bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of hap2 deletion on mnp/vp transcription in Pleurotus ostreatus grown on lignocellulosic substrates
Authors: Kayama Keita , Nakazawa Takehito , Yamaguchi Iori , Kawauchi Moriyuki , Sakamoto Masahiro , Honda Yoichi 
Published: November 2024

Abstract
The regulatory mechanisms governing expression of genes encoding lignin-modifying enzymes (LME) in white-rot fungi remain largely unexplored. Although molecular cloning has identified CCAAT-boxes frequently located 5′-upstream of these genes, their role in transcriptional regulation is not well understood. This study examines the function of hap2, a gene encoding a hypothetical protein homologous to a component of the CCAAT-binding Hap complex, in the white-rot fungus Pleurotus ostreatus. Deletion of hap2 resulted in significantly reduced Mn2+-dependent peroxidase activity and lignin-degrading capacity compared to the parental strain 20b grown on beech wood sawdust (BWS) medium. Real-time PCR revealed that vp2 transcript levels were significantly lower in hap2 deletants than in 20b grown when cultured on the three solid media consisting of BWS, holocellulose, or Avicel, but not on yeast-malt-glucose (YMG) agar plates. Additionally, glutathione S-transferase (GST) pulldown and electrophoretic mobility shift assays demonstrated that recombinant P. ostreatus Hap2, Hap3, and Hap5 expressed in Escherichia coli form a complex capable of binding to the CCAAT sequence 5′-upstream of vp2 in vitro. These results suggest that Hap2, as part of the CCAAT-binding complex, is essential for transcriptional upregulation of vp2 in P. ostreatus growing on lignocellulosic substrates.

Key points
• P. ostreatus hap2 deletants were generated.
• Lignin-degrading capacity was significantly reduced in the hap2 deletants.
• vp2 was significantly downregulated upon hap2 deletion.
Overcoming immunosuppression in cancer: how ketogenic diets boost immune checkpoint blockade
Authors: Stefan Victoria E. , Weber Daniela D. , Lang Roland , Kofler Barbara 
Published: November 2024

Abstract
Immune checkpoint blockade (ICB) is now part of the standard of care in the treatment of many forms of cancer, yet it lacks efficacy in some patients, necessitating adjunct therapies to support the anti-tumor immune response. Ketogenic diets (KDs), i.e., high-fat low-carbohydrate diets, have been shown to have antiproliferative and immunomodulatory effects in various preclinical cancer studies. Here, we review current knowledge of the complex interplay of KDs and the anti-tumor immune response in the context of ICB therapy, to update our understanding of diet-induced immunometabolic reprogramming in cancer. Preclinical cancer studies have revealed increased activation of and infiltration by tumor-fighting immune cells, especially CD8+ T cells, but also M1 macrophages and natural killer cells, in response to a KD regimen. In contrast, immune-suppressive cells such as regulatory CD4+ T lymphocytes, M2 macrophages, and myeloid-derived suppressor cells were reported to be decreased or largely unaffected in tumors of KD-fed mice. KDs also showed synergism with ICB therapy in several preclinical tumor studies. The observed effects are ascribed to the ability of KDs to improve immune cell infiltration and induce downregulation of immune-inhibitory processes, thus creating a more immunogenic tumor microenvironment. The studies reviewed herein show that altering the metabolic composition of the tumor microenvironment by a KD can boost the anti-tumor immune response and diminish even immunotherapy-resistant as well as immunologically "cold" tumors. However, the exact underlying mechanisms remain to be elucidated, requiring further studies before KDs can be successfully implemented as an adjunct tumor therapy to improve survival rates for cancer patients.
Leveraging homologous recombination deficiency for sarcoma
Authors: Planas-Paz Lara , Pauli Chantal 
Published: November 2024

Abstract
Background
Homologous recombination deficiency (HRD) in tumors correlates with poor prognosis and metastases development. Determining HRD is of major clinical relevance as it can be treated with PARP inhibitors (PARPi). HRD remains poorly investigated in sarcoma, a rare and heterogeneous cancer of mesenchymal origin.

