bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ubiquitin-specific protease 25 ameliorates ulcerative colitis by regulating the degradation of phosphor-STAT3
Authors: Liu Zhengru , Liu Jian , Wei Yuping , Li Jinting , Zhang Jixiang , Yu Rong , Yang Qian , Miao Yinglei , Dong Weiguo 
Published: January 2025

AbstractUbiquitin-specific protease 25 (USP25), a member of the deubiquitination family, plays an important role in protein ubiquitination, degradation, inflammation, and immune regulation. However, the role and mechanism of USP25 in ulcerative colitis (UC) remain unclear. To study the role and mechanism of USP25 in UC, bioinformatics analysis and research are conducted on clinical patients with UC, Usp25 knockout (Usp25−/−) mice, intestinal epithelial cell-specific knockout signal transducer and activator of transcription 3 (Stat3) (Villin-Cre Stat3fl/fl) mice, and human colonic epithelial cells. Results show that the expression of USP25 is decreased in patients with UC and mice with dextran sulfate sodium salt (DSS)-induced colitis and that USP25 deficiency exacerbates UC by destroying the intestinal mucosal barrier, however, overexpression of USP25 can alleviate colitis. Mechanistically, USP25 reduces the degradation of phosphor-STAT3Y705 at lysine 409 by catalyzing K48-linked deubiquitination. Further, this study demonstrates the aggravation of DSS-induced colitis by intestinal epithelial cell-specific knockout Stat3 in mice, while Stat3 overexpression by adeno-associated virus attenuates colitis in DSS-induced Usp25−/− mice. Together, these results showed that USP25 ameliorates UC by regulating the degradation of phosphor-STAT3. Collectively, USP25 is a specific STAT3 regulator that can be targeted in UC.
Roles of immunoglobulin GM and KM allotypes and Fcγ receptor 2 A genotypes in humoral immunity to a conserved microbial polysaccharide in pulmonary diseases
Authors: Pandey Janardan P. , Nietert Paul J. , Namboodiri Aryan M. , Kimball Christine , Flume Patrick A. 
Published: January 2025

AbstractImmunoglobulin GM (γ marker) and KM (κ marker) allotypes—encoded by immunoglobulin heavy chain G (IGHG) and immunoglobulin κ constant (IGKC) genes—have been shown to be associated with immune responsiveness to a variety of self and nonself antigens. The aim of the present investigation was to determine whether allelic variation at the GM and KM loci was associated with antibody responsiveness to poly-N-acetyl-D-glucosamine (PNAG), a broadly-conserved surface polysaccharide expressed by many microbial pathogens. In addition, we wished to determine whether Fcγ receptor 2 A (FCGR2A) genotypes, which have been shown to be risk factors for some pathogens, also influenced antibody responses to PNAG. DNA from 257 patients with various pulmonary diseases (PD) was genotyped for several GM, KM, and FCGR2A alleles, and plasma were characterized for anti-PNAG IgG antibodies. The levels of IgG4 antibodies to PNAG were associated with FCGR2A genotypes (p = 0.01). Also, KM and FCGR2A alleles epistatically contributed to anti-PNAG IgG3 antibody responses: subjects with KM 1/1 or KM 1/3 and homozygous for the R allele of FCGR2A had the highest levels of anti-PNAG IgG3 antibodies compared to all other genotype combinations. If confirmed by larger studies, these results are potentially relevant to immunotherapy against many PNAG-expressing infectious pathogens.
MPicker: visualizing and picking membrane proteins for cryo-electron tomography
Authors: Yan Xiaofeng , Li Shudong , Huang Weilin , Wang Hao , Zhao Tianfang , Huang Mingtao , Zhou Niyun , Shen Yuan , Li Xueming 
Published: January 2025

AbstractAdvancements in cryo-electron tomography (cryoET) allow the structure of macromolecules to be determined in situ, which is crucial for studying membrane protein structures and their interactions in the cellular environment. However, membranes are often highly curved and have a strong contrast in cryoET tomograms, which masks the signals from membrane proteins. These factors pose difficulties in observing and revealing the structures of membrane proteins in situ. Here, we report a membrane-flattening method and the corresponding software, MPicker, designed for the visualization, localization, and orientation determination of membrane proteins in cryoET tomograms. This method improves the visualization of proteins on and around membranes by generating a flattened tomogram that eliminates membrane curvature and reduces the spatial complexity of membrane protein analysis. In MPicker, we integrated approaches for automated particle picking and coarse alignment of membrane proteins for sub-tomogram averaging. MPicker was tested on tomograms of various cells to evaluate the method for visualizing, picking, and analyzing membrane proteins.
Brainstem serotonin amplifies nociceptive transmission in a mouse model of Parkinson’s disease
Authors: Grivet Zoé , Aby Franck , Verboven Aude , Bouali-Benazzouz Rabia , Sueur Benjamin , Maingret François , Naudet Frédéric , Dhellemmes Thibault , De Deurwaerdere Philippe , Benazzouz Abdelhamid , Fossat Pascal 
Published: January 2025

