bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Functional Map of Ultraconserved Regions in Humans, Mice and Rats
Authors: Nichio Bruno Thiago de Lima , Oliveira Liliane Santana , Rodrigues Ana Carolina , Mathias Carolina , Gradia Daniela Fiori , Urbanski Alysson Henrique , Passetti Fabio , Camargo Victória Larissa Schimidt , Cury Sarah Santiloni , Schnepper Amanda Piveta , Carvalho Robson Francisco , Calin George A. , Oliveira Jaqueline Carvalho , Paschoal Alexandre Rossi 
Published: August 2024

Abstract

BACKGROUND: Ultraconserved regions (UCRs) encompass 481 DNA segments exceeding 200 base pairs (bp), displaying 100% sequence identity across humans, mice, and rats, indicating profound conservation across taxa and pivotal functional roles in human health and disease. Despite two decades since their discovery, many UCRs remain to be explored owing to incomplete annotation, particularly of newly identified long non-coding RNAs (lncRNAs), and limited data aggregation in large-scale databases. This study offers a comprehensive functional map of 481 UCRs, investigating their genomic and transcriptomic implications: (i) enriching UCR annotation data, including ancestral genomes; (ii) exploring lncRNAs containing T-UCRs across pan-cancers; (iii) elucidating UCR involvement in regulatory elements; and (iv) analyzing population single-nucleotide variations linked to motifs, expression patterns, and diseases.
RESULTS: Our results indicate that, although a high number of protein-coding transcripts with UCRs (1,945 from 2,303), 1,775 contained UCRs outside CDS regions. Focusing on non-coding transcripts, 355 are mapped in 85 lncRNA genes, with 35 of them differentially expressed in at least one TCGA cancer type, seven lncRNAs strongly associated with survival time, and 23 differentially expressed according to single-cell cancer analysis. Additionally, we identified regulatory elements in 373 UCRs (77.5%), and found 353 SNP-UCRs (with at least 1% frequency) with potential regulatory effects, such as motif changes, eQTL potential, and associations with disease/traits. Finally, we identified 4 novel UCRs that had not been previously described.
CONCLUSION: This report compiles and organizes all the above information, providing new insights into the functional mechanisms of UCRs and their potential diagnostic applications.
Nano zinc supplementation compared with other zinc forms: effects on growth performance, serum concentrations, and economic evaluation in broiler chickens
Authors: Saber Hamada S. , Alian Heba A. 
Published: August 2024

Abstract

The current study's aim was to assess how different zinc sources affected the broilers' growth performance, economic evaluation, and serum concentrations. One-day-old "Cobb" broiler chicks (n = 192) with an average initial body weight of 44.10 g and were randomly distributed into 6 groups. The 1st, 2nd, and 3rd groups were supplied with inorganic zinc oxide, inorganic zinc sulphate monohydrate, and organic zinc methionine, respectively, at a level of 100 mg Zn/kg diet. While the 4th, 5th, and 6th groups were supplied with nano zinc oxide (NZnO) at a level of 20, 10, and 5 mg Zn/kg diet, respectively. The study exposed that NZnO at a level of 5 mg Zn/kg (G6) achieved a significant improvement (P < 0.05) in final body weight and cumulative body weight gain, feed conversion ratio, and feed efficiency. Nano zinc oxide in G5 and G6 significantly achieved the best results in economic efficiency enhancement (P < 0.05). NZnO (G6) increased superoxide dismutase activity and HDL (high-density lipoprotein) levels either significantly (P < 0.05) compared to G1, G2, G3, and G4 or numerically with G5. The addition of NZnO lessens blood serum MDA (malondialdehyde), alanine aminotransferase and aspartate aminotransferase (ALT, AST), and creatinine levels. The nano zinc oxide in G4, G5, and G6 achieved the best performance, enhanced antioxidant activity, and improved lipid profiling, liver, and kidney functions. The positive results were more noticeable in the G6. Therefore, applying NZnO (5 mg Zn/kg diet) is a new promising feed additive in the broiler industry.
Spatial analysis of propagation thresholds from meteorological to hydrological droughts in the São Francisco River catchment, Brazil
Authors: Magalhães Lucas , Raposo Vinicius , Costa Veber 
Published: August 2024

