bluuebunny/crossref_metadata_2025_split huggingface dataset:
k-core genes underpin structural features of breast cancer
Authors: Dorantes-Gilardi Rodrigo , García-Cortés Diana , Hernández-Lemus Enrique , Espinal-Enríquez Jesús 
Published: August 2021

AbstractGene co-expression networks (GCNs) have been developed as relevant analytical tools for the study of the gene expression patterns behind complex phenotypes. Determining the association between structure and function in GCNs is a current challenge in biomedical research. Several structural differences between GCNs of breast cancer and healthy phenotypes have been reported. In a previous study, using co-expression multilayer networks, we have shown that there are abrupt differences in the connectivity patterns of the GCN of basal-like breast cancer between top co-expressed gene-pairs and the remaining gene-pairs. Here, we compared the top-100,000 interactions networks for the four breast cancer phenotypes (Luminal-A, Luminal-B, Her2+ and Basal), in terms of structural properties. For this purpose, we used the graph-theoretical k-core of a network (maximal sub-network with nodes of degree at least k). We developed a comprehensive analysis of the network k-core ($$k=30$$

k
=
30

) structures in cancer, and its relationship with biological functions. We found that in the Top-100,000-edges networks, the majority of interactions in breast cancer networks are intra-chromosome, meanwhile inter-chromosome interactions serve as connecting bridges between clusters. Moreover, core genes in the healthy network are strongly associated with processes such as metabolism and cell cycle. In breast cancer, only the core of Luminal A is related to those processes, and genes in its core are over-expressed. The intersection of the core nodes in all subtypes of cancer is composed only by genes in the chr8q24.3 region. This region has been observed to be highly amplified in several cancers before, and its appearance in the intersection of the four breast cancer k-cores, may suggest that local co-expression is a conserved phenomenon in cancer. Considering the many intricacies associated with these phenomena and the vast amount of research in epigenomic regulation which is currently undergoing, there is a need for further research on the epigenomic effects on the structure and function of gene co-expression networks in cancer.
Circulating tumor DNA sequencing in colorectal cancer patients treated with first-line chemotherapy with anti-EGFR
Authors: Lim Yoojoo , Kim Sheehyun , Kang Jun-Kyu , Kim Hwang-Phill , Jang Hoon , Han Hyojun , Kim Hyoki , Kim Min Jung , Lee Kyung-Hun , Ryoo Seung-Bum , Park Ji Won , Jeong Seung-Yong , Park Kyu Joo , Kang Gyeong Hoon , Han Sae-Won , Kim Tae-You 
Published: August 2021

AbstractCirculating tumor DNA (ctDNA) may reveal dynamic tumor status during therapy. We conducted serial ctDNA analysis to investigate potential association with clinical outcome in metastatic colorectal cancer (mCRC) patients receiving chemotherapy. Tissue KRAS/NRAS wild-type mCRC patients were enrolled and treated with first-line cetuximab-containing chemotherapy. ctDNA isolated from plasma were analyzed by next generation sequencing (NGS) with 16 targeted gene panel. Among 93 patients, 84 (90.3%) had at least 1 somatic mutation in baseline ctDNA samples (average 2.74). Five patients with KRAS or NRAS hotspot mutation in the ctDNA showed significantly worse progression-free survival (PFS) (p = 0.029). Changes in average variant allele frequency (VAF) in ctDNA showed significant correlation with tumor size change at the time of first response evaluation (p = 0.020) and progressive disease (PD) (p = 0.042). Patients whose average VAF decreased below cutoff (< 1%) at the first evaluation showed significantly better PFS (p < 0.001), and the average VAF change further discriminated the PFS in the patients in partial response (p = 0.018). At the time of PD, 54 new mutations including KRAS and MAP2K1 emerged in ctDNA. ctDNA sequencing can provide mutation profile that could better reflect tumor mutation status and predict treatment outcome.
The switch of DNA states filtering the extrinsic noise in the system of frequency modulation
Authors: Lo Shih-Chiang , You Chao-Xuan , Chen Bo-Ren , Hsieh Ching-Chu , Li Cheng-En , Shu Che-Chi 
Published: August 2021

