bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative transcriptome analysis of Salmonella resistance in Beijing-You chickens and Guang Ming broilers
Authors: Wang Zixuan , Wang Hailong , Sánchez Astrid Lissette Barreto , Thiam Mamadou , Zhang Jin , Li Qinghe , Zheng Maiqing , Wen Jie , Zhao Guiping , Wang Qiao 
Published: June 2022

Abstract
BackgroundSalmonella is a food-borne pathogen that can infect animals and humans. It is currently the most common bacterial pathogen that negatively affects poultry industry. Although different chicken breeds have been observed to exhibit diverse resistance to Salmonella infection, the underlying genetic mechanisms remain unclear and the genes involved in this differential disease resistance need to be identified. To overcome this knowledge gap, we used a liver transcriptome analysis to screen differentially expressed genes (DEGs) in two different chicken breeds (local Beijing You (BY) and commercial Guangming No. 2 broiler line B (GM)) before and after Salmonella infection. We also performed weighted gene co-expression network analysis (WGCNA) to detect hub genes, and employed selection signal analysis of candidate genes. ResultsTranscriptome analysis showed that there were 329 differentially expressed genes in Guang Ming (GM) broilers Salmonella infection group and control group, of which 173 were up-regulated and 156 were down regulated. In Beijing You (BY) chickens, there were 563 DEGs between the Salmonella infection group and control group , including 220 up-regulated and 343 down-regulated genes. Using the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, we found that some genes were significantly enriched in immune-related signaling pathways, such as Toll-like receptor signaling pathway, Salmonella infection. Three promising genes (EGR1, JUN and FOS) were eventually identified, which were significantly and differentially expressed in the same breed under different conditions, and in the two breeds after Salmonella infection. Hub genes, such as PPFIA4 and ZNF395, were also identified using WGCNA, which were associated with the heterophils/lymphocytes ratio, an indicator of disease resistance. Conclusionsthe present study identified several genes and pathways associated with resistance to Salmonella infection, and found that BY had greater resistance to Salmonella infection than GM. The results obtained provide valuable resources for investigating the mechanisms of resistance to Salmonella infection in different chicken breeds.
Water intake, hydration status and related hydration biomarkers among physically active male young adults in Beijing, China: a cross-sectional study
Authors: Zhang Na , Zhang Jianfen , Wang Xing , Li Yibin , Yan Yi , Ma Guansheng 
Published: June 2022

Abstract
Studies on the water intake of athletes in daily life are insufficient. The objective was to determine the water intake and hydration status among physically active male young adults. In this cross-sectional studies study, 111 physically active male young adults were recruited. The amount of daily total drinking fluid intake (TDF) among participants was recorded and evaluated in real time over 7 days using the “7-day 24-hour fluid intake questionnaire” (liq. In7). The daily water intake from food (WFF) was calculated using the weighing, duplicate portion and direct-drying method over 3 days. All urine samples over 3 days were collected, and urine biomarkers were determined. According to 24-h urine osmolality, the participants were divided into three groups with Euhydrated status, middle hydration and hypohydration statuses. Finally, 109 participants completed the study. The median daily total water intake (TWI), TDF and WFF were 2701, 1789 and 955 mL, respectively. Among participants, 17 participants (16%) were in Euhydrated status, 47 participants (43%) were in hypohydration, and 45 participants (41%) were in middle hydration. There were statistical significances in the 24-h urine volume, osmolality, urine specific gravity, and concentrations of K, Na and Cl in different hydration statuses (χ2 = 28.212, P < 0.01; χ2 = 91.341, P < 0.01; χ2 = 47.721, P < 0.01; χ2 = 41.548, P < 0.01; χ2 = 46.863, P < 0.01; χ2 = 40.839, P < 0.01). Moderate-intensity correlations were found between the TDF and 24-h urine volume, 24-h urine osmolality, 24-h urine Na concentration, morning urine osmolality, and morning urine Na concentration (r = 0.408, P < 0.01; r=-0.378, P < 0.01; r=-0.325, P < 0.01; r=-0.344, P < 0.01; r=-0.329, P < 0.01). There were also moderate intensity correlations between the TDF and 24-h urine osmolality, morning urine osmolality, and morning urine Na concentration (r=-0.365, P < 0.01; r=-0.371, P < 0.01; r=-0.322, P = 0.01). Increased and higher moderate-intensity correlations were found between plain water and 24-h urine volume, 24-h urine osmolality, 24-h urine K and Na concentration, morning urine osmolality, and morning urine Na concentration (r = 0.374, P < 0.01; r=-0.520, P < 0.01; r=-0.312, P < 0.01; r=-0.355, P < 0.01; r=-0.446, P < 0.01; r=-0.378, P < 0.01). Insufficient water intake and hypohydration were common among physically active male young adults. The amount and type of water intake was correlated with hydration status and urine biomarkers.
BEPC-RF:A Stellar Spectral Classification Algorithm Based on Transformer and PCA Double Feature Extraction
Authors: Li Shuangchuan , Tu Liangping , Li Jianxi , Wang Xiaoming , Tu Dongxin , Feng Xueqi , Li Juan 
Published: June 2022

