bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reduced Branched-Chain Amino Acid Intake Improved High-Fat Diet-Induced Nonalcoholic Fatty Pancreas Disease in Mice
Authors: Lu Jun , Pan Ting , Gao Jie , Cai Xinghua , Zhang Huihui , Sha Wenjun , Lei Tao 
Published: January 2024

Objective
To explore the effects of branched-chain amino acids (BCAAs) on nonalcoholic fatty pancreas disease (NAFPD) and its possible mechanism in high-fat diet (HFD) induced mice.

Materials and Methods
Pancreatic morphology and lipid infiltration was assessed by hematoxylin-eosin staining and immunohistochemistry, and lipid levels in the pancreas were determined using colorimetric enzymatic method. Relevant mechanism was investigated using western blotting and biochemical test.

Results
In HFD-fed mice, dietary BCAAs restriction could attenuate body weight increase, improve glucose metabolism, and reduce excessive lipid accumulation in the pancreas. Furthermore, expression of AMPKα and downstream uncoupling protein 1 were upregulated, while genes related to mammalian target of rapamycin complex 1 (mTORC1) signal pathway and lipid de novo synthesis were suppressed in HFD-BCAA restriction group compared with HFD and HFD-high BCAAs fed mice. In addition, BCAA restriction upregulated expression of BCAAs related metabolic enzymes including PPM1K and BCKDHA, and decreased the levels of BCAAs and branched chain keto acid in the pancreas. However, there was no difference in levels of lipid content in the pancreas and gene expression of AMPKα and mTORC1 between HFD and HFD-high BCAAs groups.

Conclusions
Branched-chain amino acid restriction ameliorated HFD-induced NAFPD in mice by activation of AMPKα pathway and suppression of mTORC1 pathway.
Is it Smoke and Mirrors? Detection of Inferior Vena Cava Thrombus by Focused Cardiac Ultrasound
Authors: Soma Gauthami , DeGuardi John , Iqbal Ammarah U. , Leviter Julie , Riera Antonio 
Published: January 2024

Abstract
Inferior vena cava assessment is a standard component of focused cardiac ultrasound, traditionally used to qualify intravascular volume status. In this case series, we demonstrate that pediatric focused cardiac ultrasound can also diagnose inferior vena cava thrombi and masses, while distinguishing them from a potentially benign smoke-like artifact.
Evaluation of Mandibular Lingual and Foramen Location in Class I, Class II, and Class III Patients and its Significance in Sagittal Split Ramus Osteotomy
Authors: Wang Yu , Zhang Dong , Guo Xiaoshuang , Jin Xiaolei 
Published: January 2024

The precise location of the mandibular lingual (ML) and foramen (MF) is clinically significant because they are crucial anatomic markers for the inferior alveolar nerve protection in sagittal split ramus osteotomy. To determine the position of the ML and MF among subjects with class I, class II, and class III skeletal patterns to obtain information that could be useful for interventions in mandibular ramus. A retrospective study of 324 mandibular ramus from 162 patients was performed to evaluate the distance from the MF to the occlusal plane (OP) and the distance of the ML to the MF, OP, and the margin of the mandible ramus. The MF was more often located below the OP in class III (55.1%), compared with class I (29.0%) and class II (45.3%) patients (P<0.05). The distance from the ML to the MF in skeletal Class III patients (10.15 ± 1.56 mm) was found to be greater than class I (9.25 ± 1.52 mm) and class II (8.34 ± 1.79 mm) patients (P<0.001). And the distance from the ML to the OP was shown to be longer in class III (9.40 ± 2.53 mm) than in class I (6.85 ± 2.55 mm) and class II (6.99 ± 2.53 mm) patients (P<0.001). Therefore, we believe that a low medial horizontal cut at the height of OP is dangerous for Class III patients. And the safe zone for the high medial horizontal cut over the ML should be determined according to the patient’s skeletal patterns.
Treatment Strategy of Intracranial Anterior Circulation Aneurysm Presenting with Cerebral Ischemia: A Single-Center Experience
Authors: Guo Wenqiang , Wang Xingdong , Tong Xiaoguang 
Published: January 2024

Objective:
To investigate the clinical characteristics and treatment strategy of anterior circulation aneurysm presenting with cerebral ischemia.

