bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient joint compression and encryption approach based on compressed sensing with multiple chaotic systems
Authors: Wang Jingya , Song Xianhua , El-Latif Ahmed A. Abd 
Published: April 2022

Abstract
This paper puts forward a new algorithm that utilizes compressed sensing and two chaotic systems to complete image compression and encryption concurrently. Firstly, the hash function is utilized to obtain the initial parameters of two chaotic maps, which are 2D-SLIM and 2D-SCLMS map respectively. Secondly, a sparse coefficient matrix is transformed from the plain image through discrete wavelet transform. In addition, one of the chaotic sequences created by 2D-SCLMS system performs pixel transformation on the sparse coefficient matrix. The other chaotic sequences created by 2D-SLIM are utilized to generate a measurement matrix and perform compressed sensing operations. Subsequently, the matrix rotation is combined with row scrambling and column scrambling, respectively. Finally, the bit-cycle operation and the matrix double XOR is implemented to acquire the ciphertext image. Simulation experiment analysis manifests that the compressed encryption scheme has advantages in compression performance, key space and sensitivity, and is resistant to statistical attacks, violent attacks and noise attacks.
NSMCE2, a Novel Super-Enhancer-Regulated Gene, is Linked to Poor Prognosis and Therapy Resistance in Breast Cancer
Authors: Benedetto Carolina Di , Oh Justin , Choudhery Zainab , Shi Weiquan , Valdes Gilmer , Betancur Paola 
Published: April 2022

Abstract
Background
Despite today’s advances in the treatment of cancer, breast cancer-related mortality remains high, in part due to the lack of effective targeted therapies against breast tumor types that do not respond to standard treatments. Therefore, identifying additional breast cancer molecular targets is urgently needed. Super-enhancers are large regions of open chromatin involved in the overactivation of oncogenes. Thus, inhibition of super-enhancers has become a focus in clinical trials for its therapeutic potential. Here, we aimed to identify novel super-enhancer dysregulated genes highly associated with breast cancer patients’ poor prognosis and negative response to treatment.
Methods
Using existing datasets containing super-enhancer-associated genes identified in breast tumors and public databases comprising genomic and clinical information for breast cancer patients, we investigated whether highly expressed super-enhancer-associated genes correlate to breast cancer patients’ poor prognosis and to patients’ poor response to therapy. Our computational findings were experimentally confirmed in breast cancer cells by pharmacological SE disruption and gene silencing techniques.
Results
We bioinformatically identified two novel super-enhancer-associated genes – NSMCE2 and MAL2 – highly upregulated in breast tumors, for which high RNA levels significantly and specifically correlate with breast cancer patients’ poor prognosis. Through in-vitro pharmacological super-enhancer disruption assays, we confirmed that super-enhancers upregulate NSMCE2 and MAL2 transcriptionally, and, through bioinformatics, we found that high levels of NSMCE2 strongly associate with patients’ poor response to chemotherapy, especially for patients diagnosed with aggressive triple negative and HER2 positive tumor types. Finally, we showed that decreasing NSMCE2 gene expression by super-enhancer blockade or by directly silencing it increases breast cancer cells’ sensitivity to chemotherapy treatment.
Conclusions
Our results indicate that moderating the transcript levels of NSMCE2 could improve patients’ response to standard chemotherapy consequently improving disease outcome. Our approach offers a new avenue to identify a signature of tumor specific genes that are not frequently mutated but dysregulated by super-enhancers. As a result, this strategy can lead to the discovery of potential and novel pharmacological targets for improving targeted therapy and the treatment of breast cancer.
Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylatepathway in the propionate-producer Anaerotignum neopropionicum
Authors: Suarez-Diez Maria , Benito-Vaquerizo Sara , Parera-Olm Ivette , de Vroet Thijs , Schaap Peter J. , Sousa Diana Z , Santos Vitor A.P. Martins dos 
Published: April 2022