AbstractParkinson’s disease arises from the degeneration of dopaminergic neurons in the substantia nigra pars compacta, leading to motor symptoms such as akinesia, rigidity, and tremor at rest. The non-motor component of Parkinson’s disease includes increased neuropathic pain, the prevalence of which is 4 to 5 times higher than the general rate. By studying a mouse model of Parkinson’s disease induced by 6-hydroxydopamine, we assessed the impact of dopamine depletion on pain modulation. Mice exhibited mechanical hypersensitivity associated with hyperexcitability of neurons in the dorsal horn of the spinal cord (DHSC). Serotonin (5-HT) levels increased in the spinal cord, correlating with reduced tyrosine hydroxylase (TH) immunoreactivity in the nucleus raphe magnus (NRM) and increased excitability of 5-HT neurons. Selective optogenetic inhibition of 5-HT neurons attenuated mechanical hypersensitivity and reduced DHSC hyperexcitability. In addition, the blockade of 5-HT2A and 5-HT3 receptors reduced mechanical hypersensitivity. These results reveal, for the first time, that PD-like dopamine depletion triggers spinal-mediated mechanical hypersensitivity, associated with serotonergic hyperactivity in the NRM, opening up new therapeutic avenues for Parkinson’s disease-associated pain targeting the serotonergic systems.
Bathymetry of the Antarctic continental shelf and ice shelf cavities from circumpolar gravity anomalies and other data
Authors: Charrassin Raphaelle , Millan Romain , Rignot Eric , Scheinert Mirko 
Published: January 2025

AbstractBathymetry critically influences the intrusion of warm Circumpolar Deep Water onto the continental shelf and under ice shelf cavities in Antarctica, thereby forcing ice melting, grounding line retreat, and sea level rise. We present a novel and comprehensive bathymetry of Antarctica that includes all ice shelf cavities and previously unmeasured continental shelf areas. The new bathymetry is based on a 3D inversion of a circumpolar compilation of gravity anomalies constrained by measurements from the International Bathymetric Chart of the Southern Ocean, BedMachine Antarctica, and discrete seafloor measurements from seismic and ocean robotic probes. Previously unknown troughs with thicker ice shelf cavities are revealed in many parts of Antarctica, especially East Antarctica. The greater depths of troughs on the continental shelf and ice shelf cavities imply that many glaciers are more vulnerable to ocean subsurface warming than previously thought, which may increase the projections of sea level rise from Antarctica.
Improving model performance in mapping black-soil resource with machine learning methods and multispectral features
Authors: Hu Jianfang , Tang Yulei , Yan Jiapan , Zhang Jiahong , Zhao Yuxin , Chen Zhansheng 
Published: January 2025

AbstractAccurate information on the distribution of regional black-soil resource is one of the important elements for the sustainable management of soils. And its results can provide decision makers with robust data that can be translated into better decision making. This study utilized all Sentinel-2 images covering the study area from April to July in 2022. After masking clouds, all images were synthesized monthly. Based on the revised random forest classification algorithm, model performance using different feature combination programs were evaluated to search for an efficient, high-precision method for mapping black-soil resource. The impact on model performance of adding data from temperature, precipitation and slope geographic covariates was analyzed. And the robustness of the model was verified using Landsat-8 data with lower spatial resolution. The results showed that (1) the model based on multi-temporal ensemble features for mapping black-soil resource shows the best performance, with an OA of 94.6%; (2) adding temperature covariate can effectively improve the accuracy of black-soil resource mapping; (3) compared to the sentinel data, the performance of the model based on Landsat-8 data is reduced but still plausible, verifying the robustness of the model. This study provides a robust method to improve model performance for rapid mapping of black-soil resource.
Wavefront-aberration-tolerant diffractive deep neural networks using volume holographic optical elements
Authors: Hoshi Ikuo , Wakunami Koki , Ichihashi Yasuyuki , Oi Ryutaro 
Published: January 2025

