bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of leaf transcriptome in grafted tomato seedlings inoculated with beneficial rhizobacteria Azospirillum brasiliensis and Paraburkholderia graminis
Authors: Caradonia Federica , Buti Matteo , Flore Alessia , Morcia Caterina , Ronga Domenico , Gatti Roberto , Moulin Lionel , Terzi Valeria , Francia Enrico , Milc Justyna Anna 
Published: April 2022

Abstract
Aims: Characterization of the transcriptomic responses of grafted tomato seedlings inoculated with two beneficial microorganisms.Methods: mRNA sequencing analyses were performed from leaves of grafted tomato seedlings at flowering stage, 35 days after inoculations. The differential expression analysis results were validated by carrying out a quantitative reverse transcription PCR on nine selected genes.Results and Conclusions: Root inoculations with the two beneficial bacteria can influence the genes activity also in organs distant from roots. Interactions between grafted tomato seedlings and microorganisms suggest that the interactions between tomato and microorganisms are species-specific, and affect the activity of specific sets of genes, that in turn activate and/or involve similar pathways and mechanisms. This study provides novel knowledge on the effects of inoculation of Azospirillum brasiliensis (AB) and Paraburkholderia graminis (PG)on grafted tomato seedling metabolism, and on the molecular mechanisms underlying the improved performance of tomato plants after these treatments as far as yield and stress responses are regarded. AB induced genes coding for different MYB trascrption factors known to be involved in response to biotic and abiotic stresses, PG upregulated 5 genes coding for putative late blight resistance protein homolog. Auxine responsive molecules and giberellins involved in the fruit-set and early fruit growth in tomato were mainly induced by AB.
Single-Piece Foldable Intraocular Lenses versus Three-Piece Intraocular Lenses in the Sulcus following Posterior Capsular Rupture
Authors: Torrefranca Aramis B. , Florcruz Nilo Vincent DG. , Cariño Noel S. , Kho Richard C. 
Published: April 2022

Abstract
PurposeSuccessful intraocular lens (IOL) placement in cataract surgery is synonymous with the IOL being placed in the capsular bag. When the bag is violated, the ciliary sulcus becomes an option to be able to place an intraocular lens in a near in-the-bag position. Studies report that single-piece foldable acrylic (SPA) IOLs are a poor choice for the sulcus. This study aimed to compare the visual outcomes and complications between sulcus placement of single-piece intraocular lenses and three-piece intraocular lenses.Methods: The medical records of patients were retrospectively reviewed in a single center.Results: A total of 245 patients were included in the study with mean age of 61 with male predominance. Majority of sulcus implantation occurred during phacoemulsification (87%). Around 82% (n=202) were implanted with SPA IOLs and 18% (n=43) were three-piece IOLs. Best corrected distance visual acuity (BCDVA) was 20/20 after 6 months for both groups. Comparison between two groups showed no superiority with each other. Complications notable were elevated IOP, corneal edema, loss of IOL centration and pigment dispersion. Results showed more proportions of complications with SPA IOLs than three-piece IOL. Smaller optic diameter and overall length predispose to increase in decentrations.Conclusions: We found no significant difference between the visual outcomes of three-piece IOLs with SPA IOLs. Complications were found to be more significant in SPA IOLs. Knowledge on the outcomes and complications of SPA IOLs would help ophthalmologists in their decision making and help set realistic expectations for both doctors and patients.
Single cell and spatial transcriptomic analyses reveal microglia-plasma cell crosstalk in the brain during Trypanosoma brucei infection
Authors: Quintana Juan , Chandrasegaran Praveena , Sinton Matthew , Briggs Emma , Otto Thomas , Heslop Rhiannon , Bentley-Abbot Calum , Loney Colin , de Lecea Luis , Mabbott Neil , MacLeod Annette 
Published: April 2022

