bluuebunny/crossref_metadata_2025_split huggingface dataset:
Proper chromosome alignment depends on BRCA2 phosphorylation by PLK1
Authors: Ehlén Åsa , Martin Charlotte , Miron Simona , Julien Manon , Theillet François-Xavier , Ropars Virginie , Sessa Gaetana , Beaurepere Romane , Boucherit Virginie , Duchambon Patricia , El Marjou Ahmed , Zinn-Justin Sophie , Carreira Aura 
Published: April 2020

AbstractThe BRCA2 tumor suppressor protein is involved in the maintenance of genome integrity through its role in homologous recombination. In mitosis, BRCA2 is phosphorylated by Polo-like kinase 1 (PLK1). Here we describe how this phosphorylation contributes to the control of mitosis. We identify a conserved phosphorylation site at T207 of BRCA2 that constitutes a bona fide docking site for PLK1 and is phosphorylated in mitotic cells. We show that BRCA2 bound to PLK1 forms a complex with the phosphatase PP2A and phosphorylated-BUBR1. Reducing BRCA2 binding to PLK1, as observed in BRCA2 breast cancer variants S206C and T207A, alters the tetrameric complex resulting in unstable kinetochore-microtubule interactions, misaligned chromosomes, faulty chromosome segregation and aneuploidy. We thus reveal a role of BRCA2 in the alignment of chromosomes, distinct from its DNA repair function, with important consequences on chromosome stability. These findings may explain in part the aneuploidy observed in BRCA2-mutated tumors.
Observation of quadratic Weyl points and double-helicoid arcs
Authors: He Hailong , Qiu Chunyin , Cai Xiangxi , Xiao Meng , Ke Manzhu , Zhang Fan , Liu Zhengyou 
Published: April 2020

AbstractNovel quasiparticles beyond those mimicking the elementary high-energy particles such as Dirac and Weyl fermions have attracted great interest in condensed-matter physics and materials science. Here we report an experimental observation of the long-desired quadratic Weyl points by using a three-dimensional chiral metacrystal of sound waves. Markedly different from the newly observed unconventional quasiparticles, such as the spin-1 Weyl points and the charge-2 Dirac points featuring respectively threefold and fourfold band crossings, the charge-2 Weyl points identified here are simply twofold degenerate, and the dispersions around them are quadratic in two directions and linear in the third one. Besides the essential nonlinear bulk dispersions, we further unveil the exotic double-helicoid surface arcs that emanate from a projected quadratic Weyl point and terminate at two projected conventional Weyl points. This unique global surface connectivity provides conclusive evidence for the double topological charges of such unconventional topological nodes.
Nonlinear rheological characteristics of single species bacterial biofilms
Authors: Jana Saikat , Charlton Samuel G. V. , Eland Lucy E. , Burgess J. Grant , Wipat Anil , Curtis Thomas P. , Chen Jinju 
Published: April 2020

AbstractBacterial biofilms in natural and artificial environments perform a wide array of beneficial or detrimental functions and exhibit resistance to physical as well as chemical perturbations. In dynamic environments, where periodic or aperiodic flows over surfaces are involved, biofilms can be subjected to large shear forces. The ability to withstand these forces, which is often attributed to the resilience of the extracellular matrix. This attribute of the extracellular matrix is referred to as viscoelasticity and is a result of self-assembly and cross-linking of multiple polymeric components that are secreted by the microbes. We aim to understand the viscoelastic characteristic of biofilms subjected to large shear forces by performing Large Amplitude Oscillatory Shear (LAOS) experiments on four species of bacterial biofilms: Bacillus subtilis, Comamonas denitrificans, Pseudomonas fluorescens and Pseudomonas aeruginosa. We find that nonlinear viscoelastic measures such as intracycle strain stiffening and intracycle shear thickening for each of the tested species, exhibit subtle or distinct differences in the plot of strain amplitude versus frequency (Pipkin diagram). The biofilms also exhibit variability in the onset of nonlinear behaviour and energy dissipation characteristics, which could be a result of heterogeneity of the extracellular matrix constituents of the different biofilms. The results provide insight into the nonlinear rheological behaviour of biofilms as they are subjected to large strains or strain rates; a situation that is commonly encountered in nature, but rarely investigated.
Theoretical investigation of a potentially important formation pathway of organosulfate in atmospheric aqueous aerosols
Authors: Chen Kunpeng , Zhao Jun 
Published: April 2020