Methods:
We performed a retrospective review of patients with intracranial anterior circulation aneurysms presenting with cerebral ischemia examined in the Fifth Ward of the Neurosurgery Department of Tianjin Huanhu Hospital between September 2016 and September 2023. Data were reviewed for age, sex, presentation, type and size, location, treatment modalities, postoperative complications, clinical and imaging outcomes, and follow-up outcomes.

Results:
Among the 13 patients, there were 8 males and 5 females (1.6:1). Their presentations included ischemic stroke (69.23%, 9/13) and transient ischemic attack (TIA) (30.77%, 4/13). The aneurysms were dissecting (46.15%, 6/13), saccular (30.77%, 4/13), and saccular combined with thrombosis (23.08%, 3/13) in shape. There were 6 giant aneurysms, 4 large aneurysms, and 3 microaneurysms. Three (23.08%, 3/13) aneurysms were located at the internal carotid artery (ICA) and 10 (76.92%, 10/13) were located in the middle cerebral artery (MCA). A preoperative magnetic resonance perfusion (MRP) examination was performed in all patients, and 9 (69.23%, 9/13) patients showed hypoperfusion. Treatment modalities included stent-assisted embolization, direct clipping, clipping combined with bypass, resection combined with bypass, isolated combined with bypass, proximal occlusion combined with bypass, and the internal carotid artery constriction combined with bypass. Twelve (92.31%, 12/13) patients had no postoperative complications, and temporary complications occurred in 1 (7.69%, 1/13) patient. Aneurysms disappeared in 11 cases and shrank in 2 cases postoperatively. All patients were followed up for 1 to 72 months. We found no new cerebral infarction, no subarachnoid hemorrhage, and no recurrence or enlargement of aneurysms during the follow-up.

Conclusions:
Intracranial anterior circulation aneurysm presenting with cerebral ischemia is rare. Saccular aneurysms with wide neck or thrombosis and dissected aneurysms of the anterior circulation may result in cerebral ischemic attack caused by distal vascular embolism. Individualized treatment should be performed, and cerebral revascularization is an effective treatment for patients with intracranial anterior circulation aneurysms presenting with cerebral ischemia.
mRNA-LNP COVID-19 vaccine lipids induce low level complement activation and production of proinflammatory cytokines: Mechanisms, effects of complement inhibitors, and relevance to adverse reactions
Authors: Bakos Tamás , Mészáros Tamás , Kozma Gergely Tibor , Berényi Petra , Facskó Réka , Farkas Henriette , Dézsi László , Heirman Carlo , de Koker Stefaan , Schiffelers Raymond , Glatter Kathryn Anne , Radovits Tamás , Szénási Gábor , Szebeni János 
Published: January 2024

ABSTRACTMessenger RNA-containing lipid nanoparticles (mRNA-LNPs) enabled widespread COVID-19 vaccination with a small fraction of vaccine recipients displaying acute or sub-acute inflammatory symptoms. The molecular mechanism of these adverse events (AEs) remains undetermined. Here we report that the mRNA-LNP vaccine, Comirnaty, triggers low-level complement (C) activation and production of inflammatory cytokines, which may be key underlying processes of inflammatory AEs. In serum, Comirnaty and the control PEGylated liposome (Doxebo) caused different rises of C split products, C5a, sC5b-9, Bb and C4d, indicating stimulation of the classical pathway of C activation mainly by the liposomes, while a stronger stimulation of the alternative pathway was equal with the vaccine and the liposomes. Spikevax had similar C activation as Comirnaty, but viral or synthetic mRNAs had no such effect. In autologous serum-supplemented peripheral blood mononuclear cell (PBMC) cultures, Comirnaty caused increases in the levels of sC5b-9 and proinflammatory cytokines in the following order: IL-1α < IFN-γ < IL-1β < TNF-α < IL-6 < IL-8, whereas heatinactivation of serum prevented the rises of IL-1α, IL-1β, and TNF-α. Clinical C inhibitors, Soliris and Berinert, suppressed vaccine-induced C activation in serum but did not affect cytokine production when applied individually. These findings suggest that the PEGylated lipid coating of mRNA-LNP nanoparticles can trigger C activation mainly via the alternative pathway, which may be causally related to the induction of some, but not all inflammatory cytokines. While innate immune stimulation is essential for the vaccine’s efficacy, concurrent production of C- and PBMC-derived inflammatory mediators may contribute to some of the AEs. Pharmacological attenuation of harmful cytokine production using C inhibitors likely requires blocking the C cascade at multiple points.
Urbanization of a subtropical island (Okinawa, Japan) alters physicochemical characteristics and disrupts microbial community dynamics in nearshore ecosystems
Authors: Mars Brisbin Margaret , Dudley Kenneth L. , Yonashiro Yoshitaka , Mitarai Satoshi , Ares Angela 
Published: January 2024

