-theoretic account of pornography can be refined to close this lacuna. Using tools from recent developments in discourse theory, we propose that pornography issues implicit directives, and thereby introduces bouletic components into the discourse.
Falling Interest Rates and Credit Reallocation: Lessons from General Equilibrium
Authors: Asriyan Vladimir , Laeven Luc , Martin Alberto , Van der Ghote Alejandro , Vanasco Victoria 
Published: June 2024

Abstract
We show that in a canonical model with heterogeneous entrepreneurs, financial frictions, and an imperfectly elastic supply of capital, a fall in the interest rate has an ambiguous effect on aggregate economic activity. In partial equilibrium, a lower interest rate raises aggregate investment both by relaxing financial constraints and by prompting relatively less productive entrepreneurs to invest. In general equilibrium, however, this higher demand for capital raises its price and crowds out investment by more productive entrepreneurs. When this reallocation is strong enough, a fall in the interest rate reduces aggregate output. A numerical exploration of the model suggests that this reallocation effect is quantitatively significant and—in response to persistent changes in the interest rate—stronger than the traditional balance-sheet channel. We provide evidence of the reallocation effect using U.S. firm-level data.
Brain regulation training improves emotional competences in patients with alcohol use disorder
Authors: Hack Ramona L , Aigner Martin , Musalek Michael , Crevenna Richard , Konicar Lilian 
Published: June 2024

AbstractAlcohol use disorder (AUD) is defined as the impaired ability to stop or control alcohol use despite adverse social, occupational, or health consequences and still represents one of the biggest challenges for society regarding health conditions, social consequences, and financial costs, including the high relapse rates after traditional alcohol rehabilitation treatment. Especially, the deficient emotional competence in AUD is said to play a key role in the development of AUD and hinders the interruption of substance compulsion, often leading to a viscous circle of relapse. Although the empirical evidence of a neurophysiological basis of AUD is solid and increases even further, clinical interventions based on neurophysiology are still rare for individuals with AUD. This randomized controlled trial investigates changes in emotional competences, alcohol-related cognitions, and drinking behavior before and after an established alcohol rehabilitation treatment (control group: nCG = 29) compared to before and after an optimized, add-on neurofeedback (NF) training (experimental group: nEG = 27). Improvements on the clinical–psychological level, i.e. increases in emotional competences as well as life satisfaction, were found after the experimental electroencephalography (EEG) NF training. Neurophysiological measurements via resting-state EEG indicate decreases in low beta frequency band, while alpha and theta bands remained unaffected.
Toward a Semi-Supervised Learning Approach to Phylogenetic Estimation
Authors: Silvestro Daniele , Latrille Thibault , Salamin Nicolas 
Published: June 2024

Abstract
Models have always been central to inferring molecular evolution and to reconstructing phylogenetic trees. Their use typically involves the development of a mechanistic framework reflecting our understanding of the underlying biological processes, such as nucleotide substitutions, and the estimation of model parameters by maximum likelihood or Bayesian inference. However, deriving and optimizing the likelihood of the data is not always possible under complex evolutionary scenarios or even tractable for large datasets, often leading to unrealistic simplifying assumptions in the fitted models. To overcome this issue, we coupled stochastic simulations of genome evolution with a new supervised deep-learning model to infer key parameters of molecular evolution. Our model is designed to directly analyze multiple sequence alignments and estimate per-site evolutionary rates and divergence without requiring a known phylogenetic tree. The accuracy of our predictions matched that of likelihood-based phylogenetic inference when rate heterogeneity followed a simple gamma distribution, but it strongly exceeded it under more complex patterns of rate variation, such as codon models. Our approach is highly scalable and can be efficiently applied to genomic data, as we showed on a dataset of 26 million nucleotides from the clownfish clade. Our simulations also showed that the integration of per-site rates obtained by deep learning within a Bayesian framework led to significantly more accurate phylogenetic inference, particularly with respect to the estimated branch lengths. We thus propose that future advancements in phylogenetic analysis will benefit from a semi-supervised learning approach that combines deep-learning estimation of substitution rates, which allows for more flexible models of rate variation, and probabilistic inference of the phylogenetic tree, which guarantees interpretability and a rigorous assessment of statistical support.
Impact of Prophylactic Cerclage Location on Femoral Fracture Propagation: A Biomechanical Study
Authors: Han Shuyang , Reddy Kartik I. , Lanfermeijer Nicholas D. , Frangie Robert , Ismaily Sabir K. , Gold Jonathan E. , Lundberg Hannah J. , Rodriguez-Quintana David 
Published: June 2024

OBJECTIVES:
Prophylactic cerclage cables are often placed intraoperatively about a fracture to prevent propagation. However, biomechanical data supporting optimal cable placement location are lacking. The objective of this study was to evaluate the impact of prophylactic cerclage placement location on the propagation of femoral shaft fractures.

