bluuebunny/crossref_metadata_2025_split huggingface dataset:
An oxidative stress-related lncRNA prognostic risk model for thyroid cancer
Authors: 龙 亚红 , Mi Yan xia , Zhang Wan-chun , Jin Jian-hua 
Published: April 2023

Abstract
Purpose: Oxidative stress-elated genes (OSRGs) and long non-coding RNA (lncRNA) have been reported to be associated with cancer prognosis, but the prognostic role of oxidative stress-related lncRNAs (OSRlncRNAs) in thyroid cancer (THCA) is unclear.
Methods:RNA-sequencing data and OSRGs were downloaded from public databases. Differentially expressed OSRGs (DE-OSRGs) were identified by limma or DESeq2 packages. Pearson correlation analysis was performed to screen OSRlncRNAs. Furthermore, prognostic risk model was constructed by Cox and Least Absolute Shrinkage and Selection Operator (LASSO) regression analyses. A nomogram was further developed. Moreover, functional enrichment analyses were performed on differentially expressed genes (DEGs) between high- and low-risk groups. Finally, a lncRNA-mRNA co-expression network was constructed to analyze the regulatory relationship of model lncRNA.
Results: The prognostic risk model based on two OSRlncRNA (DPP4-DT, SAP30-DT) was constructed. The predictive power of the nomogram was accurate and reliable (c-index = 0.942). The neuroactive ligand-receptor interactions, thyroid hormone synthesis, and cytokine-cytokine receptor interactions pathways are important in THCA. The co-expression network results showed that 88 DEGs were regulated by DPP4-DT.
Conclusion:The prognostic risk model constructed based on two OSRlncRNA (DPP4-DT, SAP30-DT) could effectively predict the prognosis of THCA patients and provided insights for new personalized prediction and treatment for THCA patients.
Monte Carlo simulation of the Varian TrueBeam flattened-filtered beams using a surrogate geometry in PRIMO
Authors: Rodriguez Miguel , Sempau Josep , Brualla Lorenzo 
Published: April 2023

Abstract
Background: Monte Carlo simulation of radiation transport for medical linear accelerators (linacs) requires accurate knowledge of the geometrical description of the linac head. Since the geometry of Varian TrueBeam machines has not been disclosed, the manufacturer distributes phase-space files of the linac patient-independent part to allow researchers to compute absorbed dose distributions using the Monte Carlo method. This approach limits the possibility of achieving an arbitrarily small statistical uncertainty. This work investigates the use of the geometry of the Varian Clinac 2100, which is included in the Monte Carlo system PRIMO, as a surrogate.
Methods: Energy, radial and angular distributions extracted from the TrueBeam phase space files published by the manufacturer and from phase spaces tallied with PRIMO for the Clinac 2100 were compared for the 6, 8, 10 and 15 MV flattened-filtered beams. Dose distributions in water computed for the two sets of PSFs were compared with the Varian Representative Beam Data for square fields with sides ranging from 3 to 30 cm. Output factors were calculated for square fields with sides ranging from 2 to 40 cm.
Results: Excellent agreement with the Varian Representative Beam Data was obtained for the simulations that employed the phase spaces distributed by Varian as well as for those that used the surrogate geometry, reaching in both cases Gamma (2%, 2 mm) pass rates larger than 99%, except for the 15 MV surrogate. This result supports previous investigations that suggest a change in the material composition of the TrueBeam 15 MV flattening filter. In order to get the said agreement, PRIMO simulations were run using enlarged transport parameters to compensate the discrepancies between the actual and surrogate geometries.
Conclusions: This work sustains the claim that the simulation of the 6, 8 and 10 MV flattening-filtered beams of the TrueBeam linac can be performed using the Clinac 2100 model of PRIMO without significant loss of accuracy.
Genetic evidence for a causal relationship between innate leukocytes and risk of digestive system cancers in East Asians and Europeans
Authors: Zhu Jiahao , Pang Xiangyi , Wang Xin , Wang Ren , Lian Jie , Xu Benjie , Ji Shengjun , Lu Haibo 
Published: April 2023