Abstract

Effective water management requires a deeper understanding of the spatiotemporal dynamics of droughts. In this sense, comprehending drought development, under the influence of climate conditions and catchment characteristics, can enhance the strategies for minoring its adverse impacts. Based on these arguments, this study resorts to a probabilistic approach for assessing the likelihood of occurrence of a hydrological drought at distinct levels (moderate, severe, and extreme) conditioned to the durations and severities of meteorological droughts. Critical thresholds were estimated for 50 sub-basins in the Alto São Francisco River Basin, Brazil. The duration thresholds, whose medians were 7.40, 9.60, and 11.40 months for moderate, severe, and extreme events, respectively, were not too different across the study region, for all levels, and no clear spatial patterns could be found for this statistic. The severity thresholds, on the other hand, were more structured in space, with medians 9.80, 13.10, and 15.65 for the referred levels, but much more disperse. Additionally, we analyzed the correlations among the propagation thresholds and mean annual precipitation, baseflow index, and land use characteristics of the sub-basins, but no significant relationships were identified. Our results highlighted the difficulties in describing the spatial variability of the propagation thresholds, due to the complex interactions of climate, storage, and human intervention. Despite these limitations, the proposed approach proved able to capture the joint variations of drought statistics and might be useful for water resources management, promoting better decision-making and the development of appropriate mitigation strategies.
The Economic Value of Industrial Plantation Forest Loss Due To Peat Fires in Mesuji Subdistrict, Ogan Komering Ilir, Sout Sumatera, Indonesia
Authors: Grace Tiara , Putra Prabu Kresna , Eugenie Azalea , - Agustan , Amaliyah Rizki , Avianti Evie , - Anisah , Priyadi Hari , Fernando Doni , Cahyaningtiyas Ilvi Fauziyah 
Published: August 2024

Abstract

South Sumatra has extensive peatlands, with a significant portion located in Ogan Komering Ilir Regency. Mesuji Subdistrict, part of Ogan Komering Ilir Regency, hosts Industrial Plantation Forests (IPF) where Acacia (Acacia magnum) serves as the primary forestry product. Calculating the economic value or benefits of the IPF in Mesuji Subdistrict is crucial because it represents the main source of income for the region. Since 2015, peatlands in Ogan Komering Ilir have been prone to forest fires, leading to economic losses in various sectors. Despite government rehabilitation efforts, forest fires have continued to occur annually up to 2023. This study is a qualitative analysis utilizing regional secondary data to calculate the economic value of forest fire losses in Mesuji Subdistrict, Ogan Komering Ilir Regency. Economic losses due to forest fires in Mesuji Subdistrict include the loss of benefits from industrial plantation forests such as honey production, amounting to Rp. 2,262,000; timber production, amounting to Rp. 42,023,059,000,000; water cycle regulation, amounting to Rp. 90,412,140,000; and hydrological cycle regulation, amounting to Rp. 81,171,417,000.
Genome-Wide Identification and Expression Analysis of the Trihelix Gene Family in Melon
Authors: Siddique Md Nure Adil , Jone Md Jahid Hasan , Biswas Manosh Kumar , Hossain Mohammad Rashed 
Published: August 2024

Abstract

The trihelix transcription factor plays roles in regulating plant growth and development, and responses to various abiotic stresses. In this study, a comprehensive analysis of the trihelix family genes in Cucumis melo was conducted, identifying a total of 28 genes in its genome. These genes were further categorized into five subfamilies: GT-1, GT-2, SH4, GTγ, and SIP1. The study encompassed a systematic analysis of gene structures, chromosomal distribution, tandem and segmental duplication events, conserved motifs, phylogenetic relationships, and cis-acting elements of these trihelix genes. The syntenic analysis highlighted strong collinearity between trihelix family genes in C. melo with Arabidopsis, followed by rice while showing limited collinearity with those in B. distachyon. The cis-element analysis found 73 different types of cis-acting elements that are involved in stress tolerance, hormone signaling, growth and development, and responses to light in plants. Publicly available expression data of trihelix family genes in different tissues and growth stages were analyzed. The higher expressions of the genes, CmTH07, CmTH08, CmTH10, and CmTH14 in different tissues indicate their potential roles in growth and development. Based on cis-acting elements, and phylogeny study the genes CmTH02, CmTH16, CmTH20, CmTH21, CMTH24, CmTH26, and CmTH27 indicate their possible roles in abiotic stress tolerance. These findings contribute to enhancing our overall comprehension of the melon trihelix family. Furthermore, the research offers potential candidate genes to facilitate genetic enhancements for sustaining stress resistance in melons.
Outcomes and Predictors of Mortality in Acute Mesenteric Ischemia: A Prospective Study in a Yemeni Tertiary Hospital
Authors: Al-Amry Ali Lotf , Obadiel Yasser Abdurabo , Moghalles Ghamdan Mohammed , Jowah Haitham Mohammed , AL-Mashramah Gehad 
Published: August 2024

