bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeted knockdown of ATM, ATR, and PDEδ increases Gag HIV-1 VLP production in HEK293 cells
Authors: Díaz-Maneh Andy , Pérez-Rubio Pol , Granes Cristina Rigau , Bosch-Molist Laia , Lavado-García Jesús , Gòdia Francesc , Cervera Laura 
Published: January 2025

Abstract
Several strategies have been developed in recent years to improve virus-like particle (VLP)-based vaccine production processes. Among these, the metabolic engineering of cell lines has been one of the most promising approaches. Based on previous work and a proteomic analysis of HEK293 cells producing Human Immunodeficiency Virus-1 (HIV-1) Gag VLPs under transient transfection, four proteins susceptible of enhancing VLP production were identified: ataxia telangiectasia mutated (ATM), ataxia telangiectasia and rad3-related (ATR), DNA-dependent protein kinase catalytic subunit (DNA-PKcs), and retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta (PDEδ). The knockdown of ATM, ATR, and PDEδ in HEK293 cells increased HIV-1 VLP titers in the supernatant by 3.4-, 2.1-, and 2.2-fold, respectively. Also, possible metabolic synergies between plasmids were investigated by statistical design of experiments (DoE), enabling us to identify the optimal production strategy, that was further demonstrated at lab-scale stirred tank bioreactor operated in perfusion, significantly increasing both VLPs specific and volumetric productivities to 8.3 × 103 VLPs/cellxday and 7.5 × 1012 VLPs/Lxday, respectively.

Key points
• ATM, ATR, and PDEδ knockdowns increased VLP production in HEK293 cells.
• Knockdown of ATM increased budding efficiency and extracellular vesicle concentration.
• ATM knockdown could be intensified to bioreactor scale operated in perfusion.

Graphical Abstract
Sex differences in immunotherapy outcomes and tumor-infiltrating immune cell profiles in patients with advanced renal cell carcinoma
Authors: Ishihara Hiroki , Fukuda Hironori , Mizoguchi Yukihiro , Yamashita Makiko , Aoki Kazunori , Ishiyama Ryo , Ikeda Takashi , Nemoto Yuki , Shimmura Hiroaki , Hashimoto Yasunobu , Yoshida Kazuhiko , Hirai Toshihito , Iizuka Junpei , Tokita Daisuke , Kondo Tsunenori , Nagashima Yoji , Takagi Toshio 
Published: January 2025

Abstract
Sex differences in the outcomes of advanced renal cell carcinoma (RCC) treated with immune checkpoint inhibitors (ICIs) and the profiles of tumor-infiltrating immune cells (TIICs) remain unclear. We retrospectively evaluated data from 563 patients with RCC receiving systemic therapy, including first-line dual ICI combinations (i.e., immunotherapy [IO]-IO), combinations of ICIs with tyrosine kinase inhibitors (TKIs) (i.e., IO-TKI), TKI monotherapy, and subsequent nivolumab monotherapy. Survival and tumor response were compared between the sexes in each treatment group, and TIIC profiles were compared using 116 RCC tumor samples analyzed by flow cytometry. Progression-free survival (PFS) was shorter in female than in male patients in the IO-IO (p = 0.0227) and nivolumab monotherapy (p = 0.0478) groups. Furthermore, sex remained an independent factor for shorter PFS after adjusting for covariates in the IO-IO (p = 0.0340) and nivolumab monotherapy (p = 0.0322) groups. In contrast, PFS was not significantly different between sexes in the IO-TKI or TKI monotherapy groups (p > 0.05). Overall survival and objective response rates were not significantly different between the sexes in any of the treatment groups (p > 0.05). Some TIIC populations, including that of CD8 + T cells (p = 0.0096), decreased to a greater extent in female than in male patients in the advanced-stage population. In conclusion, the effectiveness of ICIs on PFS was lower in female patients than in male patients, potentially because of the different profiles of the immune microenvironment, particularly the decreased number of CD8 + T cells in females.
Prognostic relevance of CD163+ immune cells in patients with metastatic breast cancer
Authors: Lindberg Ida , Saleh Aya , Tutzauer Julia , Gunnarsdottir Frida Björk , Rydén Lisa , Bergenfelz Caroline , Larsson Anna-Maria 
Published: January 2025