Abstract
Human African trypanosomiasis, or sleeping sickness, is caused by the protozoan parasite Trypanosoma brucei and induces profound reactivity of glial cells and neuroinflammation when the parasites colonise the central nervous system. However, the transcriptional and functional responses of the brain to chronic T. brucei infection remain poorly understood. By integrating single cell and spatial transcriptomics of the mouse brain, we identified that glial responses triggered by infection are readily detected in the proximity to the circumventricular organs, including the lateral and 3rd ventricle. This coincides with the spatial localisation of both slender and stumpy forms of T. brucei. Furthermore, in silico predictions and functional validations led us to identify a previously unknown crosstalk between homeostatic Cx3cr1+ microglia and Cd138+ plasma cells mediated by IL-10 and B cell activating factor (BAFF) signalling. This study provides important insights and resources to improve understanding of the molecular and cellular responses in the brain during infection with African trypanosomes.
Pseudogene OCT4-pg5 Upregulates OCT4B Expression to Promote Bladder Cancer Progression by Competing with miR-145-5p
Authors: Zhou Wuer , Yang Yue , Wang Wei , Yang Chenglin , Cao Zhi , Lin Xiaoyu , Zhang Huifen , Xiao Yuansong , Zhang Xiaoming 
Published: April 2022

Abstract

Background
Bladder cancer (BC) is one of the most common malignant neoplasms worldwide, and is characterized by metastasis and insensitivity to chemotherapy. We aim to construct competing endogenous RNA (ceRNA) networks to identify potential progression and prognostic markers associated with BC.
Methods
We first extracted the expression profiles of RNAs from The Cancer Genome Atlas (TCGA) database and used bioinformatic analysis to establish ceRNAs in BC. Real-time quantity PCR (RT-qPCR) was performed to measure OCT4-pg5 and OCT4B expressions in different bladder cell lines and different grades of cancer. The effects of OCT4-pg5, OCT4B and miR-145-5p on proliferation and metastasis were determined by in vitro and in vivo experiments. Luciferase reporter assay was carried out to reveal the interaction among OCT4-pg5, OCT4B and miR-145-5p. Flow cytometry was performed to explore the effects of OCT4-pg5 and OCT4B expression on the cell cycle phases distribution of T24 cells.
Results
The OCT4-pg5/miR-145-5p/OCT4B ceRNA network was related to the progression and prognosis of BC. OCT4-pg5 expression was significantly increased in BC cell lines, which was correlated with OCT4B expression and advanced tumor grade. Overexpression of OCT4-pg5 and OCT4B promoted the proliferation and invasion of BC cells, while miR-145-5p suppressed these activities. Mechanically, OCT4-pg5 3’ untranslated region (3’UTR) competed for miR-145-5p, thereby increasing OCT4B expression. In addition, OCT4-pg5 promoted EMT by activating the Wnt/β-catenin pathway and upregulating the expression levels of matrix metalloproteinases (MMPs) 2 and 9 as well as transcription factors zinc finger E-box binding homeobox (ZEB) 1 and 2. Furthermore, elevated expression of OCT4-pg5 and OCT4B reduced the sensitivity of BC cells to cisplatin by reducing apoptosis and increasing the proportion of cells in G1.
Conclusions
These findings indicate that OCT4-pg5/miR-145-5p/OCT4B axis promotes the progression of BC by inducing EMT via Wnt/β-catenin pathway and enhances the cisplatin resistance. It could be prospect for the therapeutic approaches for BC.
Biosensor Guided Polyketide Synthase Engineering for Optimization of Domain Exchange Boundaries
Authors: Englund Elias , Schmidt Matthias , Nava Alberto , Dan Qingyun , Katz Leonard , Yuzawa Satoshi , Keasling Jay 
Published: April 2022

Abstract
Type I modular polyketide synthases (PKSs) are multi-domain enzymes functioning like assembly lines. Many engineering attempts have been made for the last three decades to replace, delete and insert new functional domains into PKSs to produce novel molecules. However, the resulting PKS hybrids typically have reduced catalytic activities and are often insoluble due to misfolding. Here, we have developed a fluorescence-based biosensor method for detecting engineered PKSs with high solubility. The biosensor has been used to sort through PKS hybrids that had acyltransferase (AT) domains from other PKSs exchanged for the native AT with randomly assigned linker junctions. Importantly, we observed a significant correlation between activity and solubility. Evaluation of highly soluble mutants in vitro revealed new boundaries for AT domain exchanges that give a wild-type level of catalytic activity. Together, we have successfully developed an experimentally validated high-throughput method to efficiently screen active engineered PKSs that produce target molecules.
High performance stemming algorithm to handle multi-level inflections in Urdu Language
Authors: Jabbar Abdul , Iqbal Sajid , Ilahi Manzoor 
Published: April 2022

