cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Molecular mechanism of vinculin activation and nanoscale spatial organization in focal adhesions
Creators: name: Davidson, Michael W.
name: Waterman, Clare M.
name: Hess, Harald F.
name: Campbell, Sharon L.
name: Shtengel, Gleb
name: Baird, Michelle A.
name: Case, Lindsay B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Focal adhesions (FAs) link the extracellular matrix (ECM) to the actin cytoskeleton to mediate cell adhesion, migration, mechanosensing and signaling. FAs have conserved nanoscale protein organization, suggesting that the position of proteins within FAs regulates their activity and function. Vinculin binds different FA proteins to mediate distinct cellular functions, but how vinculin’s interactions are spatiotemporally organized within FA is unknown. Using interferometric photo-activation localization (iPALM) super-resolution microscopy to assay vinculin nanoscale localization and a FRET biosensor to assay vinculin conformation, we found that upward repositioning within the FA during FA maturation facilitates vinculin activation and mechanical reinforcement of FA. Inactive vinculin localizes to the lower integrin signaling layer in FA by binding to phospho-paxillin. Talin binding activates vinculin and targets active vinculin higher in FA where vinculin can engage retrograde actin flow. Thus, specific protein interactions are spatially segregated within FA at the nano-scale to regulate vinculin activation and function.
Extraordinary transverse magneto-optical Kerr effect in a superlens
Creators: name: Moncada-Villa, E.
name: Garcia-Martin, A.
name: Cuevas, J. C.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: It has been shown that a slab of a negative index material can behave as a superlens enhancing the imaging resolution beyond the wavelength limit. We show here that if such a slab possesses in addition some magneto-optical activity, it could act as an ideal optical filter and exhibit an extraordinary transverse magneto-optical Kerr effect. Moreover, we show that losses, which spoil the imaging resolution of these lenses, are a necessary ingredient to observe this effect.
description: 5 pages, 6 figures
Brief an Cäsar von Arx
Creators: name: Zweig, Stefan
Publisher: name: [s.n.]
Year: 1936

description: von Stefan Zweig
description: Dieser Brief existiert auch als undatiertes Original (vgl. ZBS NL ARX_C 32/40/6).
description: Deutsch
description: Verzeichnung=Description=Inventaire Juni 2022 HAN-Katalogisierungsregeln HBr
Highly oscillatory solutions of a Neumann problem for a $p$-laplacian equation
Creators: name: Boscaggin, Alberto
name: Dambrosio, Walter
Publisher: name: arXiv
Year: 2014
Subjects: subject: Classical Analysis and ODEs (math.CA)
subject: FOS: Mathematics

description: We deal with a boundary value problem of the form $-ε(ϕ_p(εu'))'+a(x)W'(u)=0,\quad u'(0)=0=u'(1),$ where $ϕ_p(s) = \vert s \vert^{p-2} s$ for $s \in \mathbb{R}$ and $p>1$, and $W:[-1,1] \to {\mathbb R}$ is a double-well potential. We study the limit profile of solutions when $ε\to 0^+$ and, conversely, we prove the existence of nodal solutions associated with any admissible limit profile when $ε$ is small enough.
Brief an Cäsar von Arx
Creators: name: Zweig, Stefan
Publisher: name: [s.n.]
Year: 1936

description: von Stefan Zweig
description: Dieser Brief existiert auch als Abschrift von unbekannter Hand; von dort stammt die Datierung (vgl. ZBS NL ARX_C 37/1/9).
description: Deutsch
description: Verzeichnung=Description=Inventaire Juni 2022 HAN-Katalogisierungsregeln HBr
Additional file 3 of Employing cognitive interviewing to evaluate, improve and validate items for measuring the health-related quality of life of women diagnosed with ovarian cancer
Creators: name: Boban, Sharolin Ann
name: Bulsara, Caroline
name: Codde, Jim
name: Cohen, Paul A.
name: Downs, Jenny
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 3: Consolidated criteria for reporting qualitative studies (COREQ): 32-item checklist. The study was carried out in accordance with the COREQ 32-item checklist, which assisted researchers in reporting important elements of the qualitative research, study design, study context, findings, evaluation, and interpretations.
Functional response to Daphnia carinata King when feeding on the filamentous diatom Melosira granulata
Creators: name: King, C. R
name: Shiel, R. J
Publisher: name: La Trobe
Year: 2023

description: Murray-Darling Freshwater Research Centre

MDFRC item.