AbstractAs the demand for computational performance in artificial intelligence (AI) continues to increase, diffractive deep neural networks (D2NNs), which can perform AI computing at the speed of light by repeated optical modulation with diffractive optical elements (DOEs), are attracting attention. DOEs are varied in terms of fabrication methods and materials, and among them, volume holographic optical elements (vHOEs) have unique features such as high selectivity and multiplex recordability for wavelength and angle. However, when those are used for D2NNs, they suffer from unknown wavefront aberrations compounded by multiple fabrication errors. Here, we propose a training method to adapt the model to be unknown wavefront aberrations and demonstrate a D2NN using vHOEs. As a result, the proposed method improved the classification accuracy by approximately 58 percentage points in the optical experiment, with the model trained to classify handwritten digits. The achievement of this study can be extended to the D2NN that enables the independent modulation of multiple wavelengths owing to their wavelength selectivity and wavelength division multiplex recordability. Therefore, it might be promising for various applications that require multiple wavelengths in parallel optical computing, bioimaging, and optical communication.
Prediction of white matter hyperintensities evolution one-year post-stroke from a single-point brain MRI and stroke lesions information
Authors: Rachmadi Muhammad Febrian , Valdés-Hernández Maria del C. , Makin Stephen , Wardlaw Joanna , Skibbe Henrik 
Published: January 2025

AbstractPredicting the evolution of white matter hyperintensities (WMH), a common feature in brain magnetic resonance imaging (MRI) scans of older adults (i.e., whether WMH will grow, remain stable, or shrink with time) is important for personalised therapeutic interventions. However, this task is difficult mainly due to the myriad of vascular risk factors and comorbidities that influence it, and the low specificity and sensitivity of the image intensities and textures alone for predicting WMH evolution. Given the predominantly vascular nature of WMH, in this study, we evaluate the impact of incorporating stroke lesion information to a probabilistic deep learning model to predict the evolution of WMH 1-year after the baseline image acquisition, taken soon after a mild stroke event, using T2-FLAIR brain MRI. The Probabilistic U-Net was chosen for this study due to its capability of simulating and quantifying the uncertainties involved in the prediction of WMH evolution. We propose to use an additional loss called volume loss to train our model, and incorporate stroke lesions information, an influential factor in WMH evolution. Our experiments showed that jointly segmenting the disease evolution map (DEM) of WMH and stroke lesions, improved the accuracy of the DEM representing WMH evolution. The combination of introducing the volume loss and joint segmentation of DEM of WMH and stroke lesions outperformed other model configurations with mean volumetric absolute error of 0.0092 ml (down from 1.7739 ml) and 0.47% improvement on average Dice similarity coefficient in shrinking, growing and stable WMH.
Vertical wind profile distribution within canopy layer based on representative geometry model using wind tunnel experiment
Authors: Zaki S. A. , H’ng Y. M. , Mohammad A. F. , Ardila‑Rey Jorge Alfredo , Alam Noor , Ahmad Mardiana Idayu 
Published: January 2025

AbstractThis study examined the mean and turbulent wind speed distribution within the canopy height of a tropical urban campus based on a representative geometry model via wind tunnel experiments. The vertical wind profiles were analysed around two high-rise buildings, Menara Razak (MR) and Residensi Tower (RT) at both wind directions (22.5° and 202.5°). To examine the influence of high-rise buildings on strong wind, the collected data of mean wind speed (u), root mean square (urms), and skewness (SK) were analysed. Effects of the wind direction, building layout or arrangement and building geometry under the canopy height were also examined. The results show that the building layout influenced the wind distribution within the target site, and the approaching wind flow direction also influenced the wind flow interaction with the building. The height of the target building (H) influenced the distance traveled by the vortices in the wake flow. For the MR and RT cases, the vortices could be affected up to a minimum distance of H and 1.5H, respectively. The study demonstrates that the building layout significantly influences the distribution of wind speeds within the canopy height of a tropical urban campus.
A novel approach to assess acid diversion efficiency in horizontal wells
Authors: Almalichy Abdulameer , Aljawad Murtada Saleh , Turzo Zoltan , Al-Yaseri Ahmed 
Published: January 2025

