bluuebunny/crossref_metadata_2025_split huggingface dataset:
UBE2A and UBE2B are recruited by an atypical E3 ligase module in UBR4
Authors: Barnsby-Greer Lucy , Mabbitt Peter D. , Dery Marc-Andre , Squair Daniel R. , Wood Nicola T. , Lamoliatte Frederic , Lange Sven M. , Virdee Satpal 
Published: January 2024

AbstractUBR4 is a 574 kDa E3 ligase (E3) of the N-degron pathway with roles in neurodevelopment, age-associated muscular atrophy and cancer. The catalytic module that carries out ubiquitin (Ub) transfer remains unknown. Here we identify and characterize a distinct E3 module within human UBR4 consisting of a ‘hemiRING’ zinc finger, a helical-rich UBR zinc-finger interacting (UZI) subdomain, and an N-terminal region that can serve as an affinity factor for the E2 conjugating enzyme (E2). The structure of an E2–E3 complex provides atomic-level insight into the specificity determinants of the hemiRING toward the cognate E2s UBE2A/UBE2B. Via an allosteric mechanism, the UZI subdomain modestly activates the Ub-loaded E2 (E2∼Ub). We propose attenuated activation is complemented by the intrinsically high lysine reactivity of UBE2A, and their cooperation imparts a reactivity profile important for substrate specificity and optimal degradation kinetics. These findings reveal the mechanistic underpinnings of a neuronal N-degron E3, its specific recruitment of UBE2A, and highlight the underappreciated architectural diversity of cross-brace domains with Ub E3 activity.
ModE-RA: a global monthly paleo-reanalysis of the modern era 1421 to 2008
Authors: Valler Veronika , Franke Jörg , Brugnara Yuri , Samakinwa Eric , Hand Ralf , Lundstad Elin , Burgdorf Angela-Maria , Lipfert Laura , Friedman Andrew Ronald , Brönnimann Stefan 
Published: January 2024

AbstractThe Modern Era Reanalysis (ModE-RA) is a global monthly paleo-reanalysis covering the period between 1421 and 2008. To reconstruct past climate fields an offline data assimilation approach is used, blending together information from an ensemble of transient atmospheric model simulations and observations. In the early period, ModE-RA utilizes natural proxies and documentary data, while from the 17th century onward instrumental measurements are also assimilated. The impact of each observation on the reconstruction is stored in the observation feedback archive, which provides additional information on the input data such as preprocessing steps and the regression-based forward models. The monthly resolved reconstructions include estimates of the most important climate fields. Furthermore, we provide a reconstruction, ModE-RAclim, which together with ModE-RA and the model simulations allows to disentangle the role of observations and model forcings. ModE-RA is best suited to study intra-annual to multi-decadal climate variability and to analyze the causes and mechanisms of past extreme climate events.
High-resolution climate projection dataset based on CMIP6 for Peru and Ecuador: BASD-CMIP6-PE
Authors: Fernandez-Palomino Carlos Antonio , Hattermann Fred F. , Krysanova Valentina , Vega-Jácome Fiorella , Menz Christoph , Gleixner Stephanie , Bronstert Axel 
Published: January 2024

AbstractHere, we present BASD-CMIP6-PE, a high-resolution (1d, 10 km) climate dataset for Peru and Ecuador based on the bias-adjusted and statistically downscaled CMIP6 climate projections of 10 GCMs. This dataset includes both historical simulations (1850–2014) and future projections (2015–2100) for precipitation and minimum, mean, and maximum temperature under three Shared Socioeconomic Pathways (SSP1-2.6, SSP3-7.0, and SSP5-8.5). The BASD-CMIP6-PE climate data were generated using the trend-preserving Bias Adjustment and Statistical Downscaling (BASD) method. The BASD performance was evaluated using observational data and through hydrological modeling across Peruvian and Ecuadorian river basins in the historical period. Results demonstrated that BASD significantly reduced biases between CMIP6-GCM simulations and observational data, enhancing long-term statistical representations, including mean and extreme values, and seasonal patterns. Furthermore, the hydrological evaluation highlighted the appropriateness of adjusted GCM simulations for simulating streamflow, including mean, low, and high flows. These findings underscore the reliability of BASD-CMIP6-PE in assessing regional climate change impacts on agriculture, water resources, and hydrological extremes.
DDCNN-F: double decker convolutional neural network 'F' feature fusion as a medical image classification framework
Authors: Veeramani Nirmala , Jayaraman Premaladha , Krishankumar Raghunathan , Ravichandran Kattur Soundarapandian , Gandomi Amir H. 
Published: January 2024