Abstract

The research about automatically classification and accurately identification of the stellar spectrum is one of the hot research topics in astronomy. In this paper, a high-performance BEPC-RF algorithm is proposed torealize the task of automatic classification of stellar spectra. The algorithm can achieve dual feature extraction based on Transformer and Principal Component Analysis (PCA). The BEPC-RF algorithm consistsof the following three steps: firstly, the PCA algorithm is applied to extract the feature vector Fpca from the denoised and normalized stellar spectra; Secondly, by removing the pseudo continuum spectrum which is fitted through the polynomial fitting method, the spectral line information is obtained; In this step, the entire wavelength range is divided into 10 different bands, and then we can get 10 trapezoidal integral values of the 10 bands, and these 10 values are the vector Finte. Then, use the Transformer model to perform feature learningon Finte to obtain another feature vector Ftrans. Finally, the feature spectrum is represented by Fspectrum=(Ftrans, Fpca), and then input it into the Random Forest (RF) algorithm to realize the automatic classification of stellar spectra. The experimental results show that the final classification accuracy rate of BEPC-RF algorithm is 0.919, which is significantly better than KLDA algorithm, KSVM algorithm, DECISION TREE algorithm, XGBOOST algorithm, ADABOOST algorithm, BAYES algorithm, KNN algorithm, RF algorithm’s classificationaccuracy rate i.e. 0.8, 0.84, 0.806, 0.836, 0.83, 0.777, 0.821, 0.85.
Palmatine suppresses acute myeloid leukemia (AML) by inducing pyroptosis via ROS/PI3K/AKT signaling
Authors: Zheng Qin , Pei Yuqing , Li Yuchen , Chen Hongqing , Zhao Ziyi , Hu Qiongying 
Published: June 2022