Abstract

Background: Acute mesenteric ischemia (AMI) is a critical vascular emergency with high mortality, often due to delayed diagnosis and intervention. This study aimed to evaluate the clinical outcomes and identify predictors of mortality among patients with AMI at a tertiary hospital in Sana'a, Yemen.
Methods: We conducted a prospective observational study involving 31 patients diagnosed with AMI between August 2022 and February 2024 at Al Thawra Modern General Hospital. Data on demographics, clinical presentation, diagnostic methods, management strategies, and outcomes were collected. Statistical analysis was performed to identify factors associated with increased mortality.
Results: The median age of the patients was 55.3 years, with a male predominance (67.7%). Severe abdominal pain was the most common presenting symptom (100%), followed by vomiting (77.4%) and nausea (64.5%). Arterial thrombosis was identified in 51.6% of the patients, and surgical intervention was performed in 80.6% of the patients. The overall mortality rate was 51.6%, with significant predictors of mortality, including delayed presentation (p < 0.01), heart failure (p = 0.02), and elevated white blood cell counts (p = 0.03).
Conclusions: AMI continues to have a high mortality rate, particularly in resource-limited settings such as Yemen. Early diagnosis and timely surgical intervention are crucial for improving survival. Managing comorbidities such as heart failure and identifying high-risk patients early are essential to reduce mortality in AMI patients. Further studies are needed to explore strategies to improve early diagnosis and optimize treatment outcomes.
Holistic Approach to Safety and Operational Stability: Analyzing VVER-1200 Reactor Dynamics in SGTR and AC Power Loss
Authors: Rah Shaon Md Tariqur , Joarder Md. Sadman Anjum , Hashan Antor Mahamudul , Rah Sharon Md Mahabubur , Ali Redar Hameed 
Published: August 2024

Abstract

VVER-1200 (Water-Water Energetic Reactor) represents a significant advancement in nuclear power generation, emphasizing the continuous analysis and enhancement of safety systems for reliable operation. The proposed study focuses on simulating combined scenarios involving steam generator tube rupture (SGTR) and AC power loss using core algorithms and models within personal computer transient analyzer (PCTRAN). Reactor kinetic equations, thermal-hydraulic balance, and safety system models are discussed to elucidate their role in simulating SGTR and AC power loss. Safety criteria, boundaries and initial conditions are outlined to provide a comprehensive understanding of the simulation framework. The analysis delves into dynamic behavior of VVER-1200, placing emphasis on thermal-hydraulic implications, essential reactor parameters, and radiation monitoring to facilitate impact evaluation. Continuous monitoring and maintenance of safety systems are underscored to ensure stable core cooling, particularly during proposed transient conditions. Through meticulous analysis and comparison with established benchmarks, this study contributes to bolstering the safety and reliability of VVER-1200 reactors by identifying vulnerabilities, assessing mitigation strategies, and refining emergency response protocols. Practical implications of this study offer a crucial understanding of reactor behavior, safety system performance, and emergency response strategies, thereby improving safety, optimizing operational practices, and reducing risks in nuclear reactor accidents.
Setreasure: Andoid-Based Learning Media on Sets Material
Authors: Ahmadah Intan Fathimah , Risqi Erlyanna Nur , Solehah Mar'atus 
Published: August 2024

