bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative in-silico proteomic analysis discerns potential granuloma proteins of Yersinia pseudotuberculosis
Authors: Aswal Manisha , Garg Anjali , Singhal Neelja , Kumar Manish 
Published: February 2020

AbstractYersinia pseudotuberculosisis one of the three pathogenic species of the genusYersinia. Most studies regarding pathogenesis ofY. pseudotuberculosisare based on the proteins related to Type III secretion system, which is a well-known primary virulence factor in pathogenic Gram-negative bacteria, includingY. pseudotuberculosis. Information related to the factors involved inY. pseudotuberculosisgranuloma formation is scarce. In the present study we have used a computational approach to identify proteins that might be potentially involved in formation ofY. pseudotuberculosisgranuloma. A comparative proteome analysis and conserved orthologous protein identification was performed between two different genera of bacteria -MycobacteriumandYersinia, their only common pathogenic trait being ability to form necrotizing granuloma. Comprehensive analysis of orthologous proteins was performed in proteomes of seven bacterial species. This includedM. tuberculosis,M. bovisandM. avium paratuberculosis- the known granuloma formingMycobacteriumspecies,Y. pestisandY. frederiksenii- the non-granuloma formingYersiniaspecies and,Y. enterocolitica- that forms micro-granuloma and,Y. pseudotuberculosis- a prominent granuloma formingYersiniaspecies.In silicoproteome analysis indicated that seven proteins (UniProt id A0A0U1QT64, A0A0U1QTE0, A0A0U1QWK3, A0A0U1R1R0, A0A0U1R1Z2, A0A0U1R2S7, A7FMD4) might play some role inY. pseudotuberculosisgranuloma. Validation of the probable involvement of the seven proposedY. pseudotuberculosisgranuloma proteins was done using transcriptome data analysis and, by mapping on a composite protein-protein interaction map of experimentally provedM. tuberculosisgranuloma proteins (RD1 locus proteins, ESAT-6 secretion system proteins and intra-macrophage secreted proteins). Though, additional experiments involving knocking out of each of these seven proteins are required to confirm their role inY. pseudotuberculosisgranuloma our study can serve as a basis for further studies onY. pseudotuberculosisgranuloma.
S-endoglin expression is induced in hyperoxia and contributes to altered pulmonary angiogenesis in bronchopulmonary dysplasia development
Authors: Lee Yeongseok , Lee Juyoung , Nam Soo Kyung , Hoon Jun Yong 
Published: February 2020

AbstractAltered pulmonary angiogenesis contributes to disrupted alveolarization, which is the main characteristic of bronchopulmonary dysplasia (BPD). Transforming growth factor β (TGFβ) plays an important role during lung vascular development, and recent studies have demonstrated that endoglin is engaged in the modulation of TGFβ downstream signalling. Although there are two different isoforms of endoglin, L- and S-endoglin, little is known about the effect of S-endoglin in developing lungs. We analysed the expression of both L- and S-endoglin in the lung vasculature and its contribution to TGFβ-activin-like kinase (ALK)-Smad signalling with respect to BPD development. Hyperoxia impaired pulmonary angiogenesis accompanied by alveolar simplification in neonatal mouse lungs. S-endoglin, phosphorylated Smad2/3 and connective tissue growth factor levels were significantly increased in hyperoxia-exposed mice, while L-endoglin, phosphor-Smad1/5 and platelet-endothelial cell adhesion molecule-1 levels were significantly decreased. Hyperoxia suppressed the tubular growth of human pulmonary microvascular endothelial cells (ECs), and the selective inhibition of ALK5 signalling restored tubular growth. These results indicate that hyperoxia alters the balance in two isoforms of endoglin towards increased S-endoglin and that S-endoglin attenuates TGFβ-ALK1-Smad1/5 signalling but stimulates TGFβ-ALK5-Smad2/3 signalling in pulmonary ECs, which may lead to impaired pulmonary angiogenesis in developing lungs.
A Nonpeptide Oxytocin Receptor Agonist for a Durable Relief of Inflammatory Pain
Authors: Hilfiger Louis , Zhao Qian , Kerspern Damien , Inquimbert Perrine , Andry Virginie , Goumon Yannick , Darbon Pascal , Hibert Marcel , Charlet Alexandre 
Published: February 2020

