bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Utility of Rapid Whole Genome Sequencing in Neonatal Patients Receiving Extracorporeal Membrane Oxygenation (ECMO)
Authors: Amin Milan , Wigby Kristen , Suttner Denise , Niemi Anna-Kaisa , Guidugli Lucia , Carroll Jeanne 
Published: September 2024

Abstract

Objective
The objective of this study is to describe the impact of rapid and ultra-rapid whole genome sequencing (rWGS/urWGS) on the care of neonatal intensive care (NICU) patients who require extracorporeal membrane oxygenation (ECMO).
Study Design
This is a retrospective cohort study at a single-center NICU in a tertiary children’s hospital. The study population includes NICU patients treated with ECMO from May 2017 to September 2023. Patients were evaluated for whether whole genome was completed, speed of testing (rapid vs ultra-rapid), diagnostic rate, and clinical utility.
Result
Twenty-six (72%) patients had rWGS/urWGS. A diagnosis associated with the patient’s phenotype was made in 12 patients (46%). A change in clinical management was made due to rWGS/urWGS in 10 patients (38%) including avoidance of imaging studies, decisions regarding goals of care, and screening studies.
Conclusion
This study demonstrates a high diagnostic rate and clinical utility of rWGS/urWGS for NICU patients requiring ECMO.
Transcriptome analysis of Oral Squamous Cell Carcinoma Utilizing Expression Datasets of Middle-aged Indian Males
Authors: Nayarisseri Anuraj , Bisht Niyati , Bandaru Srinivas , Kunsavalikar Srushti , Bhati Durvi , Swami Radhika D , Kumar Abhishek , Chaudhary Rinku , Chopra Ishita , Khan Arshiya , Sharma Khushboo , Singh Sanjeev Kumar 
Published: September 2024

Abstract

Oral squamous cell carcinoma (OSCC) is a major contributor to disease burden and mortality, particularly in rural India. This study aims to identify genes associated with OSCC through differential expression analysis utilizing datasets (BioProject: PRJNA853478) obtained from middle-aged Indian males. Differential expression analysis, transcript assembly, and functional enrichment were performed using standard Tuxedo II suite protocols, along with the StringTie, Ballgown, and KOBAS packages. The comprehensive analysis identified genes like NOTCH1, PTEN, and NCBP2 as significantly associated with OSCC. Furthermore, our findings contrast with existing studies, as we did not observe a significant association of crucial mediators of OSCC such as PROS1 and CTBP1 genes, which may be attributed to ethnic variations and differing sampling strategies. Importantly, we observed a significant enrichment of DNA repair pathways, particularly mismatch repair genes suggesting these pathways as promising prognostic and therapeutic targets for OSCC. Overall, our findings have identified key genes associated with OSCC, and the expression profiling of these genes may serve as valuable prognostic markers for the detection of OSCC, particularly in the context of the Indian population.
Saccharomyces cerevisiae fermentation of high molecular weight hyaluronic acid enhanced the antioxidant capacity in skin fibroblasts
Authors: Zhang Meng , Shi Doudou , Cui Mimi , Li Jinyong , Cheng Wenjing , Pu Chunhong , Zhang Jiachan , Wang Changtao 
Published: September 2024

Abstract

In this study, fermented hyaluronic acid (FHA) was obtained by fermentation of HA with molecular weight between 120 and 130W with two strains of Saccharomyces cerevicae (CICC 1308 and CICC 1747). Active substance content and spectral analysis revealed a substantial decrease in FHA molecular weight, accompanied by changes in monosaccharide composition, yet the chemical structure of FHA remained unchanged. Secondly, FHA exhibited a strong ability to scavenge DPPH and hydroxyl radicals. In H2O2-induced human skin fibroblasts (HSF), FHA was found to enhance superoxide dismutase (SOD) and catalase (CAT) activities while reducing malondialdehyde (MDA) levels. Pretreated FHA could regulate the nuclear translocation of Nrf2 through the Nrf2/Keap1/HO-1 signaling pathway, thereby regulating the transcription of downstream genes and the expression of antioxidant enzymes. These findings indicate that FHA possesses antioxidant properties, making it a valuable natural ingredient in cosmetics for safeguarding skin health.
ModVAR: A Multimodal Framework for Comprehensive Driver Variant Prediction in Cancer
Authors: Wang Zhe , Yang Hai , Chen Yijia , Zhou Tianyi , Wang Yingzhuo , Zhou Qin , Xiao Ting , Zhang Qian , Zhang Jing , Li Dongdong 
Published: September 2024