Objective
We aimed (i) to investigate predictive biomarkers of HRD in several independent sarcoma cohorts using a cross-functional strategy by combining genomic, transcriptomic and phenotypic approaches and (ii) to evaluate the therapeutic potential of PARPi and DNA damage response (DDR)-based therapies ex vivo.

Materials and methods
We performed a comprehensive genomic and transcriptomic characterization of sarcoma using datasets from The Cancer Genome Atlas (TCGA) and Therapeutically Applicable Research to Generate Effective Treatments (TARGET), and our own bone and soft tissue sarcoma cohorts. We evaluated PARP1/2 and WEE1 inhibition ex vivo in patient-derived sarcoma cell models as monotherapy and in combination with chemotherapeutic agents to identify synergistic effects.

Results
Firstly, we identified genomic traits of HRD in a subset of sarcomas associated with molecular alterations in homologous recombination repair (HRR) pathway genes and high chromosomal instability. Secondly, we identified and validated distinct SARC-HRD transcriptional signatures that predicted sensitivity to PARPi. Finally, we showed functional defects in HRR in sarcoma cells that were associated with functional dependency towards PARPi and WEE1i and support the clinical use of RAD51 as a predictive biomarker for PARPi sensitivity.

Conclusion
We provide a personalized oncological approach to potentially improve the treatment of sarcoma patients. We encourage the evaluation of gene expression signatures to enhance the identification of patients who might benefit from DDR-based therapies.
Neutron tomography studies of buddhist bronze sculptures
Authors: Lehmann Eberhard H. , Mannes David , Speidel Markus 
Published: November 2024

AbstractWe have developed neutron tomography as a new tool to study the interior of ancient works of art. The present paper details the principles of the method and summarizes also some of the latest results, particularly concerning Mongolian Buddhist statues of the 17./18th century. It is shown that offering deposits made of organic and ceramic materials, even when fully enclosed in a cast metallic statue, can be examined in a non-invasive way. Within certain limits this concerns composition, size, structure and position of the interior deposits. Such studies can contribute to understand the history of ritual practices and their goals. They can also contribute to evaluate whether a statue has been properly cleaned and filled during consecration and is therefore fit for religious service. Such studies can also help to form an opinion of whether a statue is genuine.
Risk factors for wound complications after associating liver partition and portal vein ligation for staged hepatectomy (ALPPS) compared to repeated liver resection - a propensity score matching analysis
Authors: Khajeh Elias , Sabetkish Nastaran , Ramouz Ali , Werba Alexander , Klotz Rosa , Michalski Christoph W. , Mehrabi Arianeb , Pianka Frank 
Published: November 2024

Abstract
Aim
Sufficient liver function is crucial in extracellular matrix growth, hemostasis, and wound healing. Repeated abdominal surgery is a known risk factor for the development of wound complications. This study aimed to evaluate this high-risk constellation in patients undergoing associated liver partition and portal vein ligation for staged hepatectomy (ALPPS) and repeated liver resections (RLR) in comparison to single liver resection (SLR).

Method
Forty patients who underwent ALPPS between 2011 and 2020 were evenly matched with patients undergoing RLR or SLR (n = 40 per group) using propensity scores. Postoperative outcomes were compared and factors associated with wound complications were analyzed.

Results
Postoperative wound complications were significantly more frequent in ALPPS group (p = 0.001). The reoperation rate was not significantly different between the three groups (p = 0.143). However, surgical reintervention due to wound complications occurred more frequently in the ALPPS group in relation to RLR and SLR (17.5% vs. 7.5% and 5% respectively). Length of stay was significantly longer in the ALPPS group (p = 0.033). ALPPS was an independent risk factor for postoperative wound complication (OR = 8.55, 95% CI:1.07–68.44, p = 0.043). Risk factor analysis identified age ≥ 60 years (OR = 27.64, 95% CI:3.09-246.75, p = 0.003), BMI ≥ 30 kg/m2 (OR = 30.21, 95% CI:3.35-271.83, p = 0.002), and low postoperative albumin levels (OR = 168.41, 95% CI:7.76-3651.18, p = 0.001) as independent predictors of postoperative wound complications after major liver resection.