The functional response of D. carinata feeding on M. granulata was determined from laboratory trials conducted at 20-22ºC, using a range of food concentrations (F) from 0.14 to 33.8µg (dry weight) mL-1. The functional response could be described by an lvlev model: I (ingestion rate, ng µg-1 h-1) = 200 - 205 × exp (- 0.036 × F). The ingestion rate at the highest food concentration (33.8 µg mL-1) was 140 ng µg-1 h-1, and there was no evidence to suggest that M. granulata either interfered with feeding at high densities or was a difficult food item for D. carinata to handle.
Elucidating role of salivary proteins in denture stomatitis using a proteomic approach
Creators: name: Byrd, Warren C.
name: Border, Michael B.
name: Baxter, Sarah Schwartz
name: Ross, Gary F.
name: Loewy, Zvi
name: Carlson, Jim
name: Barros, Silvana
name: Dibble, Christopher F.
name: Mack, C. Russell
name: Bencharit, Sompop
name: Offenbacher, Steven
name: Altarawneh, Sandra K.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Denture stomatitis (DS) is the most common oral pathology among denture wearers, affecting over one-third of this group. DS is usually associated with C. albicans. However, unlike other oral candidiasis, most DS patients have intact host immunity. The presence of a denture alone is usually sufficient for DS. Saliva and its protein contents can theoretically predispose some denture wearers to DS and others resistant toward DS. Here we proposed for the first time to define salivary proteomic profiles of denture wearers with and without DS. SELDI-TOF/MS analysis suggests that there is a proteomic differentiation among control, localized and generalized DS. Based on initial SELDI-TOF/MS profiling, we further used reversed phase liquid chromatography, MALDI-TOF/MS, and LC-MS/MS to characterize the salivary proteins associated with DS. Nineteen proteins based on SELDI-TOF/MS profiling were found including cystatin-SN, statherin, kininogen-1, desmocollin-2, carbonic anhydrase-6, peptidyl-prolyl cis–trans isomerase A like peptides, cystatin C, and several immunoglobulin fragments. The proteomic content gives evidence of the interaction between host tissue, saliva, and candida. Further examination in larger populations of these proteins may help to gain a better understanding of DS pathological processes and improve DS treatments.
(:unas) unassigned
Creators: name: (:Unkn) Unknown
Publisher: name: Universita' degli Studi di Salerno
Year: 2024

description: Besides edutaining its audience, the theatre is also an effective means for historical and heritage preserva tion. This, however, is partly dependent on the thea tre director whose job involves manipulating the spatial medium and arts of the theatre to project a playwright’s message. Although museums are pri marily established to preserve cultural heritage and some part of history, they also entertain in their own unique way. Drawing on this, the museum and the theatre could serve similar functions in society, even though they seem to have been cast apart from each other to function independently. In a concrete way, therefore, both the museum and the theatre can achieve greater results if creatively merged to com plement each other. It is within this context that this paper adopts the historical-analytic, participant ob servation and literary methods to investigate ‘mu seuming’ the theatre for historical and heritage preservation, using Israel Wekpe’s theatrical pro duction of Idia that was staged on 26th December, 2020, at the SIO Events Centre, Benin City, as para digm. The article argues that the museum and the theatre have similar intents and should be made to complement each other whenever it is artistically possible; that one (the museum) can be used to pro mote the other (the theatre) and vice versa, if re sourcefully manipulated for cultural communica tion. It concludes that the creative and artistic com bination of both would not only make history and heritage preservation easy but also entertaining and interesting. It recommends that theatre directors should use realistic artefacts to establish their spa tial setting whenever they encounter a historical play to direct, and not to hesitate to visit the museum as that can be a source of inspiration that could be resourcefully deployed.
Additional file 1 of Applying mixed methods to pilot feasibility studies to inform intervention trials
Creators: name: Aschbrenner, Kelly A.
name: Kruse, Gina
name: Gallo, Joseph J.
name: Plano Clark, Vicki L.
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: Additional file 1.
H+ exchange and nutrient uptake by roots of the emergent hydrophytes, Cyperus involucratus Rottb., Eleocharis sphacelata R. Br. and Juncus ingens N. A. Wakef
Creators: name: Sorrell, Brian K
name: Orr, Philip T
Publisher: name: La Trobe
Year: 2023

description: Murray-Darling Freshwater Research Centre

MDFRC item.