Abstract
Stemming is an essential step in varied Natural Language Processing (NLP) applications. It is used to reduce different variants of the query words to a standard form to avoid the vocabulary mismatch issue in Information Retrieval (IR) systems. There are a lot of stemming algorithms in English language, but Urdu NLP still in its infancy. A stemmer develops and evaluates in a language cannot be efficiently used for other languages. Urdu has the highly inflected and complex morphological structure, and most of the current Urdu stemmers remove a few numbers of affixes and leads to inefficient results. In this context, according to the best of our knowledge, this is a first comprehensive effort towards the proposition and evaluation of a novel Urdu Text Stemmer (UTS) that cope with multi-level inflection and derivation forms in Urdu text. The experimental evaluation of the proposed scheme has been conducted on the text-based and words-based custom developed corpus. The proposed stemming technique is rigorously evaluated and compared with state-of-the-art stemming algorithms. Experimental results demonstrate that UTS outperforms existing Urdu stemmers and achieves an accuracy of 94.92% and 91.8% on word and text corpus, respectively.
Analysis of economic recovery forecasts in the post-COVID-19 era - China as an example
Authors: Li Xin 
Published: April 2022

Abstract
Since the outbreak of the new crown epidemic, it has dealt a severe blow to economies around the world. How to quickly recover the traumatized economies in the post-epidemic era is now an important task. This paper constructs a prediction model based on the data of five major epidemics similar to the current one that occurred in history. Based on the prediction model built, we make a comprehensive forecast and individual economic indicators forecast for China's economy after the current epidemic, and the forecast results show that the overall economy of the country name and import and export can basically recover to the pre-epidemic level in about one year, and the recovery time for tourism and air transportation is longer and requires a slow recovery. This result is also very much in line with China's reality. China has already gained some experience in this kind of economic recovery, and a summary of these experiences will provide inspiration to other economies.
Vision-related Quality of Life in Low-vision Patients Who Underwent Epiretinal Membrane Surgery
Authors: Horozoglu Fatih , Sener Hidayet , Polat Osman Ahmet , Sever Ozkan , Yuksel Turgut , Evereklioglu Cem 
Published: April 2022

Abstract
PurposeTo evaluate vision-related quality of life (VR-QOL) in patients with preoperative low vision who had previously removed epiretinal membrane (ERM) with pars plana vitrectomy, and compared the results with the control group (CG).MethodsIn this retrospective and nonrandomized clinical study, 20 subjects with unilateral ERM and 20 healthy subjects as CG were included in the study. The Turkish-translated National Eye Institute Visual Function Questionnaire-25 (NEI VFQ-25) was used. In all cases, under local anesthesia, the two-step 23 G vitrectomy was performed with a similar technique by the same experienced vitreoretinal surgeon.ResultsThe preoperative best corrected visual acuity (BCVA) in ERM group was 1.04±0.41. Postoperative visual improvement reached statistical significance (p<0.001) and postoperative 6th month BCVA was 0.61±0.41. The postoperative 6th month composite score of NEI VFQ-25 was significantly lower in patients with ERM than in the CG (p=0.017). The preoperative subscale scores were significantly lower in the patients with ERM than in the CG in general vision, ocular pain, near activities and distance activities (p<0.001, p=0.005, p<0.001, p=0.003, respectively).ConclusionsThe NEI VFQ-25 questionnaire can discriminate ERM patients from healthy individuals, and visual acuity does not fully reflect VR-QOL. Impaired binocular vision may be associated with the deterioration of VR-QOL in patients with ERM in the postoperative period.
Study on Classification of Metal Objects by Fluxgate Magnetometer Cube Structure
Authors: han songtong , Zhang Bo , wen zhu 
Published: April 2022

