bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficacy and Safety of Precision-Guided Transjugular Extrahepatic Portosystemic Shunt (TEPS) in the Management of Cavernous Transformation of the Portal Vein with Portal Hypertension: A Case Series
Authors: Zhang Liu , Zhu Yi-jiang , Wang Xue-qing , Wang Rui-feng , Dong Li , Yin Liang , Lv Wei-fu , Cheng De-lei , Zhou Chun-Ze 
Published: November 2023

Abstract
Background and Aims: Performing a Transjugular intrahepatic portal system shunt (TIPS) in patients with portal vein cavernous transformation (CTPV) poses significant challenges. As an alternative, transjugular extrahepatic portal vein shunt (TEPS) may offer a potential solution for these patients. Nonetheless, the effectiveness and safety of TEPS remain uncertain. This case series study aimed to evaluate the efficacy and safety of TEPS in treating patients with CTPV portal hypertension complications.
Methods:The study encompassed a cohort of twenty-two patients diagnosed with CTPV who underwent TEPS procedures.Of these, thirteen patients manifested recurrent hemorrhagic episodes subsequent to conventional therapies, eight patients grappled with recurrent or refractory ascites, and one patient experienced acute bleeding but refused endoscopic treatment. Comprehensive postoperative monitoring was conducted for all patients to rigorously evaluate both the technical and clinical efficacy of the intervention,as well as long-term outcomes.
Results:The overall procedural success rate among the 22 patients was 95.5% (21/22).During the TEPS procedure, nine patients were guided by percutaneous splenic access, three patients were guided by percutaneous hepatic access, five patients were guided by transmesenteric vein access from the abdomen, and two patients were guided by catheter marking from the hepatic artery. Additionally, guidance for three patients was facilitated by pre-existing TIPS stents.The postoperative portal pressure gradient following TEPS demonstrated a statistically significant decrease compared to preoperative values (24.95±3.19 mmHg vs. 11.48±1.74 mmHg, P<0.01).Although three patients encountered perioperative complications, their conditions ameliorated following symptomatic treatment, and no procedure-related fatalities occurredDuring a median follow-up period of 14 months, spanning a range of 5 to 39 months, we observed four fatalities. Specifically, one death was attributed to hepatocellular carcinoma, while the remaining three were ascribed to chronic liver failure.During the follow-up period, no instances of shunt dysfunction were observed.
Conclusions:Precision-guided TEPS appears to be a safe and efficacious intervention for the management of CTPV.
Site quality for Araucaria angustifolia plantations at subtropical Cambisol is driven by soil organisms' assemblage and the litter and soil compartments
Authors: Souza Tancredo , Dobner Mário , Nascimento Gislaine dos Santos , Silva Lucas Jónatan Rodrigues da 
Published: November 2023

Abstract
Soil quality is a driver for biodiversity enrichment, soil fertility, and soil organic matter dynamics. Different soil quality levels at Araucaria angustifolia plantations may influence the soil organisms, and the interaction between litter and soil compartments by providing habitat and nutrients in different pathways. Our aim was to present a deeper view of the litter-soil compartments, and soil organisms community composition associated with three degrees of site quality (low-, average-, and high-quality sites), which reflect productivity levels, at the highlands of southern Brazil. The non-metric multidimensional scaling (NMDS) grouped the influence of soil quality degrees in three groups considering the dissimilarities on the soil organisms among each other. The ordination of the soil organisms, richness, and Shannon’s diversity in each studied soil quality degree had a stress value of 0.08. The structural equation models indicated that the loss of soil quality showed a negative relationship among soil organisms’ assemblage, and soil-litter compartments. Our results highlighted the importance of considering soil biotic and abiotic attributes for achieving high productivity levels from A. angustifolia plantations within its natural occurrence range.
Recurrent circuits encode visual center-surround computations in the mouse superior colliculus
Authors: Kardamakis Andreas , Cui Peng , Song Kuisong , Mariatos-Metaxas Dimitrios , Isla Arturo , Femenia Teresa , Lazaridis Iakovos , Meletis Konstantinos , Kumar Arvind 
Published: November 2023

