bluuebunny/crossref_metadata_2025_split huggingface dataset:
Computational Prediction of Candidate miRNAs and their Targets	from Medicago truncatula Non-Protein-Coding	Transcripts
Authors: Wen Jiayu , Frickey Tancred , Weiller Georg F. 
Published: January 2025

Identification and analysis of miRNAs enhances our understanding of the important roles that small RNAs play in complex regulatory networks. It is often difficult to perform large-scale validation of miRNA expression that is predicted from genomic regions. Expressed transcripts provide an alternative resource to facilitate identification of miRNAs and their targets. We developed a computational pipeline to scan for miRNA genes from polyadenylated transcripts that were associated with limited protein coding potentials, corresponding to the intergenic regions of Medicago truncatula genomic sequences. Each predicted miRNA was required to have a near perfect match with target genes. We also searched for miRNA conservation in other plant species, clustered highly similar miRNAs, and provided a functional classification of target genes. The data is represented in the Medicago-MIRATdb (MiRNA And Target gene Data Base). The database provides detailed information on the sequences of the predicted miRNAs, their precursors, and potential target genes. It also details sequence source information such as the EST library, tissue category, and the number of EST clones. Information regarding miRNA conservation in other species, functional classification of target genes, and clusters of similar miRNAs is also provided. The web interface to the database provides researchers with the ability to narrow their search for miRNAs and target genes of interest by using a variety of filters. To our knowledge, this work represents the first systematic effort to identify candidate miRNAs and targets in the model legume M. truncatula. The database is freely accessible at http://bioinfoserver.rsbs.anu.edu.au/utils/MIRATdb/Medicago/v1/.
MaXlab: A Novel Application for the Cross Comparison and	Integration of Biological Signatures from Microarray Studies
Authors: Khalid Sabah , Khan Mohsin , Gorle Chandrasekhar Babu , Fraser Karl , Wang Ping , Liu Xiaohui , Li Suling 
Published: January 2025

Microarray gene expression datasets are continually being placed in public repositories. As a result, one of the most important emerging challenges is that which enables researchers to take full advantage of such previously accumulated data to discover or validate common genes in similar biological systems. In light of this we have designed the MaXlab software to not only cross-compare available array data from different laboratories but also extract further knowledge from gene expression patterns embedded within published data. More importantly MaXlab offers a flexible and automated solution applicable for microarray technologies including cDNA and Affymetrix gene chips generating expression profiles for common genes with biological significance. We have identified several sets of genes previously unknown to be commonly expressed across studies investigating related biological questions. Among them is the identification of 17 genes involved in the dysregulation of immune tolerance including the crucial transcription factor Egr2. In addition, we have identified 175 genes commonly expressed in basal and luminal breast tumours in response to the chemotherapeutic drug doxorubicin. The universal expression and characterisation of these encouraging genes identified through MaXlab suggests that they may play a common role in the mechanism of disease and hence act as an incentive for further investigation for identifying potential therapeutic targets. Overall, MaXlab is an attractive application for molecular biologists extracting the intersection between microarray datasets together with the gene expression profiles, from which biologists are able to infer further biological insights. The software together with file formats and additional material is freely available at http://www.immuno-software.org.
QColors: An algorithm for conservative viral quasispecies reconstruction from short and non-contiguous next generation sequencing reads
Authors: Huang Austin , Kantor Rami , DeLong Allison , Schreier Leeann , Istrail Sorin 
Published: January 2025