AbstractOrganic sulfate plays important roles in modulating properties of atmospheric aerosols. Recent studies showed that organic sulfate was likably interpreted as inorganic sulfate in field measurements using advanced instruments such as Aerosol Mass Spectrometer and the major contributor to organic sulfate was thought to be hydroxymethanesulfonate (HMS). This study proposed that besides HMS, its isomer hydroxymethyl sulfite (HMSi), which has not been identified in atmospheric aerosols, can emerge as the product of aqueous reactions between sulfur dioxide and formaldehyde. Results from quantum chemical modeling showed that formation of HMS and HMSi was several orders of magnitude faster than that of their corresponding conjugate acids, HMSA and HMHSi. In addition, water involvement can largely accelerate respectively the formation rate of HMS/HMSA and HMSi, but decelerate that of HMHSi, demonstrating the non-negligible role of water in the formation process. Furthermore, our kinetic model implemented with the calculated parameters indicates that HMSi/HMHSi but not HMS/HMSA can significantly alter the pH values of atmospheric aqueous aerosols and HMHSi is the most abundant species among HMS/HMSA and HMSi/HMHSi. Therefore, the newly-discovered pathway via HMSi/HMHSi formation should be of great concern and its kinetic parameters should be implemented in future models of atmospheric chemistry.
Receptor-interacting serine/threonine kinase 1- and 3-dependent inflammation induced in lungs of chicken infected with Pasteurella multocida
Authors: Li Weitian , Tang Qiyu , Dai Na , Feng Weikuan , Xie Changqing , Cheng Guofu , Liu Xiaoli , Zhang Wanpo , Hu Xueying , Gu Changqin 
Published: April 2020

AbstractFowl cholera is a serious, highly contagious disease caused by the bacterium Pasteurella multocida (P. multocida) in a range of avian species and is characterized by an acute form of septicaemia. The pathogenic mechanism of chicken lung injury caused by the bacterium is unclear. Therefore, P. multocida Q (a reference standard strain isolated from chicken) and 1G1 (a clinic isolated strain from duck) were selected to infect chickens, establishing fowl cholera-induced laying hen models. Several important proteins involved in the process of lung injury were identified and quantified using immunohistochemistry and WB. The results showed that chicken lungs infected with bacteria for 24 h showed congestion and edema. The inflammatory factors HMGB1 and IL-6, intercellular matrix MMP, the cell apoptosis-associated caspase-3 and necrotic apoptosis signal molecules RIPK1 and RIPK3 were widely expressed in the lungs of group Q and were significantly different compared with those of 1G1 group and uninfected group (P < 0.05). The results indicated that RIPK1 and RIPK3 are involved in the injury process of chicken lungs after infection with P. multocida, and the mechanisms of lung injury induced by different strains are different.
Predictive Analytics for Retention in Care in an Urban HIV Clinic
Authors: Ramachandran Arthi , Kumar Avishek , Koenig Hannes , De Unanue Adolfo , Sung Christina , Walsh Joe , Schneider John , Ghani Rayid , Ridgway Jessica P. 
Published: April 2020

AbstractConsistent medical care among people living with HIV is essential for both individual and public health. HIV-positive individuals who are ‘retained in care’ are more likely to be prescribed antiretroviral medication and achieve HIV viral suppression, effectively eliminating the risk of transmitting HIV to others. However, in the United States, less than half of HIV-positive individuals are retained in care. Interventions to improve retention in care are resource intensive, and there is currently no systematic way to identify patients at risk for falling out of care who would benefit from these interventions. We developed a machine learning model to identify patients at risk for dropping out of care in an urban HIV care clinic using electronic medical records and geospatial data. The machine learning model has a mean positive predictive value of 34.6% [SD: 0.15] for flagging the top 10% highest risk patients as needing interventions, performing better than the previous state-of-the-art logistic regression model (PPV of 17% [SD: 0.06]) and the baseline rate of 11.1% [SD: 0.02]. Machine learning methods can improve the prediction ability in HIV care clinics to proactively identify patients at risk for not returning to medical care.
RNA-Seq of human whole blood: Evaluation of globin RNA depletion on Ribo-Zero library method
Authors: Harrington Christina A. , Fei Suzanne S. , Minnier Jessica , Carbone Lucia , Searles Robert , Davis Brett A. , Ogle Kimberly , Planck Stephen R. , Rosenbaum James T. , Choi Dongseok 
Published: April 2020