Abstract
Background Microbial production of propionate from diluted streams of ethanol (e.g., deriving from syngas fermentation) is a sustainable alternative to the petrochemical production route. Yet, few ethanol-fermenting propionigenic bacteria are known, and understanding of their metabolism is limited. Anaerotignum neopropionicum is a propionate-producing bacterium that uses the acrylate pathway to ferment ethanol and CO2 to propionate and acetate. In this work, we used computational and experimental methods to study the metabolism of A. neopropionicum and, in particular, the pathway for conversion of ethanol into propionate.Results Our work describes iANEO_SB607, the first genome-scale metabolic model (GEM) of A. neopropionicum. The model was built combining the use of automatic tools with an extensive manual curation process, and it was validated with experimental data from this and published studies. The model predicted growth of A. neopropionicum on ethanol, lactate, sugars and amino acids, matching observed phenotypes. In addition, the model was used to implement a dynamic flux balance analysis (dFBA) approach that accurately predicted the fermentation profile of A. neopropionicum during batch growth on ethanol. A systematic analysis of the metabolism of A. neopropionicum combined with model simulations shed light into the mechanism of ethanol fermentation via the acrylate pathway, and revealed the presence of the electron-transferring complexes NADH-dependent reduced ferredoxin:NADP+ oxidoreductase (Nfn) and acryloyl-CoA reductase-EtfAB, identified for the first time in this bacterium.Conclusions The realisation of the GEM iANEO_SB607 is a stepping stone towards the understanding of the metabolism of the propionate-producer A. neopropionicum. With it, we have gained insight into the functioning of the acrylate pathway and energetic aspects of the cell, with focus on the fermentation of ethanol. Overall, this study provides a basis to further exploit the potential of propionigenic bacteria as microbial cell factories.
Circumflex arterial sulcus of the scapula (sulcus arteriae circumflexae scapulae). Its anatomy and clinical relevance
Authors: Strnad Tomáš , Bartoníček Jan , Tuček Michal , Naňka Ondřej 
Published: April 2022

Abstract
Introduction: The circumflex scapular artery (CSA) has been described in detail in the literature, but the groove, i.e., the circumflex sulcus (CFS), formed by the artery on the lateral pillar of the scapula has been completely neglected. The aim of the present study was to describe the variability and anatomy of the CFS. Material and method: The study was based on the examination of 103 pairs of dry bone specimens of adult scapulae, i.e., 206 specimens, including 92 (46 pairs) male and 114 (57 pairs) female specimens. In the first step, quantitative criteria were defined for assessment of the CFS presence and type. Subsequently, statistical analysis of the obtained data was performed.Results: The study revealed considerable variability of the arterial groove, which was well-developed in 33% (type A), shallow in 40% (type B), and absent in 27% (type C) of cases. The mean distance between CFS and the infraglenoid tubercle was 3.3 cm (range, 2.5–5.4), which corresponds to the proximal third of the lateral border of the scapula. Conclusion: The study has confirmed variability of the arterial groove (CFS) and its localization in relation to the inferior glenoid rim. The findings are clinically important, particularly in relation to the Judet approach to scapular fractures.
Comprehensive Analysis of CXCL genes in Human Kidney Clear Cell Carcinoma
Authors: Shen Junwen , Wang Rongjiang , Chen Yu , Fang Zhihai , Tang Jianer , Yao Jianxiang , gao jianguo , chen xiaonong , shi xinli 
Published: April 2022

Abstract
Introduction: the predictive value for survival outcomes and mechanisms of the CXCL gene family in kidney Clear Cell Carcinoma (KIRC).Objective: We evaluated the predictive value for survival outcomes and mechanisms of the CXCL gene family in Kidney Clear Cell Carcinoma (KIRC). Methods: Transcriptional and survival data of CXCL genes in KIRC patients were retrieved from Oncomine and GEPIA databases to assess their functions. Mutations’ data were downloaded from the cBioPortal, while immune cell components data were obtained from TIMER databases. Enrichment analysis was performed using the STRING database. In vitro assays were performed to validate our findings. Results: A total of 8 CXCL (CXCL2/5/9/10/11/12/13/16) genes were found to be differentially expressed in KIRC tissues. Among them, only CXCL2 and CXCL5 had survival values. In vitro assays revealed that upregulated CXCL2 promotes renal cancer cell proliferation, migration and invasion. Additionally, CXCL2 exhibited an effect on three KIRC immune cell components (B cells, CD4 T cells, and Neutrophils). After evaluating the miRNA sequences upstream of CXCL2, it was established that hsa-miR-532-5p/CXCL2 pathways are potentially involved in the regulatory mechanisms. Finally, we established a prospective signature (CXCL1/5/13) for improved survival outcomes among KIRC patients.Conclusion: Among KIRC patients, 8 CXCL genes were differentially expressed, however, only CXCL2 and CXCL5 exhibited a significant survival value. Upregulated CXCL2 promotes renal cancer cell progression.
Preparation of Nano-SiO2 by silica sol in-situ complexation protective precipitation method
Authors: Yang Yubing , Yang Yuxiang , NI Chaoying 
Published: April 2022