Abstract
Purpose Palmatine (PAL) is widely identified as an isoquinoline alkaloid among the representatives of the Berberidaceae botanical family. Palmatine exerts suppressive effects on several kinds of cancer. Several natural products were found to suppress acute myeloid leukemia (AML); however, the effects of Palmatine on AML are still unknown. In this study, we aim to evaluate the effects of PAL on AML.Methods Several AML cell lines, including HL-60, OCI-AML3, Molm-13 and KG-1 cells were employed to evaluate the effects of PAL. Cell proliferation, migration, invasion, tumor formation in soft agar were evaluated. PAL’s effects on ROS accumulation and subsequent induction of pyroptosis were measured. Results PAL promoted the cleavage of caspase-3 and PARP1 and induced apoptosis. PAL treatment also caused the release of lactic dehydrogenase (LDH) and the depolarization of the mitochondrial membrane potential and subsequently induced the pyroptosis-specific cleavage of caspase-1, caspase-5 and gasdermin D, which was reversed by pyroptosis inhibitor VX765. After PAL treatment for 6-24 hours, PAL treatment increased ROS in HL-60 and KG-1 cells. Abolishment of ROS with N-acetyl cysteine (NAC) attenuated LDH release, which was similar to the effect of VX765, indicating that palmatine contributes to the suppression of AML partially by inducing pyroptosis. Furthermore, we found that palmatine-induced ROS accumulation inhibited PI3K and AKT phosphorylation and abolished ROS-mediated reactivation of PI3K/AKT signaling, which was similar to the effects of the PI3K activator 740Y-P. Conclusion Taken together, these results indicate that palmatine induces cell death mainly by inducing ROS accumulation and ROS/PI3K/AKT signaling.
In search of Triatominae (Hemiptera: Reduviidae) using mice-baited traps along the peninsula of Baja California, Mexico
Authors: Waleckx Etienne , Verdugo Juan José Rios , Amblard-Rambert Antoine , Basulto Gerardo Enrique Medina , López-Valencia Gilberto , Haro Ana Paulina 
Published: June 2022

Abstract
During a 3000 kms-exploratory fieldtrip along the peninsula of Baja California, Mexico, we used mice-baited traps in search of Triatominae. Specimens of Paratriatoma hirsuta and Dipetalogaster maxima were collected.
Analysis of tumour dose-response data from animal experiments via two TCP models accounting for tumor hypoxia and resensitization
Authors: Stavrev Pavel Vassilev , Stavreva Nadejda , Ruggieri Ruggero , Nahum Alan Ephraim , Pressyanov Dobromir 
Published: June 2022

Abstract
Purpose

To treat animal dose-response data exhibiting inverse dose-response behavior with two tumor control probability (TCP) models accounting for tumor hypoxia and reoxygenation leading to resensitization of the tumor

Methods

One of the tested TCP models uses a modified linear-quadratic (LQ) model of cell survival where both α and β radiosensitivities increase in time during the treatment due to reoxygenation of the hypoxic tumor sub-population. The other TCP model deals with two types of hypoxia – chronic and acute – and accounts for tumor re-sensitization via oxygenation of the chronically hypoxic and fluctuating oxygenation of the acutely hypoxic sub-populations. The two models are fit using the maximum likelihood method to the data of Fowler et al on mice mammary tumors irradiated to different doses using different fractionated schedules. These data are chosen since as many as five of the dose-response curves show an inverse dose behavior, which is interpreted as due to re-sensitization.

Results

The p-values of the fits of both models to the data render them statistically acceptable. A performed comparison test shows that both models describe the data equally well. It is also demonstrated that the most sensitive (oxic) tumor component has no impact on the treatment outcome.

Conclusion

The ability of the tested models to predict and describe the impact of resensitization on the treatment outcome is thus proven. It is also demonstrated that prolonged treatment schedules can be more beneficial than shorter ones. However, this may be true only for schedules with small number of fractions, i.e. for hypo-fractionated treatments only.
Single-cell full-length isoform sequencing reveals an abundance of 3’ prime partial transcripts in maternally inherited RNAs
Authors: Xiao Chuan-Le , Wang Chaoyang , Shi Zhuoxing , Huang Qingpei , Hu Kunhua , Liu Rong , Su Dan , Lin Zhuobin , Fan Xiaoying 
Published: June 2022