We immersed the root systems of three emergent aquatic monocots (Cyperus involucratus Rottb., Eleocharis sphacelata R. Br. (both Cyperaceae), and Juncus ingens N. A. Wakef. (Juncaceae)) in nutrient agar gels with pH indicators and pH microelectrodes to study H+ exchange by root systems. For all three species, the pH changed at the tips of the adventitious roots and around young laterals. Older, lignified surfaces had little effect on pH. The pH changes around the laterals were affected by the form of nitrogen in the nutrient gel When NO3− was supplied as the N source, there was a small pH increase, whereas NH4+ enhanced H+ release, causing the pH adjacent to the laterals to decrease below 4.5. In contrast, root tips acidified the media, irrespective of the nutrient composition. H+ exchange was quantified from titrimetric assays of H+ exchange in nutrient solutions. There was a net H+ efflux from the roots of all three species into complete nutrient solutions with NH4+ as the N source, ranging from 246 μmol H+ h−1 g−1 d. wt for C. involucratus, to 32 μmol H+ h−1 g−1 d. wt for J. ingens. The H+ efflux into similar nutrient solutions with NO3− as the N source ranged from −89 μmol H+ h−1 g−1 d. wt for C. involucratus to −0.8μmol H+ h−1 d. wt for J. ingens. By assuming that H+ exchange was mainly located in the laterals, rates of H+ excretion as high as 542 μmol H+ h−1 g−1 d. wt can be calculated for C. involucratus in NH4+ solutions. Rates of H+ excretion by C. involucratus were scarcely affected by solutions of most Other ions. The NH4+-induced H+ release was dramatically reduced by H+ pump inhibitors, attaining only 18% of control rates with 50 μM diethylstilbestrol and 38% of control rates with 5 μM dicyclohexylcarbodiimide.
Network representations and methods for the analysis of chemical and biochemical pathways
Creators: name: Schnell, Santiago
name: Sandefur, Conner I.
name: Mincheva, Maya
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Systems biologists increasingly use network representations to investigate biochemical pathways and their dynamic behaviours. In this critical review, we discuss four commonly used network representations of chemical and biochemical pathways. We illustrate how some of these representations reduce network complexity but result in the ambiguous representation of biochemical pathways. We also examine the current theoretical approaches available to investigate the dynamic behaviour of chemical and biochemical networks. Finally, we describe how the critical chemical and biochemical pathways responsible for emergent dynamic behaviour can be identified using network mining and functional mapping approaches.
Salivary proteins associated with hyperglycemia in diabetes: a proteomic analysis
Creators: name: Baxter, Sarah Schwartz
name: Byrd, Warren C.
name: Offenbacher, Steven
name: Carlson, Jim
name: Howard-Williams, Escher L.
name: Buse, John B.
name: Wu, Michael C.
name: Border, Michael B.
name: Urrutia, Eugene
name: Bencharit, Sompop
name: Kohltfarber, Heidi
name: Mayo, Mary Virginia
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Effective monitoring of glucose levels is necessary for patients to achieve greater control over their diabetes. However, only about a quarter of subjects with diabetes who requires close serum glucose monitoring, regularly check their serum glucose daily. One of the potential barriers to patient compliance is the blood sampling requirement. Saliva and its protein contents can be altered in subjects with diabetes, possibly due to changes in glycemic control. We propose here that salivary proteomes of subjects with diabetes may be different based on their glycemic control as reflected in A1C levels. A total of 153 subjects with type 1 or 2 diabetes were recruited. Subjects in each type of diabetes were divided into 5 groups based on their A1C levels; <7, 7–8, 8–9, 9–10, >10. To examine the global proteomic changes associated with A1C, the proteomic profiling of pooled saliva samples from each group was created using label-free quantitative proteomics. Similar proteomic analysis for individual subjects (N=4, for each group) were then applied to examine proteins that may be less abundant in pooled samples. Principle component analysis (PCA) and cluster analysis (p<0.01 and p<0.001) were used to define the proteomic differences. We, therefore, defined the salivary proteomic changes associated with A1C changes. This study demonstrates that differences exist between salivary proteomic profiles in subjects with diabetes based on the A1C levels.
A Stable Human-Cell System Overexpressing Cystic Fibrosis Transmembrane Conductance Regulator Recombinant Protein at the Cell Surface
Creators: name: Kappes, John C.
name: Bajrami, Bekim
name: Yao, Xudong
name: Hildebrandt, Ellen
name: Urbatsch, Ina L.
name: Ray, Marjorie
name: Dai, Qun
name: Diego, Pamela Ann
name: Riordan, John R.
name: Mulky, Alok
name: Aleksandrov, Andrei A.
name: DeLucas, Lawrence J.
name: Naren, Anjaparavanda P.
name: Wu, Xing
name: Ding, Haitao
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Recent human clinical trials results demonstrated successful treatment for certain genetic forms of cystic fibrosis (CF). To extend treatment opportunities to those afflicted with other genetic forms of CF disease, structural and biophysical characterization of CF transmembrane conductance regulator (CFTR) is urgently needed. In this study, CFTR was modified with various tags, including a His10 purification tag, the SUMOstar (SUMO*) domain, an extracellular FLAG epitope, or an enhanced green fluorescent protein (EGFP), each alone or in various combinations. Expressed in HEK293 cells, recombinant CFTR proteins underwent complex glycosylation, compartmentalized with the plasma membrane, and exhibited regulated chloride-channel activity with only modest alterations in channel conductance and gating kinetics. Surface CFTR expression level was enhanced by the presence of SUMO* on the N-terminus. Quantitative mass-spectrometric analysis indicated approximately 10% of the total recombinant CFTR (SUMO*-CFTRFLAG-EGFP) localized to the plasma membrane. Trial purification using dodecylmaltoside for membrane protein extraction reproducibly recovered 178 ± 56 μg SUMO*-CFTRFLAG-EGFP per billion cells at 80% purity. Fluorescence size-exclusion chromatography indicated purified CFTR was monodisperse. These findings demonstrate a stable mammalian cell expression system capable of producing human CFTR of sufficient quality and quantity to augment futrure CF drug discovery efforts, including biophysical and structural studies.
Organic matter degradation and nutrient regeneration in Australian fresh waters: III. Size fractionation of phosphatase activity
Creators: name: Boon, Paul I
Publisher: name: La Trobe
Year: 2023

description: Murray-Darling Freshwater Research Centre

MDFRC item.