AbstractOxytocin possesses several physiological and social functions, among which an important analgesic effect. For this purpose, oxytocin binds mainly to its unique receptor, both in the central nervous system and in the peripheral nociceptive terminal axon in the skin. However, despite its interesting analgesic properties and its current use in clinics to facilitate labor, oxytocin is not used in pain treatment. Indeed, it is rapidly metabolized, with a half-life in the blood circulation estimated at five minutes and in cerebrospinal fluid around twenty minutes in humans and rats. Moreover, oxytocin itself suffers from several additional drawbacks: a lack of specificity, an extremely poor oral absorption and distribution, and finally, a lack of patentability. Recently, a first non-peptide full agonist of oxytocin receptor (LIT-001) of low molecular weight has been synthesized with reported beneficial effect for social interactions after peripheral administration. In the present study, we report that a single intraperitoneal administration of LIT-001 in a rat model induces a long-lasting reduction in inflammatory pain-induced hyperalgesia symptoms, paving the way to an original drug development strategy for pain treatment.
Keel bone fractures induce a depressive-like state in laying hens
Authors: Armstrong E. A. , Rufener C. , Toscano M. J. , Eastham J. E. , Guy J. H. , Sandilands V. , Boswell T. , Smulders T. V. 
Published: February 2020

AbstractIn commercial flocks of laying hens, keel bone fractures (KBFs) are prevalent and associated with behavioural indicators of pain. However, whether their impact is severe enough to induce a depressive-like state of chronic stress is unknown. As chronic stress downregulates adult hippocampal neurogenesis (AHN) in mammals and birds, we employ this measure as a neural biomarker of subjective welfare state. Radiographs obtained longitudinally from Lohmann Brown laying hens housed in a commercial multi-tier aviary were used to score the severity of naturally-occurring KBFs between the ages of 21–62 weeks. Individual birds’ transitions between aviary zones were also recorded. Focal hens with severe KBFs at 3–4 weeks prior to sampling (n = 15) had lower densities of immature doublecortin-positive (DCX+) multipolar and bipolar neurons in the hippocampal formation than focal hens with minimal fractures (n = 9). KBF severity scores at this time also negatively predicted DCX+cell numbers on an individual level, while hens that acquired fractures earlier in their lives had fewer DCX+neurons in the caudal hippocampal formation. Activity levels 3–4 weeks prior to sampling were not associated with AHN. KBFs thus lead to a negative affective state lasting at least 3–4 weeks, and management steps to reduce their occurrence are likely to have significant welfare benefits.
Vaginal microbiota diverges in sows with low and high reproductive performance after porcine reproductive and respiratory syndrome vaccination
Authors: Sanglard L. P. , Schmitz-Esser S. , Gray K. A. , Linhares D. C. L. , Yeoman C. J. , Dekkers J. C. M. , Niederwerder M. C. , Serão N. V. L. 
Published: February 2020

AbstractPrevious studies have demonstrated evidence for a relationship between the vaginal microbiome and reproductive performance, suggesting the vaginal microbiota may serve as a tool to predict farrowing outcomes in commercial pigs. In this study, we compared the vaginal microbiome in sows with low and high farrowing performance and used it to classify animals with contrasting reproductive outcomes in commercial sows following immune challenge with porcine respiratory and reproductive syndrome (PRRS) vaccination. Eighteen microbes were differentially abundant (q-value < 0.05) between the Low and High farrowing performance groups. Among them, Campylobacter, Bacteroides, Porphyromonas, Lachnospiraceae unclassified, Prevotella, and Phascolarctobacterium were also selected in the discriminant and linear regression analyses, and could be used as potential biomarkers for reproductive outcomes. The correct classification rate in the two groups was 100%. In conclusion, this study demonstrates that vaginal microbiota collected after PRRS vaccination could be potentially used to classify sows into having low or high farrowing performance in commercial herds.
Dual functional highly luminescence B, N Co-doped carbon nanodots as nanothermometer and Fe3+/Fe2+ sensor
Authors: Mohammed Lazo Jazaa , Omer Khalid M. 
Published: February 2020