AbstractMelanoma is a severe skin cancer that involves abnormal cell development. This study aims to provide a new feature fusion framework for melanoma classification that includes a novel ‘F’ Flag feature for early detection. This novel ‘F’ indicator efficiently distinguishes benign skin lesions from malignant ones known as melanoma. The article proposes an architecture that is built in a Double Decker Convolutional Neural Network called DDCNN future fusion. The network's deck one, known as a Convolutional Neural Network (CNN), finds difficult-to-classify hairy images using a confidence factor termed the intra-class variance score. These hirsute image samples are combined to form a Baseline Separated Channel (BSC). By eliminating hair and using data augmentation techniques, the BSC is ready for analysis. The network's second deck trains the pre-processed BSC and generates bottleneck features. The bottleneck features are merged with features generated from the ABCDE clinical bio indicators to promote classification accuracy. Different types of classifiers are fed to the resulting hybrid fused features with the novel 'F' Flag feature. The proposed system was trained using the ISIC 2019 and ISIC 2020 datasets to assess its performance. The empirical findings expose that the DDCNN feature fusion strategy for exposing malignant melanoma achieved a specificity of 98.4%, accuracy of 93.75%, precision of 98.56%, and Area Under Curve (AUC) value of 0.98. This study proposes a novel approach that can accurately identify and diagnose fatal skin cancer and outperform other state-of-the-art techniques, which is attributed to the DDCNN ‘F’ Feature fusion framework. Also, this research ascertained improvements in several classifiers when utilising the ‘F’ indicator, resulting in the highest specificity of + 7.34%.
Tuning of liver circadian transcriptome rhythms by thyroid hormone state in male mice
Authors: de Assis Leonardo Vinicius Monteiro , Harder Lisbeth , Lacerda José Thalles , Parsons Rex , Kaehler Meike , Cascorbi Ingolf , Nagel Inga , Rawashdeh Oliver , Mittag Jens , Oster Henrik 
Published: January 2024

AbstractThyroid hormones (THs) are important regulators of systemic energy metabolism. In the liver, they stimulate lipid and cholesterol turnover and increase systemic energy bioavailability. It is still unknown how the TH state interacts with the circadian clock, another important regulator of energy metabolism. We addressed this question using a mouse model of hypothyroidism and performed circadian analyses. Low TH levels decreased locomotor activity, food intake, and body temperature mostly in the active phase. Concurrently, liver transcriptome profiling showed only subtle effects compared to elevated TH conditions. Comparative circadian transcriptome profiling revealed alterations in mesor, amplitude, and phase of transcript levels in the livers of low-TH mice. Genes associated with cholesterol uptake, biosynthesis, and bile acid secretion showed reduced mesor. Increased and decreased cholesterol levels in the serum and liver were identified, respectively. Combining data from low- and high-TH conditions allowed the identification of 516 genes with mesor changes as molecular markers of the liver TH state. We explored these genes and created an expression panel that assesses liver TH state in a time-of-day dependent manner. Our findings suggest that the liver has a low TH action under physiological conditions. Circadian profiling reveals genes as potential markers of liver TH state.
Pregnancy-induced remodeling of the murine reproductive tract: a longitudinal in vivo magnetic resonance imaging study
Authors: Suarez Aileen C. , Gimenez Clara J. , Russell Serena R. , Wang Maosen , Munson Jennifer M. , Myers Kristin M. , Miller Kristin S. , Abramowitch Steven D. , De Vita Raffaella 
Published: January 2024

