bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proteasomal stimulation by MK886 and its derivatives can rescue tau-induced neurite pathology
Authors: Liao Elly E. , Yang Mu , Braun Anthony R , Ferguson David , Sachs Jonathan N 
Published: October 2022

Abstract
Proteasomal degradation of intrinsically disordered proteins, such as tau, is a critical component of proteostasis in both ageing and neurodegenerative diseases. In this study, we investigated proteasomal activation by MK886 (MK). We previously identified MK as a lead compound capable of modulating tau oligomerization in a cellular FRET assay and rescuing P301L tau-induced cytotoxicity. We first confirmed a robust proteasomal activation by MK using a cellular proteasomal tau-GFP cleavage assay. We then show that MK treatment can significantly rescue tau-induced neurite pathology in differentiated SHSY5Y neurospheres. Due to this compelling result, we designed a series of seven MK analogs to determine if proteasomal activity is sensitive to structural permutations. Using a combination of proteasome, tau aggregation, neurite outgrowth, inflammation, and autophagy assays, we identified two essential substituents of MK that are required for compound activity: 1) Removal of the N-chlorobenzyl group from MK negated both proteasomal and autophagic activity and reduced neurite outgrowth; and 2) removal of the indole-5-isopropyl group significantly improved neurite outgrowth and autophagy activity but reduced its anti-inflammatory capacity. Overall, our results suggest that the combination of proteasomal/autophagic stimulation and anti-inflammatory properties of MK and its derivatives can decrease tau-tau interactions and help rebalance dysfunctional proteostasis. Further development of MK to optimize its proteasomal, autophagic, and anti-inflammatory targets may lead to a novel therapeutic that would be beneficial in ageing and neurodegenerative diseases.
Endovascular Treatment of Aorto-iliac Occlusive Disease with TASC II C and D Lesions: Ten Year’s Experience of Clinical Technique
Authors: Dong Xiangjun , Peng ZiQian , Zheng Chuansheng , Ren Yanqiao , Su Yangbo , Liang Huimin , Sun Tao , Chen Lei 
Published: October 2022

Abstract
Objectives: The purpose of this study was to evaluate the therapeutic efficacy and safety of endovascular treatment aorto-iliac occlusive disease (AIOD) with TransAtlantic Inter-Society Consensus II (TASC II) C and D lesions. In addition, ten years of experience with interventional procedures and treatment options in our center were also worthy of further discussion.
Methods: Between January 2011 and December 2020, a total of 26 consecutive AIOD patients with TASC-II C and D lesions treated endovascular approach were enrolled in this study. Patients' demographic and clinical data were collected, and the safety and efficacy of endovascular therapy were evaluated. In addition, operation procedures were also described.
Results: The mean age of patients was 62.2±7 years (49-57 years), and the mean body mass index of patients was 24.2±2.6 kg/m2. Fifteen patients (57.7%) were Rutherford 4, 5 each (19.2%) were Rutherford 3 and 5, and 1 (3.8%) was Rutherford 2. No other serious complications occurred except death in 3 patients. Most of the patients (73.1%) had a history of smoking, and hypertension and hyperlipidemia were common comorbidities. Endovascular therapy was successfully performed in 25 patients, and the technical success rate was 96.2%. The patient's ankle-brachial index improved significantly postoperatively compared with preoperatively (preoperative 0.33±0.14 vs 1.0±0.09, P<0.001). The primary patency rates were 100%, 95.7%, and 91.3% at 1, 3, and 5 years, while the secondary patency rates were 100%. No treatment-related deaths or serious complications occurred.
Conclusions: Endovascular treatment of AIOD patients with TASC-II C and D lesions is safe and has a high rate of middle-term and long-term primary patency.
Revealing the novel pyroptosis-related therapeutic targets for sepsis based on the machine learning
Authors: Chen Ying , wang xingkai , Wang Jiaxin , Zong Junwei , Wan Xianyao 
Published: October 2022