AbstractPeripheral blood is a highly accessible biofluid providing a rich source of information about human physiology and health status. However, for studies of the blood transcriptome with RNA sequencing (RNA-Seq) techniques, high levels of hemoglobin mRNAs (hgbRNA) present in blood can occupy valuable sequencing space, impacting detection and quantification of non-hgbRNAs. In this study, we evaluated two methods for preparing ribosomal RNA (rRNA)-depleted sequencing libraries for RNA-Seq of whole blood, one of which is also designed to deplete hgbRNAs. Two experiments were performed: one evaluating library performance across 6 human blood samples and the other examining library reproducibility and performance in a two-subject subset. We find that addition of hgbRNA depletion to the rRNA-depletion protocol for library preparation from blood RNA effectively reduces highly abundant hgbRNA reads; however, it does not result in a statistically significant increase in differentially expressed genes in our patient-control study. Bioinformatic removal of globin gene counts in non-hgbRNA depleted libraries provides improvement in overall performance of these libraries. We conclude that use of a standard ribosomal RNA depletion method for library preparation coupled with bioinformatic removal of globin gene counts is sufficient for reproducible and sensitive measurement of both coding and noncoding RNAs in the blood transcriptome.
Novel insight into theacrine metabolism revealed by transcriptome analysis in bitter tea (Kucha, Camellia sinensis)
Authors: Wang Songlin , Chen Jiedan , Ma Jianqiang , Jin Jiqiang , Chen Liang , Yao Mingzhe 
Published: April 2020

AbstractKucha (Camellia sinensis) is a kind of unique wild tea resources in southwest China, containing sizeable amounts of theacrine (1,3,7,9-tetramethyluric acid) and having a special bitter taste both in fresh leaves and made tea. Theacrine has good healthy function locally. But the molecular mechanism of theacrine metabolism in Kucha was still unclear. In order to illuminate the biosynthesis and catabolism of theacrine in Kucha plants, three tea cultivars, C. sinensis ‘Shangyou Zhongye’ (SY) with low-theacrine, ‘Niedu Kucha 2’ (ND2) with middle-theacrine and, ‘Niedu Kucha 3’ (ND3) with high-theacrine, were used for our research. Purine alkaloid analysis and transcriptome of those samples were performed by High Performance Liquid Chromatography (HPLC) and RNA-Seq, respectively. The related gene expression levels of purine alkaloid were correlated with the content of purine alkaloid, and the results of quantitative real-time (qRT) PCR were also confirmed the reliability of transcriptome. Based on the data, we found that theacrine biosynthesis is a relatively complex process, N-methyltransferase (NMT) encoded by TEA024443 may catalyze the methylation at 9-N position in Kucha plant. Our finding will assist to reveal the molecular mechanism of theacrine biosynthesis, and be applied to selection and breeding of Kucha tea cultivars in the future.
Enhanced myostatin expression and signalling promote tubulointerstitial inflammation in diabetic nephropathy
Authors: Verzola Daniela , Milanesi Samantha , Viazzi Francesca , Ansaldo Francesca , Saio Michela , Garibaldi Silvano , Carta Annalisa , Costigliolo Francesca , Salvidio Gennaro , Barisione Chiara , Esposito Pasquale , Garibotto Giacomo , Picciotto Daniela 
Published: April 2020

AbstractMyostatin (MSTN), a family member of the transforming growth factor (TGF)-β super family, has been detected in the tubuli of pig kidney, but its role in the human kidney is not known. In this study we observed upregulation of MSTN mRNA (~8 to 10-fold increase) both in the glomeruli and tubulointerstitium in diabetic nephropathy (DN). In DN, immunoreactive MSTN was mainly localized in the tubuli and interstitium (∼4–8 fold increase), where it colocalized in CD45+ cells. MSTN was also upregulated in the glomeruli and the arterial vessels. Tubulointerstitial MSTN expression was directly related to interstitial fibrosis (r = 0.54, p < 0.01). In HK-2 tubular epithelial cells, both high (30 mmol) glucose and glycated albumin upregulated MSTN mRNA and its protein (p < 0.05–0.01). MSTN-treated HK-2 cells underwent decreased proliferation, together with NF-kB activation and CCL-2 and SMAD 2,3 overexpression. In addition, MSTN induced intracellular ROS release and upregulated NADPH oxidase, effects which were mediated by ERK activation. In conclusion, our data show that MSTN is expressed in the human kidney and overexpressed in DN, mainly in the tubulointerstitial compartment. Our results also show that MSTN is a strong inducer of proximal tubule activation and suggest that MSTN overexpression contributes to kidney interstitial fibrosis in DN.
Habitual use of GPS negatively impacts spatial memory during self-guided navigation
Authors: Dahmani Louisa , Bohbot Véronique D. 
Published: April 2020