Abstract
In order to classification the kinds of metal objects, we propose a recognition method based on ResNet-18. First, we built a magnetic field feature collector that we called FMCAS (Fluxgate magnetometer cube arrangement structure), using 8 fluxgate magnetometer sensor array structures to ensure a distance of 400mm between each sensitive unit. We use FMCAS to collect the magnetic field data of a survey line along the east-west direction on the north side of the measured target. Next, we change the location and type of the target and build a database of magnetic target models, which enriches the diversity of the training dataset. Construct the magnetic flux density tensor matrix to create the experimental dataset. Finally, we use the improved ResNet-18 to train the data to get the recognition classification recognizer. The recognition accuracy of this approach is 84.1%, according to the test results from 107 groups of validation sets. The target with larger magnetic moment has the best recognition effect, with a recognition accuracy rate of 96.3%, a recall rate of 96.4%, and a precision rate of 96.4%. Experimental results show that our improved RestNet-18 network can effectively handle the classification of metal objects.
New Thienopyridine Scaffold as An Antidementia Lead: In Silico Study and Biological Screening
Authors: mahmoud ZeinabMahmoud , Mohamed Lamia W. , Mohamed Khaled O. , Sayed Hadeer S. , Fattah May A. Abd El , El-Malah Afaf 
Published: April 2022

Abstract
New thienopyridine tacrine analogues were efficiently synthesized. Series 2 and 4 enclosed fourteen new compounds. They were screened against their acetyl cholinesterase, butyryl cholinesterase and β-amyloid protein inhibition. In acetyl cholinesterase inhibition assay, 2h showed IC50 value 26.4 ± 0.03 ng/mL excelling tacrine itself. 2e possessed excellent IC50 values 1.7 ± 0.07 and 14.7 ± 0.03 ng/mL for both the butyryl cholinesterase and β-amyloid protein inhibition assays, sequentially. The in silico ADME studies were investigated for the promising members (2c, 2d, 2e, 2h, 2i, and 4e) and all the results were illustrated. A comparative docking study was conducted between the promising members and both tacrine and donepezil in both acetyl and butyryl choline active sites. The results revealed extra binding patterns.
Production of a canine model of Parkinson’s disease using somatic cell nuclear transfer
Authors: Lee Ji Hye , Kwon Kyu , Park Chan Kyu , Kim Keun Jung , Kim Eun Young , Kim Min Kyu 
Published: April 2022

Abstract
Dogs have been considered a suitable model to study human neurodegenerative diseases, such as Alzheimer’s disease and Parkinson’s disease (PD), and brain aging, because of their long lifespan and the similarities of disease presentation and clinical response in humans and dogs. Further, it is possible to evaluate the visible cognition/motion ability of patients with brain dysfunction. In the present study, we aimed to generate a canine model of PD that overexpresses the human DJ-1 (hDJ-1) gene using the somatic cell nuclear transfer (SCNT) technique. The hDJ-1 gene was transfected into canine fetal fibroblasts, which were used to produce cloned embryos. Reconstructed embryos were transferred into the oviduct of surrogate mothers, one of which gave birth to one dog. The cloned dog was depressed, and his movements were slow and fewer, resulting in an abnormal phenotype, as observed via imaging analyses, such as positron emission tomography (PET) and magnetic resonance imaging (MRI) analyses; these findings were similar to the symptoms of PD in humans. In addition, exogenous hDJ-1 was successfully transmitted to the next generation without silencing. We confirmed that the puppies exhibited the same behavior and imaging analysis as the hDJ-1 transgenic (TG) dog. Using SCNT, we generated TG dogs with PD that overexpressed the hDJ-1 gene. Human PD-like phenotypes have been confirmed in the TG dogs. To the best of our knowledge, this is the first report that describes the establishment of a canine model of PD. Furthermore, TG dogs could be used in preclinical trials of drugs for the treatment of PD.
WITHDRAWN: Can latency-reversing drugs reawaken dormant retrovirus infection? A mathematical analysis
Authors: Chen S. 
Published: April 2022