METHODS:
The diaphysis of 14 fresh-frozen cadaveric femora were included. Volumetric bone mineral density in the femoral shaft was obtained from quantitative computed tomography scans. For each specimen, a 5-mm longitudinal fracture was created proximally to simulate a pre-existing fracture. After reaming of the femoral canal, a 3 degrees tapered wedge was advanced with an MTS machine at 0.2 mm/s until failure. The tests were conducted with a CoCr cable placed at varying distances (5 mm, 10 mm, 15 mm, 20 mm, and cableless) from the distal tip of the initial fracture. A compression loadcell was used to measure the cable tension during the tests. The axial force, displacement, and cable tension were monitored for comparison between groups.

RESULTS:
In the cableless group, the mean force needed to propagate the fracture was 1017.8 ± 450.3 N. With the addition of a cable at 5 mm below the fracture, the failure force nearly doubled to 1970.4 ± 801.1 N (P < 0.001). This also led to significant increases in stiffness (P = 0.006) and total work (P = 0.001) when compared with the control group. By contrast, in the 15 and 20 mm groups, there were no significant changes in the failure force, stiffness, and total work as compared with the control group (P > 0.05).

CONCLUSIONS:
Propagation of femoral shaft fracture was effectively resisted when a prophylactic cable was placed within 5 mm from the initial fracture, whereas cables placed more than 10 mm below the initial fracture were not effective in preventing fracture propagation.
Revision Rates After Single-Level Cervical Disc Arthroplasty Versus Anterior Cervical Discectomy and Fusion
Authors: Gordon Adam M. , Elali Faisal R. , Saleh Ahmed 
Published: June 2024

Study Design.
A retrospective case-control study.

Objectives.
This study aimed to compare rates and risk factors for all-cause 5-year revisions for patients undergoing primary single-level cervical disc arthroplasty (CDA) versus anterior cervical discectomy and fusion (ACDF).

Summary of Background Data.
Prospective studies have compared patient-reported outcomes, adjacent segment degeneration, and long-term revisions between CDA and ACDF. Despite these high-level evidence studies, well-powered, large investigations have not been adequately reported.

Patients and Methods.
A nationwide database was queried for patients undergoing primary single-level CDA or ACDF for degenerative cervical spine pathology. Further inclusion criteria consisted of patients having a minimum 5-year follow-up. Patients undergoing CDA were in a 1:5 ratio matched to patients undergoing ACDF by age, sex, comorbidities, and overall Elixhauser comorbidity index (ECI). Objectives were to compare the rates and risk factors of all-cause 5-year revisions for those undergoing single-level CDA versus ACDF. Multivariate logistic regression models computed the odds ratios (ORs) of revisions within 5 years. P values of less than 0.001 were significant.

Results.
A total of 32,953 patients underwent single-level CDA (N=5,640) or ACDF (N=27,313) with a 5-year minimum follow-up. The incidence of all-cause revisions within 5 years was 1.24% for CDA and 9.23% for ACDF (P<0.001). After adjustment, patients undergoing single-level ACDF had significantly higher odds of all-cause revisions within 5 years (OR: 8.09; P<0.0001). Additional patient-specific factors associated with revisions were a history of reported drug abuse (OR: 1.51; P<0.0001), depression (OR: 1.23; P<0.0001), cardiac arrhythmias (OR: 1.21; P=0.0008), hypertension (OR: 1.20; P=0.0006), and tobacco use (OR: 1.18; P=0.0003).

Conclusions.
In this study of nearly 33,000 single-level cervical spine surgeries with minimum 5-year follow-up, all-cause revision rates were significantly lower for patients undergoing CDA. Surgeons may use this data to counsel patients regarding 5-year revisions following single-level CDA or ACDF.

Level of Evidence.
III.