Abstract

Background
Immune dysregulation plays an important role in cancer onset and development. The causal relationships between innate leukocytes prior to cancer and the risk of digestive system cancers remain unknown. This study assesses the causal correlations between white blood cells (WBC) and digestive system cancer risk in East Asians and Europeans.
Methods
Summary-level data of WBC-related genetic variation were extracted from Biobank Japan (107,964 and 62,076 participants), and a recent large-scale meta-analysis (563,946 participants). Summary-level data for the cancers were obtained from Biobank Japan (212,978 individuals) and the FinnGen consortium (178,802 participants). Univariable and multivariable Mendelian randomization (MR) analysis was performed in East Asians and Europeans separately.
Results
Univariable MR analysis demonstrated the significant association between circulating eosinophil counts and risk of colorectal cancer (CRC) in the East Asians (odds ratio (OR) = 0.80, 95% confidence interval (CI): 0.69–0.92, P = 0.002) and a suggestive relationship in the European population (OR = 0.86, 95% CI: 0.77–0.97, P = 0.013). An inverse suggestive association was observed between levels of basophil and risk of gastric cancer (GC) in East Asians (OR = 0.83, 95% CI: 0.72–0.97, P = 0.019). The multivariable MR analysis showed the independent causal effect of eosinophil count on CRC risk in East Asians (OR = 0.72, 95% CI: 0.57–0.92, P = 0.009) and Europeans (OR = 0.80, 95% CI: 0.70–0.92, P = 0.002). Circulating basophils served as the negative causal factor in GC risk in East Asians (OR = 0.80, 95% CI: 0.67–0.94, P = 0.007).
Conclusions
Our MR analyses reveal the genetically causal effect of blood eosinophils on decreased risk of CRC in both Europeans and East Asians, and of basophils on decreased risk of GC in Europeans.
A Novel Nested Production Function Approach
Authors: Pal Samidh 
Published: April 2023

Abstract
This paper presents a new nested production function that is specifically designed for analyzing capital and labor intensity of manufacturing industries in developing and developed regions. The paper provides a rigorous theoretical foundation for this production function. The analysis shows that the production function can be used to accurately estimate the level of capital and labor intensity in industries, as well as to analyze the capacity utilization of these industries.
Conservation status of vascular epiphytes in the Neotropics
Authors: Carmona-Higuita Maria Judith , Mendieta-Leiva Glenda , Gómez-Díaz Jorge Antonio , Villalobos Fabricio , Ramos Flavio Nunes , Elias João Pedro Costa , Jiménez-López Derio Antonio , Zuluaga Alejandro , Holst Bruce , Kessler Michael , Mathieu Guido , Zizka Alexander , Zotz Gerhard , Krömer Thorsten 
Published: April 2023

Abstract
The Neotropical realm hosts some of the Earth’s most species-rich biodiversity hotspots, with vascular epiphytes significantly contributing to this diversity. However, many regions of the Neotropics where epiphytic species of restricted distribution are reported coincide with threatened ecosystems, such as the tropical montane cloud forest. Moreover, epiphytes may be especially vulnerable to land use and climate change impacts due to their dependence on host trees. We assessed the conservation status of vascular epiphytes in the Neotropics for the families that represent over 80% of the global epiphyte diversity (Araceae, Bromeliaceae, Orchidaceae, Piperaceae, and Polypodiaceae) and identified geographical centers of accumulation of threatened epiphyte species. We gathered information from free-access web repositories, specific epiphytic plant databases, and scientific and grey literature. We assessed the extinction risk of 11,446 epiphyte species following IUCN Red List guidelines, using Criterion B (geographic range size). We found nearly 60% (6,721 species) to be threatened, with 1,766 critically endangered (CR), 3,537 endangered (EN), and 1,418 vulnerable (VU). The threatened species are mainly found in the centers of endemism of vascular epiphytes in Central America, the northern Andes, and the Atlantic Forest. Our study emphasises that the centers of threatened species largely coincide with diversity hotspots, highlighting epiphytes as an especially vulnerable group that requires urgent conservation actions.
Groundwater level dynamic simulation and soil salinization prediction of the closed hydrogeological unit in the arid irrigation area
Authors: Lian Haidong , Sun Zhaojun , Xu Cundong , Gu Fengyou , Liu Zijin , He Jun 
Published: April 2023