AbstractMammalian pregnancy requires gradual yet extreme remodeling of the reproductive organs to support the growth of the embryos and their birth. After delivery, the reproductive organs return to their non-pregnant state. As pregnancy has traditionally been understudied, there are many unknowns pertaining to the mechanisms behind this remarkable remodeling and repair process which, when not successful, can lead to pregnancy-related complications such as maternal trauma, pre-term birth, and pelvic floor disorders. This study presents the first longitudinal imaging data that focuses on revealing anatomical alterations of the vagina, cervix, and uterine horns during pregnancy and postpartum using the mouse model. By utilizing advanced magnetic resonance imaging (MRI) technology, T1-weighted and T2-weighted images of the reproductive organs of three mice in their in vivo environment were collected at five time points: non-pregnant, mid-pregnant (gestation day: 9–10), late pregnant (gestation day: 16–17), postpartum (24–72 h after delivery) and three weeks postpartum. Measurements of the vagina, cervix, and uterine horns were taken by analyzing MRI segmentations of these organs. The cross-sectional diameter, length, and volume of the vagina increased in late pregnancy and then returned to non-pregnant values three weeks after delivery. The cross-sectional diameter of the cervix decreased at mid-pregnancy before increasing in late pregnancy. The volume of the cervix peaked at late pregnancy before shortening by 24–72 h postpartum. As expected, the uterus increased in cross-sectional diameter, length, and volume during pregnancy. The uterine horns decreased in size postpartum, ultimately returning to their average non-pregnant size three weeks postpartum. The newly developed methods for acquiring longitudinal in vivo MRI scans of the murine reproductive system can be extended to future studies that evaluate functional and morphological alterations of this system due to pathologies, interventions, and treatments.
A comparative study of language learners’ ICT attitudes and behavior pre- and post-COVID-19
Authors: Habók Anita , Nguyen Lan Anh Thuy 
Published: January 2024

AbstractAlong with the adoption of hybrid teaching and learning modes, the integration of ICT into language instruction in higher education during the COVID-19 pandemic has afforded teachers and students increased opportunities to engage with technology. This quantitative study uses a self-report questionnaire to examine language learners’ attitudes and behavior tied to the role of ICT in learning before and after the COVID-19 pandemic. Firstly, the study confirms the questionnaire’s validity for assessing ICT attitudes and behavior in the Hungarian educational context. Additionally, the measurement invariance and differential item functioning of the assessment tool pre- and post-COVID-19 show that attitudes and the frequency of ICT use remain consistent at both the construct and item levels. Overall, the results demonstrate significant variations between the two student groups in attitudes and behavior tied to the use of ICT tools in language learning. The findings show that the post-COVID-19 group exhibits higher attitudes, and an increased frequency of technology use is observed compared to the pre-COVID-19 period. Furthermore, the study indicates that attitudes before COVID-19 do not strongly influence habitual technology use for language learning, while the opposite is true for the post-COVID-19 period.
Quantifying motor adaptation in a sport-specific table tennis setting
Authors: Carius Daniel , Kaminski Elisabeth , Clauß Martina , Schewe Yannick , Ryk Lenja , Ragert Patrick 
Published: January 2024

AbstractStudies on motor adaptation aim to better understand the remarkable, largely implicit capacity of humans to adjust to changing environmental conditions. So far, this phenomenon has mainly been investigated in highly controlled laboratory setting, allowing only limited conclusions and consequences for everyday life scenarios. Natural movement tasks performed under externally valid conditions would provide important support on the transferability of recent laboratory findings. Therefore, one major goal of the current study was to create and assess a new table tennis paradigm mapping motor adaptation in a more natural and sport-specific setting. High-speed cinematographic measurements were used to determine target accuracy in a motor adaptation table tennis paradigm in 30 right-handed participants. In addition, we investigated if motor adaptation was affected by temporal order of perturbations (serial vs. random practice). In summary, we were able to confirm and reproduce typical motor adaptation effects in a sport-specific setting. We found, according to previous findings, an increase in target errors with perturbation onset that decreased during motor adaptation. Furthermore, we observed an increase in target errors with perturbation offset (after-effect) that decrease subsequently during washout phase. More importantly, this motor adaptation phenomenon did not differ when comparing serial vs. random perturbation conditions.
Combination of high resolution MRI with 3D-printed needle guides for ex vivo myocardial biopsies
Authors: Reiss Simon , Thielmann Julien , Fischer Johannes , Lottner Thomas , Maier Alexander , Westermann Dirk , von zur Mühlen Constantin , Heidt Timo , Bock Michael 
Published: January 2024