Abstract
The interaction of retinal center-surround processes with early visual subcortical and cortical circuits forms the basis for saliency computations. The subcortical circuit mechanisms contributing to surround modulation, however, remain unclear. We developed an optogenetic approach to functionally delineate visual center and surround zones of individual neurons in the superficial layers of the superior colliculus (SCs). We demonstrate that local circuit interactions within the SCs are sufficient to generate visual surround suppression. Notably, surround network activation leads to decreases in center excitation rather than increases in synaptic inhibition. Using a range of complementary methods, we reveal the identity of a SCs-based circuit with two key interacting circuit motifs, recurrent excitation and feedback inhibition, capable of modulating levels of center excitation when the visual surround is active. We propose that subcortical and cortical visual circuits are both recurrent-based and have evolved to independently perform surround modulation, thus enabling parallel saliency computations across multiple levels.
Fractional Hitting Sets for Efficient Multiset Sketching
Authors: ́e Timoth ́e Rouz , Martayan Igor , Marchet Camille , Limasset Antoine 
Published: November 2023

Abstract

The exponential increase in publicly available sequencing data and genomic resources necessitates the development of highly efficient methods for data processing and analysis. Locality-sensitive hashing techniques have successfully transformed large datasets into smaller, more manageable sketches while maintaining comparability using metrics such as Jaccard and containment indices. However, fixed-size sketches encounter difficulties when applied to divergent datasets.
Scalable sketching methods, such as sourmash, provide valuable solutions but still lack resource-efficient, tailored indexing. Our objective is to create lighter sketches with comparable results while enhancing efficiency. We introduce the concept of Fractional Hitting Sets, a generalization of Universal Hitting Sets, which uniformly cover a specified fraction of the k-mer space. In theory and practice, we demonstrate the feasibility of achieving such coverage with simple but highly efficient schemes.
By encoding the covered k-mers as super-k-mers, we provide a space-efficient exact representation that also enables optimized comparisons. Our novel tool, SuperSampler, implements this scheme, and experimental results with real bacterial collections closely match our theoretical findings.
In comparison to sourmash, SuperSampler achieves similar outcomes while utilizing an order of magnitude less space and memory and operating several times faster. This highlights the potential of our approach in addressing the challenges presented by the ever-expanding landscape of genomic data.
SuperSampler is an open-source software and can be accessed at github.com/TimRouze/supersampler. The data required to reproduce the results presented in this manuscript is available at github.com/TimRouze/supersampler/experiments.
Neuronal Glycogen Breakdown Mitigates Tauopathy via Pentose Phosphate Pathway-Mediated Oxidative Stress Reduction
Authors: Kapahi Pankaj , Bar Sudipta , Wilson Kenneth , Hilsabeck Tyler , Alderfer Sydney , Dammer Eric , Burton Jordan , Shah Samah , Holtz Anja , Carrera Enrique , Beck Jennifer , Chen Jackson , Kauwe Grant , Tracy Tara , Seyfried Nicholas , Schilling Birgit , Ellerby Lisa 
Published: November 2023

Abstract
Tauopathies encompass a range of neurodegenerative disorders, such as Alzheimer's disease (AD) and frontotemporal dementia (FTD). Unfortunately, current treatment approaches for tauopathies have yielded limited success, underscoring the pressing need for novel therapeutic strategies. We observed distinct signatures of impaired glycogen metabolism in the Drosophila brain of the tauopathy model and the brain of AD patients, indicating a link between tauopathies and glycogen metabolism. We demonstrate that the breakdown of neuronal glycogen by activating glycogen phosphorylase (GlyP) ameliorates the tauopathy phenotypes in flies and induced pluripotent stem cell (iPSC) derived neurons from FTD patients. We observed that glycogen breakdown redirects the glucose flux to the pentose phosphate pathway to alleviate oxidative stress. Our findings uncover a critical role for increased GlyP activity in mediating the neuroprotection benefit of dietary restriction (DR) through the cAMP-mediated protein kinase A (PKA) activation. Our studies identify impaired glycogen metabolism as a key hallmark for tauopathies and offer a promising therapeutic target in tauopathy treatment.
Non-linear relationship between blood urea nitrogen to albumin (BUN/ALB) ratio and 3-month outcomes with acute ischemic stroke: a second analysis based on a prospective cohort study
Authors: Liu Ren-li , Peng Gang-gang , Zhou Pan , Hu Hao-fei , Deng Zhe 
Published: November 2023