AbstractGlobal Positioning System (GPS) navigation devices and applications have become ubiquitous over the last decade. However, it is unclear whether using GPS affects our own internal navigation system, or spatial memory, which critically relies on the hippocampus. We assessed the lifetime GPS experience of 50 regular drivers as well as various facets of spatial memory, including spatial memory strategy use, cognitive mapping, and landmark encoding using virtual navigation tasks. We first present cross-sectional results that show that people with greater lifetime GPS experience have worse spatial memory during self-guided navigation, i.e. when they are required to navigate without GPS. In a follow-up session, 13 participants were retested three years after initial testing. Although the longitudinal sample was small, we observed an important effect of GPS use over time, whereby greater GPS use since initial testing was associated with a steeper decline in hippocampal-dependent spatial memory. Importantly, we found that those who used GPS more did not do so because they felt they had a poor sense of direction, suggesting that extensive GPS use led to a decline in spatial memory rather than the other way around. These findings are significant in the context of society’s increasing reliance on GPS.
Alkyl-carbon chain length of two distinct compounds and derivatives are key determinants of their anti-Acanthamoeba activities
Authors: Mooney Ronnie , Masala Mariana , Martial Theo , McGinness Charles , Henriquez Fiona Luisa , Williams Roderick Adeyinka Malcolm 
Published: April 2020

AbstractThe opportunistic pathogen, Acanthamoeba castellanii is the causative agent for the sight threatening infection Acanthamoeba keratitis (AK). It is commonly associated with contact lens wearers, and prevalence is increasing at an alarming rate due to an inadequate preventive strategy to protect the lens from this protist. This problem is compounded by the lack of an effective acanthamoebocide, particularly with cysticidal activity in the contact lens solutions. We have used cytotoxicity assays and a variety of biophysical approaches to show that two molecules with tails made of alkyl carbon, alkylphosphocholines (APCs) and quaternary ammonium compounds (QACs) had significant chain-length dependent efficacy against A. castellanii trophozoites, the latter producing death via permeabilization, and DNA complexing. QACs were more effective than APCs and had activity against cysts. Conversely, the QAC with 12 alkyl carbon chain, was non toxic, its presence increased A. castellanii trophozoites biomass and delayed encystation by 96 h. Interestingly, it was unable to induce excystation and increased trophozoite sensitivity to APC16. These results present a mono- and multi-inhibitor management strategy effective against trophozoites and cysts that may be useful for formulating into contact lense cleaning solutions and reducing AK incidence.
Soyasapogenol-A targets CARF and results in suppression of tumor growth and metastasis in p53 compromised cancer cells
Authors: Omar Amr , Kalra Rajkumar Singh , Putri Jayarani , Elwakeel Ahmed , Kaul Sunil C. , Wadhwa Renu 
Published: April 2020

AbstractWe screened some phytochemicals for cytotoxic activity to human cancer cells and identified Soyasapogenol-A (Snol-A) as a potent candidate anti-cancer compound. Interestingly, Soyasapogenin-I (Snin-I) was ineffective. Viability assays endorsed toxicity of Snol-A to a wide variety of cancer cells. Of note, wild type p53 deficient cancer cells (SKOV-3 and Saos-2) also showed potent growth inhibitory effect. Molecular analyses demonstrated that it targets CARF yielding transcriptional upregulation of p21WAF1 (an inhibitor of cyclin-dependent kinases) and downregulation of its effector proteins, CDK2, CDK-4, Cyclin A and Cyclin D1. Targeting of CARF by Snol-A also caused (i) downregulation of pATR-Chk1 signaling leading to caspase-mediated apoptosis and (ii) inactivation of β-catenin/Vimentin/hnRNPK-mediated EMT signaling resulting in decrease in migration and invasion of cancer cells. In in vivo assays, Snol-A caused suppression of tumor growth in subcutaneous xenograft model and inhibited lung metastasis in tail vein injection model. Taken together, we demonstrate that Snol-A is a natural inhibitor of CARF and may be recruited as a potent anti-tumor and anti-metastasis compound for treatment of p53-deficient aggressive malignancies.
The feasibility of differentiating colorectal cancer from normal and inflammatory thickening colon wall using CT texture analysis
Authors: Wang Xiao , Yuan Mingyuan , Mi Honglan , Suo Shiteng , Eteer Khalid , Li Suqin , Lu Qing , Xu Jianrong , Hu Jiani 
Published: April 2020