AbstractUsing an acid to stimulate a heterogeneous carbonate reservoir during matrix acidizing may lead to over-treating the high permeability zones, leaving low permeability zones untreated. This is particularly exacerbated in long horizontal sections, necessitating the use of acid diverters for effective acid distribution across the formation. In previous studies, conventional core flooding systems were utilized where single inlet and outlet lines were used or, at best, two outlet lines for dual-core flooding. This paper proposes a new method for simulating matrix acidizing in horizontal wells by introducing five injection points and two outlet lines. The injection points are perpendicular to the core samples to simulate multiple perforations in a horizontal well while the outlet lines are parallel. Four experiments were conducted in this study using Indiana limestone cores that were 1.5 inches in diameter. For the first three tests, the length of the core was 12 inches, and the cores’ average permeabilities were 16 mD. For the fourth one, two 6-inch length cores with different average permeability (10 and 50 mD) were employed. Hydrochloric acid was used in the first experiment, while hydrochloric acid with viscoelastic surfactant (VES) was used in subsequent experiments. To the best of our knowledge, this is the first study to introduce a multi-point injection system with enhanced coverage and distribution, resulting in a more precise representation of acidizing a horizontal well.
Examining the effect of personality on user acceptance of conditionally automated vehicles
Authors: Nordhoff S. , Lehtonen E. 
Published: January 2025

AbstractAutomated vehicle acceptance (AVA) research has grown substantially in the past few years. There is a paucity of research on the role of the big five personality traits on attitudes towards automated vehicles (AVs) and AVA. This is a critical shortcoming given that personality is considered a critical factor explaining technology adoption. Our major theoretical contribution is the integration of the most popular personality measure – the big five – and one of the most influential technology acceptance models – Unified Theory of Acceptance and Use of Technology (UTAUT2). A questionnaire was administered to 9,339 respondents from nine countries to predict the behavioral intention to use conditionally automated vehicles (CondAVs). The original UTAUT2 was extended by trust and driver engagement and the big five personality traits openness, conscientiousness, extraversion, agreeableness, and neuroticism. Structural equation modeling was applied to examine the direct effects of these constructs on behavioral intention and the indirect effects of the personality traits on the independent constructs of the extended UTAUT2. The results have shown positive effects of social influence, trust, and performance expectancy on the behavioral intention to use CondAVs. Most of the hypotheses pertaining to the role of the personality traits on the UTAUT2 constructs were supported, but the effects were relatively small (< 0.25). Our findings support the usefulness of UTAUT2 in evaluating the success of AVs, providing crucial insights into the factors driving the acceptance of CondAVs. The cross-country analysis provides further insights into the role of an individual’s personality for AVA. Our study yields important implications for practitioners. Given the small effect sizes of personality, designing CondAVs around the personalities of their customers during development and commercialization may be ineffective to promote trust and acceptance.
The assessment of chemical composition and biological activity of faba bean pods as a potential feed additive utilized in piglets nutrition
Authors: Vlasova Inna , Krüsselmann Philip , Kostenko Yuliia , Obrębski Maciej , Granica Sebastian , Vahjen Wilfried , Zentek Jürgen , Równicki Marcin , Piwowarski Jakub P. 
Published: January 2025

AbstractThe study addresses the utilization of food waste by-products from faba bean (Vicia faba L.) pods (FBP) as an alternative feed supplement to promote sustainable piglet growth by reducing antimicrobial use. Objectives include evaluation of FBP in terms of nutritional components (proximate composition, fibres, minerals), phytochemical composition (total phenols, HPLC-MS profiling), and in vitro biological activities. Air-dried FBP from the cultivar ‘Bizon’ contained high levels of crude protein (144 g/kg), dietary fibre (413 g/kg), potassium (27.8 g/kg), and iron (126 mg/kg). Phytochemical analysis of methanolic extract from FBP revealed significant levels of polyphenols, including vestitol, piscidic acid, hydroxyeucomic acid, quercetin, and kaempferol glycosides with no detectable tannins. The extract showed negligible activity against porcine digestive enzymes (α-amylase, lipase, and trypsin) (IC50 > 4 mg/mL) and demonstrated a dose-dependent antibacterial activity against Escherichia coli and Salmonella enterica in concentrations of 1–8 mg/mL. The extract had low cytotoxicity (IC50 = 432.6 µg/mL) against IPEC-J2 – cells derived from porcine jejunal epithelium. The results indicate that FBP ‘Bizon’ is a valuable source of bioactive compounds with antibacterial properties, without adverse effects on porcine enzymes or IPEC-J2 cells, supporting its potential as a sustainable feed in piglet nutrition, in line with circular economy concepts.
Inosine monophosphate dehydrogenase 2 (IMPDH2) modulates response to therapy and chemo-resistance in triple negative breast cancer
Authors: da Silva Fernandes Tatiane , Gillard Bryan M. , Dai Tao , Martin Jeffrey C. , Chaudhry Kanita A. , Dugas Scott M. , Fisher Alyssa A. , Sharma Pia , Wu RongRong , Attwood Kristopher M. , Dasgupta Subhamoy , Takabe Kazuaki , Rosario Spencer R. , Bianchi-Smiraglia Anna 
Published: January 2025