Abstract
Objective
There is still little evidence on the relationship between blood urea nitrogen to albumin (BUN/ALB) ratio and 3-month outcomes in patients with acute ischemic stroke (AIS). Therefore, this study aimed to explore the association between BUN/ALB ratio and 3-month poor outcomes in AIS patients.
Methods
A retrospective study of 1868 AIS participants was conducted in a Korean hospital from January 2010 to December 2016. Binary logistic regression, smooth curve fitting, and subgroup sensitivity analysis were used to analyze the association between BUN/ALB ratio and 3-month poor outcomes.
Results
After adjusting covariates, the results of the binary logistic regression model suggested that the relationship between the BUN/ALB ratio and the risk of 3-month poor outcomes for AIS patients was not statistically significant in model II. However, there was a special nonlinear relationship between them, and the inflection point of the BUN/ALB ratio was 0.326. On the left side of the inflection point, 0.1-unit increase in the BUN/ALB ratio reduces the risk of 3-month poor outcomes by 42% (OR = 0.58, 95% CI: 0.40 to 0.83, P = 0.0033). On the right side of the inflection point, the relationship is not statistically significant.
Conclusion
There is a nonlinear relationship with saturation effect between BUNALB ratio and 3-month poor outcomes in AIS patients. Maintaining a patient's BUN/ALB ratio of around 0.326 can reduce the risk of 3-month poor outcome in AIS patients.
Forecasting the fate of vertically propagating dikes from geodetic data
Authors: Aoki Yosuke 
Published: November 2023

Abstract

Magmas, especially mafic ones, usually intrude into the upper crust as dikes. The intruded dike is often arrested before reaching the surface to make an eruption. Many geophysical observations, including geodetic measurements, have documented dike intrusions and arrests. Also, many theoretical considerations and analog experiments explored the mechanics of dike propagation and arrest. However, insights gained from theoretical considerations, analog experiments, and geophysical observations have yet to be well reconciled. This study attempts to reconcile geodetic measurements with insights gained from theoretical considerations and analog experiments to investigate how to forecast whether an intruded dike results in an eruption or not. This study considers four causes of dike arrests: (1) solidification of the intruded magma, (2) insufficient volume of dike intrusion, (3) negative buoyancy acting on the intruded magma, and (4) stress perturbation near the dike tip by a large earthquake. Then, this study investigates the cause of dike arrests associated with the 1997 and 1998 seismic swarm off the Izu Peninsula, Japan, and the 2015 failed eruption of Sakurajima volcano as an example. This study suggests that the dike intrusions associated with the 1997 and 1998 seismic swarm off the Izu Peninsula are caused by insufficient volume of the intruded dike, the loss of buoyancy acting on the intruded magma, or both. The failed eruption of the 2015 Sakurajima eruption cannot be caused by magma solidification but is most likely by insufficient volume. To investigate the contribution of geodetic data in understanding the cause of dike arrests, it is essential to consider the characteristics of geodetic data. They are: (1) geodetic data constrain the intruded volume and the location relatively well, (2) geodetic data cannot constrain the geometry of the intruded dike very well, (3) an assumption of the host rock as homogeneous halfspace underestimates the depth and volume of the intruded dike. These limitations indicate that geodetic data cannot fully understand the cause of dike arrests. Independent information gained from, for example, the location of dike-induced earthquakes, seismic structures, or density structure from gravity anomalies or muon radiography helps better understand the cause of dike arrests.
Reassessing Human Genetic Diversity in T Cell Studies.
Authors: Scheeren Ferenc , Slieker Roderick , Warmerdam Daniel , Vermeer Maarten , Doorn Remco van , Heemskerk Mirjam 
Published: November 2023