Abstract
Isoform expression in preimplantation embryos has been extensively investigated, and many novel isoforms have been identified. However, the regulation patterns of different types of transcripts along the developing stages remainsunexplored. We quantified the expression of full-length isoforms in over one hundred single blastomeres from the mouse oocyte to blastocyst stage and found that the 3’ prime partial transcripts that lack stop codonswere highly accumulated in oocytes and zygotes. A typical 3’ prime partial isoform,Ncl-S-350, was demonstratedto be not a transcription by-productbutto function in the ZGA process. SRSF4 was identified to be responsible for generating these 3’ prime partial transcripts in mouse embryonic stem cells (mESCs), and both Ncl-S-350 and Srsf4 overexpression could convert mESCs to a 2-cell (2C)-like state. Our work reveals the important role of isoform switch regulation in early embryonic development and lays the foundation for an alternative way of acquiring totipotent cells.
P2Y6R: A Promising New Target in Inflammatory Diseases and Advances in its Antagonists
Authors: Wang Yuanhui , Pei Yuanyuan , Yao Yongfang , Cheng Weyland , Li Yinchao , Duan Yongtao 
Published: June 2022

Abstract:
P2Y receptors (P2YRs) are G protein-coupled receptors that are activated by
extracellular nucleotides. The P2Y6 receptor (P2Y6R) is specifically activated by UDP,
causing PKC activation and intracellular calcium ion release through the PLC pathway.
Based on receptor tissue distribution and related pathways, several studies have reported
that P2Y6R plays a physiological role in mediating inflammation, which suggests that
P2Y6R could be a promising molecular target for the treatment of inflammatory diseases.
In the past ten years, several P2Y6R antagonists have been discovered as new therapeutic
strategies for inflammatory diseases. In this article, we systematically summarize the role
of P2Y6R in inflammation and highlight the anti-inflammatory mechanism of a key
P2Y6R antagonist, MRS2578. Insight into recent progress on the discovery of P2Y6R antagonists
is also discussed.
Functional Analysis of Wild-Type and 27 CYP3A4 Variants on Dronedarone Metabolism
In vitro
Authors: Wang Chen-Chen , Lan Tian 
Published: June 2022

Background:
Cytochrome P450 (P450) is the largest family of enzymatic proteins in the human liver, and
its features have been studied in physiology, medicine, biotechnology, and phytoremediation.

Objective:
The aim of this study was to assess the catalytic activities of 28 human CYP3A4 alleles by using dronedarone
as a probe drug in vitro, including 7 novel alleles recently found in the Han Chinese population.

Methods:
We expressed 28 CYP3A4 alleles in insect microsomes and incubated them with 1-100 μM of dronedarone
at 37 °C for 40 minutes to obtain the metabolites of N-debutyl-dronedarone.

Results:
Compared with the wild type of CYP3A4, the 27 defective alleles can be classified into four categories.
Three alleles had no detectable enzyme activity leading to a lack of kinetic parameters of N-debutyl-dronedarone; the
other three alleles slightly despaired when it comes to intrinsic clearance values compared with the features of the
wild type. Sixteen alleles exhibited 35.91%~79.70% relative values (in comparison to the wild-type) and could be
defined as the “moderate decrease group”. The rest of the alleles showed a considerable decrease in intrinsic clearance
values, ranging from 11.88%~23.34%. Therefore they were classified as a “significantly decreased group”.
More specifically, 18 CYP3A4 alleles exhibited a substrate inhibition trend toward dronedarone when the concentration
rises to 20 μM.

Conclusion:
The outcomes of this novel study on the metabolism of dronedarone by CYP3A4 alleles can be used as
experimental data support for the individualized use of this modern drug.
Therapeutic Targeting of Overexpressed MiRNAs in Cancer Progression
Authors: Lee Sau Har , Brianna Brianna 
Published: June 2022