Abstract

Aiming at problems such as inaccurate simulation of groundwater level in closed hydrogeological units, difficult quantitative prediction of soil salinization degree, and unclear water and salt migration, a three-dimensional simulation model of groundwater was established, and the development trend of groundwater level and soil salinization was predicted. The groundwater level simulation results are consistent with the changing trend of the observational data and the simulation model can be used to predict groundwater levels in closed hydrogeological units. When climate scenarios and human activity change are set as future scenarios, the average groundwater buried depth will continue to decrease in the next 10 years, the area with a groundwater buried depth of 0–5 m will exceed 50%, and even the groundwater will overflow to the surface. The change of soil salt content is predicted quantitatively and the salinization degree will develop from ‘saline–alkali soil’ and ‘mild saline–alkali soil’ to ‘medium saline–alkali soil’. The process of water and salt migration in three key hydrologic zones, namely ‘irrigation infiltration’, ‘solute migration’, and ‘water and salt accumulation’, is revealed in the closed hydrogeological unit. The research results can provide new ideas for the improvement of soil and water environment problems.
Characterizing groundwater quality for a safe supply of water using WQI and GIS in Bahir Dar city, northwest Ethiopia
Authors: Asmamaw Menen , Debie Ermias 
Published: April 2023

Abstract
Although both urban and rural residents benefit from drinking enough high-quality water in the right amounts, the degree of contamination from artificial sources has been increasing. The study aims to assess the quality and availability of groundwater potential in Bahir Dar City using geographic information systems (GIS)-based ordinary kriging (OK) and analytical hierarchy process methods, respectively. The concentrations of pH, alkalinity, Escherichia coli, nitrite manganese, and iron in the groundwater of built-up areas were found to exceed the limits set by the World Health Organization. The groundwater quality distribution contained 69.6% of good water, 19.6% of the excellent class, and 10.8% of the poor class. The high potential of groundwater, particularly in the Lake Tana shoreline sedimentation areas, revealed the poor quality class. The results suggest that improving groundwater quality should be prioritized in areas with high potential groundwater availability.
Study on the Analgesic Activity of Peptide from Conus achates
Authors: Liu Xiujie , Wang Fuli , Yu Huilan , Liu Changcai , Xia Junmei , Ma Yangde , Jiang Hui 
Published: April 2023

Background:
As a peptide originally discovered from Conus achates by mass spectrometry
and cDNA sequencing, Ac6.4 contains 25 amino acid residues and three disulfide bridges. Our
previous study found that this peptide possesses 80% similarity to MVIIA by BLAST and that MVIIA
is a potent and selective blocker of N-type voltage-sensitive calcium channels in neurons.

Objective:
To recognize the target protein and analgesic activity of Ac6.4 from Conus achates.

MethodS:
In the present study, we synthesized Ac6.4, expressed the Trx-Ac6.4 fusion protein, tested
Ac6.4 for its inhibitory activity against Cav2.2 in CHO cells and investigated Ac6.4 and Trx-Ac6.4 for
their analgesic activities in mice.

Results:
Data revealed that Ac6.4 had strong inhibitory activity against Cav2.2 (IC50 = 43.6 nM). After
intracranial administration of Ac6.4 (5, 10, 20 μg/kg) and Trx-Ac6.4 (20, 40, 80 μg/kg), significant
analgesia was observed. The analgesic effects (elevated pain thresholds) were dose-dependent.

Conclusion:
This study expands our knowledge of the peptide Ac6.4 and provides new possibilities for
developing Cav2.2 inhibitors and analgesic drugs.
Novel Computational Methods for Cancer Drug Design
Authors: Talluri Sekhar , Kamal Mohammad Amjad , Malla Rama Rao 
Published: April 2023

Abstract:
Cancer is a complex and debilitating disease that is one of the leading causes
of death in the modern world. Computational methods have contributed to the successful
design and development of several drugs. The recent advances in computational methodology,
coupled with the avalanche of data being acquired through high throughput genomics,
proteomics, and metabolomics, are likely to increase the contribution of computational
methods toward the development of more effective treatments for cancer. Recent
advances in the application of neural networks for the prediction of the native conformation
of proteins have provided structural information regarding the complete human proteome.
In addition, advances in machine learning and network pharmacology have provided
novel methods for target identification and for the utilization of biological, pharmacological,
and clinical databases for the design and development of drugs. This is a review
of the key advances in computational methods that have the potential for application
in the design and development of drugs for cancer.
The Role of MiR-29 in the Mechanism of Fibrosis
Authors: Wang Min , Huo Zhiying , He Xiaoyan , Liu Fuyou , Liang Jingtao , Wu Lijuan , Yang Dongdong 
Published: April 2023