Conclusion
Patients undergoing ALPPS and RLR are faced with a high risk of developing wound complications. Older age, obesity, a history of previous abdominal surgery, and a decreased postoperative albumin level were independent risk factors for wound complications.
Phase Ib study of the oral PI3Kδ inhibitor linperlisib in patients with advanced solid tumors
Authors: Li Jin , Xue Junli , Liu Tianshu , Feng Yi , Xu Nong , Huang Jianjin , Yin Yongmei , Zhang Jun , Mou Haibo , Shentu Jiangzhong , Bao Hanying , Xu Zusheng , Xu Zuhong 
Published: November 2024

Abstract

Background
Patients with advanced solid tumors have a suboptimal prognosis. This study investigated the safety and feasibility of linperlisib, a selective phosphatidylinositol 3-kinase delta isoform (PI3Kδ) inhibitor, for treating patients with advanced solid tumors.

Methods
In this phase Ib, single-arm, open-label, multi-center clinical trial, patients with histologically confirmed advanced solid tumors from eight centers in China were enrolled to receive oral linperlisib (80 mg/day). The primary endpoint was safety.

Results
Between August 2019 and June 2022, 94 patients were enrolled in the trial and received the study treatment. The most common (≥ 20%) treatment emergent adverse events (TEAEs) of all grades irrespective of causality were increased aspartate aminotransferase (AST) (26.6%), proteinuria (26.6%), decreased appetite (25.5%), increased alanine aminotransferase (ALT) (22.3%), weight loss (21.3%), and anemia (21.3%). The most common grade ≥ 3 TEAEs were diarrhea (4.3%), increased AST (3.2%), increased ALT (3.2%), neutropenia (3.2%), anemia (3.2%), increased blood alkaline phosphatase (3.2%). The objective response rate (ORR) was 1.1% (95% confidence interval [CI] 0.0–5.8), and the disease control rate (DCR) was 37.2% (95% CI 27.5–47.8). As of the data cutoff, the median follow-up time was 4.2 months (95% CI 2.8–6.9). The median progression-free survival (PFS) was 1.85 months (95% CI 1.79–1.88). The median overall survival (OS) was not reached.

Conclusion
Linperlisib showed an acceptable safety profile and preliminary clinical benefit in patients with a range of advanced solid tumors. Further studies of linperlisib safety and efficacy are warranted.
Technical Note: Neural Network Architectures for Self-Supervised Body Part Regression Models with Automated Localized Segmentation Application
Authors: Fei Michael , McMillan Alan B. 
Published: November 2024

AbstractThe advancement of medical image deep learning necessitates tools that can accurately identify body regions from whole-body scans to serve as an essential pre-processing step for downstream tasks. Typically, these deep learning models rely on labeled data and supervised learning, which is labor-intensive. However, the emergence of self-supervised learning is revolutionizing the field by eliminating the need for labels. The purpose of this study was to compare neural network architectures of self-supervised models that produced a body part regression (BPR) slice score to aid in the development of anatomically localized segmentation models. VGG, ResNet, DenseNet, ConvNext, and EfficientNet BPR models were implemented in the MONAI/Pytorch framework. Landmark organs were correlated to slice scores and mean absolute error (MAE) was calculated from the predicted slice and the actual slice of various organ landmarks. Four localized DynUNet segmentation models (thorax, upper abdomen, lower abdomen, and pelvis) were developed using the BPR slice scores. Dice similarity coefficient (DSC) was compared between the localized and baseline segmentation models. The best performing BPR model was the EfficientNet architecture with an overall 3.18 MAE, compared to the VGG baseline model with a MAE of 6.29. The localized segmentation model significantly outperformed the baseline in 16 out of 20 organs with a DSC of 0.88. Enhanced neural networks like EfficientNet have a large performance increase in localizing anatomical structures in a CT compared in BPR task. Utilizing BPR slice score is shown to be effective in anatomically localized segmentation tasks with improved performance.
A bird’s-eye view reveals no fixed differences in plumage coloration between divergent populations of Painted Buntings
Authors: Podkowa Pawel , Hogan Benedict G. , Stoddard Mary Caswell , Hill Geoffrey E. 
Published: November 2024

