bluuebunny/crossref_metadata_2025_split huggingface dataset:
Versatile function of NF-ĸB in inflammation and cancer
Authors: Ma Qiang , Hao Shuai , Hong Weilong , Tergaonkar Vinay , Sethi Gautam , Tian Yu , Duan Chenyang 
Published: July 2024

AbstractNuclear factor-kappaB (NF-ĸB) plays a crucial role in both innate and adaptive immune systems, significantly influencing various physiological processes such as cell proliferation, migration, differentiation, survival, and stemness. The function of NF-ĸB in cancer progression and response to chemotherapy has gained increasing attention. This review highlights the role of NF-ĸB in inflammation control, biological mechanisms, and therapeutic implications in cancer treatment. NF-ĸB is instrumental in altering the release of inflammatory factors such as TNF-α, IL-6, and IL-1β, which are key in the regulation of carcinogenesis. Specifically, in conditions including colitis, NF-ĸB upregulation can intensify inflammation, potentially leading to the development of colorectal cancer. Its pivotal role extends to regulating the tumor microenvironment, impacting components such as macrophages, fibroblasts, T cells, and natural killer cells. This regulation influences tumorigenesis and can dampen anti-tumor immune responses. Additionally, NF-ĸB modulates cell death mechanisms, notably by inhibiting apoptosis and ferroptosis. It also has a dual role in stimulating or suppressing autophagy in various cancers. Beyond these functions, NF-ĸB plays a role in controlling cancer stem cells, fostering angiogenesis, increasing metastatic potential through EMT induction, and reducing tumor cell sensitivity to chemotherapy and radiotherapy. Given its oncogenic capabilities, research has focused on natural products and small molecule compounds that can suppress NF-ĸB, offering promising avenues for cancer therapy.
Papillary tumor of the pineal region: analysis of DNA methylation profiles and clinical outcomes in 76 cases
Authors: Wu Zhichao , Dazelle Karen , Abdullaev Zied , Chung Hye-Jung , Dahiya Sonika , Wood Matthew , Lee Han , Lucas Calixto-Hope G. , Mao Qinwen , Robinson Lorraina , Fernandes Igor , McCord Matthew , Pytel Peter , Conway Kyle S. , Yoda Rebecca , Eschbacher Jennifer M. , Maher Ossama M. , Hasselblatt Martin , Mobley Bret C. , Raisanen Jack M. , Hatanpaa Kimmo J. , Byers Joshua , Lehman Norman L. , Cimino Patrick J. , Pratt Drew , Quezado Martha , Aldape Kenneth 
Published: July 2024

AbstractPapillary tumor of the pineal region (PTPR) is an uncommon tumor of the pineal region with distinctive histopathologic and molecular characteristics. Experience is limited with respect to its molecular heterogeneity and clinical characteristics. Here, we describe 39 new cases and combine these with 37 previously published cases for a cohort of 76 PTPR’s, all confirmed by methylation profiling. As previously reported, two main methylation groups were identified (PTPR-A and PTPR-B). In our analysis we extended the subtyping into three subtypes: PTPR-A, PTPR-B1 and PTPR-B2 supported by DNA methylation profile and genomic copy number variations. Frequent loss of chromosome 3 or 14 was found in PTPR-B1 tumors but not in PTPR-B2. Examination of clinical outcome showed that nearly half (14/30, 47%) of examined patients experienced tumor progression with significant difference among the subtypes (p value = 0.046). Our analysis extends the understanding of this uncommon but distinct neuroepithelial tumor by describing its molecular heterogeneity and clinical outcomes, including its tendency towards tumor recurrence.
NTRK-fused central nervous system tumours: clinicopathological and genetic insights and response to TRK inhibitors
Authors: Kim Eric Eunshik , Park Chul-Kee , Kim Seung-Ki , Phi Ji Hoon , Paek Sun Ha , Choi Jung Yoon , Kang Hyoung Jin , Lee Joo Ho , Won Jae Kyung , Yun Hongseok , Park Sung-Hye 
Published: July 2024