Abstract

Cancer's genomic complexity poses significant challenges in identifying the crucial driver variants that fuel oncogenesis. To overcome these obstacles, we present ModVAR, an innovative multimodal model that seamlessly integrates DNA sequences, protein tertiary structures, and cancer omics data to predict driver variants with exceptional precision. Leveraging pre-trained models DNAbert2 and ESMFold, combined with a novel self-supervised strategy for omics data, ModVAR consistently outperforms 14 leading prediction methods. It achieves an outstanding AUROC of 0.985 in clinical benchmarks and 0.952 in experimental assay-related benchmarks, underscoring its effectiveness in identifying both clinically and experimentally validated variants. ModVAR also excels in predicting cancer indels, with an AUROC of 0.901, and demonstrates remarkable generalization with an AUROC of 0.981 for non-cancer disease variants. These results underscore ModVAR's robustness and versatility, positioning it as a powerful tool in genomics and precision medicine. Additionally, its application to COSMIC has generated a publicly available resource of 3,971,946 annotated variants, driving an advancement in cancer research and personalized therapy.
EcoNicheS: enhancing ecological niche modeling, niche overlap and connectivity analysis using shiny dashboard and R Package
Authors: Sunny Armando , Marmolejo Clere , López-Vidal Rodrigo , Falconi-Briones Fredy , Bolom-Huet René 
Published: September 2024

Abstract

EcoNicheS is a novel, user-friendly tool designed to facilitate ecological niche modeling and species distribution modeling, niche overlap and connectivity analysis and support biodiversity conservation efforts. This R package offers a streamlined workflow for researchers and conservation practitioners to assess habitat suitability and predict species distributions in response to environmental changes. Leveraging the power of R programming and the Shinydashboard, EcoNicheS provides an intuitive interface for data input, model parameterization, and visualization of results. By integrating species occurrence data with environmental variables, users can generate robust predictions of species distributions, aiding in the identification of priority areas for conservation and management actions. EcoNicheS incorporates advanced modeling techniques to account for uncertainty and variability in species-environment relationships, enhancing the accuracy and reliability of predictions. Through a combination of user-friendly features and sophisticated analytical capabilities, EcoNicheS empowers researchers and conservation practitioners to effectively assess and mitigate threats to biodiversity in a rapidly changing world.
Machine learning regression-based prediction model for the autonomous control of coagulant dosing in smart water purification plants
Authors: Shin Donggi , Lee Jong Yun 
Published: September 2024

ABSTRACT

The global issue of water scarcity is escalating due to urbanization and increased demand. This paper proposes a machine learning (ML) regression-based model for automatic coagulant dosing control in smart water purification plants (SWPPs).1 The model uses random forest (RF), light gradient boosting machine (LGBM), extreme gradient boosting (XGB), and k-nearest neighbors (KNN) algorithms. Performance metrics include MAE, MSE, RMSE, MAPE, and R2. The RF algorithm showed superior performance, with MAE of 0.005, MSE of 0.002, RMSE of 0.05, and MAPE of 0.000 for anion-poly aluminum chloride dosing, and MAE of 0.007, MSE of 0.00, RMSE of 0.02, and MAPE of 0.000 for Polymax dosing. The RF model's performance is due to its robust handling of large datasets and ensemble learning approach. Limitations include testing only two coagulants and reliance on historical data. These findings suggest integrating advanced water management, energy systems, and facility management to make SWPPs feasible and efficient, establishing a foundation for future applications of ML in chemical processes.
Recent Advances in the Linkers of Drug Conjugates
Authors: Deng Shirui , Wen Xiaoan , Wang Jinzheng 
Published: September 2024

Abstract:
Drug conjugates have emerged as a pivotal research focus in the field of targeted
cancer therapy. They represent a widely explored prodrug strategy that significantly
enhances the therapeutic index of drugs while minimizing side effects. The stability and
selective cleavage of the linker within drug conjugates are critical for the therapeutic efficacy
and targeted treatment achieved by these conjugates. In this review, we have categorized
the linkers based on their cleavage mode and summarized the chemical properties,
advantages, and limitations of various types of cleavable linkers. Particularly, examples
have been provided to illustrate their specific potential for development.
Study on Shenbao Tablet in Treating Kidney-yang Deficiency Syndromebased on Metabolomics
Authors: Zhou Qing-gang , Han Bao-xia , Yi Huan , Geng Zhao , Gou Xiao-jun 
Published: September 2024

Aim:
The aim of this study was to elucidate the mechanism of action of Shenbao tablets
using metabolomics approach.