AbstractSubtropical and tropical islands are undergoing rapid urbanization as human populations and tourism expand worldwide. Urbanization disrupts coastal ecosystems by replacing forests and other natural habitats with roads, parking lots, and buildings. These impervious surfaces increase the amount of runoff and pollution that reaches coastal ecosystems. Urbanization also comes with increased industry, waste treatment needs, fishing and aquaculture pressure, and coastline engineering. Despite the major changes to coasts that accompany urbanization, specific impacts on marine ecosystems can be difficult to measure due to missing baselines. Here, we take advantage of a large gradient in urbanization on the subtropical island of Okinawa, Japan, to evaluate the impact of urbanization on nearshore ecosystems. We measured physicochemical parameters and assessed bacterial community composition every two weeks for one year at two nearshore sites adjacent to watersheds with >70% urban land use and two nearshore sites adjacent to watersheds with >70% rural land use. Our results show that urbanization increases freshwater input and nutrient loading to nearshore ecosystems and profoundly alters the microbial community, overriding the natural seasonal succession observed at rural sites. At urban sites, we detected multiple bacterial species that are fecal indicators and human or marine organism pathogens. The altered physicochemical conditions and microbial communities at urban sites can contribute to the degradation of nearby coral reefs. Results highlight the importance of a “ridge-to-reef” management mindset, as restoring natural coastlines could buffer the impact of urbanization on the marine environment.
Acoustic Signatures of the Cerrado: Machine Learning Reveals Unique Soundscapes Across Diverse Phytogeographies
Authors: Daleffi da Silva Bruno , Padovese Linilson 
Published: January 2024

ABSTRACTThis article explores the application of machine learning techniques in acoustic ecology to classify the formations of the Brazilian Cerrado (Forest, Savanna, and Grassland) based on their soundscapes. Considering the Cerrado’s importance for biodiversity and hydrology, as well as the challenges faced by the biome in the face of agricultural expansion, the study seeks more efficient and economical methods for identifying its physiognomies.Five statistical models were developed and evaluated, using both traditional Machine Learning and Deep Learning, with the use of Mel-Frequency Cepstral Coefficients (MFCCs) and spectrogram images as input variables. The performance of these models was measured by accuracy, precision, and recall metrics, revealing a superiority of the Convolutional Neural Network (CNN), which, despite requiring greater computational cost and training time, provided high precision in the classifications and valuable insights through the application of the LIME explainability technique.Moreover, the study proposes a majority vote classification methodology for frequently observed events, enabling reliable classifications through models with moderate performance. It is concluded that the choice of the ideal model for the classification of soundscapes of the Cerrado should consider a balance between accuracy, operational complexity, and efficiency. The conclusions of this study offer relevant directions for future research and the application of monitoring technologies in conservation and recovery efforts of biomes.
Differentially polarized macrophages show diverse proangiogenic characteristics under normo- and hyperglycemic conditions
Authors: Shariatzadeh Mahnaz , Payán Gómez César , Dik Willem A. , Leenen Pieter J. M. 
Published: January 2024