Next generation sequencing technologies have recently been applied to characterize mutational spectra of the heterogeneous population of viral genotypes (known as a quasispecies) within HIV-infected patients. Such information is clinically relevant because minority genetic subpopulations of HIV within patients enable viral escape from selection pressures such as the immune response and antiretroviral therapy. However, methods for quasispecies sequence reconstruction from next generation sequencing reads are not yet widely used and remains an emerging area of research. Furthermore, the majority of research methodology in HIV has focused on 454 sequencing, while many next-generation sequencing platforms used in practice are limited to shorter read lengths relative to 454 sequencing. Little work has been done in determining how best to address the read length limitations of other platforms. The approach described here incorporates graph representations of both read differences and read overlap to conservatively determine the regions of the sequence with sufficient variability to separate quasispecies sequences. Within these tractable regions of quasispecies inference, we use constraint programming to solve for an optimal quasispecies subsequence determination via vertex coloring of the conflict graph, a representation which also lends itself to data with non-contiguous reads such as paired-end sequencing. We demonstrate the utility of the method by applying it to simulations based on actual intra-patient clonal HIV-1 sequencing data.
A Osseointegration of Dental Implants in Atrophic Regions. The use of Densah Burs, Osseodensification Technique, in Sinus Lift Procedures. A Clinical Case and Review Literature.
Authors: Koshovari Alba , Muca Amela , Berdica Leart , Bushati Teona , Fejza Laura , Kaja Oltjon , Koci Ardita 
Published: January 2025

Introduction: Atrophic posterior maxillary regions pose a significant challenge in dental medicine, where dental implant stability is hard to achieve. The innovative osseo-densification, a new biomechanical technique that aims to solve this problem without removing any bone tissue, is a topic of great interest and potential in our field.
Case report: The patient, A.K., a 44-year-old smoking female, was presented to the clinic concerned with the lack of ability to eat from her left side as a result of the extraction of her upper molars. After a 3D radiographic scan was conducted, it was confirmed that there was considerable bone loss in the upper left posterior region and a proximity with the maxillary sinus. As part of the treatment plan, an Osseo-densification technique in crystal maxillary sinus elevation would be used for two implant placements in the first and second molar regions.
Conclusions: The osseo-densification technique in crestal sinus lifting was shown to be a dependable and less invasive option for treating considerable posterior maxillary bone loss. However, conclusive findings are still needed for this technique, emphasizing the need for continuous research and learning in our field.
Understanding the Dynamics of the Political Use of Religion in Bangladesh: Causes, Process, and Consequences
Authors: Siddika Ayesha , Islam Shafiul , Saara Khan Amia , Akter Sathi Halima 
Published: January 2025

This paper attempts to understand how religion plays a pivotal role in politics with a focus on the process through which amalgamation of religion and politics usually takes place, and how such amalgamation impacts the political sphere in Bangladesh. By using Riaz’s political expediency theory, this paper argues that the political use of religion was institutionalized by the military regimes to consolidate their power base and while for democratic governments, the primary reason to use religion as a political agenda was to gain mass popularity. However, this tendency always possesses the risk of falling out of balance and creating communal tension. The purpose led to materializing drastic steps such as state- sponsored patronization, constitutional modification, depiction of religious attitudes by political leaders, political expediency, and application of digital platforms for political purpose, that eventually caused the amalgamation of religion and politics. The impact of such amalgamation is found primarily negative, including restricting attitude toward liberal ideology and threat to minorities.
Social Science Review, Vol. 41(1), June 2024, Page 39-56.
PENGARUH WAKTU PEMANASAN TERHADAP KARAKTERISTIK PULP DARI PELEPAH PISANG DENGAN MENGGUNAKAN METODE ACETOSOLV
Authors: Tiara Greenastya Febrianis , Hardjono  
Published: January 2025