Background:
Kidney-Yang deficiency is a common syndrome type in traditional Chinese Medicine
(TCM) syndrome typology, closely related to disorders of multiple metabolic pathways and
is the root cause and underlying syndrome type of many diseases. Shenbao tablets can significantly
improve the main symptoms of kidney yang deficiency syndrome, but the mechanism of
action of Shenbao tablets on kidney yang deficiency syndrome is still unknown.

Methods:
The rats were intraperitoneally injected with hydrocortisone once a day for 40 days to
simulate the syndrome. Traditional pharmacodynamic indicators (body mass, biochemical indicators
and pathology) were used to evaluate the efficacy of the medicine. Serum, urine and feces
were collected from rats. UPLC/MS metabolomics method was used to study the overall metabolic
profile of serum, while GC/MS metabolomics method was used to study the metabolic
spectrum of urine and feces.

Results:
Results showed that the syndrome was significantly improved in the treatment group,
and obvious metabolic disorders were observed in rats with the syndrome, with 47 potential biomarkers
identified. Pathway analysis showed that nicotinate and nicotinamide metabolism, glycine,
serine and trione metabolism, aminoacyl tRNA biosynthesis, glycoxylate and dicarboxylate
metabolism were the major ways for Shenbao tablet to improve kidney-yang deficiency syndrome.

Conclusion:
The mechanism of action of Shenbao tablet in improving the syndrome involves the
regulation of energy metabolism, amino acid metabolism, bile acid metabolism, fatty acid metabolism
and intestinal microorganisms. This work shows that metabolomics is a promising tool
for studying the essence of syndrome theory in TCM and the mechanisms of TCM.
The Protective Effect of Astragalus Polysaccharide on Experimental Autoimmune Encephalomyelitis in Mice by Activating the AMPK/JAK/STAT3/Arginase-1 Signaling Pathway
Authors: Wang Jin-Li , Li Bin , He Xue-Xin , Gao Chang-Yu , Wang Jue-Qiong , Guo Ruo-Yi , Fan Jing-Yi , Zhang Ya-Nan , Quan Mo-Yuan , Song Shuang , Xie Tao 
Published: September 2024

Objective:
This study aimed to investigate the protective effect and mechanism of
Astragalus polysaccharide (APS) on autoimmune encephalomyelitis.

Methods:
C57BL/6 mice were randomly divided into the blank control group, EAE group, and
APS intervention group (n=15/group). The Experimental Autoimmune Encephalomyelitis (EAE)
mouse model was established by active immunization. The pathological changes in the spinal
cord were evaluated by Hematoxylin-eosin (HE) and Luxol Fast Blue (LFB) staining. The number
of CD11b+ Gr-1+ myeloid-derived suppressor cells (MDSCs) in the spleen tissues of mice in
each group was determined by immunofluorescence staining. The expression of Arginase-1 in
the spinal cord and spleen of each group was detected by immunofluorescence double staining.
The TNF-α, IL-6, and Arginase-1 levels in the spleen were detected by ELISA assay. A western
blot was used to detect the protein expression of the AMPK/JAK/STAT3/Arginase-1 signaling
pathway.

Results:
After the intervention of APS, the incidence of autoimmune encephalomyelitis in mice
of the APS group was significantly lower than that in the EAE group, and the intervention of
APS could significantly delay the onset time in the EAE mice, and the score of neurological
function deficit in mice was significantly lower than that in EAE group (P < 0.05). APS intervention
could reduce myelin loss and improve the inflammatory response of EAE mice. Moreover,
it could induce the expression of CD11b+ GR-1 + bone MDSCs in the spleen and increase
the expression of Arginase-1 in the spinal cord and spleen. This study further demonstrated that
APS can protect EAE mice by activating the AMPK/JAK/STAT3/Arginase-1 signaling pathway.

