cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
(1691) Edward Baines jnr
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
MOLECULAR CHARACTERIZATION OF K26 GENE OF LEISHMANIA INFANTUM, ISOLATE BY HUMAN PATIENTS FROM SICILY REGION
Creators: name: Giambanco
name: Bruno, F.
name: Castelli, G.
name: Migliazzo A
name: Reale, S.
name: F, Vitale
Publisher: name: INFN Open Access Repository
Year: 2018

description: Human Leishmaniasis is an emerging problem in Italy and increase in the Sicily region.
 In the present work, we explored the genetic polymorphism of Leishmania isolates from twenty-five cases of human
 Leishmaniasis: two cases of visceral Leishmaniasis (VL) and twenty-three of cutaneous Leishmaniasis (CL). The
 characterization is carried out in comparison with twenty five human isolates of leishmania and one reference strain, L.
 infantum MHOM/TN/80IPT1 (MON-1). MON-1 is the most common zymodeme responsible for Leishmaniasis in Italy.
 The aim of the study is to genotype Leishmania isolates from Sicily by PCR ,analyzing size polymorphism of K26 gene
 to discriminate between MON-1 and non MON-1 zymodemes. K26 is a protein belonging to the Hydrofilic acylated
 surface protein B (HASPB) family. It is characterized by repeated aminoacidal domains and shows polymorphisms. The
 k26 polymorphism of MON-1 zymodeme is determinate in the size of 626 bp. The analysis show that all the 25 isolates
 belong to the L. infantum species, in particular the product size of 626 bp is detect in six patients affected by cutaneous
 Leishmaniasis. The molecular tools applied in this study can constitute a helpful support for parasite tracking and for a
 better understanding of the epidemiological evolution of Leishmaniasis.
Supplemental Methods.pdf from Molecular palaeontology illuminates the evolution of ecdysozoan vision.
Creators: name: Fleming, James F.
name: Kristensen, Reinhardt Møbjerg
name: Sørensen, Martin Vinther
name: Tae-Yoon S. Park
name: Kazuharu Arakawa
name: Blaxter, Mark
name: Rebecchi, Lorena
name: Guidetti, Roberto
name: Williams, Tom A.
name: Roberts, Nicholas W.
name: Vinther, Jakob
name: Pisani, Davide
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: 40308 Palaeontology (incl. Palynology)
subject: FOS: Earth and related environmental sciences

description: A PDF file describing our methods in greater detail, alongside the new opsin family nomenclature
Impaired Regulatory Volume Decrease in Freshly Isolated Cholangiocytes from Cystic Fibrosis Mice: IMPLICATIONS FOR CYSTIC FIBROSIS TRANSMEMBRANE CONDUCTANCE REGULATOR EFFECT ON POTASSIUM CONDUCTANCE
Creators: name: Cho, Won Kyoo
name: Zinzow, Wendy
name: Siegrist, Vicki J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Various K(+) and Cl(-) channels are important in cell volume regulation and biliary secretion, but the specific role of cystic fibrosis transmembrane conductance regulator in cholangiocyte cell volume regulation is not known. The goal of this research was to study regulatory volume decrease (RVD) in bile duct cell clusters (BDCCs) from normal and cystic fibrosis (CF) mouse livers. Mouse BDCCs without an enclosed lumen were prepared as described (Cho, W. K. (2002) Am. J. Physiol. 283, G1320-G1327). The isotonic solution consisted of HEPES buffer with 40% of the NaCl replaced with isomolar amounts of sucrose, whereas hypotonic solution was the same as isotonic solution without sucrose. The cell volume changes were indirectly assessed by measuring cross-sectional area (CSA) changes of the BDCCs using quantitative videomicroscopy. Exposure to hypotonic solutions increased relative CSAs of normal BDCCs to 1.20 +/- 0.01 (mean +/- S.E., n = 50) in 10 min, followed by RVD to 1.07 +/- 0.01 by 40 min. Hypotonic challenge in CF mouse BDCCs also increased relative CSA to 1.20 +/- 0.01 (n = 53) in 10 min but without significant recovery. Coadministration of the K(+)-selective ionophore valinomycin restored RVD in CF mouse BDCCs, suggesting that the impaired RVD was likely from a defect in K(+) conductance. Moreover, this valinomycin-induced RVD in CF mice was inhibited by 5-nitro-2'-(3-phenylpropylamino)-benzoate, indicating that it is not from nonspecific effects. Neither cAMP nor calcium agonists could reverse the impaired RVD seen in CF cholangiocytes. Our conclusion is that CF mouse cholangiocytes have defective RVD from an impaired K(+) efflux pathway, which could not be reversed by cAMP nor calcium agonists.