AbstractThere is a special node, which the large noise of the upstream element may not always lead to a broad distribution of downstream elements. This node is DNA, with upstream element TF and downstream elements mRNA and proteins. By applying the stochastic simulation algorithm (SSA) on gene circuits inspired by the fim operon in Escherichia coli, we found that cells exchanged the distribution of the upstream transcription factor (TF) for the transitional frequency of DNA. Then cells do an inverse transform, which exchanges the transitional frequency of DNA for the distribution of downstream products. Due to this special feature, DNA in the system of frequency modulation is able to reset the noise. By probability generating function, we know the ranges of parameter values that grant such an interesting phenomenon.
A bagging dynamic deep learning network for diagnosing COVID-19
Authors: Zhang Zhijun , Chen Bozhao , Sun Jiansheng , Luo Yamei 
Published: August 2021

AbstractCOVID-19 is a serious ongoing worldwide pandemic. Using X-ray chest radiography images for automatically diagnosing COVID-19 is an effective and convenient means of providing diagnostic assistance to clinicians in practice. This paper proposes a bagging dynamic deep learning network (B-DDLN) for diagnosing COVID-19 by intelligently recognizing its symptoms in X-ray chest radiography images. After a series of preprocessing steps for images, we pre-train convolution blocks as a feature extractor. For the extracted features, a bagging dynamic learning network classifier is trained based on neural dynamic learning algorithm and bagging algorithm. B-DDLN connects the feature extractor and bagging classifier in series. Experimental results verify that the proposed B-DDLN achieves 98.8889% testing accuracy, which shows the best diagnosis performance among the existing state-of-the-art methods on the open image set. It also provides evidence for further detection and treatment.
Associations between ultrasound measurements and hematochemical parameters for the assessment of liver metabolic status in Holstein–Friesian cows
Authors: Giannuzzi Diana , Tessari Rossella , Pegolo Sara , Fiore Enrico , Gianesella Matteo , Trevisi Erminio , Ajmone Marsan Paolo , Premi Michele , Piccioli-Cappelli Fiorenzo , Tagliapietra Franco , Gallo Luigi , Schiavon Stefano , Bittante Giovanni , Cecchinato Alessio 
Published: August 2021

AbstractMetabolic disorders, including hepatic lipidosis and ketosis, severely affect animal health status and welfare with a large economic burden in dairy herds. The gold standard for diagnosing hepatic lipidosis is the liver biopsy, which is impractical and invasive for the screening at farm level. Ultrasound (US) imaging is a promising technique for identifying liver dysfunction, but standardized specifications in physiological conditions are needed. Herein, we described the features of four US measurements, namely the liver predicted triacylglycerol (pTAG) content, liver depth (LD), and portal vein area (PVA) and depth (PVD) and we investigated their associations with a set of hematochemical (HC) indicators in 342 clinically healthy Holstein Friesian dairy cows. Liver pTAG content was negatively associated with hematocrit and positively with globulin, whereas PVA was negatively associated with thiol group levels, and LD positively with ceruloplasmin. We found significant interactions between some HC parameters and parity: in particular, creatinine, thiol groups and globulin for PVA, and aspartate aminotransferase, paraoxonase and ceruloplasmin for PVD. This study offers new insights on variations in liver function occurring after calving and pave the way for the potential use of minimally invasive techniques for prompt detection of metabolic disorders in dairy herds.
Deep learning-based single-shot phase retrieval algorithm for surface plasmon resonance microscope based refractive index sensing application
Authors: Thadson Kitsada , Visitsattapongse Sarinporn , Pechprasarn Suejit 
Published: August 2021

AbstractA deep learning algorithm for single-shot phase retrieval under a conventional microscope is proposed and investigated. The algorithm has been developed using the context aggregation network architecture; it requires a single input grayscale image to predict an output phase profile through deep learning-based pattern recognition. Surface plasmon resonance imaging has been employed as an example to demonstrate the capability of the deep learning-based method. The phase profiles of the surface plasmon resonance phenomena have been very well established and cover ranges of phase transitions from 0 to 2π rad. We demonstrate that deep learning can be developed and trained using simulated data. Experimental validation and a theoretical framework to characterize and quantify the performance of the deep learning-based phase retrieval method are reported. The proposed deep learning-based phase retrieval performance was verified through the shot noise model and Monte Carlo simulations. Refractive index sensing performance comparing the proposed deep learning algorithm and conventional surface plasmon resonance measurements are also discussed. Although the proposed phase retrieval-based algorithm cannot achieve a typical detection limit of 10–7 to 10–8 RIU for phase measurement in surface plasmon interferometer, the proposed artificial-intelligence-based approach can provide at least three times lower detection limit of 4.67 × 10–6 RIU compared to conventional intensity measurement methods of 1.73 × 10–5 RIU for the optical energy of 2500 pJ with no need for sophisticated optical interferometer instrumentation.
A novel bis(pyrazolyl)methane compound as a potential agent against Gram-positive bacteria
Authors: Seguí Pedro , Aguilera-Correa John J. , Domínguez-Jurado Elena , Sánchez-López Christian M. , Pérez-Tanoira Ramón , Ocaña Ana V. , Castro-Osma José A. , Esteban Jaime , Marcilla Antonio , Alonso-Moreno Carlos , Pérez-Martínez Francisco C. , Molina-Alarcón Milagros 
Published: August 2021