Abstract
Background
Sepsis is one of the most lethal diseases worldwide. Pyroptosis as a unique form of cell death and the mechanism of interaction with sepsis is not yet clear. The aim of this study is to uncover pyroptosis genes associated with sepsis and to provide early therapeutic targets for the treatments of sepsis.
Methods
Based on the GSE134347 dataset, sepsis-related genes were mined by differential expression analysis and WGCNA. Subsequently, the sepsis-related genes were analyzed for enrichment and a protein-protein interaction (PPI) network was constructed. We performed unsupervised consensus clustering of sepsis patients based on 33 pyroptosis related genes (PRGs) provided by prior reviews. We finally obtained the PRGs mostly associated with sepsis by machine learning prediction models combined with the GeneCards database and prior reviews. The GSE32707 dataset served as an external validation dataset to validate the model and PRGs via receiver operating characteristic (ROC) curves. NetworkAnalyst online tool was utilized to create a ceRNA network of lncRNAs and miRNAs around PRGs mostly associated with sepsis.
Results
A total of 170 genes associated with sepsis and 13 hub genes were acquired by WGCNA and PPI network. The results of the enrichment analysis implied that these genes were mainly involved in the regulation of the inflammatory response and the positive regulation of bacterial and fungal defense responses. Prolactin signaling pathway and IL-17 signaling pathway were the primary enrichment pathways. Thirty-three PRGs can effectively classify septic patients into two subtypes, implying that there is a reciprocal relationship between sepsis and pyroptosis. Eventually, NLRC4 was considered as the PRG most strongly associated with sepsis. The validation results of the prediction model and NLRC4 based on ROC curves were 0.74 and 0.67, respectively, both of which showed better predictive values. Meanwhile, the ceRNA network consisting of 6 lncRNAs and 2 miRNAs was constructed around NLRC4.
Conclusion
NLRC4 as the PRG mostly associated with sepsis could be considered as a potential target for treatment. The 6 lncRNAs and 2 miRNAs centered on NLRC4 could serve as a further research direction to uncover the deeper pathogenesis of sepsis.
Label-free Macrophage Phenotype Classification Using Machine Learning Methods
Authors: Hourani Tetiana , Perez-Gonzalez Alexis , Khoshmanesh Khashayar , Luwor Rodney , Achuthan Adrian A. , Baratchi Sara , O’Brien-Simpson Neil M. , Al-Hourani Akram 
Published: October 2022

Abstract
Macrophages are heterogeneous innate immune cells that are functionally shaped by their surrounding microenvironment. Diverse macrophage populations have multifaceted differences related to their morphology, metabolism, expressed markers, and functions, where the identification of the different phenotypes is of an utmost importance in modelling immune response. While expressed markers are the most used signature to classify phenotypes, multiple reports indicate that macrophage morphology and autofluorescence are also valuable clues that can be used in the identification process. In this work, we investigated macrophage autofluorescence as a distinct feature for classifying six different macrophage phenotypes, namely: M0, M1, M2a, M2b, M2c, and M2d. The identification was based on extracted signals from multi-channel/multi-wavelength flow cytometer. To achieve the identification, we constructed a dataset containing 152,438 cell events each having a response vector of 45 optical signals fingerprint. Based on this dataset, we applied different supervised machine learning methods to detect phenotype specific fingerprint from the response vector, where the fully connected neural network architecture provided the highest classification accuracy of 75.8% for the six phenotypes compared simultaneously. Furthermore, by restricting the number of phenotypes in the experiment, the proposed framework produces higher classification accuracies, averaging 92.0%, 91.9%, 84.2%, and 80.4% for a pool of two, three, four, five phenotypes, respectively. These results indicate the potential of the intrinsic autofluorescence for classifying macrophage phenotypes, with the proposed method being quick, simple, and cost-effective way to accelerate the discovery of macrophage phenotypical diversity.
How Salt (NaCl) stress modulates histidine kinase-based signalling systems
Authors: Dabravolski Siarhei A. , Isayenkov Stanislav 
Published: October 2022

Abstract
Salt stress is a global environmental problem, which affects various biochemical and physiological processes in plants and significantly decreases the quantity and quality of the yield. NaCl is the main driver of NaCl-mediated effects because the accumulation of sodium ions (Na+) in plant tissues disrupts the homeostasis of other ions and may lead to secondary stresses. Two-component signalling (TCS) is an evolutionally conserved histidine-kinase based system utilised by many organisms to react to inner and environmental stimuli and stresses. In this review, we focus on the effect of NaCl on histidine-kinase based signalling systems (TCS) in bacteria and its advanced form multi-step phosphorely (MSP) in plants. Further, we discuss available data on the sodium-sensing approach employed by bacteria and plants, current limitations and future prospects in this area. Also, based on the analysed experimental and evolutional data, we suggested some potential directions for the future investigation of the salt-sensing mechanisms in plants.
DFFNDDS: Prediction of Synergistic Drug Combinations With Dual Feature Fusion Networks
Authors: Xu Mengdie , Zhao Xinwei , Wang Jingyu , Feng Wei , Wen Naifeng , Wang Chunyu , Wang Junjie , Liu Yun , Zhao Lingling 
Published: October 2022