AbstractPurposeAngiogenesis is a vital process involved in the formation of new blood vessels from existing ones. Macrophages play a crucial role in initiating endothelial activation and inflammation, and are involved in the pathological angiogenesis. Traditionally, macrophages have been classified, with the pro-angiogenic activity attributed to the M2 phenotype. However, recent evidence challenges the notion that only M2 macrophages possess pro-angiogenic properties. This study aims to investigate the pro- and anti-angiogenic properties of human polarized macrophages in normo- and hyper-glycemic conditions, in order to gain a better insight into the angiogenic capacity of M1- and M2-like macrophages in diabetes.MethodsA comprehensive bioinformatic analysis of pro- and anti-angiogenic gene expression profiles related in M1-vs. M2-polarized macrophages was performed based on a large previously published dataset. The most contributing differentially expressed genes in angiogenesis were selected for further validation. Macrophages were generated and polarized by culturing CD14+monocytes and their stimulation with any of IFN-γ, IL-4, or IL-6 cytokines. Polarized macrophages were immunophenotyped using flow cytometry, and their expression of the selected genes were measured using qPCR. Finally, the proangiogenic capacity of the cells was assessed in anin vitro3-D endothelial tubule formation assay, containing GFP-expressing human retinal endothelial cells, pericytes, and pro-angiogenic growth factors.ResultsIL-4 and IL-6 induce distinct M2-like phenotypes in macrophages with mixed pro- and anti-angiogenic gene expressions. Hyperglycemia has a mild negative effect on the expression of M2-associated markers, however it does not significantly affect the angiogenic properties of macrophages.ConclusionOur data support the concept of a spectrum model for macrophage polarization, indicating that the angiogenic status of polarized macrophages is not limited to the M2-phenotype, but is rather mediated by microenvironmental cues, and can result in diverse phenotypic characteristics. The effect of hyperglycemia on the angiogenic capacity of macrophages requires more comprehensive investigation.
Computational Transcriptomic and Comparative Genomic Analysis of dead box RNA Helicase gene AT2G45810 Expressed in Plants Arabidopsis thaliana
Authors: Emon Mohammed , Hosen Akram , Bhajan Sujay Kumar , Jewel Zilhas Ahmed , Ali Md. Sarafat 
Published: January 2024

AbstractArabidopsis thalianais a short life cycle, small genome, and Brassicaceae family winter annual small flowering plants. It is popularly used as a model organism in genetics and plant biology research, and it is essential to understanding the molecular biology of many plant features, including light sensing and flower formation. It also plays a key role in the science of agronomy, and plant transcriptomics as well as genomics. When it comes to the development of multicellular creatures, transcriptional programs are crucial. The constantly active growth of different organ systems is supported by transcriptional programs. Arabidopsis embryos possess remarkable transcriptomes compared to other plant tissues comprising somatic embryo differentiation circumstances operating during plant embryogenesis. Here we show that the transcriptomic analysis of the genome dead box RNA helicase gene AT2G45810 ofArabidopsis thalianaAraport11 species which revealed the specific gene expression patterns of Arabidopsis tissue-specific information of developmental map, embryo, single cell, DNA damage, cellular interactions, pathway analysis, etc., throughIn Silicoor computational approaches. In this particular study, we used the TAIR, Phytozome, and plant comparative genomics portal for retrieving and identification of specific genes of interest. Next, we used web-based Bar utoronto tools to visualize other data, including functional genomics. Their protein and gene expression tools facilitate the exploration of promoters, the identification of protein-protein interactions, the viewing of expression patterns as electronic fluorescent pictographs or heatmaps, and more.
IOBR2: Multidimensional Decoding Tumor Microenvironment for Immuno-Oncology Research
Authors: Zeng Dongqiang , Fang Yiran , Luo Peng , Qiu Wenjun , Wang Shixiang , Shen Rongfang , Gu Wenchao , Huang Xiatong , Mao Qianqian , Lai Yonghong , Xu Xi , Shi Min , Yu Guangchuang , Liao Wangjun 
Published: January 2024