Pulp adalah material yang digunakan untuk membuat kertas. Bahan baku yang biasa digunakan dalam industri pulp dan kertas adalah kayu. Eksploitasi hutan yang terus menerus dilakukan untuk memenuhi kebutuhan industri tersebut akan berdampak terhadap ketersediaan kayu dan mengakibatkan banyak permasalahan global. Alternatif bahan baku pembuatan pulp dan kertas sangat diperlukan, salah satunya adalah pelepah pisang. Pembuatan pulp dari pelepah pisang dapat dilakukan melalui metode acetosolv, yaitu metode yang menggunakan asam asetat sebagai pelarut organik. Kualitas pulp yang dihasilkan dapat dipengaruhi oleh beberapa faktor, salah satunya yaitu waktu pemanasan. Penelitian ini bertujuan untuk mengetahui waktu pemanasan terbaik dan mengetahui pengaruh waktu pemanasan terhadap karakteristik pulp. Waktu pemanasan yang digunakan adalah 30 menit, 45 menit, dan 60 menit. Proses pembuatan pulp meliputi size reduction dan pengeringan pelepah pisang, pencampuran dan pemanasan serbuk pelepah pisang dengan asam asetat, dan pembilasan campuran menggunakan etanol dan air. Pulp yang dihasilkan selanjutnya dilakukan pengujian karakteristik berupa nilai yield, kadar air, kadar abu, kadar lignin, dan kadar selulosa. Dari hasil penelitian, diperoleh nilai yield tertinggi sebesar 71% pada waktu pemanasan 60 menit, kadar air terendah sebesar 3% pada waktu pemanasan 60 menit, kadar abu terendah sebesar 2% pada waktu 60 menit, kadar lignin terendah sebesar 13% pada waktu 30 menit, dan kadar selulosa tertinggi sebesar 87% pada waktu 30 menit. Berdasarkan hasil penelitian, diperoleh kesimpulan bahwa waktu pemanasan terbaik adalah 60 menit dan semakin lama waktu pemanasan akan menurunkan yield, kadar air, kadar abu, dan kadar lignin serta meningkatkan kadar selulosa pulp yang dihasilkan.
Brucella suis ΔmapB outer membrane vesicles as an acellular vaccine against systemic and mucosal B. suis infection
Authors: González Florencia Muñoz , Bialer Magali G. , Cerutti Maria L. , Estein Silvia M. , Ramis Lila Y. , Baldi Pablo C. , Zorreguieta Ángeles , Ferrero Mariana C. 
Published: January 2025

IntroductionSwine brucellosis, caused by Brucella suis, is a worldwide infectious zoonotic disease. Currently, there are no available human or porcine vaccines to protect against B. suis infection, which is primarily acquired through the mucosa. We recently described B. suis MapB, the homologous protein of TamB, the inner membrane component of the TAM system. Our findings indicate that MapB is involved in bacterial cell envelope homeostasis. In this study, we characterize the outer membrane vesicles (OMVs) of B. suis 1330 (wt) and those of B. suis ΔmapB (ΔmapB) mutant strain and evaluate their vaccine potential in mice.MethodsOMVs were isolated using the ultracentrifugation method and characterized through electron microscopy, Dynamic Light Scattering, SDS-PAGE and proteomics. Immunogenicity was assessed by intramuscular immunization of mice with wt OMVs or ΔmapB OMVs, followed by the measurement of antigen-specific antibody levels and functional assays to evaluate the protective capacity of the antibodies. Cellular immunity was assessed by characterizing cytokine secretion through ELISA after in vitro stimulation of spleen cells with heat-killed B. suis. To determine the level of protection conferred by immunization, mice were challenged with virulent B. suis via intraperitoneal or intratracheal routes, and the bacterial load was quantified post-challenge.ResultsDynamic Light Scattering of the OMVs from both strains revealed the presence of spherical structures of 90-130 nm. Proteomic analysis identified 94 and 95 proteins in the wt and ΔmapB OMVs, respectively, including several known Brucella immunogens. Both OMVs showed immunoreactivity with sera from Brucella-infected pigs. Intramuscular immunization of mice with both OMVs induced antigen-specific IgG in serum, with the ΔmapB OMVs group showing higher titers compared to the wt OMVs group. Serum antibodies from both OMVs groups reduced B. suis adherence and invasion of lung epithelial cells and enhanced its phagocytosis by macrophages. Upon in vitro antigen stimulation, spleen cells from mice immunized with ΔmapB OMVs secreted higher levels of interleukin-17 and especially gamma interferon compared to cells from mice immunized with wt OMVs, suggesting the induction of a stronger T helper 1 response in the ΔmapB OMVs group. While immunization with both wt and ΔmapB OMVs achieved the same level of protection following intratracheal infection with B. suis (p&lt;0.01), immunization with ΔmapB OMVs provided higher levels of protection against intraperitoneal infection.DiscussionOverall, these results demonstrate that the B. suis ΔmapB OMVs are immunogenic and capable of inducing both cellular and humoral immune responses that protect against mucosal and systemic B. suis challenges.
Analysis of the safety and efficacy of flow diverter device in the treatment of tandem aneurysms in the internal carotid artery
Authors: Wan Jun , Xu Ligang , Jiang Yeqing , Zhang Lei , Wang Zhenyu , Zhang Xiaolong , Wang Shengzhang 
Published: January 2025