AbstractIn birds, the process of speciation is closely associated with transitions in ornamentation, including coloration, plumage pattern, and song. To investigate the origins of these shifts and their connection to genetic changes, we conducted a study on one of the most highly ornamented songbirds, the Painted Bunting (Passerina ciris). The male Painted Buntings exhibits a stunning array of colors, with a red chest, blue head, green back, green coverts, and pink rump. In addition, Painted Buntings show a high level of genetic structure, with eastern and western populations that have fixed genetic differences in both nuclear and mitochondrial genes. Using non-invasive spectrophotometry techniques, we measured the coloration of six plumage patches on 88 museum specimens of male Painted Buntings in definitive plumage from across the range of the species. We predicted that there would be divergence between the genetically distinct eastern and western populations in ornamental coloration that is perceptible to a bunting but imperceptible to a human observer. However, we measured no consistent nor substantial difference in the plumage coloration of males from different populations. The observation of substantial divergence in nuclear and mitochondrial genotype with no change in ornamental coloration between populations of a brightly colored bird has important implications for the role of sexual selection in the process of speciation.
Wnt-5a Signaling Mediates Metaplasticity at Hippocampal CA3–CA1 Synapses in Mice
Authors: Parodi Jorge , Mira Rodrigo G. , Fuenzalida Marco , Cerpa Waldo , Serrano Felipe G. , Tapia-Rojas Cheril , Martinez-Torres Ataulfo , Inestrosa Nibaldo C. 
Published: November 2024

AbstractWnt signaling plays a role in synaptic plasticity, but the specific cellular events and molecular components involved in Wnt signaling-mediated synaptic plasticity are not well defined. Here, we report a change in the threshold required to induce synaptic plasticity that facilitates the induction of long-term potentiation (LTP) and inhibits the induction of long-term depression (LTD) during brief exposure to the noncanonical ligand Wnt-5a. Both effects are related to the metaplastic switch of hippocampal CA3–CA1 synaptic transmission, a complex mechanism underlying the regulation of the threshold required to induce synaptic plasticity and of synaptic efficacy. We observed an early increase in the amplitude of field excitatory postsynaptic potentials (fEPSPs) that persisted over time, including after washout. The first phase involves an increase in the fEPSP amplitude that is required to trigger a spontaneous second phase that depends on Jun N-terminal kinase (JNK) and N-methyl D-aspartate receptor (NMDAR) activity. These changes are prevented by treatment with secreted frizzled-related protein 2 (sFRP-2), an endogenous antagonist of Wnt ligands. Here, we demonstrate the contribution of Wnt-5a signaling to a process associated with metaplasticity at CA3–CA1 synapses that favors LTP over LTD.
Graphical Abstract
Embodied learning of science concepts through augmented reality technology
Authors: Mansour Nasser , Aras Ceren , Staarman Judith Kleine , Alotaibi Sarah Bader Mohsen 
Published: November 2024

AbstractAugmented Reality (AR) revolutionizes educational approaches by providing an immersive experience that superimposes virtual 3D elements onto the physical environment. This integration of virtual and real worlds addresses the challenge of understanding abstract concepts by enabling three-dimensional visualization and interaction. This study aims to assess the role of embodied cognition in science learning through AR technology, analyze its impact on collaborative, inquiry-based learning in primary science, and understand students' perceptions of its influence on their engagement and comprehension in collaborative science tasks. Data collection methods for this study included three focus group interviews and five video observations involving ten grade 5 students, totaling 23 participants, in a primary science classroom. The analysis utilized content, thematic, and multimodal frameworks to evaluate student interactions. The findings indicated that the use of AR significantly enhanced the students' learning experiences. Students' comprehension of complex scientific concepts improved through active engagement with 3D models using the AR application. The AR app's 3D virtual shapes encouraged students to move around more during lessons, likely because these shapes were engaging and offered various perspectives. The use of embodied learning was enhanced with the support of AR technology, as students were constantly in motion around the table, using their fingers to manipulate objects and explore 3D forms from different angles.
Ecomorphology of Longnose Gar (Lepisosteus osseus): on the influence of size, sex, and river location
Authors: Doll Jason C. , Fisher Ian , Selby Aaron , Jacquemin Stephen J. , Sinopoli Daniel , David Solomon R. 
Published: November 2024