Continuous centrifugation and tangential flow ultrafiltration were used to size-fractionate and concentrate suspended particles from various turbid rivers of south-eastern Australia. These preparative steps produced highly concentrated samples, but the high load of suspended solids (up to 3.28 gl-1) did not interfere with the determination of phosphatase activity with an enzyme assay using p-nitrophenyl phosphate as the substrate. Phosphomonoesterase activity was an order of magnitude greater than phosphodiesterase activity; acid, neutral and alkaline phosphatases were detected. Most neutral (pH 7.5) and alkaline (pH 9.0) phosphatase activity was in the 0.2 - 1 mum size fraction: the next most active fractions were usually the 1-25 mum and the 100,000 daltons - 0.2 mum classes. Activity associated with free enzymes (i.e., that in the 10,000 - 100,000 daltons fraction) was usually low. Similar profiles were obtained with p-nitrophenyl phosphate and methylumbelliferyl phosphate substrates. Across the various size fractions within each river-water sample, phosphatase activity was usually more highly correlated with organic-matter content than with dry-matter content. Phosphatase activity was poorly related to chlorophyll-a contents. Phosphatase-producing bacteria were detected in all particulate fractions. The high activity in the 0.2 - 1 mum size fraction of turbid rivers might, therefore, be a function of either phosphatases associated with planktonic bacteria, or phosphatases adsorbed to the organic coating of suspended inorganic particles. In the coarser fractions, the additional contribution of attached bacteria cannot be excluded.
Voltage Induced Dynamical Quantum Phase Transitions in Exciton Condensates
Creators: name: Park, Moon Jip
name: Hankiewicz, E. M.
name: Gilbert, Matthew J.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We explore non-analytic quantum phase dynamics of dipolar exciton condensates formed in a system of 1D quantum layers subjected to voltage quenches. We map the exciton condensate physics on to the pseudospin ferromagnet model showing an additional oscillatory metastable and paramagnetic phase beyond the well-known ferromagnetic phase by utilizing a time-dependent, non-perturbative theoretical model. We explain the coherent phase of the exciton condensate in quantum Hall bilayers, observed for currents equal to and slightly larger than the critical current, as a stable time-dependent phase characterized by persistent charged meron flow in each of the individual layers with a characteristic AC Josephson frequency. As the magnitude of the voltage quench is further increased, we find that the time-dependent current oscillations associated with the charged meron flow decay, resulting in a transient pseudospin paramagnet phase characterized by partially coherent charge transfer between layers, before the state relaxes to incoherent charge transfer between the layers.
description: 7 Pages, 7 figures
Are There Good Mistakes? A Theoretical Analysis of CEGIS
Creators: name: Jha, Susmit
name: Seshia, Sanjit A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Logic in Computer Science (cs.LO)
subject: Artificial Intelligence (cs.AI)
subject: Machine Learning (cs.LG)
subject: Programming Languages (cs.PL)
subject: FOS: Computer and information sciences