Conclusion:
After the intervention of APS, myelin loss and inflammatory response of EAE mice
were effectively controlled. APS promoted the secretion of Arginase-1 by activating MDSCs and
inhibited CD4+T cells by activating AMPK/JAK/STAT3/Arginase-1 signaling pathway, thus
improving the clinical symptoms and disease progression of EAE mice.

conclusion:
The EAE animal model was established successfully. After the intervention of APS, myelin loss and inflammatory response of EAE mice were effectively controlled. APS promoted the secretion of Arginase-1 by activating MDSCs and inhibited CD4+T cells by activating AMPK/JAK/STAT3/Arginase-1 signaling pathway, thus improving the clinical symptoms and disease progression of EAE mice.
Exploring Phytochemical Compounds: A Computational Study for HIV-1 Reverse Transcriptase Inhibition
Authors: Bandi Jyotsna , Chunduru Madhan , Mangamuri Satya Tulasi , Nelapati Anand Kumar , Naravula Jalaja , Mulpuru Viswajit 
Published: September 2024

Background:
HIV-1 is the most virulent type, causing most AIDS cases worldwide.
Therapeutics like NRTIs and NNRTIs terminate replication by terminating polymerization reactions.
Natural-based therapeutics are increasingly being used to reduce side effects and combat disease.

Method:
The study focuses on identifying phytochemical compounds that effectively inhibit the
HIV-1 reverse transcriptase process using molecular docking and molecular dynamic simulations.

Result:
Molecular docking results show anisomelolide has a significantly stronger binding affinity
(-29.9992KJ/mol) compared to nevirapine (-13.34696 KJ/mol), forming more hydrogen bonds and
hydrophilic interactions, indicating a more stable and specific binding. MD simulations further
support these findings, with anisomelolide exhibiting lower RMSD and RMSF values, suggesting
greater structural stability and lower flexibility. Interaction energy analysis reveals robust binding
and stability for anisomelolide over time. Additionally, hydrogen bond analysis indicates more frequent
and stronger interactions for anisomelolide.

Conclusion:
The phytochemical compound anisomelolide exhibits superior binding affinity, structural
stability, and interaction dynamics, making it a promising candidate for drug development
against HIV-1 RT.
Reflections on the Union of October 17 Review of Soyuz 17 oktyabrya. Politicheskii klass Rossii: vzlet i padenie [Union of October 17. Russian political class: Rise and fall], by K.A. Solov'ev (Moscow: Novoe literaturnoe obozrenie, 2023)
Authors: Егоров А.Н. 
Published: September 2024

Анализируется научно-популярная работа профессора Национального исследовательского университета «Высшая школа экономики» К.А. Соловьева, посвященная одной из ведущих партий России начала ХХ в. – Союзу 17 октября. Рецензируемая книга является удачной попыткой в научно-популярном плане довести до широкого круга читателей ключевые проблемы взаимодействия власти и общества в период Думской монархии на примере деятельности партии октябристов. Работа опирается на широкий комплекс разнообразных источников и учитывает сложившуюся историографическую традицию изучения октябризма. Автор рассматривает дискуссионные вопросы политической идентификации октябристов, особенности взаимодействия депутатов Государственной думы и правительства, проблемы формирования политической культуры имперской России и пр. Подчеркивается серьезный вклад рецензируемой работы в осмысление дискуссионных проблем политического развития России начала ХХ в.
The reviewer considers the popular science work by Kirill A. Solov'ev, a professor at the National Research University Higher School of Economics, dedicated to the Union of October 17, one of the leading parties in Russia in the early twentieth century. The book under review is a successful attempt to bring the key problems of the interaction between power and society during the period of the Duma monarchy to a wide range of readers in a popular science way with special reference to the activities of the Octobrist Party. The work is based on a wide range of different sources and takes into account the established historiographical tradition of studying the Octobrists. The author examines the controversial issues of the Octobrists’ political identification, the peculiarities of interaction between the deputies of the State Duma and the government, the problems of forming the political culture of imperial Russia, etc. Emphasis is placed on the serious contribution of the work under review to the understanding of the controversial problems of the political development of Russia in the early twentieth century.
Count V.N. Kokovtsov in the mirror of documentary materials Review of Gosudarstvennaya i obshchestvennaya deyatel'nost' V.N. Kokovtsova: dokumental'naya monografiya [State and public activities of V.N. Kokovtsov: A documentary monograph], by M.V. Zaitsev, and M.V. Kovalev (St Petersburg: Nestor-Istoriya, 2022)
Authors: Климович Л.В. 
Published: September 2024