AbstractEcomorphology is essential to understanding the evolution and biogeography of species. However, morphological studies that focus on nongame or ‘rough’ fish groups such as Gar (Lepisosteidae), outside of a phylogenetic context, are comparatively rare. Herein, we investigate the effects of sex, size, and location in a river to assess the potential for sexual dimorphism, allometry, habitat, or some combination to drive observed morphologic variation. Our dataset includes 230 Longnose Gars (Lepisosteus osseus) made up of both males and females of a wide range of sizes collected from three different sites corresponding to the upper, middle, and lower Great Pee Dee River in South Carolina. Dorsal and lateral photographs were taken from each specimen and landmarked for 2D geometric morphometric analyses. Discriminant function analyses (DFA) were also conducted on a few linear trusses to compare the accuracy of sex-related shape aspects that emerged from morphometrics as a possible field-based tool to help fisheries managers understand their stock populations. Overall, location was a statistically significant predictor of shape, yet the differences were not biologically meaningful. Additionally, sex and size were strong predictors of shape, with the greatest differences seen in the largest individuals. DFA of field measurements found that the Snout Length-to-Total Length ratio accurately predicted sex 71% of the time, with females having longer snouts than males. Differences in ratio between sexes can allow tentative sex assignments without lethal gonadal inspection. This study presents the first standardized whole-body 2D geometric morphometrics protocol for Longnose Gar.
Learning to speak mathematically at the Japanese supplementary school in Sweden: critical cases of praxeological anomaly
Authors: Aoki Mayu , Asami-Johansson Yukiko , Winsløw Carl 
Published: November 2024

AbstractNatural language is known to play a crucial and specific role for children’s learning in school mathematics. Not only does it carry special vocabulary, but subtle differences between natural languages may lead to surprising challenges, for instance, for learners who are not taught mathematics in their mother tongue. In this paper, the anthropological theory of didactic (ATD) is used as a main framework, and we analyse some praxeological anomalies from the teaching of fractions at Japanese schools abroad, while learners attend, at the same time, a regular school in some other language (in this case, the local language, Swedish). Our findings indicate that these praxeological anomalies arise not only from linguistic disparities related to specialised vocabulary and syntax for elementary mathematics but also from institutional and curricular differences. This study gives new insights on these language challenges related to mathematics as taught at expatriate schools, particularly in the case of Japanese.
A comparison of statistical and machine learning models for spatio-temporal prediction of ambient air pollutant concentrations in Scotland
Authors: Zhu Qiangqiang , Lee Duncan , Stoner Oliver 
Published: November 2024

AbstractThe spatio-temporal prediction of air pollutant concentrations is vital for assessing regulatory compliance and for producing exposure estimates in epidemiological studies. Numerous approaches have been utilised for making such predictions, including land use regression models, additive models, spatio-temporal smoothing models and machine learning prediction algorithms. However, relatively few studies have compared the predictive performance of these models thoroughly, which is one of the novel contributions of this paper. For the specific challenge of predicting monthly average concentrations of NO$$_{2}$$

2

, PM$$_{10}$$

10

and $$\hbox {PM}_{2.5}$$

PM

2.5

in Scotland, we find that random forests typically outperform (or are as good as) more traditional statistical prediction approaches. Additionally, we utilise the best performing model to provide a new data resource, namely, predictions of monthly average concentrations (with uncertainty quantification) of the above pollutants on a regular 1 km$$^{2}$$

2

grid for all of Scotland between 2016 and 2020.