AbstractBackground Neurotrophic tropomyosin receptor kinase (NTRK) gene fusions are found in 1% of gliomas across children and adults. TRK inhibitors are promising therapeutic agents for NTRK-fused gliomas because they are tissue agnostic and cross the blood–brain barrier (BBB). Methods We investigated twelve NGS-verified NTRK-fused gliomas from a single institute, Seoul National University Hospital. Results The patient cohort included six children (aged 1–15 years) and six adults (aged 27–72 years). NTRK2 fusions were found in ten cerebral diffuse low-grade and high-grade gliomas (DLGGs and DHGGs, respectively), and NTRK1 fusions were found in one cerebral desmoplastic infantile ganglioglioma and one spinal DHGG. In this series, the fusion partners of NTRK2 were HOOK3, KIF5A, GKAP1, LHFPL3, SLMAP, ZBTB43, SPECC1L, FKBP15, KANK1, and BCR, while the NTRK1 fusion partners were TPR and TPM3. DLGGs tended to harbour only an NTRK fusion, while DHGGs exhibited further genetic alterations, such as TERT promoter/TP53/PTEN mutation, CDKN2A/2B homozygous deletion, PDGFRA/KIT/MDM4/AKT3 amplification, or multiple chromosomal copy number aberrations. Four patients received adjuvant TRK inhibitor therapy (larotrectinib, repotrectinib, or entrectinib), among which three also received chemotherapy (n = 2) or proton therapy (n = 1). The treatment outcomes for patients receiving TRK inhibitors varied: one child who received larotrectinib for residual DLGG maintained stable disease. In contrast, another child with DHGG in the spinal cord experienced multiple instances of tumour recurrence. Despite treatment with larotrectinib, ultimately, the child died as a result of tumour progression. An adult patient with glioblastoma (GBM) treated with entrectinib also experienced tumour progression and eventually died. However, there was a successful outcome for a paediatric patient with DHGG who, after a second gross total tumour removal followed by repotrectinib treatment, showed no evidence of disease. This patient had previously experienced relapse after the initial surgery and underwent autologous peripheral blood stem cell therapy with carboplatin/thiotepa and proton therapy. Conclusions Our study clarifies the distinct differences in the pathology and TRK inhibitor response between LGG and HGG with NTRK fusions.
New perspectives, additions, and amendments to plant endemism in a North African flora
Authors: Abd El-Ghani Monier , Hosni Hasnaa , Shamso Eman , Ellmouni Faten 
Published: July 2024

Abstract
Background
Endemism is essential in biodiversity, biogeography, and conservation tasks. Based on herbarium specimens kept in some local herbaria, many published literature, and available information, we compiled a comprehensive list and an updated assessment of the Egyptian endemic and near-endemic taxa. The application of quantitative approaches to the distribution patterns, conservation status, and habitat preference of endemic taxa in Egypt was provided. Comparisons of the near-endemic taxa with other neighbouring flora were explained. For each taxon, the distribution patterns, most preferable habitat, biological spectrum, and taxa among 14 phytogeographical regions (Operational Geographical Units; OGUs) of Egypt were determined.

Results
In this study, 19 endemics (out of 70) and 76 near-endemics (out of 181) are newly added taxa. Differentiation indices represented the taxonomic degrees of differentiation among endemic taxa. Two different indices were used to assess endemism: single-region endemic taxa (SRET) and multiple-region endemic taxa (MRET). Most endemic and near-endemic taxa were recorded from the mountainous Sinai (S) and the Mareotis sector of the Mediterranean coastal land (Mm). Generally, the most represented families in endemic and near-endemic areas were Asteraceae, Caryophyllaceae, Lamiaceae, and Fabaceae. More than 60% of the endemic taxa occurred in the sandy plains, wadis (desert valleys), and rocky plains and mountains. Applying hierarchical cluster analysis to the occurrences of 70 endemic taxa in the 14 studied OGUs revealed five main floristic groups (I–V), each characterized by certain OGUs. We provided eight groups of near-endemic taxa that represented their extension in neighbouring countries.

Conclusions
The presented data will help to fill the gap in our knowledge of endemism, provide baseline information to understand biogeographical processes and facilitate further cooperation toward conservation purposes.
Effects of thermophilic and acidophilic microbial consortia on maize wet-milling steeping
Authors: Sun Yaqin , Xia Wenjing , Tang Langjun , Xiu Zhilong , Jin Weiwu , Wang Xiaoyan , Tao Jin , Liu Haijun , An Hongyan , Li Yi , Tong Yi 
Published: July 2024