description: Counterexample-guided inductive synthesis CEGIS is used to synthesize programs from a candidate space of programs. The technique is guaranteed to terminate and synthesize the correct program if the space of candidate programs is finite. But the technique may or may not terminate with the correct program if the candidate space of programs is infinite. In this paper, we perform a theoretical analysis of counterexample-guided inductive synthesis technique. We investigate whether the set of candidate spaces for which the correct program can be synthesized using CEGIS depends on the counterexamples used in inductive synthesis, that is, whether there are good mistakes which would increase the synthesis power. We investigate whether the use of minimal counterexamples instead of arbitrary counterexamples expands the set of candidate spaces of programs for which inductive synthesis can successfully synthesize a correct program. We consider two kinds of counterexamples: minimal counterexamples and history bounded counterexamples. The history bounded counterexample used in any iteration of CEGIS is bounded by the examples used in previous iterations of inductive synthesis. We examine the relative change in power of inductive synthesis in both cases. We show that the synthesis technique using minimal counterexamples MinCEGIS has the same synthesis power as CEGIS but the synthesis technique using history bounded counterexamples HCEGIS has different power than that of CEGIS, but none dominates the other.
description: In Proceedings SYNT 2014, arXiv:1407.4937
Ataxia Telangiectasia-Mutated Dependent DNA Damage Checkpoint Functions Regulate Gene Expression in Human Fibroblasts
Creators: name: Bushel, P. R.
name: Paules, R. S.
name: Zhou, Y.
name: Kaufmann, W. K.
name: Simpson, D. A.
name: Cao, F.
name: Zhou, T.
name: Chou, J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: The relationships between profiles of global gene expression and DNA damage checkpoint functions were studied in cells from patients with ataxia telangiectasia (AT). Three telomerase-expressing AT fibroblast lines displayed the expected hypersensitivity to ionizing radiation (IR) and defects in DNA damage checkpoints. Profiles of global gene expression in AT cells were determined at 2, 6 and 24 h after treatment with 1.5 Gy IR or sham-treatment, and were compared to those previously recognized in normal human fibroblasts. Under basal conditions 160 genes or ESTs were differentially expressed in AT and normal fibroblasts, and these were associated by gene ontology with insulin-like growth factor binding and regulation of cell growth. Upon DNA damage, 1091 gene mRNAs were changed in at least two of the three AT cell lines. When compared with the 1811 genes changed in normal human fibroblasts after the same treatment, 715 were found in both AT and normal fibroblasts, including most genes categorized by gene ontology into cell cycle, cell growth and DNA damage response pathways. However, the IR-induced changes in these 715 genes in AT cells usually were delayed or attenuated in comparison to normal cells. The reduced change in DNA-damage-response genes and the attenuated repression of cell-cycle-regulated genes may account for the defects in cell cycle checkpoint function in AT cells.
Photometric binaries, mass functions, and structural parameters of 78 Galactic open clusters
Creators: name: Cordoni, Giacomo
name: Milone, Antonino P.
name: Marino, Anna F.
name: Vesperini, Enrico
name: Dondoglio, Emanuele
name: Legnardi, Maria Vittoria
name: Mohandasan, Anjana
name: Carlos, Marilia
name: Lagioia, Edoardo P.
name: Jang, Sohee
name: Ziliotto, Tuila
Publisher: name: arXiv
Year: 2023
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Binary stars play a crucial role in our understanding of the formation and evolution of star clusters and their stellar populations. We use Gaia Data Release 3 to homogeneously analyze 78 Galactic open clusters and the unresolved binary systems they host, each composed of two main sequence (MS) stars. We first investigated the structural parameters of these clusters, such as the core radius and the central density, and determined the cluster mass function (MF) and total mass by interpolating the density profile of each cluster. We measured the fraction of binaries with a large mass ratio and the fraction of blue straggler stars (BSSs), and finally investigated possible connections between the populations of binary stars and BSSs with the main parameters of the host cluster. {Remarkably, we find that the MFs of 78 analyzed open clusters follow a similar trend and are well reproduced by two single power-law functions, with a change in slope around masses of 1$M_{\odot}$. The fraction of binary stars ranges from $\sim$15\% to more than $\sim$60\% without significant correlation with the mass and the age of the host cluster. Moreover, we detect hints of a correlation between the total fraction of binary stars and the central density of the host cluster. We compared the fraction of binary stars with that of BSSs, finding that clusters with high and low central density exhibit different trends. The fraction of binaries does not significantly change with the mass of the primary star and the mass ratio. The radial distribution of binary stars depends on cluster age. The binaries of clusters younger than $\sim$800\,Myr typically show a flat radial distribution, with some hints of a double peak. In contrast, the binaries of the remaining clusters are more centrally concentrated than the single stars, which is similar to what is observed in globular clusters.
description: 27 pages, 27 figures, accepted for publication in Astronomy & Astrophysics
Increased Expression of Androgen Receptor Coregulator MAGE-11 in Prostate Cancer by DNA Hypomethylation and Cyclic AMP
Creators: name: Wilson, E. M.
name: Karpf, A. R.
name: Bai, S.
name: James, S. R.
name: Mohler, J. L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Melanoma antigen gene protein-A11 (MAGE-11) of the MAGE family of cancer-germline antigens increases androgen receptor (AR) transcriptional activity through its interaction with the AR NH2-terminal FXXLF motif. The present study investigated the regulatory mechanisms that control MAGE-11 expression during androgen deprivation therapy and prostate cancer progression. Studies include the CWR22 xenograft model of human prostate cancer, clinical specimens of benign and malignant prostate, and prostate cancer cell lines. MAGE-11 mRNA levels increased 100 to 1500 fold during androgen deprivation therapy and prostate cancer progression, with highest levels in the castration-recurrent CWR22 xenograft and clinical specimens of castration-recurrent prostate cancer. Pyrosequencing of genomic DNA from prostate cancer specimens and cell lines indicated the increase in MAGE-11 resulted from DNA hypomethylation of a CpG island in the 5´ promoter of the MAGE-11 gene. Sodium bisulfite sequencing of genomic DNA from benign and malignant prostate tumors and prostate cancer cell lines revealed DNA hypomethylation at individual CpG sites at the transcription start site were most critical for MAGE-11 expression. Cyclic AMP also increased MAGE-11 expression and AR transcriptional activity in prostate cancer cell lines. However, cyclic AMP did not alter DNA methylation of the promoter and its effects were inhibited by extensive DNA methylation in the MAGE-11 promoter region. Increased expression of the AR coregulator MAGE-11 through promoter DNA hypomethylation and cyclic AMP provides a novel mechanism for increased AR signaling in castration-recurrent prostate cancer.
HiRSE Seminar Series 2022 - Celebration 10 years of the RSE Movement 2012-2022
Creators: name: Wyatt, Claire
Publisher: name: Zenodo
Year: 2022
Subjects: Research Software Engineering, Community Building, Research Software Engineers