Abstract
Drug combination therapies are promising clinical treatments for curing patients. However, efficiently identifying valid drug combinations remains challenging because the number of available drugs has increased rapidly. In this study, we proposed a deep learning model called the Dual Feature Fusion Network for Drug-Drug Synergy prediction (DFFNDDS) that utilizes a fine-tuned pretrained language model and dual feature fusion mechanism to predict synergistic drug combinations. The dual feature fusion mechanism fuses the drug features and cell line features at the bit-wise level and the vector-wise level. We demonstrated that DFFNDDS outperforms competitive methods and can serve as a reliable tool for identifying synergistic drug combinations.
Improving 1d Convolutional Neural Network (1d Cnn) Performance in Processing Tabular Datasets Using Principal Component Analysis
Authors: Surendro Kridanto , Rachmatullah Muhammad Ibnu Choldun , Santoso Judhi 
Published: October 2022

Abstract
Convolutional Neural Network (CNN) has been used significantly in various applications to process data that have spatial or temporal relationship, such as image and video recognition, medical image analysis, natural language processing, and speech recognition. This study used CNN to process tabular datasets with unknown spatial and temporal relationship between attributes. It used a principal component analysis (PCA) process to obtain the relationship between the attributes, which are connected based on their variance values and expected to provide a spatial relationship. Therefore, after being transformed with PCA, the dataset remains in the tabular form but between attributes already have a relationship. Because the transformed dataset is still a one-dimensional dataset, the CNN model used is 1D CNN which is more suitable for processing one-dimensional data. To compare the performance of 1D CNN against the original dataset and the dataset that has been transformed with PCA, the Iris and Covertype datasets were used. By using the Wilcoxon difference test, it turns out that two datasets that have been transformed with PCA provide better performance than using the original dataset. Furthermore, the PCA implementation to the NCI-60 dataset using 1D CNN performed better compared to previous research. This research has an accuracy of 83.34%. The previous research transformed the dataset into a two-dimensional image classified using 2D CNN at an accuracy of 75.4%.
Analysis of clinical characteristics of patients with rhinitis in Guangzhou, China
Authors: Zhu Huiqing , Huang Zhifeng , An Nairui , Liu Tingting , Chen Tong , Sun Baoqing 
Published: October 2022

Abstract
Background: High prevalence of allergic rhinitis (AR) and asthma (AS) produces a considerable burden on patients and society, and it has negative impact on patients’ life, daily activities and work productivity.
Methods: A total of 270 patients withallergic rhinitis were recruited, of whom 177 (65.6%) combined with asthma (AR&AS). All patients filled out a standardized questionnaire againstrespiratory allergic diseases. Skin prick test (SPT) and or serological specific immunoglobulin E (sIgE) test for 9 common inhalation allergens.
Results: House dust mites (HDMs)were the main aeroallergen in patients with respiratory allergic diseases, and the positive rates were all more than 60%. The age of AR&AS patients was higher than that of AR patients (P < 0.05), and the patients with AR only are more likely to have a family history of allergy. Almost all (94%) of patients with AR only develop nasal and eye symptoms when exposed to cold air. The reporting rate of rhinitis symptoms caused by pollen exposure is 33.33%~44.07%, while the reporting rate of rhinitis symptoms caused by furry animal exposure were about 25%. The incidence of rhinitis symptoms in moderate to severe patients was higher than that in mild patients (all P<0.05). 41.94% of patients reported symptoms of cough in AR patients, and among the patients with AR&AS, 97.18% reported the symptoms of wheezing, 70.06% reported chest tightness and 75.14% reported cough. The reporting rate of AR&AS patients was higher than that of AR patients. And the percentage of pulmonary symptoms reported by children was significantly lower than that of adults.
Conclusions: HDMs are the main allergen causing respiratory allergic diseases. The introduction of different types of AR will help to better understand the risk factors and progress of patients with AR, and may help to put forward more targeted prevention strategies and treatment.
Genetic characterization of HIV-1 viruses among antiretroviral therapy failure individuals in Suzhou City, China
Authors: DONG Zefeng , XU Zhihui , ZHOU Ying , TIAN Runfang , ZHOU Kai , WANG Di , YA Xuerong , SHEN Qiang 
Published: October 2022