Abstract
In this study, nanosilica particles were prepared from self-made silica gel under the protection of citric acid in situ complexation and ethyl acetate as the latent acid reagent. The effects of ethyl acetate, citric acid, reaction temperature, and reaction time on the particle size of nanosilica were studied. The optimum process parameters were determined as follows: V ethyl acetate: V silica sol = 9:50, citric acid addition amount 3.64%, reaction time 8 h, and reaction temperature 70 ℃. The products were characterized by IR, XRD, and TEM analyses. The results show that the silica prepared using this method has good dispersion, and the average controllable particle size is 19.44 nm. The method has the advantage of a simple preparation process and is expected to achieve industrial production.
Urbanization and depressive symptoms among middle-aged and older adults in China
Authors: Hong Chenlu , Luo Yanan 
Published: April 2022

Abstract
Background: As a health transition, urbanization plays an important role in individuals’ health. However, it is difficult to isolate healthy migrant effect between urbanization and health. This study examined the effects of urbanization on depressive symptoms and its possible pathways among Chinese middle-aged and older adults independent of the influence of health-selective migration.Methods: Using the baseline survey of the China Health and Retirement Longitudinal Study, this study compared the depressive symptoms among three groups (urbanized rural residents, rural non-migrants and urban non-migrants). The 10-item Center for Epidemiologic Studies Depression Scale (CESD-10) short form was used to measure depressive symptoms. Logistic regression models and Structural Equation Model (SEM) were applied to examine the association between urbanization and depressive symptoms and the corresponding potential mechanisms.Results: Compared with urbanized rural residents, rural residents were more likely to have depressive symptoms (OR=1.19, 95% CI=1.07, 1.32), and urban residents were associated with a decreased risk of depressive symptoms (OR=0.81, 95% CI: 0.70, 0.94). A large proportion of the association between urbanization and depressive symptoms were mainly mediated by social participation, income and living conditions.Conclusions: Planned urbanization had an independent impact on decreased depressive symptoms. Improvements in social participation, income and living conditions are the main drivers behind this relationship. Additionally, urbanization compensates for the negative impact on depressive symptoms from disadvantaged early life conditions, but it cannot completely eliminate the gap between urbanized rural people and urban non-migrants.
Synergistic antibacterial effect of highly permeable curcumin and ciprofloxacin containing self-emulsifying drug delivery system against urinary tract bacterial infections
Authors: Ameer Nabeela , Hanif Muhammad , Azeem Muhammad , Mahmood Khalid , Chugtai Fazal Rahman Sajid , Ramzan Nasreen , Aziz Mubashir , Pandey Kapil 
Published: April 2022

Abstract
Antibacterial properties of curcumin (Cur) and ciprofloxacin (Cip) against urinary tract bacterial infections can be improved by using self-emulsifying drug delivery system (SEDDS). Previously prepared Cur-SEDDS (lauroglycol FCC, tween 80, transcutol HP) alone and its combination with ciprofloxacin (Cip) were used to investigate the antibacterial activity against Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa. Minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), dose response curve, checkerboard assay and time kill assay were performed to investigate the synergistic effect of Cur and Cip. FTIR, polydispersity index (PDI), zeta potential, permeability coefficient (Kp), cell viability assay of Cur, Cip and Cur-Cip containing SEDDS were performed. Average PDI of all SEDDS was 0.3±0.97 with negative charge -10.56±0.67mV at pH 6.8 and encapsulation efficiency 93.88%. Interestingly, Cur and Cip showed synergistic behavior at average MIC of 72±0.45 and 0.33±0.98 against three microorganisms. Stability analysis using Rgui software (R 4.1.3 version) estimates shelf life of 16 months. Improvement in the permeation rate was up to 10 times of Cur and 3 times of Cip in case of SEDDS as compared to their pure form. Enhanced permeation through SEDDS and synergistic antibacterial effect will help in establishing its therapeutic usefulness especially for bacterial urinary tract infections in humans.
Commensal Oral Microbiota Influences Ulcerative Oral Mucositis Clinical Course in Allogeneic Stem Cell Transplant Recipients
Authors: Bruno Julia , Heidrich Vitor , Knebel Franciele H. , de Molla Vinícius Campos , Parahyba Claudia Joffily , Miranda-Silva Wanessa , Asprino Paula Fontes , Tucunduva Luciana , Rocha Vanderson , Novis Yana , Arrais-Rodrigues Celso , Camargo Anamaria Aranha , Fregnani Eduardo Rodrigues 
Published: April 2022