This study aims to determine the feasibility of developing the SETREASURE learning media that has been developed and to determine the students' responses to the SETREASURE learning media. SETREASURE is aimed at seventh grade students, especially on set material. This research was conducted using the Research and Development method with the ADDIE development procedure (Analyze, Design, Development, Implementation, and Evaluation) using the Construct2 application and the web2apk. The data collection technique used a validation questionnaire in material validation sheets, media validation sheets, and student response questionnaires. The developed learning media application is equipped with material especially on in seventh grade. The feature of application, such as explanations, videos, sample questions, practice questions, and game score results.The data analysis technique in the form of an assessment score was carried out quantitatively. Based on the validation results of the learning media, SETREASURE is very feasible with a score of 83.33% on the material aspect and 81.67% on the media aspect with a note of slight improvement, as well as the results of the student response questionnaire were given a percentage of 83.21%. Students also gave a positive response to the SETREASURE learning media so that it can be stated that this learning media is very interesting for students.Keywords: Construct2, Learning Game, Mathematics Learning Media, Sets
Evaluación de los servicios ambientales del bosque urbano “Caja de Agua” (Lima, Perú) mediante i-Tree Eco y i-Tree Canopy
Authors: Huaman Rosa , Giacomotti José , Calixto Arlet 
Published: August 2024

El presente estudio tuvo como objetivo evaluar el bosque urbano “Caja de Agua” de 3.06 ha, ubicado en el distrito de San Juan Lurigancho, en la provincia de Lima, Perú, utilizando los programas i-Tree Eco y i-Tree Canopy. Se realizó un censo forestal en el área de estudio en el cual se midieron todos los individuos arbóreos y arborescentes con un diámetro a la altura del pecho (DAP) mayor a 2.5 cm a 1.30 m del suelo. Se registraron un total de 765 individuos, agrupados en 43 especies, 40 géneros y 22 familias botánicas. Con i-Tree Eco se estimaron los servicios ambientales proporcionados por el arbolado de "Caja de Agua", los cuales fueron la eliminación de 256.9 kg/año de contaminantes del aire (CO, O3, SO2, NO2, PM2.5 y PM10), la captura anual de 16.44 toneladas métricas de carbono, el almacenamiento de 172 toneladas métricas de carbono y la producción de 43.83 toneladas métricas de oxígeno al año. Las especies forestales que otorgaron los mayores servicios ambientales fueron Eucalyptus camaldulensis Dehnh., Ligustrum lucidum W.T. Aiton, Fraxinus americana L. y Ceiba speciosa (A. St.-Hil.) Ravenna, influenciadas por su abundancia y área foliar. Utilizando el programa i-Tree Canopy se clasificaron cuatro tipos de cobertura en el bosque urbano "Caja de Agua" (arbórea/arbustiva, suelo desnudo, herbácea y construcciones) mediante la fotointerpretación de imágenes satelitales disponibles en Google Earth, determinando una disminución de su cobertura arbórea en los últimos 14 años. Los resultados indican que el bosque urbano “Caja de Agua” proporciona servicios ambientales para la ciudad, el cual debe ser conservado para el beneficio de la comunidad local.
Single-cell RNA-sequencing Analysis Reveals the Promoting Role of the Hedgehog Pathway in Epithelial Cells during Cervical Cancer Progression
Authors: Ji Chen , Wang Yiyi , Jiang Yingchun , Wang Yan 
Published: August 2024

Aim:
This study explored the role of the Hedgehog pathway in epithelial cells
during cervical cancer [CC] progression, providing new insights for improving current
CC treatment.

Background:
Abnormal activation of the Hedgehog signaling pathway is associated
with the malignant transformation of CC epithelial cells. Single-cell atlas of CC and the
role of Hedgehog pathway in epithelial cells during CC progression remain to be explored.

Objective:
To comprehensively analyze the mechanism of Hedgehog pathway activation
in CC epithelial cells and its impact on tumor progression by applying single-cell RNA
sequencing [scRNA-seq] analysis.

Methods:
The scRNA-seq data were acquired from the Gene Expression Omnibus
[GEO] database and then processed with the Seurat package. FindNeighbors and Find-
Clusters functions were applied to cluster the cells. The CellMarker database was used
for subgroup annotation. Differentially expressed genes [DEGs] in each cell subgroup
were filtered by FindAllMarkers function. Biological function analysis for the gene set
of interest was performed using Clusterprofiler package. AUCell function was employed
to calculate the score of the Hedgehog pathway. The differentiation trajectory in epithelial
cell subtypes was generated by performing Pseudotime analysis. Finally, protein-protein
network [PPI] was used to investigate the interactions between the Hedgehog pathway
and other pathways enriched in the gene set of interest.