Abstract
The Major Histocompatibility Complex class I (MHC-I) system plays a vital role in immune responses by presenting antigens to T cells. Allele specific technologies, including recombinant MHC-I technologies, have been extensively used in T cell analyses for COVID-19 patients and are currently used in the development of immunotherapies for cancer. However, the immense diversity of MHC-I alleles presents challenges. The genetic diversity serves as the foundation of personalized medicine, yet it also poses a potential risk of exacerbating healthcare disparities based on MHC-I alleles. To assess potential biases, we analyzed (pre)clinical publications focusing on COVID-19 studies and TCR-based clinical trials. Our findings reveal an underrepresentation of MHC-I alleles associated with Asian, Australian and African descent. Ensuring diverse representation is vital for advancing personalized medicine and global healthcare equity, transcending genetic diversity. Addressing this disparity is essential to unlock the full potential of T cells for enhancing diagnosis and treatment across all individuals.
Spontaneous Donor Defects and Voltage–Assisted Hole Doping in Beta-Gallium Oxides under Multiple Epitaxy Conditions
Authors: Luo Guangfu , Nie Chenxi , Liu kai , Ke Chengxuan , Jiang Xisong , He Yifeng , Deng Yonghong , Yan Yanhua 
Published: November 2023

Abstract

Beta-phase gallium oxide (β-Ga2O3) is prone to the spontaneous formation of donor defects but poses a formidable challenge in achieving high-quality p-type doping, mainly due to its exceptionally low valence band maximum (VBM). In this study, we utilize first-principles computations to investigate the origin of spontaneous donor defects in β-Ga2O3 grown by three typical techniques: molecular beam epitaxy (MBE), metal organic chemical vapor deposition (MOCVD), and halide vapor phase epitaxy (HVPE). Our findings elucidate that the primary donor defects vary with the growth techniques, specifically Gai33+ for MBE, Hi2+ for MOCVD, and (2VGa1+Gai2+2VO1)+ for HVPE. Employing a recently developed voltage–assisted doping method, we demonstrate that the dominant spontaneous donors can be significantly reduced accompanied by a noticeable increase in acceptors, leading to a stepwise reduction of Fermi level to 0.54, 0.88, and 2.10 eV above VBM for the MOCVD, HVPE, and MBE methods, and a hole concentration of 4.3 × 1017, 8.7 × 1011, and 2.7 × 10-9 cm-3, respectively, at room temperature without the use of external dopants. By further introducing Mg doping, we identify a strategy that reduces the Fermi level to 0.39 eV above VBM for both the MBE and HVPE experiments, achieving a high hole concentration of ~1020 cm-3 at room temperature. Furthermore, our study uncovers an intriguing phenomenon that defects of identical composition can concurrently exhibit two distinct charge states under specific Fermi levels, as was often overlooked in the conventional understanding.
Study on The Bottom-Type Back Scattering Layer Precursor to The Equatorial Plasma Bubble
Authors: chang qihai , zheng ming , zheng xuanyu , wang xiaomeng , liu yifei , zhang gaosai 
Published: November 2023

Abstract
The bottom-type scattering layer precursor to the equatorial plasma bubble is named by its belt feature in the temporal record of the coherent scattering radar. Its spatial structure is rarely studied and has not been clearly described so far. Through the data observed by the coherent scattering radar and digisonde at Fuke observatory, we argued that the shape of the bottom-type scattering layer in space should be a plasma structure of a quasi-circular cross-section extending along the geomagnetic field with the quasi-static velocity feature. Such a plasma structure along the geomagnetic field line at the F region bottom has the characteristics of a waveguide. Based on this derived result, it’s proposed the possible origination of the equatorial plasma bubble. On the condition that the state of plasma density in the waveguide greater than that of the background reversed, the transverse bipolar electric field of the hybrid electric eigen-mode in the waveguide excited by resonance break out of the boundary, and the equatorial plasma bubble will generate. Electromagnetic disturbances such as Alfven wave and ULF wave etc. may be the source of exciting the hybrid electric eigen-modes of plasma waveguide.
Finite variation sensitivity analysis in the design of isotropic metamaterials through discrete topology optimization
Authors: Cunha Daniel Candeloro , Pavanello Renato 
Published: November 2023