AbstractThis study was designed to propose alternative therapeutic compounds to fight against bacterial pathogens. Thus, a library of nitrogen-based compounds bis(triazolyl)methane (1T–7T) and bis(pyrazolyl)methane (1P–11P) was synthesised following previously reported methodologies and their antibacterial activity was tested using the collection strains of Staphylococcus aureus, Enterococcus faecalis, Escherichia coli, and Pseudomonas aeruginosa. Moreover, the novel compound 2P was fully characterized by IR, UV–Vis and NMR spectroscopy. To evaluate antibacterial activity, minimal inhibitory concentrations (MICs), minimal bactericidal concentrations (MBCs), minimum biofilm inhibitory concentrations (MBICs), and minimum biofilm eradication concentrations (MBECs) assays were carried out at different concentrations (2–2000 µg/mL). The MTT assay and Resazurin viability assays were performed in both human liver carcinoma HepG2 and human colorectal adenocarcinoma Caco-2 cell lines at 48 h. Of all the synthesised compounds, 2P had an inhibitory effect on Gram-positive strains, especially against S. aureus. The MIC and MBC of 2P were 62.5 and 2000 µg/mL against S. aureus, and 250 and 2000 µg/mL against E. faecalis, respectively. However, these values were > 2000 µg/mL against E. coli and P. aeruginosa. In addition, the MBICs and MBECs of 2P against S. aureus were 125 and > 2000 µg/mL, respectively, whereas these values were > 2000 µg/mL against E. faecalis, E. coli, and P. aeruginosa. On the other hand, concentrations up to 250 µg/mL of 2P were non-toxic doses for eukaryotic cell cultures. Thus, according to the obtained results, the 2P nitrogen-based compound showed a promising anti-Gram-positive effect (especially against S. aureus) both on planktonic state and biofilm, at non-toxic concentrations.
A stokes polarimetric light microscopy view of liquid crystal droplets
Authors: Gou J. , Shen T. H. , Bao P. , Ramos Angulo J. L. , Evans S. D. 
Published: August 2021

AbstractThe optical characteristics of materials, such as their magnetooptical effects, birefringence, optical activities, linear and circular dichroism, are probed via the polarisation states of light transmitted through or reflected from the specimens. As such, the measurements of the polarisation states play an important role in many research disciplines. Experimentally, Stokes parameters provide a full description of the polarisation states of light. We report the implementation of a dual- photoelastic modulator based polarimeter in a light microscope, enabling the determination of Stokes parameters at each pixel. As a case study, polarimetric images of liquid crystal droplets of different internal structures are obtained, showing their distinct polarisation characteristics. We demonstrate that the prototype Stokes polarimetric microscope allows the quantitative determination of the polarisation characteristics of light at the object plane and enables the access of the information of full polarisation states as compared to a conventional cross polariser microscope. This work shows that Stokes polarimetric microscopy may find potential applications in a wide range of research fields.
Decidualized endometrial stromal cells present with altered androgen response in PCOS
Authors: Khatun Masuma , Meltsov Alvin , Lavogina Darja , Loid Marina , Kask Keiu , Arffman Riikka K. , Rossi Henna-Riikka , Lättekivi Freddy , Jääger Kersti , Krjutškov Kaarel , Rinken Ago , Salumets Andres , Piltonen Terhi T. 
Published: August 2021