Тема государственной и общественной деятельности выдающихся деятелей императорской России периода царствования Николая II и их роли в социально-экономическом развитии страны начала ХХ в. по-прежнему актуальна и требует введения в оборот новых источников. Рецензируемая документальная монография, подготовленная историками М.В. Зайцевым и М.В. Ковалевым, вносит заметный вклад в изучение политической судьбы графа В.Н. Коковцова, как во время его службы на Родине, так и в эмиграции. В ней собраны материалы из российских и зарубежных архивов, большая часть которых впервые стала доступна российским исследователям. Логичная структура монографии охватывает все этапы жизненного пути Коковцова и позволяет увидеть, как проявлялась его личность в профессиональном плане. Книга будет полезна историкам и всем тем, кто интересуется темой личности в истории, а также имперским периодом России и Русским Зарубежьем.
The topic of state and public activities of prominent figures of imperial Russia during the reign of Nicholas II and their role in the socio-economic development of the country at the beginning of the twentieth century is still relevant and requires the introduction of new sources. The reviewed documentary monograph prepared by historians M. Zaitsev and M. Kovalev makes a significant contribution to the study of the political fate of Count Vladimir.N. Kokovtsov both during his service in his homeland and in emigration. It contains materials from Russian and foreign archives, most of which have become available to Russian researchers for the first time. The logical structure of the monograph covers all stages of Kokovtsov’s life and allows the reader to see how his personality manifested itself in his professional activities. The book will be useful to historians and all those who are interested in the role of the individual in history as well as the imperial period of Russia and Russian Diaspora.
Biglieri, P. y Cadahia, L. (2021). Siete ensayos sobre el populismo. Hacia una perspectiva teórica renovada. Barcelona: Herder Editorial (232 páginas)
Authors: Maiarú Julieta 
Published: September 2024

Reseña de Biglieri, P. y Cadahia, L. (2021). Siete ensayos sobre el populismo. Hacia una perspectiva teórica renovada. Barcelona: Herder Editorial (232 páginas).
Computed tomographic findings of nasal and paranasal disease in domestic rabbits highlight maxillary sinusitis and close association with dental disease: 100 studies (2004–2024)
Authors: Mikoni Nicole , Guzman David Sanchez-Migallon , Beaufrère Hugues , Phillips Kathryn 
Published: September 2024

Abstract

OBJECTIVE
To describe CT findings and epidemiologic features of nasal and paranasal disease of rabbits (Oryctolagus cuniculus).

METHODS
An electronic search was performed for rabbits that underwent skull CT from 2004 to 2024 and had findings consistent with nasal/paranasal or maxillary dental disease. History, signalment, and physical examination findings were recorded and reevaluated retrospectively for evidence of changes to the nasal passages, paranasal sinuses, and nearby associated anatomy. Data were analyzed with descriptive statistics, ordinal mixed logistic regression, and correlation analysis.

RESULTS
100 studies from 69 rabbits were reviewed. Lop-eared rabbits represented 30 of 69 cases. Upper respiratory signs (48 of 69 [69.6%]) and dental-related disorders (21 of 69 [31.9%]) were primary complaints. Rhinitis (49 of 69 [71.0%]), sinusitis (50 of 69 [72.5%]), and both (40 of 69 [60.0%]) were most diagnosed, with turbinate destruction (48 of 69 [69.6%]) and alveolar bone loss of adjacent teeth (51 of 69 [73.9%]) being common findings. Sinusitis was most common in the ventral (48 of 50 [96.0%]) and dorsal (33 of 50 [66.0%]) recesses of the maxillary sinus. Multiple CT variables were significantly correlated (P < .05); of those, maxillary alveolar bone loss of the incisor teeth and the second premolar tooth were, respectively, correlated with rhinitis grade and with sinusitis and sinusitis grade within the ventral recess of the maxillary sinus (P < .001).

CONCLUSIONS
Computed tomographic evaluation allowed characterization of nasal and paranasal disease in rabbits and the association of rhinitis, sinusitis, and dental disease.

CLINICAL RELEVANCE
The correlation between the maxillary dentition, rhinitis, and sinusitis highlights the need for thorough evaluation in CT of the teeth in rabbits with upper respiratory signs.