AbstractTriple negative breast cancer (TNBC) is one of the deadliest subtypes of breast cancer, whose high frequency of relapse is often due to resistance to chemotherapy. Here, we identify inosine monophosphate dehydrogenase 2 (IMPDH2) as a contributor to doxorubicin resistance, in multiple TNBC models. Analysis of publicly available datasets reveals elevated IMPDH2 expression to associate with worse overall TNBC prognosis in the clinic, including lower recurrence-free survival post adjuvant/neoadjuvant therapy. Importantly, both genetic depletion and pharmacological inhibition of IMPDH2 leads to reduction of pro-tumorigenic phenotypes in multiple doxorubicin-resistant TNBC models, both in vitro and in vivo. Overall, we propose IMPDH2 as a novel vulnerability that could be leveraged therapeutically to suppress and/or prevent the growth of chemo-resistant lesions.
Worse survival of hepatocellular cancer patients with membranous insulin receptor overexpression
Authors: Heckl Steffen Markus , Schneider Carolin , Kercher Lukas , Behrens Hans-Michael , Gundlach Jan-Paul , Bernsmeier Alexander , Schmidt Stephan , Krüger Sandra , Braun Felix , Günther Rainer , Becker Thomas , Schreiber Stefan , Röcken Christoph 
Published: January 2025

AbstractHepatocellular cancer (HCC) therapy is in need for an ideal companion diagnostic. Preclinical experimental studies have identified the insulin receptor (IR) and its synergistic counterpart, the IGF1 receptor (IGF1R), as relevant in HCC development, and the ligands IGF1 and IGF2 have been found to be elevated in HCC. This study aimed to bridge the gap to the clinical setting and explore whether the IR or the IGF1R would be of prognostic significance and would be associated with clinicopathologic parameters in HCC patients. In our retrospective cohort study located at the University Hospital Schleswig-Holstein, Campus Kiel, Germany, HCC samples of 139 patients were examined for IR and IGF1R expression by immunohistochemistry. A HistoScore was correlated with clinicopathological characteristics and survival. IR overexpression was frequently observed and was associated with clinicopathological parameters and survival. Membranous IR expression was associated with worse tumor specific survival (p = 0.043). Intriguingly, membranous IR expression was associated with worse tumor specific survival (p = 0.017) in the subgroup of patients undergoing sorafenib therapy. IGF1R expression was not associated with survival. In conclusion, our results suggest that membranous IR expression plays a role in HCC prognosis and treatment resistance, inspiring future validation as a potential companion diagnostic in HCC.
Systemic lupus erythematosus is associated with an increased risk of cervical artery dissection
Authors: Trager Robert J. , Lynn Benjamin P. , Baumann Anthony N. , Chu Eric Chun-Pu 
Published: January 2025

AbstractLimited evidence suggests that autoimmune diseases are associated with an increased risk of cervical artery dissection (CeAD). We hypothesized individuals with systemic lupus erythematosus (SLE) would have an increased risk of CeAD following SLE diagnosis compared to matched non-lupus controls. We queried a de-identified United States electronic medical records network (TriNetX, Inc.) for individuals aged 10 and older from 2012 to 2020, for two cohorts: (1) SLE and (2) non-lupus controls, excluding those with prior CeAD. We used propensity matching to control for confounding variables and calculated the risk ratio (RR) for CeAD occurring over four years’ follow-up, secondarily exploring cumulative incidence. After matching, both cohorts contained 77,008 patients, who were mostly female (89%). The incidence and risk of CeAD was significantly greater among those with SLE compared to matched non-lupus controls [95% CI] (0.08% vs. 0.04%; RR = 2.33 [1.49;3.66]; P < 0.0001). These findings support the hypothesis that SLE is a risk factor for CeAD. Additional research is needed to identify the mechanisms that may underly the SLE-CeAD association and examine the potential association between other autoimmune diseases and CeAD.