Abstract
Metastatic breast cancer (MBC) is generally considered an incurable disease and even though new treatments are available, the median survival is approximately three years. The introduction of immune therapies for MBC highlights the importance of the immune system in cancer progression and treatment. CD163+ anti-inflammatory myeloid cells, including tumor associated macrophages (TAMs), are known to be of relevance in early breast cancer but their role in MBC is not yet established. Here we determine the levels of CD163+ immune cells in 139 patients with newly diagnosed MBC by using Immunohistochemistry (IHC) and gene expression analyses (GEX). We aim to determine changes and distribution of CD163+ immune cells during tumor progression from primary tumors (PT) to lymph node metastases (LNM) and distant metastases (DM). In addition, we evaluate associations between CD163+ immune cells, clinicopathological factors and disease outcome (progression-free and overall survival; PFS and OS, respectively). Despite similar distribution, high levels of CD163+ immune cells in the tumor nest of PT, but not in LNM or DM, associated with adverse prognostic features including higher grade and molecular subtype, as well as with shorter PFS and OS, however this observation was not significant after adjusted multivariate analyses. Finally, high levels of CD163+ immune cells in PT, as well as GEX in PT and synchronous LNM associated with shorter OS from the initial diagnosis. These results indicate that evaluating the levels of CD163+ immune cells may identify MBC patients with a worse prognosis. Unraveling the role of CD163+ immune cells in the complex immune responses in MBC is highly relevant for improving future immune therapies.
Characterization of the adaptive immune response in a mouse model for HPV-positive head and neck squamous cell carcinoma with implications to human disease
Authors: Oliveri Franziska , Neher Linda , Pscheid Ronja , Sewald Isabel , Gowdavally Sowmya , Betzler Annika C. , Hallitsch Jaqueline , Greve Jens , Laban Simon , Schmid Sebastian , Hoffmann Thomas K. , Schuler Patrick J. , Brunner Cornelia 
Published: January 2025

Abstract
Head and neck squamous cell carcinoma (HNSCC) is the seventh most common cancer worldwide with a poor prognosis for survival. Risk factors include alcohol and tobacco abuse and infection with human papilloma virus (HPV). To enhance anti-tumor immune responses immunotherapeutic approaches are approved for recurrent metastatic disease but only approx. 20% of patients respond to checkpoint blockade of the PD-1/PD-L1 axis. Therefore, preclinical research is needed to better understand molecular and cellular processes and to identify new therapeutic targets. Immunocompetent mouse models can serve these purposes but only few are currently available for HPV-positive HNSCC. Here, we established a mouse cell line overexpressing the oncogenes E6/E7 of the HPV16 genome as well as a constitutively active form of H-Ras and studied the anti-tumor immune response upon orthotopic tumor growth at the floor of the mouth. Moreover, we analyzed the same immunoregulatory pathways in samples of HPV-positive cancer patients. T cells in the tumor of mice and humans exhibited high expression of CD39 and CD73, two ectoenzymes involved in the production of immunosuppressive adenosine from ATP, along with increased expression of PD-1, LAG-3 and GITR. Additionally, B cell responses were elevated in tumor-bearing mice, seen as an increase of germinal center, immunoregulatory marginal zone and follicular B cell subtypes. Taken together, this study suggests that the generated mouse model shares characteristics with human disease and can thus be used as a platform to study anti-tumor responses in HPV-positive HNSCC which will help to identify novel therapeutic targets.
Identification of immune suppressor candidates utilizing comparative transcriptional profiling in histiocytic sarcoma
Authors: Lenz Jennifer A. , Peng Brandon , Assenmacher Charles‑Antoine , King Austin , Zhang Paul J. , Maki Robert G. , Blanco M. Andres , Radaelli Enrico , Atherton Matthew J. 
Published: January 2025