ObjectiveTo investigate the clinical efficacy and safety of flow diverter device (FDD) in the treatment of tandem aneurysms in the internal carotid artery.Materials and methodsThis study was a retrospectively observational study involving two neurointerventional centers. Sixteen Patients with tandem aneurysms in the internal carotid artery treated with FDD and Digital Subtraction Angiography (DSA) follow-up in Huashan Hospital Affiliated with Fudan University and Jing’an District Central Hospital Affiliated with Fudan University from 2020.08 to 2023.12 were included. The outcomes included the angiographic occlusion rate of aneurysms, complications, and the modified Rankin Scale score. The risk factors of complete occlusion of tandem aneurysms were explored by logistic regression analysis.ResultsA total of 38 aneurysms were included, including 21 aneurysms of 8 patients in the Pipeline Embolization Device (PED) group and 17 aneurysms of 8 patients in the Tubridge Flow Diverter (TFD) group. A total of 16 FDD stents were implanted, 8 in each PED and TFD group, with a technical success rate of 100%. The median value of maximum aneurysm diameter (Dmax) was 4.27 (3.57–5.41) mm. Among them, 28 aneurysms had a maximum diameter of &lt;5 mm (73.7%), 10 aneurysms had a maximum diameter of 5–15 mm (26.3%). All patients were followed up clinically for a median of 25.5 months (15.5–28.7 months). There were no deaths and symptomatic complications. The modified Rankin Scale scores (mRS) of 16 patients were all less than 2. All patients were examined by angiography with a median of 14 months (6–27 months). Among them, there were 5 Consensus Grading Scale for Endovascular Aneurysm Occlusion (CGSFEAO) grade 5 (13.2%), 1 CGSFEAO grade 4 (2.6%), 1 CGSFEAO grade 2 (2.6%) and 31 CGSFEAO grade 0 (81.6%). The complete occlusion rate of intracranial aneurysm in the whole study was 81.6%, including 85.7% in the PED group and 76.5% in the TFD group, and there was no significant statistical difference between the two groups. Statistically significant variables were not found in univariate logistic regression analysis.ConclusionFDD is safe and effective in treating tandem aneurysms in the internal carotid artery with a high occlusion rate and few complications. TFD is comparable to PED in the treatment of intracranial tandem aneurysms.
Tinea Capitis Induced by Barber Shaving: Isolation of Trichophyton tonsurans
Authors: Addari Giampaolo , Corbeddu Marialuisa , Mugheddu Cristina , Chessa Mariangela , Vivanet Grazia , Ferreli Caterina , Atzori Laura 
Published: January 2025

Background/Objective: Tinea capitis is a common scalp fungal infection with significant implications for public health, particularly in regions where proper hygiene and access to healthcare are limited. Emerging evidence suggests that this disease, particularly in young male individuals, may be related to certain unsanitary practices in barbershop settings, such as the use of contaminated shaving equipment. To increase awareness of the risk of scalp dermatophyte infections by disclosing different cases of tinea capitis that had arisen shortly after hairdressing procedures and providing a comprehensive review of the existing literature. Patients and Methods: 10 cases of young, adult male patients developed tinea capitis after haircuts carried out at different local barbershops in Sardinia. A collection of data regarding age, sex, location of the disease, clinical manifestations as well as direct microscopy and cultural investigations were performed. Results: Clinical manifestations varied among patients, exhibiting both non-inflammatory and inflammatory features, cultural investigations were positive for Trichophyton tonsurans. Patients were treated with griseofulvin or terbinafine in combination with topical antimycotics. Two cases out of the ten patients developed scarring alopecia. Conclusions: Outbreaks of T. tonsurans-induced tinea capitis, linked to hairdressing, have been recorded in many different countries. Timely diagnosis and therapy are crucial, since any delay can result in disease dissemination and potential complications such as scarring alopecia, particularly in the inflammatory forms.
Skatole Alleviates Osteoarthritis by Reprogramming Macrophage Polarization and Protecting Chondrocytes
Authors: Wang Weiyun , Chu Yaru , Lu Yunkun , Xu Jie , Zhao Weixuan , Liang Zhuo , Guo Xueqiang , Xi Lingling , Han Tao , Shen Yaping , Song Wenjuan , Tang Yanhua , Wen Mengnan , Qian Zhuang , Wang Lei , Fan Zhenlin , Zhou Guangdong , Ren Wenjie 
Published: January 2025