AbstractTo understand the ecology of species and promote biotechnology through beneficial strain selection for improving starch yield in maize wet-milling steeping, bacterial diversity and community structure during the counter-current steeping process in a commercial steeping system were characterized and investigated. The microbial diversity in the steeping liquor, which consisted of 16 phyla, 131 families, and 290 genera, was more abundant compared to those present on the surface of unsteeped maize. As the counter-current steeping progressed, exposing newer maize to the older steepwater, Lactobacillus dominated, replacing Rahnella, Pseudomonas, Pantoea, and Serratia. The thermophilic and acidophilic microbial consortia were enriched through adaptive evolution engineering and employed to improve starch yield. Several steeping strategies were evaluated, including water alone, SO2 alone, mono-culture of B. coagulans, microbial consortia, and a combination of consortium and SO2. Combining the microbial consortium with SO2 significantly increased the starch yield to, about 66.4 ± 0.5%, a 22% and 46% increase over SO2 alone and the consortium alone, respectively. Scanning electron microscope (SEM) of steeped maize structure indicated that the combination of consortium and SO2 disrupted the protein matrix and widened gaps between starch granules in maize endosperm. This released proteins into the steepwater and left starch granules in the aleurone layer. The steeping strategy of using thermophilic and acidophilic microbial consortium as additives shows potential application as an environmentally friendly alternative to conventional maize steeping procedures.
Influence of temperature on the compression properties of expanded thermoplastic polyurethane (ETPU)
Authors: Meuchelböck Johannes , Peiffer Carlo , Walter Lena , Dippold Marcel , Munro Peter , Ruckdäschel Holger 
Published: July 2024

AbstractThis study explores how expanded thermoplastic polyurethane (ETPU) responds to temperature and compression at various temperatures. Dynamic mechanical thermal analysis (DMTA) was used to understand the temperature influence at small deformations. To investigate the deformation behavior at different compression stages we employed in-situ CT measurements and 3D strain mapping. Through quasi-static compression tests at temperatures from − 50 to 120 °C, we determined the influence of temperature on compression modulus, elastic stress, stress at 50% deformation, densification, and energy absorption. Remarkably, ETPU demonstrates robust recovery after compression, particularly within the − 50 to 60 °C temperature range. Subsequent compression tests show consistent or even slightly increased compression properties, such as a 10% increase in energy absorption for samples previously tested at − 40 °C, indicating that ETPU can withstand prior exposure to different temperatures.
Deep learning systems for forecasting the prices of crude oil and precious metals
Authors: Foroutan Parisa , Lahmiri Salim 
Published: July 2024

AbstractCommodity markets, such as crude oil and precious metals, play a strategic role in the economic development of nations, with crude oil prices influencing geopolitical relations and the global economy. Moreover, gold and silver are argued to hedge the stock and cryptocurrency markets during market downsides. Therefore, accurate forecasting of crude oil and precious metals prices is critical. Nevertheless, due to the nonlinear nature, substantial fluctuations, and irregular cycles of crude oil and precious metals, predicting their prices is a challenging task. Our study contributes to the commodity market price forecasting literature by implementing and comparing advanced deep-learning models. We address this gap by including silver alongside gold in our analysis, offering a more comprehensive understanding of the precious metal markets. This research expands existing knowledge and provides valuable insights into predicting commodity prices. In this study, we implemented 16 deep- and machine-learning models to forecast the daily price of the West Texas Intermediate (WTI), Brent, gold, and silver markets. The employed deep-learning models are long short-term memory (LSTM), BiLSTM, gated recurrent unit (GRU), bidirectional gated recurrent units (BiGRU), T2V-BiLSTM, T2V-BiGRU, convolutional neural networks (CNN), CNN-BiLSTM, CNN-BiGRU, temporal convolutional network (TCN), TCN-BiLSTM, and TCN-BiGRU. We compared the forecasting performance of deep-learning models with the baseline random forest, LightGBM, support vector regression, and k-nearest neighborhood models using mean absolute error (MAE), mean absolute percentage error, and root mean squared error as evaluation criteria. By considering different sliding window lengths, we examine the forecasting performance of our models. Our results reveal that the TCN model outperforms the others for WTI, Brent, and silver, achieving the lowest MAE values of 1.444, 1.295, and 0.346, respectively. The BiGRU model performs best for gold, with an MAE of 15.188 using a 30-day input sequence. Furthermore, LightGBM exhibits comparable performance to TCN and is the best-performing machine-learning model overall. These findings are critical for investors, policymakers, mining companies, and governmental agencies to effectively anticipate market trends, mitigate risk, manage uncertainty, and make timely decisions and strategies regarding crude oil, gold, and silver markets.
Subcarrier modulated navigation signal processing in GNSS: a review
Authors: Yao Zheng , Qi Yunhan , Lu Mingquan 
Published: July 2024