AbstractHyperandrogenic women with PCOS show disrupted decidualization (DE) and placentation. Dihydrotestosterone (DHT) is reported to enhance DE in non-PCOS endometrial stromal cells (eSCCtrl); however, this has not been assessed in PCOS cells (eSCPCOS). Therefore, we studied the transcriptome profile of non-decidualized (non-DE) and DE eSCs from women with PCOS and Ctrl in response to short-term estradiol (E2) and/or progesterone (P4) exposure with/without (±) DHT. The non-DE eSCs were subjected to E2 ± DHT treatment, whereas the DE (0.5 mM 8-Br-cAMP, 96 h) eSCs were post-treated with E2 and P4 ± DHT, and RNA-sequenced. Validation was performed by immunofluorescence and immunohistochemistry. The results showed that, regardless of treatment, the PCOS and Ctrl samples clustered separately. The comparison of DE vs. non-DE eSCPCOS without DHT revealed PCOS-specific differentially expressed genes (DEGs) involved in mitochondrial function and progesterone signaling. When further adding DHT, we detected altered responses for lysophosphatidic acid (LPA), inflammation, and androgen signaling. Overall, the results highlight an underlying defect in decidualized eSCPCOS, present with or without DHT exposure, and possibly linked to the altered pregnancy outcomes. We also report novel factors which elucidate the mechanisms of endometrial dysfunction in PCOS.
Dereplication of antimicrobial biosurfactants from marine bacteria using molecular networking
Authors: Patiño Albert D. , Montoya-Giraldo Manuela , Quintero Marynes , López-Parra Lizbeth L. , Blandón Lina M. , Gómez-León Javier 
Published: August 2021

AbstractBiosurfactants are amphiphilic surface-active molecules of microbial origin principally produced by hydrocarbon-degrading bacteria; in addition to the bioremediation properties, they can also present antimicrobial activity. The present study highlights the chemical characterization and the antimicrobial activities of biosurfactants produced by deep-sea marine bacteria from the generaHalomonas,Bacillus,Streptomyces, andPseudomonas. The biosurfactants were extracted and chemically characterized through Chromatography TLC, FT-IR, LC/ESI–MS/MS, and a metabolic analysis was done through molecular networking. Six biosurfactants were identified by dereplication tools from GNPS and some surfactin isoforms were identified by molecular networking. The half-maximal inhibitory concentration (IC50) of biosurfactant fromHalomonassp. INV PRT125 (7.27 mg L−1) andHalomonassp. INV PRT124 (8.92 mg L−1) were most effective against the pathogenic yeastCandida albicansATCC 10231. For Methicillin-resistantStaphylococcus aureusATCC 43300, the biosurfactant fromBacillussp. INV FIR48 was the most effective with IC50values of 25.65 mg L−1and 21.54 mg L−1forC. albicans, without hemolytic effect (< 1%), and non-ecotoxic effect in brine shrimp larvae (Artemia franciscana), with values under 150 mg L−1, being a biosurfactant promising for further study. The extreme environments as deep-sea can be an important source for the isolation of new biosurfactants-producing microorganisms with environmental and pharmaceutical use.
Low-dose rapamycin does not impair vascular integrity and tubular regeneration after kidney transplantation in rats
Authors: Hoff Uwe , Markmann Denise , Nieminen-Kelhä Melina , Budde Klemens , Hegner Björn 
Published: August 2021

AbstractmTOR inhibitors offer advantages after kidney transplantation including antiviral and antitumor activity besides facilitating low calcineurin inhibitor exposure to reduce nephrotoxicity. Concerns about adverse effects due to antiproliferative and antiangiogenic properties have limited their clinical use particularly early after transplantation. Interference with vascular endothelial growth factor (VEGF)-A, important for physiologic functioning of renal endothelial cells and tubular epithelium, has been implicated in detrimental renal effects of mTOR inhibitors. Low doses of Rapamycin (loading dose 3 mg/kg bodyweight, daily doses 1.5 mg/kg bodyweight) were administered in an allogenic rat kidney transplantation model resulting in a mean through concentration of 4.30 ng/mL. Glomerular and peritubular capillaries, tubular cell proliferation, or functional recovery from preservation/reperfusion injury were not compromised in comparison to vehicle treated animals. VEGF-A, VEGF receptor 2, and the co-receptor Neuropilin-1 were upregulated by Rapamycin within 7 days. Rat proximal tubular cells (RPTC) responded in vitro to hypoxia with increased VEGF-A and VEGF-R1 expression that was not suppressed by Rapamycin at therapeutic concentrations. Rapamycin did not impair proliferation of RPTC under hypoxic conditions. Low-dose Rapamycin early posttransplant does not negatively influence the VEGF network crucial for recovery from preservation/reperfusion injury. Enhancement of VEGF signaling peritransplant holds potential to further improve outcomes.
Cleavage and activation of LIM kinase 1 as a novel mechanism for calpain 2-mediated regulation of nuclear dynamics
Authors: Rodríguez-Fernández L. , Company S. , Zaragozá R. , Viña J. R. , García-Trevijano E. R. 
Published: August 2021