Abstract
Histiocytic sarcoma (HS) is a rare yet lethal malignancy with no established standard of care therapies. A lack of pre-clinical models limits our understanding of HS pathogenesis and identification of therapeutic targets. Canine HS shares multiple clinical and genetic similarities with human HS, supporting its use as a unique translational model. Prior studies have investigated the immunogenicity of HS. Although increased tumor infiltrating lymphocyte (TIL) density is associated with favorable outcomes in canine HS, virtually all canine patients eventually succumb to progressive disease consistent with ultimate failure of anti-tumor immunity. To investigate potential regulators of the immune tumor microenvironment (TME), we undertook a comparative transcriptional approach of three long-lived cases of canine pulmonary HS with heavy T cell infiltrate and three short-lived cases of splenic HS that lacked significant T cell inflammation and compared these data to corresponding grossly normal tissues from dogs undergoing necropsy. This comparison identified PDCD1, encoding the immune checkpoint PD-1, and SPP1, encoding the secreted pro-tumorigenic protein osteopontin, as positive differentially expressed genes (DEGs) in canine HS. TXNIP, encoding the tumor suppressor TXNIP, was the most significant negative DEG. Comparative transcriptomic studies revealed conservation of enriched (including SPP1) and depleted (including TXNIP) DEGs between canine and human HS patients. Immunohistochemistry demonstrated osteopontin in the TMEs of canine and human HS. Collectively, we uncover PD-1, osteopontin, and TXNIP as putative actionable targets in HS and further establish canine HS as a preclinical platform to screen novel immunotherapeutic approaches for this deadly disease.
Understanding the impact of spatial immunophenotypes on the survival of endometrial cancer patients through the ProMisE classification
Authors: Hattori Satomi , Yoshikawa Nobuhisa , Liu Wenting , Matsukawa Tetsuya , Kubokawa Mei , Yoshida Kosuke , Yoshihara Masato , Tamauchi Satoshi , Ikeda Yoshiki , Yokoi Akira , Shimizu Yusuke , Niimi Kaoru , Kajiyama Hiroaki 
Published: January 2025

Abstract

Objectives
We focused on how the immunophenotypes based on the distribution of CD8-positive tumor-infiltrating lymphocytes (TILs) relate to the endometrial cancer (EC) molecular subtypes and patients’ prognosis.

Patients and methods
Two cohorts of EC patients (total n = 145) were analyzed and categorized using the Molecular Risk Classifier for Endometrial cancer (ProMisE): POLEmut (POLE mutation), MMRd (mismatch repair deficiency), NSMP (no specific molecular profile), and p53abn (p53 abnormality). CD8-positive TILs, within the central tumor and the invasive margin, were examined by using immunohistochemical staining and advanced image-analysis software. It was investigated whether these immunophenotypes correlate with the molecular subtypes and patients' survival. RNA-sequencing (RNA-seq) was used to explore tumor-derived factors influencing these immunophenotypes.

Results
Three distinct immunophenotypes (inflamed, excluded, and desert) based on the CD8-positive TIL patterns were identified in EC patients. Notably, the inflamed phenotype was most frequently observed in the POLEmut and MMRd subtypes, while the desert phenotype was predominant in the NSMP subtype; however, other immunophenotypes were also observed. All p53abn subtype showed the non-inflamed (excluded or desert) phenotype. The prognosis was markedly poorer in the patients with the non-inflamed phenotype than in those with the inflamed phenotype. The RNA-seq analysis showed that the expression of MYC target genes and type-1 interferon response genes was enriched in the non-inflamed phenotype in MMRd and NSMP subtypes, respectively.

Conclusion
Evaluating not only the molecular classification but also the immunophenotype may lead to more personalized immunotherapy in EC and elucidating the mechanisms that underlie the formation of the three immunophenotypes could lead to the discovery of new immunotherapy targets.
Detection of H3F3A K27M or BRAF V600E in liquid biopsies of brain tumor patients as diagnostic and monitoring biomarker: impact of tumor localization and sampling method
Authors: Madlener Sibylle , Stepien Natalia , Senfter Daniel , Mayr Lisa , Laemmerer Anna , Hedrich Cora , Baumgartner Alicia , Lötsch-Gojo Daniela , Sterba Jaroslav , Pokorna Petra , Kiesel Barbara , Widhalm Georg , Eckert Franziska , Preusser Matthias , Rössler Karl , Azizi Amedeo , Peyrl Andreas , Czech Thomas , Haberler Christine , Slavc Irene , Kasprian Gregor , Dorfer Christian , Furtner Julia , Gojo Johannes 
Published: January 2025