Abstract
Oral mucositis (OM) is a complex acute cytotoxicity of antineoplastic treatment that affects 40%-85% of patients undergoing hematopoietic stem-cell transplantation. OM is associated with prolonged hospitalization, increased extensive pharmacotherapy, need for parenteral nutrition, and elevated treatment costs. As OM onset relates with the mucosal microenvironment status, with a particular role for microbiota-driven inflammation, we aimed to investigate whether the oral mucosa microbiota was associated with the clinical course of OM in patients undergoing allogeneic hematopoietic stem-cell transplantation. We collected oral mucosa samples from 30 patients and analyzed the oral mucosa microbiota by 16S rRNA sequencing. A total of 13 patients (43%) developed ulcerative OM. We observed that specific taxa were associated with oral mucositis grade and time to oral mucositis healing. Porphyromonas relative abundance at preconditioning was positively correlated with ulcerative OM grade (Spearman ρ = 0.61, p = 0.028) and higher Lactobacillus relative abundance at ulcerative OM onset was associated with shortened ulcerative OM duration (p = 0.032). Additionally, we generated a machine-learning-based bacterial signature that uses pre-treatment microbial profiles to predict whether a patient will develop OM during treatment. Our findings suggest that further research should focus on host-microbiome interactions to better prevent and treat OM.
Steady-state estradiol triggers a unique innate immune response to allergen resulting in increased airway hyper-reactivity yet decreased eosinophils and ILC2.
Authors: Warren Kristi , Deering-Rice Cassandra , Huecksteadt Tom , Trivedi Shubhanshi , Venossa Alessandro , Reilly Christopher , Sanders Karl , Clayton Frederic , Wyatt Todd A. , Poole Jill A , Heller Nicola M. , Leung Daniel , III Robert Paine 
Published: April 2022

Abstract
Rationale: Asthma is a chronic airway condition that occurs more often in women than men during reproductive years. In males, testosterone attenuates allergic inflammation while estrogens are thought to exacerbate asthma through the estrogen receptors on airway epithelial cells. Population studies have looked at all types of asthma, and collectively shown that long-term use of oral contraceptives decreased the onset of asthma in women of reproductive age. In the current study, we hypothesized that steady-state levels of estrogen would reduce airway inflammation and airway hyperresponsiveness to methacholine challenge. Methods: Ovariectomized BALB/c mice (Ovx) were implanted with subcutaneous hormone pellets (estrogen, OVX-E2; or placebo, OVX-Pl) that deliver consistent levels of estrogen [49 ± pg/mL] followed by ovalbumin sensitization and challenge. In conjunction with methacholine challenge, immune phenotyping was performed to correlate inflammatory proteins and immune populations with better or worse pulmonary outcomes measured by invasive pulmonary mechanics techniques. Results: Histologic analysis showed an increase in total cell infiltration around the airways and vasculature leading to an increased inflammatory score in ovarectomized (OVX) animals with steady-state estrogen pellets (OVX-E2-OVA) as compared to other groups including female-sham operated (F-Sham-OVA) and OVX implanted with a placebo pellet (OVX-Pl-OVA). Airway resistance (Rrs) and lung elastance were increased in OVX-E2-OVA in comparison to F-Sham-OVA following aerosolized intratracheal methacholine challenges. Immune phenotyping revealed that steady-state estrogen reduced CD3+ T cells, CD19+ B cells, ILC2 and eosinophils across all experiments. Inflammatory cytokines (IL-5 and IL-13) were also decreased in OVX-E2-OVA treated animals in comparison to Female-Sham-OVA mice. ILC2 that were sorted and stimulated with exogenous IL-33 had less cytokine and chemokine expression when they were isolated from OVX-E2-OVA animals indicating that estrogen suppresses IL-33 mediated activation of ILC2. Conclusions: Therapeutically targeting estrogen receptors may have a limiting effect on eosinophils, ILC2 and potentially other immune populations that may improve asthma symptoms in those females that experience perimenstrual worsening of asthma, with the caveat, that long-term use of estrogens or hormone receptor modulators may be detrimental to the lung microenvironment over time.
An approach for prioritizing candidate genes from RNA-seq using preclinical cocaine craving datasets as a test case
Authors: Vannan Annika , Dell'Orco Michela , Perrone-Bizzozero Nora I. , Neisewander Janet L. , Wilson Melissa A. 
Published: April 2022