Lissajous rocking ratchet
Creators: name: Platonov, S.
name: Kästner, B.
name: Schumacher, H. W.
name: Kohler, S.
name: Ludwig, S.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Breaking time-reversal symmetry (TRS) in the absence of a net bias can give rise to directed steady-state non-equilibrium transport phenomena such as ratchet effects. Here we present, theoretically and experimentally, the concept of a Lissajous rocking ratchet as an instrument based on breaking TRS. Our system is a semiconductor quantum dot (QD) with periodically modulated dot-lead tunnel barriers. Broken TRS gives rise to single electron tunneling current. Its direction is fully controlled by exploring frequency and phase relations between the two barrier modulations. The concept of Lissajous ratchets can be realized in a large variety of different systems, including nano-electrical, nano-electromechanical or superconducting circuits. It promises applications based on a detailed on-chip comparison of radio-frequency signals.
IκB Kinase α and p65/RelA Contribute to Optimal Epidermal Growth Factor-induced c- fos Gene Expression Independent of IκBα Degradation
Creators: name: Baldwin Jr., Albert S.
name: Anest, Vasiliki
name: Cogswell, Patricia C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Mitogenic activation of expression of immediate-early genes, such as c-fos, is controlled through signal-induced phosphorylation of constitutively bound transcription factors that is correlated with a nucleosomal response that involves inducible chromatin modifications, such as histone phosphorylation and acetylation. Here we have explored a potential role for the transcription factor NF-kappaB and its associated signaling components in mediating induction of c-fos gene expression downstream of epidermal growth factor (EGF)-dependent signaling. Here we show that EGF treatment of quiescent fibroblast does not induce the classical pathway of NF-kappaB activation through IkappaB kinase (IKK)-directed IkappaBalpha phosphorylation. Interestingly, efficient induction of c-fos transcription requires IKKalpha, one of the subunits of the IkappaB kinase complex. The NF-kappaB subunit, p65/RelA, is found constitutively associated with the c-fos promoter, and knock-out of this transcription factor significantly reduces c-fos gene expression. Importantly, EGF induces the recruitment of IKKalpha to the c-fos promoter to regulate promoter-specific histone H3 Ser(10) phosphorylation in a manner that is independent of p65/RelA. Collectively, our data demonstrate that IKKalpha and p65/RelA contribute significantly to EGF-induced c-fos gene expression in a manner independent of the classical, IkappaBalpha degradation, p65/RelA nuclear accumulation response pathway.