AbstractGliomas are the most common brain tumor type in children and adolescents. To date, diagnosis and therapy monitoring for these tumors rely on magnetic resonance imaging (MRI) and histopathological as well as molecular analyses of tumor tissue. Recently, liquid biopsies (LB) have emerged as promising tool for diagnosis and longitudinal tumor assessment potentially allowing for a more precise therapeutic management. However, the optimal strategy for monitoring gliomas by LB remains to be determined. In this study, we analyzed circulating tumor DNA (ctDNA) from 78 liquid biopsies (plasma n = 44, cerebrospinal fluid n = 34 (CSF)) of 35 glioma patients, determining H3F3A K28M (K27M) and BRAF V600E mutation allele frequency using droplet digital PCR (ddPCR). All results were correlated to clinically relevant parameters including diagnostic imaging and CSF aspiration site (ventricular vs lumbar) with respect to tumor localization. Regarding diagnostic accuracy, the calculated sensitivity score in the H3F3A K27M cohort was 84.61% for CSF and 73.68% for plasma. In the BRAF V600E cohort, we determined a sensitivity of 83.3% in plasma and 80% in CSF. The overall specificity was 100%. With respect to the CSF aspiration, the intra-operatively obtained CSF demonstrated 100% detection rate, followed by ventricular CSF obtained via Ommaya Reservoir/shunt puncture (93%) and CSF obtained via lumbar puncture (66%). Notably, this further correlated with the proximity of the CSF site to tumor localization. Longitudinal CSF monitoring demonstrated a good correlation to clinical and radiological disease evolution. Importantly, we show for the first time that monitoring BRAF V600E by ddPCR could serve as treatment response assessment in gliomas. In summary, our observation may inform recommendations with regard to location of CSF aspiration when incorporating LB into future treatment protocols.
Pedestrian thermal comfort mapping for evidence-based urban planning; an interdisciplinary and user-friendly mobile approach for the case study of Dresden, Germany
Authors: Gallacher Claire , Boehnke Denise 
Published: January 2025

Abstract
In the face of climate change and increasing urbanisation, ensuring outdoor thermal comfort is becoming an increasingly crucial consideration for sustainable urban planning. However, informed decision-making is limited by the challenge of obtaining high-resolution thermal comfort data. This study introduces an interdisciplinary, low-resource, and user-friendly methodology for thermal comfort mapping, employing a self-built low-cost meteorological device for mobile climate monitoring. This device was utilised in the city center of Dresden, Germany to collect air temperature, humidity, pressure, surface temperature, global radiation, and globe temperature data as key inputs for the calculation of thermal comfort indices. These measurements were then used to calculate the Universal Thermal Climate Index (UTCI) using the RayMan Pro urban climate modelling program. Due to the limited resource capacities of urban planning departments, clear priority areas must be identified. Therefore, an exemplary approach for the prioritisation of consistent hotspots using the highest 5% of UTCI values was developed. The spatial variances in UTCI were validated through mobile pedestrian thermal comfort questionnaires, which allowed for the comparison of objective and subjective estimates of thermal comfort and gave the basis on which to make holistic and practical suggestions for urban planning interventions. This paper demonstrates an accessible and interdisciplinary approach to thermal comfort mapping which can empower urban planning stakeholders with scientifically informed and cost-effective decision-making tools for climate-adapted urban development.
How Balanced Can Permutations Be?
Authors: Beniamini Gal , Lavee Nir , Linial Nati 
Published: January 2025

AbstractA permutation $$\pi \in \mathbb {S}_n$$

π
∈

S
n

is k-balanced if every permutation of order k occurs in $$\pi $$
π
equally often, through order-isomorphism. In this paper, we explicitly construct k-balanced permutations for $$k \le 3$$

k
≤
3

, and every n that satisfies the necessary divisibility conditions. In contrast, we prove that for $$k \ge 4$$

k
≥
4

, no such permutations exist. In fact, we show that in the case $$k \ge 4$$

k
≥
4

, every n-element permutation is at least $$\Omega _n(n^{k-1})$$

Ω
n

(

n

k
-
1

)

far from being k-balanced. This lower bound is matched for $$k=4$$

k
=
4

, by a construction based on the Erdős–Szekeres permutation.
Evaluation of physico-chemical characteristics of biochar produced from red bell pepper waste biomass
Authors: Christophe Nsaka Ntumba , Veronica Ngole Jeme 
Published: January 2025

Abstract
Different types of biomasses are utilised for biochar production, but agricultural solid wastes remain a viable feedstock because of its availability and lower cost. This study investigated the possibility of producing biochar from red bell pepper wastes (RBPW) using slow carbonisation (300 and 400 °C) without chemical modification and characterising the produced biochar in an endeavour to elucidate on its potential use for environmental remediation. Proximate analysis, physical and chemical properties of the biomass and biochars were investigated using standard methods and analytical instruments. The yields of biochars from RBPW were found to be 25.8 and 23.5%, respectively, for biochar produced at carbonisation temperatures of 300 and 400 °C. Elemental analysis showed the presence of elements with concentration patterns that followed the order Fe > Na > Ca > K > Mg > Mn > Zn in the biomass and biochars though the biochars had higher concentrations than the biomass. The specific surface areas and pore volumes of both biomass and biochars were found to be low (< 0.706 and 0.0280 cm2/g, respectively) as per the BET results. FTIR results showed the presence of oxygen-containing functional groups on the surface of both biomass and biochars. The surface of biomass had more acidic sites as opposed to biochars which had more basic sites. RBPW has shown typically acceptable chemical, physical and thermal properties for the production of biochar. Further studies are required to understand whether chemical activation would improve their surface properties and the conditions under which they can be used.