AbstractTo investigate the diagnostic value of texture analysis (TA) for differentiating between colorectal cancer (CRC), colonic lesions caused by inflammatory bowel disease (IBD), and normal thickened colon wall (NTC) on computed tomography (CT) and assess which scanning phase has the highest differential diagnostic value. In all, 107 patients with CRC, 113 IBD patients with colonic lesions, and 96 participants with NTC were retrospectively enrolled. All subjects underwent multiphase CT examination, including pre-contrast phase (PCP), arterial phase (AP), and portal venous phase (PVP) scans. Based on these images, classification by TA and visual classification by radiologists were performed to discriminate among the three tissue types. The performance of TA and visual classification was compared. Precise TA classification results (error, 2.03–12.48%) were acquired by nonlinear discriminant analysis for CRC, IBD and NTC, regardless of phase or feature selection. PVP images showed a better ability to discriminate the three tissues by comprising the three scanning phases. TA showed significantly better performance in discriminating CRC, IBD and NTC than visual classification for residents, but there was no significant difference in classification between TA and experienced radiologists. TA could provide useful quantitative information for the differentiation of CRC, IBD and NTC on CT, particularly in PVP images.
Comparison of auditory spatial bisection and minimum audible angle in front, lateral, and back space
Authors: Aggius-Vella Elena , Kolarik Andrew J. , Gori Monica , Cirstea Silvia , Campus Claudio , Moore Brian C. J. , Pardhan Shahina 
Published: April 2020

AbstractAlthough vision is important for calibrating auditory spatial perception, it only provides information about frontal sound sources. Previous studies of blind and sighted people support the idea that azimuthal spatial bisection in frontal space requires visual calibration, while detection of a change in azimuth (minimum audible angle, MAA) does not. The influence of vision on the ability to map frontal, lateral and back space has not been investigated. Performance in spatial bisection and MAA tasks was assessed for normally sighted blindfolded subjects using bursts of white noise presented frontally, laterally, or from the back relative to the subjects. Thresholds for both tasks were similar in frontal space, lower for the MAA task than for the bisection task in back space, and higher for the MAA task in lateral space. Two interpretations of the results are discussed, one in terms of visual calibration and the use of internal representations of source location and the other based on comparison of the magnitude or direction of change of the available binaural cues. That bisection thresholds were increased in back space relative to front space, where visual calibration information is unavailable, suggests that an internal representation of source location was used for the bisection task.
A three-dimensional bioprinted model to evaluate the effect of stiffness on neuroblastoma cell cluster dynamics and behavior
Authors: Monferrer Ezequiel , Martín-Vañó Susana , Carretero Aitor , García-Lizarribar Andrea , Burgos-Panadero Rebeca , Navarro Samuel , Samitier Josep , Noguera Rosa 
Published: April 2020

AbstractThree-dimensional (3D) bioprinted culture systems allow to accurately control microenvironment components and analyze their effects at cellular and tissue levels. The main objective of this study was to identify, quantify and localize the effects of physical-chemical communication signals between tumor cells and the surrounding biomaterial stiffness over time, defining how aggressiveness increases in SK-N-BE(2) neuroblastoma (NB) cell line. Biomimetic hydrogels with SK-N-BE(2) cells, methacrylated gelatin and increasing concentrations of methacrylated alginate (AlgMA 0%, 1% and 2%) were used. Young’s modulus was used to define the stiffness of bioprinted hydrogels and NB tumors. Stained sections of paraffin-embedded hydrogels were digitally quantified. Human NB and 1% AlgMA hydrogels presented similar Young´s modulus mean, and orthotopic NB mice tumors were equally similar to 0% and 1% AlgMA hydrogels. Porosity increased over time; cell cluster density decreased over time and with stiffness, and cell cluster occupancy generally increased with time and decreased with stiffness. In addition, cell proliferation, mRNA metabolism and antiapoptotic activity advanced over time and with stiffness. Together, this rheological, optical and digital data show the potential of the 3Din vitrocell model described herein to infer how intercellular space stiffness patterns drive the clinical behavior associated with NB patients.