Abstract

Background:The technique of using drugs to target latent virus reservoir has been introduced to reawaken the dormant virus so that the immune system can attack it. However, further tests have shown this method to fail in laboratory tests. In this work, the author tries to mathematically analyze whether drugs can be used to reawaken dormant virus reservoirs. The study uses mathematical formulas to differentiate between different relationship types, and then a model of protein reawakening dormant reservoirs is presented. Results:The results show that the amino acid sequences ARG of gag proteins of HTLV1, HTLV2, STLV1 and STLV2 match with their primer binding site GGGGGCTCG in the 3'-to-5' direction, and the amino acid sequences SPR of gag proteins of HIV1, HIV2, SIV and FIV match with their primer binding site GGCGCCCGA in the 3'-to-5' direction. The gag, gag-pol and gag-pro-pol proteins are promising for reawakening dormant retrovirus infection. Conclusions:The author hence believes that the latency-reversing drugs were involved in the process of transcription of cancer, and the genome they reawakened just happened to contain the genome of the retrovirus, which means that it was false reawakening. On the other hand, using proteins of retroviruses to reawaken them is more reliable, just like androgen receptor activates the IGF1R gene.
Dynamics of deep soil water, organic carbon and total nitrogen in response to the conversion of annual crops to long-term alfalfa pasture on the semi-arid Loess Plateau
Authors: Wang Li , Ali Nazer , Wang Zikui 
Published: April 2022

Abstract
Aims Deep soil resources was not well quantified under dryland conditions. This study aimed to quantify the changes of deep soil water, soil organic carbon (SOC), and total nitrogen (TN) in alfalfa pasture, and identify the relationships between root density and their changes.Methods Field experiment was conducted in the Loess Plateau in 2020 and 2021. Soil water, SOC, and TN contents and alfalfa root density to 1000-cm-depth were measured in alfalfa pastures and an annual crop reference field.Results Soil water depletion by alfalfa mainly occurred in the first six years with a depletion rate of 41.6, 49.1, and 62.1 mm year-1 in the shallow (0-200 cm), middle (200-500 cm), and deep (500-1000 cm) soil layers, respectively. Total depletion after six and 19 years were 916.8 and 1049.4 mm respectively. SOC content in all layers increased and peaked six years after planting, with total storage in the 0-1000-cm-profile of 74.6 kg m-2, 43.3% higher than in the reference field. TN storage in only the shallow layer continuously increased and was 52.5% higher than that in the reference field after 19 years. Root density explained the changes of soil water in the shallow and deep soil layer, SOC in the shallow and middle layer, and TN only in the shallow soil layer.Conclusions Although alfalfa pasture continuously reduced deep soil water, it showed great potential for soil carbon and nitrogen sequestration. It should be stopped early (≤6years) to increase water sustainability and maintain carbon and nitrogen sequestration efficiencies.
The quality and fertilizing potential of red deer (Cervus elaphus L.) epididymal spermatozoa stored in a liquid state – a preliminary study
Authors: Dziekońska Anna , Koziorowska-Gilun Magdalena , Kordan Władysław , Neuman Nicoletta M. , Kotlarczyk Angelika M. , Korzekwa Anna J. 
Published: April 2022

Abstract
The aim of this study was to assess the quality and fertilizing potential of red deer epididymal spermatozoa stored in a liquid state for up to 11 days (D11). In Experiment 1, sperm quality was determined. In Experiment 2, the efficiency in vitro fertilization (IVF) and artificial insemination (AI) of stored sperm were evaluated. An analysis of sperm quality on D5 of storage revealed a decrease (P < 0.05) in motility, morphology, and a higher proportion of apoptotic spermatozoa. On D1, D7 and D10, the total motility of sperm for IVF and AI was determined at 82.6%, 71.0% and 64.8%, respectively. The results of IVF and AI demonstrated that the fertilizing potential of spermatozoa differ between days of storage. The percentage of blastocysts was higher when oocytes were fertilized with D1 (17.4%) than and D7 (8.5%) and D10 sperm (10.5%). Differences were noted in the pregnancy rates of inseminated hinds. The insemination with D1, D7 and D10 sperm led to live births (33% on D7 and D10). The results indicate that the quality of red deer epididymal spermatozoa remains satisfactory during ten days of storage in a liquid state, and that these spermatozoa maintain their fertility potential.