Abstract:
MicroRNAs (miRNAs) are non-coding RNAs involved in the modulation of various bio-logical processes, and their dysregulation is greatly associated with cancer progression as miRNAs can act as either tumour suppressors or oncogenes, depending on their intended target, mechanism of actions, and expression levels. This review paper aims to shed light on the role of overexpressed miRNAs in cancer progression. Cancer cells are known to upregulate specific miRNAs to inhibit the expression of genes regulating the cell cycle, such as PTEN, FOXO1, SOX7, caspases, KLF4, TRIM8, and ZBTB4. Inhibition of these genes promotes cancer development and survival by indu-cing cell growth, migration, and invasion while evading apoptosis, which leads to poor cancer sur-vival rates. Therefore, the potential of antisense miRNAs in treating cancer is also explored in this review. Antisense miRNAs are chemically modified oligonucleotides that can reverse the action of overexpressed miRNAs. Currently, the therapeutic potential of antisense miRNAs is being validated in both in vitro and in vivo models. Studies have shown that antisense miRNAs could slow down the progression of cancer while enhancing the action of conventional anticancer drugs. These fin-dings provide hope for future oncologic care as this novel intervention is in the process of clinical translation.
Identification of HnRNP Family as Prognostic Biomarkers in Five Major
Types of Gastrointestinal Cancer
Authors: Wang Lili , Yu Qian , Chen Xianghan , Gong Ruining , Wang Jia , Ma Boyi , Lei Ke , Ren He , Wang Jigang , Zhao Chenyang 
Published: June 2022

Background:
Heterogeneous nuclear ribonucleoproteins (hnRNPs), a large family of RNAbinding
proteins, have been implicated in tumor progression in multiple cancer types. However, the
expression pattern and prognostic value of hnRNPs in five gastrointestinal (GI) cancers, including gastric,
colorectal, esophageal, liver, and pancreatic cancer, remain to be investigated.

Objective:
The current research aimed to identify prognostic biomarkers of the hnRNP family in five
major types of gastrointestinal cancer.

Methods:
Oncomine, Gene Expression Profiling Interactive Analysis (GEPIA), and Kaplan-Meier
Plotter were used to explore the hnRNPs expression levels concerning clinicopathological parameters
and prognostic values. The protein level of hnRNPU was validated by immunohistochemistry (IHC) in
human tissue specimens. Genetic alterations of hnRNPs were analyzed using cBioportal, and Gene
Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to
illustrate the biological functions of co-expressed genes of hnRNPs.

Results:
The vast majority of hnRNPs were highly expressed in five types of GI cancer tissues compared
to their adjacent normal tissues, and mRNA levels of hnRNPA2B1, D, Q, R, and U were significantly
different in various GI cancer types at different stages. In addition, Kaplan-Meier analysis revealed
that the increased hnRNPs expression levels were correlated with better prognosis in gastric
and rectal cancer patients (log-rank p < 0.05). In contrast, patients with high levels of hnRNPs exhibited
a worse prognosis in esophageal and liver cancer (log-rank p < 0.05). Using immunohistochemistry,
we further confirmed that hnRNPU was overexpressed in gastric, rectal, and liver cancers. In addition,
hnRNPs genes were altered in patients with GI cancers, and RNA-related processing was correlated
with hnRNPs alterations.

Conclusion:
We identified differentially expressed genes of hnRNPs in tumor tissues versus adjacent
normal tissues, which might contribute to predicting tumor types, early diagnosis, and targeted therapies
in five major types of GI cancer.
Hepatocyte Growth Factor Delivered by Nanocomposites for Gene Therapy
of Bleomycin-Induced Pulmonary Fibrosis in Rats
Authors: Guo Qi , Lu Yuxin , Cheng Xiaochen , Xiao Fengjun , Zhang Qinglin , Gao Peng , Du Li 
Published: June 2022

Background:
Pulmonary fibrosis (PF) is a chronic and progressive interstitial lung disease.
There is no effective treatment for PF. Hepatocyte growth factor (HGF) has anti-inflammatory and antifibrotic
effects but has limited potential owing to its short half-life.