Abstract
Background: This retrospective study was aimed to characterize the distribution of HIV-1 genotypes and prevalence of drug-resistance mutations in antiretroviral therapy (ART) failure individuals in Suzhou City, China.
Methods: Polgene of HIV-1 viruses in EDTA anticoagulant plasma samples of 398 ART failure HIV-infected individuals were successfully amplified by using an in-house assay. Drug resistance mutations were analyzed by using the Stanford HIV Drug Resistance Database system (https://hivdb.stanford.edu/hivdb/by-mutations/). HIV-1 genotypes were determined by REGA HIV subtyping tool (version 3.46, https://www.genomedetective.com/app/typingtool/hiv). Near full-length genomes (NFLG) of HIV-1 viruses were obtained by next generation sequencing method.
Results: Sequences analysis of the pol gene revealed that CRF 01_AE (57.29%, 228/398) was the dominant subtype circulating in Suzhou City, followed by CRF 07_BC (17.34%, 69/398), subtype B (7.54%, 30/398), CRF 08_BC (6.53%, 26/398), CRF 67_01B (3.02%, 12/398) and CRF55_01B (2.51%, 10/398). The overall prevalence of drug-resistant mutations in ART failure HIV-infected individuals was 64.57% (257/398), including 45.48% (181/398) for nucleotide reverse transcriptase inhibitors (NRTIs) mutations, 63.32% (252/398) for non-nucleoside reverse transcriptase inhibitors (NNRTIs) mutations, and 3.02% (12/398) for protease inhibitors (PIs) mutations. Ten near full-length genomes (NFLG) of HIV-1 viruses were identified, including six recombinants of CRF 01_AE and subtype B, two recombinants of CRF 01_AE, subtype B and subtype C sequences, one recombinant of CRF 01_AE and subtype C and one recombinant of CRF 01_AE, subtype A1 and subtype C.
Conclusions: The high prevalence of drug-resistant HIV-1 viruses was a serious challenge for HIV prevention and HIV-infected individuals’ treatment. Therapeutic regimens of ART failure HIV-infected individuals should be adjusted in time according to drug resistance test results. NFLG sequencing facilitates the identification of new HIV-1 recombinant strains.
The striatum drives the ergogenic effects of caffeine
Authors: Alves Ana Cristina de Bem , Speck Ana Elisa , Farias Hémelin Resende , Santos Naiara Souza dos , Pannata Gabriela , Tavares Ana Paula , Martins Leo Meira , de Oliveira Jade , Tomé Ângelo Ribeiro , Cunha Rodrigo , Aguiar Aderbal S 
Published: October 2022

Abstract
Caffeine is one of the main ergogenic resources used in exercise and sports. Previously, we presented the ergogenic mechanism of caffeine through neuronal A2AR antagonism in the central nervous system [1]. We demonstrate here that the striatum rules the ergogenic effects of caffeine through neuroplasticity changes. Thirty-four Swiss (8–10 weeks, 47 ± 1.5 g) and twenty-four C57BL6 (8–10 weeks, 23.9 ± 0.4 g) adult male mice were challenged in behavior and electrophysiology experiments using caffeine and SH-SY5Y cells for energetic metabolism. Systemic (15 mg/kg, i.p.) or striatal (bilateral, 15 µg) caffeine was psychostimulant in the open field (p < 0.05) and increased gripping muscle power (p < 0.05). Caffeine also induced long-term potentiation (LTP) in striatal slices (p < 0.05) and increased mitochondrial mass (p < 0.05) and membrane potential p < 0.05) in SH-SY5Y dopaminergic cells. In summary, our results demonstrate that caffeine stimulation in the striatum produces ergogenic effects accompanied by an LTP, possibly associated with acute increased mitochondrial metabolism observed in dopaminergic cell lines.
Root hypoxia aggravates the effects of saline tailings water on the growth and physiology of woody plants
Authors: Fleurial Killian Gérardin , Zhang Wen-Qing , Vassov Robert , Zwiazek Janusz J. 
Published: October 2022