AbstractCalpain-2 (CAPN2) is a processing enzyme ubiquitously expressed in mammalian tissues whose pleiotropic functions depend on the role played by its cleaved-products. Nuclear interaction networks, crucial for a number of molecular processes, could be modified by CAPN2 activity. However, CAPN2 functions in cell nucleus are poorly understood. To unveil CAPN2 functions in this compartment, the result of CAPN2-mediated interactions in cell nuclei was studied in breast cancer cell (BCC) lines. CAPN2 abundance was found to be determinant for its nucleolar localization during interphase. Those CAPN2-dependent components of nucleolar proteome, including the actin-severing protein cofilin-1 (CFL1), were identified by proteomic approaches. CAPN2 binding, cleavage and activation of LIM Kinase-1 (LIMK1), followed by CFL1 phosphorylation was studied. Upon CAPN2-depletion, full-length LIMK1 levels increased and CFL1/LIMK1 binding was inhibited. In addition, LIMK1 accumulated at the cell periphery and perinucleolar region and, the mitosis-specific increase of CFL1 phosphorylation and localization was altered, leading to aberrant mitosis and cell multinucleation. These findings uncover a mechanism for the role of CAPN2 during mitosis, unveil the critical role of CAPN2 in the interactions among nuclear components and, identifying LIMK1 as a new CAPN2-target, provide a novel mechanism for LIMK1 activation. CFL1 is crucial for cytoskeleton remodeling and mitosis, but also for the maintenance of nuclear structure, the movement of chromosomes and the modulation of transcription frequently altered in cancer cells. Consequently, the role of CAPN2 in the nuclear compartment might be extended to other actin-associated biological and pathological processes.
Pyk2 in dorsal hippocampus plays a selective role in spatial memory and synaptic plasticity
Authors: Mastrolia Vincenzo , al Massadi Omar , de Pins Benoit , Girault Jean-Antoine 
Published: August 2021

AbstractPyk2 is a Ca2+-activated non-receptor tyrosine kinase enriched in the forebrain, especially in pyramidal neurons of the hippocampus. Previous reports suggested its role in hippocampal synaptic plasticity and spatial memory but with contradictory findings possibly due to experimental conditions. Here we address this issue and show that novel object location, a simple test of spatial memory induced by a single training session, is altered in Pyk2 KO mice and that re-expression of Pyk2 in the dorsal hippocampus corrects this deficit. Bilateral targeted deletion of Pyk2 in dorsal hippocampus CA1 region also alters novel object location. Long term potentiation (LTP) in CA1 is impaired in Pyk2 KO mice using a high frequency stimulation induction protocol but not with a theta burst protocol, explaining differences between previous reports. The same selective LTP alteration is observed in mice with Pyk2 deletion in dorsal hippocampus CA1 region. Thus, our results establish the role of Pyk2 in specific aspects of spatial memory and synaptic plasticity and show the dependence of the phenotype on the type of experiments used to reveal it. In combination with other studies, we provide evidence for a selective role of non-receptor tyrosine kinases in specific aspects of hippocampal neurons synaptic plasticity.
Delta band activity contributes to the identification of command following in disorder of consciousness
Authors: Rivera-Lillo Gonzalo , Stamatakis Emmanuel A. , Bekinschtein Tristan A. , Menon David K. , Chennu Srivas 
Published: August 2021

AbstractThe overt or covert ability to follow commands in patients with disorders of consciousness is considered a sign of awareness and has recently been defined as cortically mediated behaviour. Despite its clinical relevance, the brain signatures of the perceptual processing supporting command following have been elusive. This multimodal study investigates the temporal spectral pattern of electrical brain activity to identify features that differentiated healthy controls from patients both able and unable to follow commands. We combined evidence from behavioural assessment, functional neuroimaging during mental imagery and high-density electroencephalography collected during auditory prediction, from 21 patients and 10 controls. We used a penalised regression model to identify command following using features from electroencephalography. We identified seven well-defined spatiotemporal signatures in the delta, theta and alpha bands that together contribute to identify DoC subjects with and without the ability to follow command, and further distinguished these groups of patients from controls. A fine-grained analysis of these seven signatures enabled us to determine that increased delta modulation at the frontal sensors was the main feature in command following patients. In contrast, higher frequency theta and alpha modulations differentiated controls from both groups of patients. Our findings highlight a key role of spatiotemporally specific delta modulation in supporting cortically mediated behaviour including the ability to follow command. However, patients able to follow commands nevertheless have marked differences in brain activity in comparison with healthy volunteers.