Abstract
The addiction field relies heavily on rodent models to probe the complex molecular mechanisms underlying drug motivation and reward. However, findings in animal research often fail to be reproduced or translated into clinical treatments. Here, we developed and applied standardized workflows to three RNA-sequencing (RNA-seq) studies in rodent self-administration models to assess reproducibility and translational viability of potential gene targets. Generally, we found low overlap of differentially-expressed genes (DEGs) across datasets using a significance level of P < 0.05, and only 1 DEG in any dataset after correcting for multiple testing (FDR < 0.05 or FDR < 0.1), raising concerns about false positives. When using a nominal P value, which is a standard used in the field, we found potential genomic targets for drug craving and withdrawal that overlap across datasets. Several of these shared genes are conserved in humans and/or are highly expressed in reward regions of the brain, but the sample sizes in all datasets limit the power to distinguish true positives from false positives. Thus, we advocate for improved RNA-seq experimental design, data collection, statistical testing, and metadata reporting that will bolster the field’s ability to communicate across research groups and advance addiction science in a more reproducible manner.
Expression of γδTCR on myeloid cells of Plasmodium yoelii nigeriensis -infected C57BL/6 mice
Authors: Chen Dianhui , Mo Feng , Liu Meiling , Liu Lin , Xing Junmin , Shi Feihu , Xie Anqi , Xie Hongyan , Pan Xingfei , Wang Xinhua , Huang Jun 
Published: April 2022

Abstract
Background: The role of CD3+γδTCR+(γδT) cells during the Plasmodium yoelii nigeriensis infection has been reported in our previous studies. However, there is a paucity of studies on the characteristics of myeloid cells which expressed γδTCR. Therefore, the aim of this study was to observe the properties of γδTCR-expressing myeloid cells in the spleen of C57BL/6 mice infected by P. yoelii NSM. Methods: Haematoxylin-eosin (HE) staining was used to observe the pathological changes in the spleens. The samples from the experimental group before and after infection underwent RNA sequencing (RNA-seq), and the differentially expressed genes (DEGs) were screened. Flow cytometry (FCM) was used to evaluate the frequency of γδTCR+ cells and the characteristics of γδTCR+ cells in Plasmodium yoelii-infected mice.Results: We observed obvious infiltration of inflammatory in infected C57BL/6 mouse spleens. The proportions of γδTCR+ cells and CD11b+ γδTCR+cells from infected group were higher than that from normal group. γδTCR+CD11b+ cells expressed high levels of activated-mediated genes and inflammatory-mediated genes. We characterized the heterogeneous pathway activities among γδTCR+CD11b+ cells from normal and infected group. The oxidative phosphorylation, respiratory electron transport chain and leukocyte activation involved in immune response pathways were up-regulated, while the alpha-beta T cell activation and myeloid leukocyte migration pathways were down-regulated. Importantly, we found that Ly6c2 was higher expressed in γδTCR+CD11b+ cells than Ly6g. Consistent with it, flow cytometry results revealed that a subset of Ly6C+Ly6G-CD11b+γδTCR+ cells was higher than Ly6G+Ly6C-CD11b+γδTCR+ cells in the spleen. Conclusions: Taken together, our data suggest the existence of a population of γδTCR-expressing myeloid cells and played potential role in the context of Plasmodium infection. The molecular markers and pathways screened warrant further study.