description: A presentation describing the journey from 2012 to 2022 of the RSE Movement primarily in the UK but also leading to RSE Chapters around the world. Includes community activites from the last six years and upcoming events for 2022/2023.
K-Ras Promotes Angiogenesis Mediated by Immortalized Human Pancreatic Epithelial Cells through Mitogen-Activated Protein Kinase Signaling Pathways
Creators: name: Fleming, J. B.
name: Brekken, R. A.
name: Matsuo, Y.
name: Guha, S.
name: Ouellette, M. M.
name: Campbell, P. M.
name: Der, C. J.
name: Aggarwal, B. B.
name: Sung, B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Activating point mutations in the K-Ras oncogene are among the most common genetic alterations in pancreatic cancer, occurring early in the progression of the disease. However, the function of mutant K-Ras activity in tumor angiogenesis remains poorly understood. Using human pancreatic duct epithelial (HPDE) and K-Ras4BG12V–transformed HPDE (HPDE-KRas) cells, we show that activated K-Ras significantly enhanced the production of angiogenic factors including CXC chemokines and vascular endothelial growth factor (VEGF). Western blot analysis revealed that K-Ras activation promoted the phosphorylation of Raf/mitogen-activated protein kinase kinase-1/2 (MEK1/2) and expression of c-Jun. MEK1/2 inhibitors, U0126 and PD98059, significantly inhibited the secretion of both CXC chemokines and VEGF, whereas the c-Jun NH2-terminal kinase inhibitor SP600125 abrogated only CXC chemokine production. To further elucidate the biological functions of oncogenic K-Ras in promoting angiogenesis, we did in vitro invasion and tube formation assays using human umbilical vein endothelial cells (HUVEC). HUVEC cocultured with HPDE-KRas showed significantly enhanced invasiveness and tube formation as compared with either control (without coculture) or coculture with HPDE. Moreover, SB225002 (a CXCR2 inhibitor) and 2C3 (an anti-VEGF monoclonal antibody) either alone or in a cooperative manner significantly reduced the degree of both Ras-dependent HUVEC invasiveness and tube formation. Similar results were obtained using another pair of immortalized human pancreatic duct–derived cells, E6/E7/st and its oncogenic K-Ras variant, E6/E7/Ras/st. Taken together, our results suggest that angiogenesis is initiated by paracrine epithelial secretion of CXC chemokines and VEGF downstream of activated oncogenic K-Ras, and that this vascular maturation is in part dependent on MEK1/2 and c-Jun signaling.
miR-93, miR-98, and miR-197 Regulate Expression of Tumor Suppressor Gene FUS1
Creators: name: Du, L.
name: Roth, J. A.
name: Prudkin, L.
name: Pertsemlidis, A.
name: Ji, L.
name: Hammond, S. M.
name: Minna, J. D.
name: Wistuba, I. I.
name: Schageman, J. J.
name: Subauste, M. C.
name: Saber, B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: FUS1 is a tumor suppressor gene located on human chromosome 3p21, and expression of Fus1 protein is highly regulated at various levels, leading to lost or greatly diminished tumor suppressor function in many lung cancers. Here we show that selected microRNAs (miRNAs) interact with the 3’ untranslated region (3’ UTR) of FUS1, leading to down-regulation of protein expression. Using computational methods, we first predicted that FUS1 is a target of three miRNAs, miR-93, miR-98 and miR-197, and then showed that exogenous over-expression of these miRNAs inhibited Fus1 protein expression. We then confirmed that the three miRNAs target the 3’UTR region of the FUS1 transcript, and that individual deletion of the three miRNA target sites in the FUS1 3’UTR restores the expression level of Fus1 protein. We further found that miR-93 and miR-98 are expressed at higher levels in small cell lung cancer cell lines (SCLC) than in non-small cell lung cancer cell lines (NSCLC) and immortalized human bronchial epithelial cells (HBECs), and that miR-197 is expressed at higher levels in both SCLC and NSCLC than in HBECs. Finally, we found that elevated miR-93 and miR-197 expression is correlated with reduced Fus1 expression in NSCLC tumor specimens. These results suggest that the three miRNAs are negative regulators of Fus1 expression in lung cancers.
Measurements of Outflow Velocities in On-Disk Plumes from EIS Hinode Observations
Creators: name: Fu, Hui
name: Xia, Lidong
name: Li, Bo
name: Huang, Zhenghua
name: Jiao, Fangran
name: Mou, Chaozhou
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: The contribution of plumes to the solar wind has been subject to hot debate in the past decades. The EUV Imaging Spectrometer (EIS) on board Hinode provides a unique means to deduce outflow velocities at coronal heights via direct Doppler shift measurements of coronal emission lines. Such direct Doppler shift measurements were not possible with previous spectrometers. We measure the outflow velocity at coronal heights in several on-disk long-duration plumes, which are located in coronal holes and show significant blue shifts throughout the entire observational period. In one case, a plume is measured 4 hours apart. The deduced outflow velocities are consistent, suggesting that the flows are quasi-steady. Furthermore, we provide an outflow velocity profile along the plumes, finding that the velocity corrected for the line-of-sight effect can reach 10 km s$^{-1}$ at 1.02 $R_{\odot}$, 15 km s$^{-1}$ at 1.03 $R_{\odot}$, and 25 km s$^{-1}$ at 1.05 $R_{\odot}$. This clear signature of steady acceleration, combined with the fact that there is no significant blue shift at the base of plumes, provides an important constraint on plume models. At the height of 1.03 $R_{\odot}$, EIS also deduced a density of 1.3$\times10^{8}$ cm$^{-3}$, resulting in a proton flux of about 4.2$\times10^9$ cm$^{-2}$s$^{-1}$ scaled to 1AU, which is an order of magnitude higher than the proton input to a typical solar wind if a radial expansion is assumed. This suggests that, coronal hole plumes may be an important source of the solar wind.
description: accepted for publication in ApJ, 13 pages, 9 figures
A 600 kpc complex radio source at the center of Abell 3718 discovered by the EMU and POSSUM surveys
Creators: name: Loi, F.
name: Brienza, M.
name: Riseley, C. J.
name: Rudnick, L.
name: Boschin, W.
name: Lovisari, L.
name: Carretti, E.
name: Koribalski, B.
name: Stuardi, C.
name: O'Sullivan, S. P.
name: Bonafede, A.
name: Filipović, M. D.
name: Hopkins, A.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Multifrequency studies of galaxy clusters are crucial for inferring their dynamical states and physics. Moreover, these studies allow us to investigate cluster-embedded sources, whose evolution is affected by the physical and dynamical condition of the cluster itself. So far, these kinds of studies have been preferentially conducted on clusters visible from the northern hemisphere due to the high-fidelity imaging capabilities of ground-based radio interferometers located there. In this paper, we conducted a multifrequency study of the poorly known galaxy cluster Abell 3718. We investigated the unknown origin of an extended radio source with a length of $\sim$612 kpc at 943 MHz detected in images from the Evolutionary Map of the Universe (EMU) and POlarisation Sky Survey of the Universe's Magnetism (POSSUM) surveys. We analyzed optical and X-ray data to infer the dynamical state of the cluster and, in particular, the merger activity. We conducted a radio spectral index study from 943 MHz up to 9 GHz. We also evaluated the polarization properties of the brightest cluster-embedded sources to understand if they are related to the radio emission observed on larger scales. [Abstract truncated due to arxiv limit! Please see the pdf version]
description: 12 pages, 10 figures; accepted for publication by A&A
Altered-Function p53 Missense Mutations Identified in Breast Cancers Can Have Subtle Effects on Transactivation
Creators: name: Edmiston, Sharon
name: Resnick, Michael A.
name: Inga, Alberto
name: Jordan, Jennifer J.
name: Conway, Kathleen
name: Wu, Lin
name: Carey, Lisa A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Mutations of the sequence-specific master regulator p53 that alter transactivation function from promoter response elements (REs) could result in changes in the strength of gene activation or spectra of genes regulated. Such mutations in this tumor suppressor might lead to dramatic phenotypic changes and diversification of cell responses to stress. We have determined “functional fingerprints” of sporadic breast cancer-related p53 mutants many of which are also associated with familial cancer proneness such as the Li-Fraumeni Syndrome and germline BRCA1/2 mutant-associated cancers. The ability of p53, wild type and mutants, to transactivate from 11 human target REs has been assessed at variable expression levels using a cellular, isogenomic yeast model system that allows for the rapid analysis of p53 function using a qualitative and a quantitative reporter. Among 50 missense mutants, 29 were classified as loss-of-function. The remaining 21 retained transactivation towards at least one RE. At high levels of galactose induced p53 expression, 12/21 mutants that retain transactivation appeared similar to WT. When the level of galactose was reduced, transactivation defects could be revealed suggesting that some breast cancer related mutants can have subtle changes in transcription. These findings have been compared with clinical data from an ongoing neoadjuvant chemotherapy treatment trial for locally advanced breast tumors. The functional and nonfunctional missense mutations may distinguish tumors in terms of demographics, appearance and relapse, implying that heterogeneity in the functionality of specific p53 mutations could impact clinical behavior and outcome.
Composition Comparison between ICMEs from Active Regions and Quiet-Sun Regions
Creators: name: Li, Jinrong
name: Song, Hongqiang
name: Lv, Qi
name: Fu, Hui
name: Li, Leping
name: Zheng, Ruisheng
name: Chen, Yao
Publisher: name: arXiv
Year: 2023
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Space Physics (physics.space-ph)
subject: FOS: Physical sciences