Abstract
Aims
Oil sands mining in the boreal forest produces large volumes of liquid tailings. Research has generally focused on the thickness and composition of the soil layers to be placed on top of the tailings during reclamation. However, tailings release water, which may seep into the root zone and affect plants. Furthermore, the interactions and combined effects of root hypoxia and root substrate chemistry on plant responses are poorly understood.
Methods
The effects of the aqueous phase of novel tailings (Non-Segregating Tailings—NST) were studied under well-aerated and hypoxic conditions in three relatively hypoxia resistant tree species [tamarack (Larix laricina), black spruce (Picea mariana), and balsam poplar (Populus balsamifera)] and three relatively sensitive tree species [lodgepole pine (Pinus contorta), jack pine (Pinus banksiana), and aspen (Populus tremuloides)] by growing them in hydroponic solutions in a controlled environment.
Results
Root hypoxic conditions further reduced the survival, growth, and physiology of plants exposed to NST. Our results confirm that NST water produces the same deleterious effects in plants as previously reported in the amalgamated oil sands tailings. In trembling aspen, salt sequestration was inhibited, and in black spruce needles hypoxia may have prevented an osmoregulative mechanism.
Conclusions
Our results highlight the potential impact of water seepage from buried tailings on reclamation success. Furthermore, hypoxic conditions can aggravate these effects by inhibiting salt stress mechanisms. We suggest that the preparation of reclamation sites impacted by tailings water should involve efforts aimed at improvement of soil aeration to minimize the detrimental effects on plants.
An integrated chromatographic strategy to discover free radical inhibitors from trace fraction of Ribes himalense Royle ex Decne
Authors: Liu Chuang , Lei Yuqing , Lv Yue , Liu Youyi , Guo Jingrou , Wu Minchen , Dang Jun 
Published: October 2022

Abstract
Efficient and rapid chromatographic strategies are indispensable for analyzing the chemical components of natural products as well as their biological functions. The current study developed an integrated chromatography-based strategy to recognize and separate trace free radical inhibitors from the traditional Tibetan medicine Ribes himalense Royle ex Decne (R. himalense). First, R. himalense was processed using medium pressure liquid chromatography (MPLC) involving polyamide as a stationary phase. Then the free radical inhibitors in target fraction (Fr4) were purified using a two-dimensional reversed-phase/reversed-phase interaction liquid chromatography (2D RP/RPLC) mode, with the procedure being directed by an online HPLC-1,1-diphenyl-2-picrylhydrazyl (HPLC-DPPH) activity screening method. Finally, three free radical inhibitors (3-caffeoylquinic acid methyl ester, rutin and myricetin-3'-α-L-rhamnopyranoside) were successfully isolated with a percentage purity above 95%, with their IC50 values being 22.5 µg/mL, 9.5 µg/mL and 15.4 µg/mL respectively. To the best of our knowledge, these free radical inhibitors are being recorded for the first time in R. himalense. Furthermore, the integrated chromatography-based strategy developed in this work was shown to be reliable and efficient, which further supplemented the chemical components of R. himalense, as well as provided methodological support for the analysis of active substances in other natural products.
Impact of seed origin and genetic drift of improved rice variety IR841 in Benin
Authors: SEDAH Paulin , DJEDATIN Gustave Lambert , Yêyinou Laura Estelle Loko , EWEDJE Eben-Ezer , OROBIYI Azize , GBEMAVO Charlemangne Dossou Seblodo Judes , TOFFA Joelle , TCHAKPA Cyrille , CUBRY Phillipe , SABOT Francois 
Published: October 2022

Abstract
Background
Rice production is important for food security in Benin, with a national production largely dominated by the cultivation of the ecotype IR841, by far the most appreciated by Beninese consumers. However, to maintain agronomical qualities of a given cultivar, the origin and quality of seeds are mandatory and at the heart of the maintenance of yield and of market requests. Following this idea, the objective of the current study was thus to investigate the genetic purity of IR841 varieties collected from rice producers across 22 villages in Benin in relation to their agronomical performances.
Results
For this, agromorphological evaluation of 72 accessions based on 13 quantitative descriptors followed by genotyping with the Illumina Infinium rice 7K SNP array of 9 accessions was carried out in the presence of 2 controls. Agromorphologic as well as genetic and phylogenetic analyses revealed two groups, the first one Okouta97, Koum47, Nana30, Man118, Ang1 and control sample IR841-2) was characterized by seed accessions provided by the formal seed system, while the second ((Koum53, Tchaka41 and Koud46) comprising seeds from local markets or from previous harvests and showing a depression in agronomic performances.
Conclusion
We showed that IR841 seed purity is mandatory for the completion of agronomical performance, and that the farmers’ choice of seeds must be guided and informed to ensure sustainability and food security