Abstract
This paper extends recently developed Finite Variation Sensitivity Analysis (FVSA) approaches to an inverse homogenization problem. It is stated as a topology optimization problem, which is used to design metamaterials with prescribed mechanical properties. The objective function depends on the homogenized Poisson's ratio, and the homogenized Young's modulus is constrained. A hexagonal base cell, discretized by the finite element method, with dihedral D3 symmetry is used, which results in metamaterials with isotropic properties. Under these conditions, elemental stiffness matrices are not all identical, and each design variable is related to six different elements. The FVSA is suitable for discrete density topology optimization methods, it is used to properly linearize the functions of binary variables, then the optimization problem can be solved through sequential integer linear programming. In this work, novel sensitivity expressions, more accurate than the ones from the mainstream approach in literature, are developed. The obtained improvements are illustrated with numerical examples.
The antimicrobial peptide Abaecin alleviates colitis in mice by regulating inflammatory signaling pathways and intestinal microbial composition
Authors: Liu Zhineng , Qin Xinyun , Nong Keyi , Fang Xin , Zhang Bin , Chen Wanyan , Wang Zihan , Wu Yijia , Shi Huiyu , Wang Xuemei , Liu Youming , Zhang Haiwen 
Published: November 2023

Abstract
Objective
The purpose of this study was to determine the effect of Abaecin on dextran sulfate sodium (DSS) -induced ulcerative colitis in mice and to explore its related mechanisms.
Methods
Twenty-four mice with similar body weight were randomly divided into 4 groups. 2.5% DSS was added to drinking water to induce colitis in mice. Mice were executed after Abaecin administration treatment, and mouse serum and tissues were collected. We measured the concentration of serum inflammatory cytokines in mice and produced colon tissue sections to observe the damage to the colonic structure. Then, we assessed the integrity of the intestinal barrier by the expression of intestinal tight junction proteins. In addition, we determined the phosphorylation levels of NF-κb/MAPK inflammatory signaling pathway proteins and the microbial composition of the intestinal flora to preliminarily investigate the alleviation mechanism of ulcerative colitis by Abaecin.
Results
The results showed that Abaecin significantly alleviated histological damage and intestinal mucosal barrier damage caused by colitis, reduced the concentration of pro-inflammatory cytokines and the phosphorylation of NF-κB / MAPK inflammatory signaling pathway proteins, and improved the composition of intestinal microorganisms.
Conclusion
These findings suggest that Abaecin may have potential prospects for the treatment of ulcerative colitis.
DiZyme: The Ultimate Resource for Nanozyme Multiple Catalytic Activity Prediction
Authors: Vinogradov Vladimir , Razlivina Julia , Dmitrenko Andrei 
Published: November 2023

Abstract
Nanozymes are unique materials with many valuable properties for applications in biomedicine, biosensing, clinical diagnostics, environmental monitoring and beyond. However, it is usually challenging to find new nanozymes. In this work, we developed a machine learning (ML) approach to search for new nanozymes and deployed a web platform DiZyme, featuring a unique database of nanozymes, catalytic activity prediction, data visualization and DiZyme Assistant interface powered by a large language model (LLM). For the first time, we enable prediction of multiple catalytic activities of nanozymes by training an ensemble learning algorithm achieving R2 = 0.75 for the Michaelis-Menten constant and R2 = 0.77 for the maximum velocity. We envision accurate prediction of multi-catalytic activity (peroxidase, oxidase, and catalase) promoting entirely novel applications for a wide range of surface-modified inorganic nanozyme compositions. The DiZyme state-of-the-art database of nanozymes contains 1210 experimental samples with a wide range of compositions and molecular features. The DiZyme Assistant based on the ChatGPT model provides users with supporting information on experimental samples, such as synthesis procedures, measurement protocols, etc. DiZyme (dizyme.aicidlab.itmo.ru) is now openly available worldwide.