AbstractMagnetic resonance imaging (MRI) provides a multitude of techniques to detect and characterize myocardial infarction. To correlate MRI findings with histology, in most cases terminal animal studies are performed; however, precise extraction and spatial correlation of myocardial tissue samples to MRI image data is difficult. In this proof of concept study, we present a 3D-printing technique to facilitate the extraction of tissue samples from myocardial regions. Initially, seven pig hearts embedded in formaldehyde were imaged on a clinical 3 T system to define biopsy targets on high resolution ex vivo images. Magnitude images and R2*-maps acquired with a 3D multi-echo gradient echo sequence and 0.58 mm isotropic resolution were used to create digital models of the cardiac anatomy. Biopsy guides were 3D-printed to steer the extraction of myocardial samples. In total, 61 tissue samples were extracted with an average offset of the tissue sample location from the target location of 0.59 ± 0.36 mm. This offset was not dependent on the distance of the target point to the epicardial surface. Myocardial tissue could be extracted from all samples. The presented method enables extraction of myocardial tissue samples that are selected by ex vivo MRI with submillimeter precision.
Enhanced vegetable production in hydroponic systems using decontamination of closed circulating fluid
Authors: Perez Shirly Lara , Ferro Rafael Basilio , Corrêa Bruna , Casarin Rene , Corrêa Thaila Quatrini , Blanco Kate Cristina , Bagnato Vanderlei Salvador 
Published: January 2024

AbstractWhile plant microorganisms can promote plants by producing natural antibiotics, they can also be vectors for disease transmission. Contamination from plant management practices and the surrounding environment can adversely affect plants, leading to infections and hindered growth due to microbial competition for nutrients. The recirculation of nutrient-rich fluids can facilitate the transport of microorganisms between vegetables in the hydroponic production system. This issue can be addressed through the application of the decontamination method in the hydroponic liquid. Ultraviolet light (UV-C) has been employed for microbiology, and its effects on lettuce were evaluated in this study. This study aims to assess the effectiveness of a decontamination system using UV-C in hydroponic solutions during nutrient recirculation in hydroponics. We evaluated the time required for lettuce plants to reach their maximum height, as well as their pigment content, phenolic compounds, antioxidant capacity, and micro and macronutrient levels. The evaluation was conducted under two photoperiods (18 and 20 hours) in lettuce samples exposed to UV-C in the hydroponic fluid, with control groups not exposed to UV-C. The application of the UV-C decontamination system in hydroponic circulation water containing nutrients accelerated plant growth while maintaining nutritional values equal to or higher than those in the control groups without such a system. The results of microorganism control highlight the potential application of this technique for enhancing and expediting vegetable production. This approach reduces production time and enhances nutrient absorption and the content of certain compounds and minerals.
Nonlinearity association between hyperuricemia and all-cause mortality in patients with chronic kidney disease
Authors: Liu Ya-Fei , Han Liang , Geng Yin-Hong , Wang Huan-Huan , Yan Jia-Hui , Tu Sheng-Hao 
Published: January 2024

AbstractControversy surrounds the role of serum uric acid and whether treatment intervention is favorable in retarding the progression of chronic kidney disease (CKD). The association of serum uric acid levels and CKD patient mortality risk needs to be further determined by large sample cohort studies. The National Health and Nutrition Examination Survey participants with CKD from 1998 to 2017 were enrolled in the study. Multivariable Cox regression models were used to reveal the association of serum uric acid concentrations and CKD mortality risks. A total of 9891 CKD patients were enrolled in the study, and 3698 individuals died during the follow-up. Increasing serum uric acid levels are independently relevant to higher mortality risks of CKD patients (HR per SD increase). A restricted cubic spline curve showed a nonlinear association between serum uric acid and CKD mortality risks (p for nonlinearity = 0.046). CKD patients with higher levels of serum uric acid (≥ 5.900 mg/dL) show a significant increase in mortality risks (HR = 1.102, 95% CI 1.043–1.165). Sensitivity analysis demonstrated that the results were stable and robust. High serum uric acid levels (≥ 5.900 mg/dL) may be associated with increased mortality risks in CKD patients.
Transcriptome-based biomarker prediction for Parkinson’s disease using genome-scale metabolic modeling
Authors: Abdik Ecehan , Çakır Tunahan 
Published: January 2024