AbstractDual functional fluorescence nanosensors have many potential applications in biology and medicine. Monitoring temperature with higher precision at localized small length scales or in a nanocavity is a necessity in various applications. As well as the detection of biologically interesting metal ions using low-cost and sensitive approach is of great importance in bioanalysis. In this paper, we describe the preparation of dual-function highly fluorescent B, N-co-doped carbon nanodots (CDs) that work as chemical and thermal sensors. The CDs emit blue fluorescence peaked at 450 nm and exhibit up to 70% photoluminescence quantum yield with showing excitation-independent fluorescence. We also show that water-soluble CDs display temperature-dependent fluorescence and can serve as highly sensitive and reliable nanothermometers with a thermo-sensitivity 1.8% °C−1, and wide range thermo-sensing between 0–90 °C with excellent recovery. Moreover, the fluorescence emission of CDs are selectively quenched after the addition of Fe2+ and Fe3+ ions while show no quenching with adding other common metal cations and anions. The fluorescence emission shows a good linear correlation with concentration of Fe2+ and Fe3+ (R2 = 0.9908 for Fe2+ and R2 = 0.9892 for Fe3+) with a detection limit of of 80.0 ± 0.5 nM for Fe2+ and 110.0 ± 0.5 nM for Fe3+. Considering the high quantum yield and selectivity, CDs are exploited to design a nanoprobe towards iron detection in a biological sample. The fluorimetric assay is used to detect Fe2+ in iron capsules and total iron in serum samples successfully.
Ablation of Myeloid Cell MRP8 Ameliorates Nephrotoxic Serum-induced Glomerulonephritis by Affecting Macrophage Characterization through Intraglomerular Crosstalk
Authors: Hata Yusuke , Kuwabara Takashige , Mori Kiyoshi , Kan Youngna , Sato Yuki , Umemoto Shuro , Fujimoto Daisuke , Kanki Tomoko , Nishiguchi Yoshihiko , Yokoi Hideki , Kakizoe Yutaka , Izumi Yuichiro , Yanagita Motoko , Mukoyama Masashi 
Published: February 2020

AbstractToll-like receptor 4 (TLR4) and one of its endogenous ligands myeloid-related protein 8 (MRP8 or S100A8), especially expressed in macrophages, play an important role in diabetic nephropathy and autoimmune disorders. However, detailed mechanisms and consequence of MRP8 expression remain unknown, partly due to embryonic lethality of MRP8 knockout mice. In this study, Myeloid lineage cell-specific MRP8 knockout mice were generated, and nephrotoxic serum-induced glomerulonephritis was developed. Mice with conditional ablation of MRP8 gene in myeloid cells exhibited less severe histological damage, proteinuria and inflammatory changes compared to control mice. Mechanism of MRP8 upregulation was investigated using cultured cells. Co-culture of macrophages with mesangial cells or mesangial cell-conditioned media, but not with proximal tubules, markedly upregulated MRP8 gene expression and inflammatory M1 phenotype in macrophages, which was attenuated in MRP8-deleted bone marrow-derived macrophages. Effects of MRP8 deletion was further studied in the context of macrophage-inducible C-type lectin (Mincle), which is critically involved in maintenance of M1 phenotype of macrophages. MRP8 ablation in myeloid cells suppressed the induction of Mincle expression on macrophages in glomerulonephritis. Thus, we propose that intraglomerular crosstalk between mesangial cells and macrophages plays a role in inflammatory changes in glomerulonephritis, and MRP8-dependent Mincle expression in macrophage may be involved in the process.
New participant stratification and combination of urinary biomarkers and confounders could improve diagnostic accuracy for overactive bladder
Authors: Firouzmand Sepinoud , Ajori Ladan , Young John S. 
Published: February 2020