Graphical Abstract
Impact of short and long-term application of low-level laser therapy on mandibular alveolar process of osteoporotic rats – a Histological and Molecular Study
Authors: El-Halwagy Mai O. , Hegazy Enas M. , Shalaby Hany K. , Mahmoud Elham F. 
Published: January 2025

AbstractThis study aims to investigate and compare the effects of short and long-term application of low-level laser therapy on the mandibular alveolar process of osteoporotic rats. Forty adult male albino rats were included in this study. After animal grouping, the experimental group received dexamethasone (0.1 mg/kg b.wt./day for 60 days) for the induction of osteoporosis, then the rats were treated using LLLT (830 nm, 100 mW, at 60 J/cm2). The lower jaw specimens were collected and processed for histological, molecular, and histomorphometric assessments. The osteoporotic group exhibited alveolar bone resorption, accompanied by significantly upregulated RANKL and downregulated OPG mRNA expression. The short-term application of laser group showed alveolar bone partial improvement with slightly downregulated RANKL and slightly upregulated OPG levels. The long-term application of laser group showed dramatic positive changes in the alveolar bone, with markedly downregulated RANKL and upregulated OPG levels. LLLT shows potential as a low-risk and impactful local management for osteoporosis, with long-term laser application demonstrably improving bone quality, quantity, and organization compared to short-term application.
Graphical abstract
Governance Considerations for Point-of-Care Ultrasound: a HIMSS-SIIM Enterprise Imaging Community Whitepaper in Collaboration with AIUM
Authors: Ma Irene W. Y. , Francavilla Michael L. , Nomura Jason T. , Kielski Adam , Fernandez Francisco , Piro Kevin , Liu Rachel , Valenzuela Josephine , Toland Michael , Koehler Jessica , Cohen Gregg , Eid Monief , Choi Wilson , Nolan James D. , Ferre Robinson M. , McBee Morgan P. , Kummer Tobias , Lanspa Michael J. , Brown Jenn Quattrone , DeStigter Kristen , Desyatnikova Stella , Bottemiller Allan 
Published: January 2025

AbstractPoint-of-care ultrasound (POCUS) has emerged as a standard of care across a variety of healthcare settings due to its ability to provide critical clinical information and as well as procedural guidance to clinicians directly at the bedside. Implementation of enterprise imaging (EI) strategies is needed such that POCUS images can be appropriately captured, indexed, managed, stored, distributed, viewed, and analyzed. Because of its unique workflow and educational requirements, reliance on traditional order-based workflow solutions may be insufficient. To improve patient care outcomes and operational efficiency, a robust governance committee for POCUS within healthcare systems that addresses pertinent institutional policies to ensure effective and sustainable implementation of enterprise imaging, appropriate to the specific clinical encounter-based workflow needs of POCUS, is critical. This white paper explores several key governance considerations in the formulation and structure of a POCUS enterprise imaging strategy, focusing on program governance, clinical governance, technology governance, information governance, and financial governance.
Destruction of chemical weapons stockpiles in the Russian Federation: a review
Authors: Rozsypal Tomas , Pejchal Jaroslav , Opravil Jakub , Haralampiev Mihail , Bocos-Bintintan Victor , Kobliha Zbynek 
Published: January 2025

AbstractChemical weapons, designed for mass harm, are posing risks of contamination, accidents, and ecological damage, and thus require their destruction. However, destruction of chemical weapons is challenging, notably in the Russian Federation due to the large scale and complexity of chemical weapons stockpiles, the diverse toxic agents stored under varying conditions, logistical and political obstacles, financial constraints, and the disposal process. Here we review the Russian Federation’s chemical weapons disposal program with an emphasis on the political context, declared chemical weapons stockpiles, methods for destruction, health and environmental issues, and nerve agents. We analyze stockpiles totaling nearly 40,000 tonnes of chemical agents across seven facilities, focusing on their composition, storage conditions, and destruction technologies. Methods such as neutralization, bituminization, and thermal destruction are compared. Environmental risks include arsenic migration and groundwater contamination near disposal sites. We observe the limitations of using bitumen salt masses as a safe disposal method.