Osteoarthritis (OA) is the most prevalent joint disease, yet effective disease-modifying OA drugs (DMOADs) remain elusive. Targeting macrophage polarization has emerged as a promising avenue for OA treatment. This study identified skatole through high-throughput screening as an efficient modulator of macrophage polarization. In vivo experiments demonstrated that skatole administration markedly reduced synovitis and cartilage damage in both destabilization of medial meniscus (DMM)-induced OA mice and monosodium iodoacetate (MIA)-induced OA rats. Mechanistically, skatole activated signal transducer and activator of transcription 6 (Stat6) signaling, promoting M2 macrophage polarization, while inhibiting nuclear factor-κB (NFκB) and mitogen-activated protein kinase (MAPK) signaling pathways to suppress M1 polarization. RNA-sequencing analysis, targeted metabolomics, and mitochondrial stress tests further revealed that skatole treatment shifted macrophages toward oxidative phosphorylation for energy production. Additionally, it up-regulated genes associated with glutathione metabolism and reactive oxygen species (ROS) pathways, reducing intracellular ROS production. The CUT&Tag assay results indicated that the downstream transcription factor p65 of NFκB can directly bind to gene loci related to inflammation, oxidative phosphorylation, and glutathione metabolism, thereby modulating gene expression. This regulatory process is inhibited by skatole. At the chondrocyte level, conditional medium from skatole-treated M1 macrophages balanced anabolism and catabolism in mouse chondrocytes and inhibited apoptosis. In IL1β-treated chondrocytes, skatole suppressed inflammation and catabolism without affecting apoptosis or anabolism. Overall, skatole maintains immune microenvironment homeostasis by modulating macrophage polarization in joints and preserves cartilage function by balancing chondrocyte anabolism and catabolism, effectively alleviating OA. These findings suggest skatole’s potential as a DMOAD.
ЭМОЦИОНАЛЬНЫЙ ИНТЕЛЛЕКТ: ПОНЯТИЕ, МОДЕЛИ И ФОРМИРОВАНИЕ
Authors: Губарева Л.И. , Чянкаева З.А. , Соловьев А.Г. , Литвинова Л.В. 
Published: January 2025

В статье представлены концепции и модели эмоционального интеллекта, а также структурно-функциональные основы и нейрофизиологические механизмы формирования эмоций. Должное внимание уделено факторам, влияющим на формирование эмоционального интеллекта и как следствие на успешность деятельности. Показаны перспективы дальнейших исследований в области поиска мозговых коррелятов эмоционального интеллекта и их взаимосвязи с другими адаптационными системами организма и свойствами личности, так как для людей, работающих по профессии типа «человек-человек», «человек-машина», эмоциональный интеллект является профессионально важным качеством.
he article presents concepts and models of emotional intelligence, as well as structural and functional foundations and neurophysiological mechanisms of emotion formation. Due attention is paid to factors influencing the formation of emotional intelligence and, as a consequence, the success of activities. The prospects for further research in the field of searching for brain correlates of emotional intelligence and their relationship with other adaptive systems of the body and personality property's are shown, since for people working in a profession such as "person-person", "person-machine" emotional intelligence is a professionally important quality.