Abstract:
Fibrosis is a pathological process characterized by tissue scarring that can occur in various
human body organs. The fibrosis of the organ is manifested as an increase in fibrous connective
tissue and a decrease in parenchymal cells in the organ tissue, leading to structural damage and
functional decline of the organ. At present, the incidence and medical burden of fibrosis are increasing
worldwide, which has presented severe negative impacts on human health. Although many of
the cellular and molecular processes for underlying fibrosis have been discerned, there are still gaps
for effective therapies and target fibrogenesis specifically. Recent studies have shown that the microRNA-
29 family (miR-29a, b, c) plays an essential role in the process of multiorgan fibrosis. It is
a class of highly conserved single-stranded noncoding RNAs composed of 20-26 nucleotides.
Through its 5' untranslated region (UTR) pairing with the 3'UTR of the target mRNA, the mRNA of
the target gene is degraded to complete the physiological process of inhibiting the transcription and
translation of the target gene. Here, we summarize the interaction of miR-29 with multiple cytokines,
describe the mechanism by which miR-29 regulates major fibrotic pathways such as TGF-
β1/Smad, PI3K/Akt/mTOR, DNA methylation，and found that miR-29 is closely linked to epithelial-
mesenchymal transition (EMT). These findings point to a common or similar regulatory mechanism
by miR-29 in fibrogenesis. Finally, we review the antifibrotic activity of miR-29 mimicked in
current studies and highlight miR-29 as a promising therapeutic reagent or target for the treatment of
pulmonary fibrosis. Besides, there is an urgent need to screen and identify small compounds to
modulate miR-29 expression in vivo.
LINC00839, LINC01671, AC093673 and AC008760 are Associated with
the Prognosis and Immune Infiltration of Clear-cell Renal Cell Carcinoma
Authors: Su Bao-Chang , Yang Sheng-Fu , Ye Xun-Da , Huang Zhang-Xiong , Song Yu-Wei , Xu San-Huang 
Published: April 2023

Background:
Clear cell renal cell carcinoma (ccRCC) is the most common type of kidney
cancer, and it is a significant global health problem causing significant morbidity and mortality. Long
noncoding RNAs (lncRNAs) have been identified as a class of gene expression regulators that play a
critical role in the immune system. However, the function of lncRNAs in the immune microenvironment
of ccRCC remains unclear.

Methods:
The least absolute shrinkage and selection operator regression techniques, robust likelihoodbased
survival modeling, and Cox regression analysis were used to identify potential prognostic
lncRNAs. The relationship between the signature and the tumor's immune infiltration was analyzed
using gene set enrichment analysis and the subset analysis of immune cells.

Results:
LINC00839, LINC01671, AC093673, and AC008760 were selected to create a risk signature.
For 3-, 5-, and 8-year overall survival rates, the areas under the receiver operating characteristic curves of
the risk signature set were 0.689, 0.721, and 0.719 in the training set and 0.683, 0.686, and 0.665 in the
validation set, respectively. A model and nomogram were constructed using the risk signature and clinical
characteristics. The C-index of the model was 0.78 in the training set and 0.773 in the validation set.

Conclusion:
The risk signature reflects the tumor's current immune infiltration and is associated with
regulatory T cell differentiation, interleukin 17 production regulation, negative regulation of inflammatory
response to an antigenic stimulus, and the IL6-JAK-STAT3 signaling pathway. This study
provides prognostic information for ccRCC patients and may also serve as a useful clue for future
immunotherapies.
A Case Report of Bone Paget's Disease with Concurrent Psoriasis and Positive
Celiac Serology
Authors: Sabooniha Fakhreddin 
Published: April 2023

Background:
Paget's disease of bone (PDB) is the second most frequent metabolic bone disease affecting about 3 percent of the Caucasian population older than
55 years. Its etiopathogenesis is unknown. While viral agents like measles and respiratory syncytial virus has been proposed, the role of genetic
susceptibility loci such as SQSTM1/p62 gene mutations have been confirmed. A new inhibitory mechanism against osteoprotegerin (OPG) via
autoantibodies has been revealed in a patient with occult celiac disease (CD) with a phenotype similar to juvenile Paget's disease, which suggests
an immunological mechanism for Paget's disease-like disorders other than genetic causes. But there is no report in the literature addressing the
shared immunological mechanisms underlying classic PDB, CD and psoriasis.