AbstractThe use of large transcriptome datasets has greatly improved our understanding of the tumor microenvironment (TME) and helped develop precise immunotherapies. The increasing popularity of multi-omics sequencing, single-cell transcriptome sequencing (scRNA), and spatial transcriptome sequencing has led to numerous new discoveries. However, these findings require clinical phenotypic validation with a large sample size. To enhance the integration of multi-omics in advancing research on the tumor microenvironment, we have developed a systematic and comprehensive analytical tool (Immuno-Oncology Biological Research 2, IOBR2) based on our prior work. IOBR2 offers six modules for TME analysis based on multi-omics data. These modules cover data preprocessing, TME estimation, TME infiltrating patterns, cellular interactions, genome and TME interaction, and visualization for TME relevant features, as well as modelling based on key features. IOBR2 integrates multiple vital microenvironmental analysis algorithms and signature estimation methods, simplifying the analysis and downstream visualization of the TME. In addition to providing a quick and easy way to construct gene signatures from single-cell data, IOBR2 also provides a way to construct a reference matrix for TME deconvolution from single-cell RNAseq. The analysis pipeline and feature visualization are user-friendly and provide a comprehensive description of the complex TME, offering insights into tumor-immune interactions. A comprehensive gitbook (https://iobr.github.io/book/) is available with a user-friendly manual and complete analysis workflow for each module.
FLAb: Benchmarking deep learning methods for antibody fitness prediction
Authors: Chungyoun Michael , Ruffolo Jeffrey , Gray Jeffrey 
Published: January 2024

AbstractThe successful application of machine learning in therapeutic antibody design relies heavily on the ability of models to accurately represent the sequence-structure-function landscape, also known as the fitness landscape. Previous protein bench-marks (including The Critical Assessment of Function Annotation [33], Tasks Assessing Protein Embeddings [23], and FLIP [6]) examine fitness and mutational landscapes across many protein families, but they either exclude antibody data or use very little of it. In light of this, we present the Fitness Landscape for Antibodies (FLAb), the largest therapeutic antibody design benchmark to date. FLAb currently encompasses six properties of therapeutic antibodies: (1) expression, (2) thermosta-bility, (3) immunogenicity, (4) aggregation, (5) polyreactivity, and (6) binding affinity. We use FLAb to assess the performance of various widely adopted, pretrained, deep learning models for proteins (IgLM [28], AntiBERTy [26], ProtGPT2 [11], ProGen2 [21], ProteinMPNN [7], and ESM-IF [13]); and compare them to physics-based Rosetta [1]. Overall, no models are able to correlate with all properties or across multiple datasets of similar properties, indicating that more work is needed in prediction of antibody fitness. Additionally, we elucidate how wild type origin, deep learning architecture, training data composition, parameter size, and evolutionary signal affect performance, and we identify which fitness landscapes are more readily captured by each protein model. To promote an expansion on therapeutic antibody design benchmarking, all FLAb data are freely accessible and open for additional contribution athttps://github.com/Graylab/FLAb.
Thermal Tolerance Plasticity and Dynamics of Thermal Tolerance inEublepharis macularius: Implications for Future Climate-Driven Heat Stress
Authors: White Emma , Kim Solyip , Wegh Garrett , Chiari Ylenia 
Published: January 2024

AbstractThe intensity and duration of heat waves, as well as average global temperatures, are expected to increase due to climate change. Heat waves can cause physiological stress and reduce fitness in animals. Species can reduce overheating risk through phenotypic plasticity, which allows them to raise their thermal tolerance limits over time. This mechanism could be important for ectotherms whose body temperatures are directly influenced by available environmental temperatures. Geckos are a large, diverse group of ectotherms that vary in their thermal habitats and times of daily activity, which could affect how they physiologically adjust to heat waves. Data on thermal physiology are scarce for reptiles, with only one study in geckos. Understanding thermal tolerance and plasticity, and their relationship, is essential for understanding how some species are able to adjust or adapt to changing temperatures. In this study, we estimated thermal tolerance and plasticity, and their interaction, in the crepuscular gecko,Eublepharis macularius, a species that is emerging as a model for reptile biology. After estimating basal thermal tolerance for 28 geckos, thermal tolerance was measured for each individual a second time at several timepoints (3, 6, or 24 h) to determine thermal tolerance plasticity. We found that thermal tolerance plasticity (1) does not depend on the basal thermal tolerance of the organism, (2) was highest after 6 hours from initial heat shock, and (3) was negatively influenced by individual body mass. Our findings contribute to the increasing body of work focused on understanding the influence of biological and environmental factors on thermal tolerance plasticity in organisms and provide phenotypic data to further investigate the molecular basis of thermal tolerance plasticity in organisms.