description: The composition, including the ionic charge states and elemental abundances of heavy elements, within interplanetary coronal mass ejections (ICMEs) has tight correlations with their source regions and eruption processes. This can help analyze the eruption mechanisms and plasma origins of CMEs, and deepen our understanding of energetic solar activities. The active regions and quiet-Sun regions have different physical properties, thus from a statistical point of view, ICMEs originating from the two types of regions should exhibit different compositional characteristics. To demonstrate the differences comprehensively, we conduct survey studies on the ionic charge states of five elements (Mg, Fe, Si, C, and O) and the relative abundances of six elements (Mg/O, Fe/O, Si/O, C/O, Ne/O, and He/O) within ICMEs from 1998 February to 2011 August through the data of advanced composition explorer. The results show that ICMEs from active regions have higher ionic charge states and relative abundances than those from quiet-Sun regions. For the active-region ICMEs, we further analyze the relations between their composition and flare class, and find a positive relationship between them, i.e., the higher classes of the associated flares, the larger means of ionic charge states and relative abundances (except the C/O) within ICMEs. As more (less) fractions of ICMEs originate from active regions around solar maximum (minimum), and active-region ICMEs usually are associated with higher-class flares, our studies might answer why ICME composition measured near 1 au exhibits the solar cycle dependence.
description: 13 pages, 4 figures
FEN1 Functions in Long Patch Base Excision Repair Under Conditions of Oxidative Stress in Vertebrate Cells
Creators: name: Nagata, K.
name: Takeda, S.
name: Adachi, N.
name: Kaufman, D. G.
name: Watanabe, M.
name: Nakamura, J.
name: Chastain, P. D.
name: Tano, K.
name: Asagoshi, K.
name: Koyama, H.
name: Sonoda, E.
name: Wilson, S. H.
name: Swenberg, J. A.
name: Kikuchi, K.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: From in vitro studies, flap endonuclease 1 (FEN1) has been proposed to play a role in the long patch (LP) base excision repair (BER) sub-pathway. Yet, the role of FEN1 in BER in the context of the living vertebrate cell has not been thoroughly explored. In the present study, we cloned a DT40 chicken cell line with a deletion in the FEN1 gene and found that these FEN1-deficient cells exhibited hypersensitivity to H2O2. This oxidant produces genotoxic lesions that are repaired by BER, suggesting that the cells have a deficiency in BER affecting survival. In experiments with extracts from the isogenic FEN1 null and wild type cell lines, the LP-BER activity of FEN1 null cells was deficient, whereas repair by the single-nucleotide BER sub-pathway was normal. Other consequences of the FEN1 deficiency also were evaluated. These results illustrate that FEN1 plays a role in LP-BER in higher eukaryotes, presumably by processing the flap-containing intermediates of BER.
(:unas) unassigned
Creators: name: (:Unkn) Unknown
Publisher: name: Universita' degli Studi di Salerno
Year: 2024