Case Presentation:
Herein, the case of a 50-year-old Caucasian man being reported with progressive bilateral hearing loss. The patient had a history of total blindness
which had developed shortly after a cranial osteotomy for optic nerve decompression without any specific diagnosis 15 years ago. He had also
been suffering chronic psoriasis vulgaris. Because of his enlarged skull, a diagnosis of bone Paget's disease was suspected and plain radiographs
revealed a polyostotic Paget's disease with characteristic radiologic signs. In searching for his refractory constipation causes, an elevated level of
tissue transglutaminase IgA (tTG IgA) antibody was demonstrated. Alendronate sodium 40 mg daily was started and a gluten-free diet was
recommended to him but he was not adherent to the treatments and lost to follow-up.

Conclusion:
This case further supports the idea of considering PDB as an osteoimmunologic disorder, like psoriasis and CD, because of similar biochemical
features, including elevated levels of Cytokines such as interleukin-6 and tumor necrosis factor- α as well as bone resorption markers such as OPG
and urinary deoxypyridinoline. So, the treatment of Paget’s disease of the bone may benefit from progresses in osteoimmunology-targeted
therapies. Also a probable causal relationship between PDB and CD either by production of neutralizing antibodies in CD against OPG or by
inducing PDB in genetically susceptible patients through oxidative stress, has been postulated here.
Objective Evaluation of Oral and Pharyngeal Areas in Autopsy Cases of
Obstructive Sleep Apnea Syndrome via Postmortem CT
Authors: Takeuchi Akiko , Hyodoh Hideki , Jin Shigeki , Tanaka Satoshi , Murakami Manabu , Minowa Kazuyuki , Matoba Kotaro 
Published: April 2023

Background:
Obstructive sleep apnea syndrome (OSAS) can cause sudden death during sleep. Previous findings have suggested that OSAS development is
related to maxillofacial morphology. Evaluation of facial morphology can determine the risk of developing the disease, and establishing an
objective method to assess the underlying etiology of OSAS-related death would be advantageous.

Objective:
The objective of this study is to determine the key features of obstructive sleep apnea syndrome (OSAS) using postmortem oral and pharyngeal
computed tomography (CT).

Methods:
We retrospectively assessed autopsy cases of patients with (n=25) and without (n=25) OSAS-related death. We used oral and pharyngeal CT
images to compare the oral and pharyngeal cavity volume (OPCV), oral and pharyngeal soft tissue volume (OPSV), oral and pharyngeal air space
volume (OPAV), and OPAV to OPCV ratio (%air). Receiver operating curve (ROC) analysis was used to determine the accuracy of OSAS
prediction. We assessed participants with body mass index (BMI) values within the normal range.

Results:
Among the 50 subjects, we observed significant between-group differences in OPSV, OPAV, and % air, whereas there were significant betweengroup
differences in OPSV and %air among 28 subjects with normal BMI values. Both comparisons suggested that OSAS-related death was
associated with low %air and high OPSV values.

Conclusion:
The % air and OPSV are useful for assessing postmortem oropharyngeal CT images. OSAS-related sudden death is likely when %air and OPSV
values are ≤20.1% and ≥127.2 ml, respectively. Among those with normal BMI values, % air and OPSV values of ≤22.8% and ≥111.5 ml,
respectively, predict OSAS-related sudden death.
Screening and in vitro Biological Evaluation of Novel Multiple Tyrosine Kinases Inhibitors as Promising Anticancer Agents
Authors: Li Xiuying , Ruan Pinglang , Jiang Gang , Zhang Weidong 
Published: April 2023

Background:
Tyrosine kinases have emerged as key stimulatory drivers in several cancer-related pathways.
This is particularly evident in non-small cell lung cancer with regulating cell growth and apoptosis and so on. Tyrosine
kinase inhibitors (TKI) are one breakthrough option that could improve the life quality of cancer patients.

Objective:
This study aims to find more effective tyrosine kinase inhibitors.

Methods:
In this study, natural products from TargetMol that may be the potential TKI for lung cancer were screened
through structure-based virtual screening and experimental validation. Moreover, the binding between the hit compounds
and tyrosine kinase was explored.

Results:
From the study findings, Gramicidin and Tannic acid have strong interactions with the four tyrosine kinases
(ALK, TRK, MET, and ABL), and this could significantly inhibit the viability of A549 cells in a concentrationdependent
manner.

Conclusion:
These findings indicated that Gramicidin and Tannic acid might be potential multiple TKI and are promising
anticancer agents that call for further study.