Methods:
To increase the transfection efficiency of pVAX-HGF, we prepared polyethyleneiminepolyethylene
glycol: polyethyleneimine/pVAX-HGF (PEG-PEI: PEI/pVAX-HGF) nanocomposite
loaded with a plasmid encoding the HGF gene. The PEG-PEI:PEI/pVAX-HGF characteristics, including
morphology, particle size, zeta-potential, and DNA entrapment efficiency, were investigated. The
pVAX-HGF nanocomposites with low toxicity and high transfection efficiency were screened by cell
viability assay and cell transfection. The antifibrotic effect of pVAX-HGF nanocomposite on PF rats
induced by bleomycin (BLM) was evaluated by pulmonary function measurement, pathological examination
and collagen content assay.

Results:
Different nanocomposites were prepared to deliver pVAX-HGF, in which mix1 (PEGPEI:
PEI/pVAX-HGF) has lower potential and better entrapment ability. PEG-PEI:PEI/pVAX-HGF
(N/P=25) nanocomposite with low toxicity and high transfection efficiency was administered to PF
rats. After treatment with mix 1/pVAX-HGF, the index of lung function(including EF50, MV, TV, PEF
and PIF) in mix 1/pVAX-HGF group was higher than that of the PF group. The number of cells in
BALF of the mix 1/pVAX-HGF group was significantly lower than that of the PF groups, and the content
of hydroxyproline(HYP) and collagen Type I (Col-I) in the lung of the mix 1/pVAX-HGF group
was much lower than that of the PF groups in the early stage. The result of pathological examination
showed that rats in the mix1/pVAX-HGF group showed obviously reduced alveolar septal thickening,
fewer infiltrated inflammatory cells and less collagen deposition.

Conclusion:
The PEG-PEI:PEI/pVAX-HGF nanocomposite can ameliorate PF induced by BLM. The
pVAX-HGF nanocomposite is a latent therapeutic strategy for PF.
Future Management of Chronic Myeloid Leukemia: From Dose Optimization
to New Agents
Authors: Breccia Massimo , Scalzulli Emilia , Pepe Sara , Colafigli Gioia , Martelli Maurizio 
Published: June 2022

Background:
The outcome of chronic myeloid leukemia (CML) patients in chronic phase has
changed after the introduction of tyrosine kinase inhibitors (TKIs). The life expectancy is actually similar
to that of the general population. Although outstanding results were achieved, about 20-30% of patients
failed to achieve molecular milestones or experienced a severe toxicity and needed to switch to a second
line.

Objective:
The aim of this review is to report on possible future management in CML, from dose optimization
to avoid long-term off-target events to new agents for the treatment of resistant and/or intolerant
patients.

Methods:
Broad research on Medline, Embase and archives from EHA and ASH congresses was performed.

Results:
New TKIs have been developed to counteract resistance and/or intolerance in the setting of
T315I mutated patients. The benefits of ponatinib dose optimization have been recently reported in the
OPTIC trial. New trials to test the dose optimization are ongoing.

Conclusion:
Reduction of the standard dose could be performed to reduce the specific TKI toxicity. Selective
TKIs could be prescribed in the future as third line treatment.
Discovery, Design, and Development of Effective and Stable Binding Compounds for Mutant EGFR Inhibition
Authors: Karnik Kshipra S. , Sarkate Aniket P. , Jambhorkar Vaishanavi S. , Wakte Pravin S. 
Published: June 2022

Background:The epidermal growth factor receptor of the tyrosine kinase family has been largely targeted in mutations associated with non-small cell lung cancer. EGFR inhibitors have been produced that bind allosterically to the C797S mutant EGFR enzyme.Objective:Here, the Waterswap tool has been used for the interpretation and visualization of trajectories of mutant EGFR-ligand complexes. Virtual screening of the generated compounds has been carried out along with its molecular docking and ADMET analysis.Methods:Out of the generated library of compounds, the top 15 have been selected. Waterswap calculated the binding free energies of the compounds and thermodynamic properties of the enumerated compounds were compared with that of standard EAI045.Results:It was observed that compound KSK-1 stabilized better than EAI045.Conclusion:Waterswap analysis offers a promising new path in the hunt for improved tools for analyzing and visualizing molecular driving forces in protein-ligand complex simulations.