AbstractOveractive bladder (OAB) is a highly prevalent symptom complex characterised by symptoms of urinary urgency, increased frequency, nocturia, with or without urge incontinence; in the absence of proven infection or other obvious pathology. The underlying pathophysiology of idiopathic OAB is not clearly known and the existence of several phenotypes has been proposed. Current diagnostic approaches are based on discordant measures, suffer from subjectivity and are incapable of detecting the proposed OAB phenotypes. In this study, cluster analysis was used as an objective approach for phenotyping participants based on their OAB characteristic symptoms and led to the identification of a low OAB symptomatic score group (cluster 1) and a high OAB symptomatic score group (cluster 2). Furthermore, the ability of several potential OAB urinary biomarkers including ATP, ACh, nitrite, MCP-1 and IL-5 and participants’ confounders, age and gender, in predicting the identified high OAB symptomatic score group was assessed. A combination of urinary ATP and IL-5 plus age and gender was shown to have clinically acceptable and improved diagnostic accuracy compared to urodynamically-observed detrusor overactivity. Therefore, this study provides the foundation for the development of novel non-invasive diagnostic tools for OAB phenotypes that may lead to personalised treatment.
Machine learning improves our knowledge about miRNA functions towards plant abiotic stresses
Authors: Asefpour Vakilian Keyvan 
Published: February 2020

AbstractDuring the last two decades, human has increased his knowledge about the role of miRNAs and their target genes in plant stress response. Biotic and abiotic stresses result in simultaneous tissue-specific up/down-regulation of several miRNAs. In this study, for the first time, feature selection algorithms have been used to investigate the contribution of individual plant miRNAs in Arabidopsis thaliana response towards different levels of several abiotic stresses including drought, salinity, cold, and heat. Results of information theory-based feature selection revealed that miRNA-169, miRNA-159, miRNA-396, and miRNA-393 had the highest contributions to plant response towards drought, salinity, cold, and heat, respectively. Furthermore, regression models, i.e., decision tree (DT), support vector machines (SVMs), and Naïve Bayes (NB) were used to predict the plant stress by having the plant miRNAs’ concentration. SVM with Gaussian kernel was capable of predicting plant stress (R2 = 0.96) considering miRNA concentrations as input features. Findings of this study prove the performance of machine learning as a promising tool to investigate some aspects of miRNAs’ contribution to plant stress responses that have been undiscovered until today.
Impaired DNA-binding affinity of novel PAX6 mutations
Authors: Lee Seowhang , Lee Seung-Han , Heo Hwan , Oh Eun Hye , Shin Jin-Hong , Kim Hyang-Sook , Jung Jae-Ho , Choi Seo Young , Choi Kwang-Dong , Lee Hakbong , Lee Changwook , Choi Jae-Hwan 
Published: February 2020

AbstractMutations in human PAX6 gene are associated with various congenital eye malformations including aniridia, foveal hypoplasia, and congenital nystagmus. These various phenotypes may depend on the mutation spectrums that can affect DNA-binding affinity, although this hypothesis is debatable. We screened PAX6 mutations in two unrelated patients with congenital nystagmus, and measured DNA-binding affinity through isothermal titration calorimetry (ITC). To elucidate phenotypic differences according to DNA-binding affinity, we also compared DNA-binding affinity among the previously reported PAX6 missense mutations within the linker region between two subdomains of the paired domain (PD). We identified two novel mutations of PAX6 gene: c.214 G > T (p.Gly72Cys) and c.249_250delinsCGC (p.Val84Alafs*8). Both were located within the linker region between the two subdomains of the PD. ITC measurement revealed that the mutation p.Val84Alafs*8 had no DNA-binding affinity, while the p.Gly72Cys mutation showed a decreased binding affinity (Kd = 0.58 μM) by approximately 1.4 times compared to the wild type-PAX6 (Kd = 0.41 μM). We also found that there was no close relationship between DNA-binding affinity and phenotypic differences. Our results suggest that the DNA-binding affinity alone might be insufficient to determine PAX6-related phenotypes, and that other modifier genes or environmental factors might affect phenotypes of the PAX6 gene.
Breaking limitation of quantum annealer in solving optimization problems under constraints
Authors: Ohzeki Masayuki 
Published: February 2020

AbstractQuantum annealing is a generic solver for optimization problems that uses fictitious quantum fluctuation. The most groundbreaking progress in the research field of quantum annealing is its hardware implementation, i.e., the so-called quantum annealer, using artificial spins. However, the connectivity between the artificial spins is sparse and limited on a special network known as the chimera graph. Several embedding techniques have been proposed, but the number of logical spins, which represents the optimization problems to be solved, is drastically reduced. In particular, an optimization problem including fully or even partly connected spins suffers from low embeddable size on the chimera graph. In the present study, we propose an alternative approach to solve a large-scale optimization problem on the chimera graph via a well-known method in statistical mechanics called the Hubbard-Stratonovich transformation or its variants. The proposed method can be used to deal with a fully connected Ising model without embedding on the chimera graph and leads to nontrivial results of the optimization problem. We tested the proposed method with a number of partition problems involving solving linear equations and the traffic flow optimization problem in Sendai and Kyoto cities in Japan.
Neural Functions Play Different Roles in Triple Negative Breast Cancer (TNBC) and non-TNBC
Authors: Tan Renbo , Li Haoyang , Huang Zhenyu , Zhou Yi , Tao Mingxin , Gao Xin , Xu Ying 
Published: February 2020