AbstractSubcarrier modulated signals are widely used in the new generation of Global Navigation Satellite Systems (GNSS) to improve spectral compatibility and ranging accuracy. The unique structure of subcarrier modulated signals poses an ambiguity threat to acquisition and tracking, rendering traditional GNSS signal processing algorithms unsuitable. Designing unambiguous acquisition and tracking as well as observation extraction techniques for subcarrier modulated signals that can realize the high ranging accuracy potential while avoiding the ambiguity threat is a topic of common interest in both academia and industry. Numerous studies have addressed the ambiguity elimination problem of subcarrier modulated signals. However, to the best of our knowledge, no updated reviews on this topic reflecting recent advances in the field have been presented in the past few years. On the one hand, the unique composite subcarrier modulated signal structure in the B1 and B2 bands of the BeiDou Navigation Satellite System (BDS) and the E5 band of the Galileo satellite navigation system (Galileo) has been gradually emphasized by academics. On the other hand, unambiguous processing methods for subcarrier modulated signals based on multidimensional tracking loops have flourished, which provides a new way to solve the ambiguity problem. An overview of the most representative subcarrier modulated signal processing techniques, focusing on the achievements made in the last decade, is presented in this article, which can be a starting point for the researchers who start their study in this area. Furthermore, we aim to present a complete review on the recent breakthroughs that have taken place within this research area, providing links to the most interesting and successful advances in this research field. Remaining challenges with prospects are also given.
Assessing the potential integration of large language models in accounting practices: evidence from an emerging economy
Authors: Toumeh Ahmad A. 
Published: July 2024

AbstractThis research intends to demonstrate the potential integration of large language models (LLMs) in accounting practices in Jordan. It is a mixed methods study that employs semi-structured interviews and content analysis of published financial reports. A total of 13 semi-structured interviews are conducted with various accounting professionals, such as accountant, financial analyst, financial controller, auditor, tax consultant, and finance manager. In addition, the study includes a thorough content analysis of financial reports, which reveals a compelling pattern highlighting the distinct narrative content richness prevalent across financial, industrial, and service sectors. The results emphasize the need for sector-specific adaptation, suggesting a paradigm shift in financial reporting practices. This study represents the initial empirical exploration in Jordan. It serves as a bridge between theory and application, offering both theoretical insights and practical guidance for accounting professionals. Ultimately, the study envisions a future where LLMs significantly enrich financial reporting practices across diverse sectors.
m6A-dependent mature miR-151-5p accelerates the malignant process of HNSCC by targeting LYPD3
Authors: Huang Fei , Ren Yuan , Hua Yufei , Wang Ying , Li Ruomeng , Ji Ning , Zeng Xin , Bai Ding , Chen Qianming , Zhou Xikun , Wu Junjie , Li Jing 
Published: July 2024

AbstractmiRNA has emerged as a crucial regulator in various of pathological and physiological processes, yet its precise mechanism of action the detailed mechanism of their action in Head and neck squamous cell carcinoma (HNSCC) remains incompletely understood. This study sheds light on the role of mi-151-5p, revealing its significantly elevated expression in tumor cells, which notably enhances the invasion and migration of HNSCC cells. This effect is achieved through directly targeting LY6/PLAUR Domain Containing 3 (LYPD3) by miR-151-5p, involving complementary binding to the 3’-untranslated regions (3’-UTR) in the mRNA of LYPD3. Consequently, this interaction accelerates the metastasis of HNSCC. Notably, clinical observations indicate a correlation between high expression of miR-151-5p and low levels of LYPD3 in clinical settings are correlated with poor prognosis of HNSCC patients. Furthermore, our investigation demonstrates that glycosylation of LYPD3 modulates its subcellular localization and reinforces its role in suppressing HNSCC metastasis. Additionally, we uncover a potential regulatory mechanism involving the facilitation of miR-151-5p maturation and accumulation through N6-methyladenosine (m6A) modification. This process is orchestrated by methyltransferase-like 3 (METTL3) and mediated by a newly identified reader, heterogeneous nuclear ribonucleoprotein U (hnRNP U). These findings collectively underscore the significance of the METTL3/miR-151-5p/LYPD3 axis serves as a prominent driver in the malignant progression of HNSCC.
Diversification of FT-like genes in the PEBP family contributes to the variation of flowering traits in Sapindaceae species
Authors: Huang Xing , Liu Hongsen , Wu Fengqi , Wei Wanchun , Zeng Zaohai , Xu Jing , Chen Chengjie , Hao Yanwei , Xia Rui , Liu Yuanlong 
Published: July 2024