Results:
A total of 9 major cell subpopulations were classified and the proportion of
epithelial cells was the highest in CC samples. Further analysis revealed that the Hedgehog
pathway was abnormally activated in STYK1+ and TP73+ epithelial cell subtypes.
Pseudo-time trajectory analysis showed that the differentiation trajectory of STYK1+
epithelial cells gradually transformed into defense-to-virus cells or into proliferation
cells, while TP73+ epithelial cells eventually differentiated into two branches of response
to estrogen and virus-induced proliferation. PPI analysis showed that the Hedgehog
pathway was involved in the proliferation and viral process of epithelial cells in CC.

Conclusion:
The current study comprehensively analyzed the features of CC samples
and differentiation trajectories of epithelial cell subtypes, as well as the role of the
Hedgehog pathway in epithelial cells during CC progression. More importantly, effective
target genes were discovered for the molecular diagnosis and precise treatment of
CC.
A Novel Cuproptosis-Related Gene Signature Predicts Prognosis in Papillary Thyroid Carcinoma Patients
Authors: Cao Jun , Zhang Shijia , Zhou Kehui , Mao Xiaochun , Zhao Ming , Shang Jinbiao , Lan Xiabin 
Published: August 2024

background:
Cuproptosis is a novel type of cell death mediated by protein lipoylation，and is closely related to mitochondrial metabolism. Clinical association of cuproptosis-related genes（CRGs）in thyroid cancer, however, remains unclear. In this study, we systematically evaluated the differential expression and genetic alterations of CRGs in papillary thyroid cancer (PTC) and constructed a CRG signature to predict the prognosis of PTC patients.

method:
We integrated the data of The Cancer Genome Atlas (TCGA) database and analyzed the expression of 10 CRGs in PTC. CRG signature was constructed by univariate Cox analysis and selection operator (LASSO) Cox regression. In addition, the signature-related molecular features were validated by a combination of functional enrichment, Cox regression, and immune infiltration analysis. Independent validation cohort data and quantitative real-time polymerase chain reaction (qRT-PCR) were used to validate the expression of differentially expressed CRG (CDKN2A).

result:
Thyroid cancer patients could be divided into two subtypes (low and high CRG score groups) and we found that overall survival (OS) of patients was lower in high CRG score group (HCSG) than in low CRG score group (LCSG) (p &amp;amp;lt; 0.001). And the area under the curve (AUC) values for 3 years, 5 years, and 8 years were 0.872, 0.941, and 0.976, respectively. Cox regression analysis showed that the CRG score could be used as an independent prognostic indicator for PTC. Functional enrichment analysis indicated that the CRG prognostic signature was also associated with the tumor immune microenvironment. In HCSG, the immune suppression type cell score is significantly higher than in LCSG. In addition, we identified the expression of CRG (CDKN2A) by qRT-PCR, and the results were consistent with the TCGA database.

conclusion:
Our CRG signature has a good predictive ability for the prognosis of PTC patients. CRGs may play an important role in tumorigenesis and could be used to predict immunotherapy efficacy of PTC.
ResUbiNet: A Novel Deep Learning Architecture for Ubiquitination Site Prediction
Authors: Duan Zixin , Liang Yafeng , Xiu Xin , Ma Wenjie , Mei Hu 
Published: August 2024

Introduction:
Ubiquitination, a unique post-translational modification, plays a cardinal
role in diverse cellular functions such as protein degradation, signal transduction, DNA repair, and
regulation of cell cycle.

Method:
Thus, accurate prediction of potential ubiquitination sites is an urgent requirement for exploring
the ubiquitination mechanism as well as the disease pathogenesis associated with ubiquitination
processes.

Results:
This study introduces a novel deep learning architecture, ResUbiNet, which utilized a protein
language model (ProtTrans), amino acid properties, and BLOSUM62 matrix for sequence embedding
and multiple state-of-the-art architectural components, i.e., transformer, multi-kernel convolution,
residual connection, and squeeze-and-excitation for feature extractions.

Conclusion:
The results of cross-validation and external tests showed that the ResUbiNet model
achieved better prediction performances in comparison with the available hCKSAAP_UbSite, RUBI,
MDCapsUbi, and MusiteDeep models.