AbstractTriple negative breast cancer (TNBC) represents the most malignant subtype of breast cancer, and yet our understanding about its unique biology remains elusive. We have conducted a comparative computational analysis of transcriptomic data of TNBC and non-TNBC (NTNBC) tissue samples from the TCGA database, focused on genes involved in neural functions. Our main discoveries are: (1) while both subtypes involve neural functions, TNBC has substantially more up-regulated neural genes than NTNBC, suggesting that TNBC is more complex than NTNBC; (2) non-neural functions related to cell-microenvironment interactions and intracellular damage processing are key inducers of the neural genes in both TNBC and NTNBC, but the inducer-responder relationships are different in the two cancer subtypes; (3) key neural functions such as neural crest formation are predicted to enhance adaptive immunity in TNBC while glia development, along with a few other neural functions, induce both innate and adaptive immunity in NTNBC. These results reveal key differences in the biology between the two cancer subtypes, particularly in terms of the roles that neural functions play. Our findings may open new doors for further investigation of the distinct biology of TNBC vs. NTNBC.
Routes to control diffusive pathways and thermal expansion in Ti-alloys
Authors: Bönisch Matthias , Stoica Mihai , Calin Mariana 
Published: February 2020

Abstractβ-stabilized Ti-alloys present several unexplored and intriguing surprises in relation to orthorhombic α″ phases. Among them are (i) the diffusion-controlled formation of transitional α″iso, α″lean and α″rich phases and ii) the highly anisotropic thermal expansion of martensitic α″. Using the prototypical Ti-Nb system, we demonstrate that the thermodynamic energy landscape reveals formation pathways for the diffusional forms of α″ and may lead to a stable β-phase miscibility gap. In this way, we derive temperature-composition criteria for the occurrence of α″iso and resolve reaction sequences during thermal cycling. Moreover, we show that the thermal expansion anisotropy of martensitic α″ gives rise to directions of zero thermal strain depending on Nb content. Utilizing this knowledge, we propose processing routes to achieve null linear expansion in α″ containing Ti-alloys. These concepts are expected to be transferable to other Ti-alloys and offer new avenues for their tailoring and technological exploitation.
A Machine-learning Approach to Forecast Aggravation Risk in Patients with Acute Exacerbation of Chronic Obstructive Pulmonary Disease with Clinical Indicators
Authors: Peng Junfeng , Chen Chuan , Zhou Mi , Xie Xiaohua , Zhou Yuqi , Luo Ching-Hsing 
Published: February 2020

AbstractPatients with chronic obstructive pulmonary disease (COPD) repeat acute exacerbations (AE). Global Initiative for Chronic Obstructive Lung Disease (GOLD) is only available for patients in stable phase. Currently, there is a lack of assessment and prediction methods for acute exacerbation of chronic obstructive pulmonary disease (AECOPD) patients during hospitalization. To enhance the monitoring and treatment of AECOPD patients, we develop a novel C5.0 decision tree classifier to predict the prognosis of AECOPD hospitalized patients with objective clinical indicators. The medical records of 410 hospitalized AECOPD patients are collected and 28 features including vital signs, medical history, comorbidities and various inflammatory indicators are selected. The overall accuracy of the proposed C5.0 decision tree classifier is 80.3% (65 out of 81 participants) with 95% Confidence Interval (CI):(0.6991, 0.8827) and Kappa 0.6054. In addition, the performance of the model constructed by C5.0 exceeds the C4.5, classification and regression tree (CART) model and the iterative dichotomiser 3 (ID3) model. The C5.0 decision tree classifier helps respiratory physicians to assess the severity of the patient early, thereby guiding the treatment strategy and improving the prognosis of patients.