AbstractMany species of Sapindaceae, such as lychee, longan, and rambutan, provide nutritious and delicious fruit. Understanding the molecular genetic mechanisms that underlie the regulation of flowering is essential for securing flower and fruit productivity. Most endogenous and exogenous flowering cues are integrated into the florigen encoded by FLOWERING LOCUS T. However, the regulatory mechanisms of flowering remain poorly understood in Sapindaceae. Here, we identified 60 phosphatidylethanolamine-binding protein-coding genes from six Sapindaceae plants. Gene duplication events led to the emergence of two or more paralogs of the FT gene that have evolved antagonistic functions in Sapindaceae. Among them, the FT1-like genes are functionally conserved and promote flowering, while the FT2-like genes likely serve as repressors that delay flowering. Importantly, we show here that the natural variation at nucleotide position − 1437 of the lychee FT1 promoter determined the binding affinity of the SVP protein (LcSVP9), which was a negative regulator of flowering, resulting in the differential expression of LcFT1, which in turn affected flowering time in lychee. This finding provides a potential molecular marker for breeding lychee. Taken together, our results reveal some crucial aspects of FT gene family genetics that underlie the regulation of flowering in Sapindaceae.
Exome Sequencing Identifies Carriers of the Autosomal Dominant Cancer Predisposition Disorders Beyond Current Practice Guideline Recommendations
Authors: Samadder N. Jewel , Gay Emily , Lindpere Vanda , Bublitz Michelle L. , Bandel Lorelei A. , Armasu Sebastian M. , Vierkant Robert A. , Ferber Matthew J. , Klee Eric W. , Larson Nicholas B. , Kruisselbrink Teresa M. , Egan Jan B. , Kemppainen Jennifer L. , Bidwell Jessa S. , Anderson Jennifer L. , McAllister Tammy M. , Walker T'Nita S. , Kunze Katie L. , Golafshar Michael A. , Klint Margaret A. , Presutti Richard J. , Bobo William V. , Sekulic Aleksander , Summer-Bolster Jolene M. , Willman Cheryl L. , Lazaridis Konstantinos N. 
Published: July 2024

PURPOSE The autosomal dominant cancer predisposition disorders hereditary breast and ovarian cancer (HBOC) and Lynch syndrome (LS) are genetic conditions for which early identification and intervention have a positive effect on the individual and public health. The goals of this study were to determine whether germline genetic screening using exome sequencing could be used to efficiently identify carriers of HBOC and LS. METHODS Participants were recruited from three geographically and racially diverse sites in the United States (Rochester, MN; Phoenix, AZ; Jacksonville, FL). Participants underwent Exome+ sequencing (Helix Inc, San Mateo, CA) and return of results for specific genetic findings: HBOC ( BRCA1 and BRCA1) and LS ( MLH1, MSH2, MSH6, PMS2, and EPCAM). Chart review was performed to collect demographics and personal and family cancer history. RESULTS To date, 44,306 participants have enrolled in Tapestry. Annotation and interpretation of all variants in genes for HBOC and LS resulted in the identification of 550 carriers (prevalence, 1.24%), which included 387 with HBOC (27.2% BRCA1, 42.8% BRCA2) and 163 with LS (12.3% MSH6, 8.8% PMS2, 4.5% MLH1, 3.8% MSH2, and 0.2% EPCAM). More than half of these participants (52.1%) were newly diagnosed carriers with HBOC and LS. In all, 39.2% of HBOC/LS carriers did not satisfy National Comprehensive Cancer Network (NCCN) criteria for genetic evaluation. NCCN criteria were less commonly met in underrepresented minority populations versus self-reported White race (51.5% v 37.5%, P = .028). CONCLUSION Our results emphasize the need for wider utilization of germline genetic sequencing for enhanced screening and detection of individuals who have LS and HBOC cancer predisposition syndromes.