AbstractParkinson's disease (PD) is the second most common neurodegenerative disease in the world. Identification of PD biomarkers is crucial for early diagnosis and to develop target-based therapeutic agents. Integrative analysis of genome-scale metabolic models (GEMs) and omics data provides a computational approach for the prediction of metabolite biomarkers. Here, we applied the TIMBR (Transcriptionally Inferred Metabolic Biomarker Response) algorithm and two modified versions of TIMBR to investigate potential metabolite biomarkers for PD. To this end, we mapped thirteen post-mortem PD transcriptome datasets from the substantia nigra region onto Human-GEM. We considered a metabolite as a candidate biomarker if its production was predicted to be more efficient by a TIMBR-family algorithm in control or PD case for the majority of the datasets. Different metrics based on well-known PD-related metabolite alterations, PD-associated pathways, and a list of 25 high-confidence PD metabolite biomarkers compiled from the literature were used to compare the prediction performance of the three algorithms tested. The modified algorithm with the highest prediction power based on the metrics was called TAMBOOR, TrAnscriptome-based Metabolite Biomarkers by On–Off Reactions, which was introduced for the first time in this study. TAMBOOR performed better in terms of capturing well-known pathway alterations and metabolite secretion changes in PD. Therefore, our tool has a strong potential to be used for the prediction of novel diagnostic biomarkers for human diseases.
Continent-island boundary and environment-shaped evolution in the marine amphipod Ampithoe marcuzzii complex (Crustacea: Eumalacostraca: Ampithoidae)
Authors: Iwasa-Arai Tammy , Siqueira Silvana G. L. , Sobral-Souza Thadeu , Leite Fosca P. P. , Andrade Sónia C. S. 
Published: January 2024

AbstractMarine amphipods are crustaceans that lack a larval phase and consequently have low dispersion rates. Despite that, these crustaceans present a remarkable ability to be transported by rafting on natural floating substrata, especially macroalgae, where they find shelter, food and a mating ground. The species Ampithoe marcuzzii is widely distributed throughout the western Atlantic Ocean. Here, it was used as a model to study seascape genomics and phylogeography in invertebrates with low dispersion capacities. We anticipated that the lineages would present isolation-by-distance patterns. However, surface currents and other abiotic variables could facilitate connectivity among distant sites. Based on mitochondrial and nuclear genes, SNPs, and environmental associations, we observed the presence of a species complex within A. marcuzzii, separating mainland and insular populations. Each species showed an independent evolutionary history, with a strong latitudinal population structure and evidence of isolation-by-distance and isolation-by-environment, characterizing the 'continent' species. Historical expansion and environmental variables were observed associated with the southeastern population, and ecological niche modeling corroborated the region as a paleorefuge. Conversely, populations from 'islands' presented complicated evolutionary histories, with closer localities genetically isolated and distant localities connected. These findings indicate that insular populations with low dispersion capacity might be more susceptible to spatial connectivity by floating substrata and to changes in surface currents. In contrast, mainland populations might be more vulnerable to local climate changes due to lack of gene flow.
β-Carboline (FG-7142) modulates fear but not anxiety-like behaviour in zebrafish
Authors: Scatterty Kale R. , Hamilton Trevor J. 
Published: January 2024

AbstractThe β-Carboline FG-7142 is a partial inverse agonist at the benzodiazepine allosteric site on the GABA-A receptor that induces anxiogenic, proconvulsant, and appetite-reducing effects in many species, including humans. Seizure-kindling effects have been well studied, however anxiogenic properties are relatively unexplored. This study aimed to investigate concentration-dependent effects of FG-7142 on anxiety-like behaviour and fear responses in zebrafish (Danio rerio) using the open-field test (OF) and novel object approach test (NOA). A U-shaped distribution was found with maximal responses in increased immobility and reduced distance moved at 10 µM in the NOA but not the OF. Follow up experiments demonstrated a lack of effect in repeated OF testing and no changes in opercular movements. Furthermore, the effect of FG-7142 was reversed with ethanol treatment. These results suggest that FG-7142 elicits a ‘freezing’ response in zebrafish via the introduction of novelty, suggesting fear-induction. These findings indicate that FG-7142 may act as an agent to promote acute fear responses in zebrafish.