description: Il breve intervento coglie, nel ricordo del primo ‘incontro’ scientifico con i lavori di Dante Della Terza, l’occasione per segnalare alcuni aspetti interessanti dell’esegesi dantesca dell’illustre italianista. In primo luogo si rileva la sua insistenza sulla necessità di leggere i singoli canti in funzione dell’«insiemezza» della cantica e della realtà globale del poema, che impone, dunque, anche l’adozione di una ‘visuale’ retrospettiva; in secondo luogo si fa riferimento, sia pure per fugaci cenni, al suo rapporto con Singleton e alla sua meritoria ‘scoperta’ di Auerbach.
description: This brief intervention, in memory of the first scientific 'encounter' with Dante Della Terza's works, takes the opportunity to point out some interesting aspects of Dante's exegesis by the illustrious Italianist. In the first place, his insistence on the necessity of reading the single cantos in function of the ‘wholeness’ of the cantica and of the global reality of the poem, which imposes, therefore, also the adoption of a retrospective "view"; in the second place, reference is made, albeit briefly, to his relationship with Singleton and his meritorious ‘discovery’ of Auerbach.
The appearance of a merging binary black hole very close to a spinning supermassive black hole
Creators: name: Zhang, Xiaoyue
name: Chen, Xian
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The mass and distance of a binary black hole (BBH) are fundamental parameters to measure in gravitational-wave (GW) astronomy. It is well-known that the measurement is affected by cosmological redshift, and recent works also showed that Doppler and gravitational redshifts could further affect the result if the BBH coalesces close to a supermassive black hole (SMBH). Here we consider the additional lensing effect induced by the nearby SMBH on the measurement. We compute the null geodesics originating within $10$ gravitational radii of a Kerr SMBH to determine the redshift and magnification of the GWs emitted by the BBH. We find a positive correlation between redshift and demagnification, which results in a positive correlation between the mass and distance of the BBH in the detector frame. More importantly, we find a higher probability for the signal to appear redshifted and demagnified to a distant observer, rather than blueshifted and magnified. Based on these results, we show that a binary at a cosmological redshift of $z_{\rm cos}=(10^{-2}-10^{-1})$ and composed of BHs of $(10-20)M_\odot$ could masquerade as a BBH at a redshift of $z_{\rm cos}\sim1$ and containing BHs as large as $(44-110)M_\odot$. In the case of extreme demagnification, we also find that the same BBH could appear to be at $z_{\rm cos}>10$ and contain subsolar-mass BHs. Such an effect, if not accounted for, could bias our understanding of the origin of the BHs detected via GWs.
Statistical Methods for Thermonuclear Reaction Rates and Nucleosynthesis Simulations
Creators: name: Iliadis, Christian
name: Longland, Richard
name: Coc, Alain
name: Timmes, F. X.
name: Champagne, Art E.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Nuclear Experiment (nucl-ex)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Rigorous statistical methods for estimating thermonuclear reaction rates and nucleosynthesis are becoming increasingly established in nuclear astrophysics. The main challenge being faced is that experimental reaction rates are highly complex quantities derived from a multitude of different measured nuclear parameters (e.g., astrophysical S-factors, resonance energies and strengths, particle and gamma-ray partial widths). We discuss the application of the Monte Carlo method to two distinct, but related, questions. First, given a set of measured nuclear parameters, how can one best estimate the resulting thermonuclear reaction rates and associated uncertainties? Second, given a set of appropriate reaction rates, how can one best estimate the abundances from nucleosynthesis (i.e., reaction network) calculations? The techniques described here provide probability density functions that can be used to derive statistically meaningful reaction rates and final abundances for any desired coverage probability. Examples are given for applications to s-process neutron sources, core-collapse supernovae, classical novae, and big bang nucleosynthesis.
description: Accepted for publication in J. Phys. G Focus issue "Enhancing the interaction between nuclear experiment and theory through information and statistics"