Association of PM2.5 and PM10 with Acute Exacerbation of Chronic Obstructive Pulmonary Disease at lag0 to lag7: A Systematic Review and Meta-Analysis
Creators: name: Li, Niuniu
name: Ma, Jianling
name: Ji, Kun
name: Wang, Liyun
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy

description: This study aimed to conduct a meta-analysis to investigate whether short-term exposure to fine (PM2.5) and coarse (PM10) particulate matter was associated with acute exacerbation of chronic obstructive pulmonary disease (AECOPD) hospitalization, emergency room visit, and outpatient visit at different lag values. PubMed, Embase, and the Cochrane Library were searched for relevant papers published up to March 2021. For studies reporting results per 1-µg/m3 increase in PM2.5, the results were recalculated as per 10-µg/m3 increase. We manually calculated the RRs for these two studies and transferred the RRs to estimate 10 µg/m3 increases in PM2.5. Automation tools were initially used to remove ineligible studies. Two reviewers independently screened the remaining records and retrieved reports. Twenty-six studies (28 datasets; 7,018,419 patients) were included. There was a significant association between PM2.5 and AECOPD events on lag0 (ES = 1.01, 95%CI: 1.01-1.02, p < 0.001; I2=88.6%, Pheterogeneity<0.001), lag1 (ES = 1.00, 95%CI: 1.00-1.01, p < 0.001; I2=82.5%, Pheterogeneity<0.001), lag2 (ES = 1.01, 95%CI: 1.01-1.01, p < 0.001; I2=90.6%, Pheterogeneity<0.001), lag3 (ES = 1.01, 95%CI: 1.00-1.01, p < 0.001; I2=88.9%, Pheterogeneity<0.001), lag4 (ES = 1.00, 95%CI: 1.00-1.01, p < 0.001; I2=83.7%, Pheterogeneity<0.001), and lag7 (ES = 1.00, 95%CI: 1.00-1.00, p < 0.001; I2=0.0%, Pheterogeneity=0.743). The subgroup analyses showed that PM2.5 influenced the rates of hospitalization, emergency room visits, and outpatient visits. Similar trends were observed with PM10. The risk of AECOPD events (hospitalization, emergency room visit, and outpatient visit) was significantly increased with a 10-µg/m3 increment in PM2.5 and PM10 from lag0 to lag7. List Of Abbreviations: particulate matter (PM2.5 and PM10); acute exacerbation of chronic obstructive pulmonary disease (AECOPD); Chronic obstructive pulmonary disease (COPD); Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA); Effect sizes [48]; confidence intervals (CIs)
(1692) Edward Baines [snr]
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Supplemental Figures_1-8.pdf from Molecular palaeontology illuminates the evolution of ecdysozoan vision
Creators: name: Fleming, James F.
name: Kristensen, Reinhardt Møbjerg
name: Sørensen, Martin Vinther
name: Tae-Yoon S. Park
name: Kazuharu Arakawa
name: Blaxter, Mark
name: Rebecchi, Lorena
name: Guidetti, Roberto
name: Williams, Tom A.
name: Roberts, Nicholas W.
name: Vinther, Jakob
name: Pisani, Davide
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: 40308 Palaeontology (incl. Palynology)
subject: FOS: Earth and related environmental sciences

description: A single PDF file containing Supplemental Figures 1 through 8, as described in the main text, alongside their figure legends
Mapping Subunit Location on the Saccharomyces cerevisiae Origin Recognition Complex Free and Bound to DNA Using a Novel Nanoscale Biopointer
Creators: name: Lee, Daniel G.
name: Bowers, Jayson L.
name: Chastain II, Paul D.
name: Bell, Stephen P.
name: Griffith, Jack D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: The Saccharomyces cerevisiae origin recognition complex (ORC) is composed of six subunits and is an essential component in the assembly of the replication apparatus. To probe the organization of this multiprotein complex by electron microscopy, each subunit was tagged on either its C or N terminus with biotin and assembled into a complex with the five other unmodified subunits. A nanoscale biopointer consisting of a short DNA duplex with streptavidin at one end was used to map the location of the N and C termini of each subunit. These observations were made using ORC free in solution and bound to the ARS1 origin of replication. This mapping confirms and extends previous studies mapping the sites of subunit interaction with origin DNA. In particular, we provide new information concerning the stoichiometry of the ORC-ARS1 complex and the changes in conformation that are associated with DNA binding by ORC. This versatile, new approach to mapping protein structure has potential for many applications.
Schrödinger Equation of a particle in an Uniformly Accelerated Frame and the Possibility of a New kind of Quanta
Creators: name: De, Sanchari
name: Chakrabarty, Somenath
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: In this article we have developed a formalism to obtain the Schr$\ddot{\rm{o}}$dinger equation for a particle in a frame undergoing an uniform acceleration in an otherwise flat Minkowski space-time geometry. We have presented an exact solution of the equation and obtained the eigenfunctions and the corresponding eigenvalues. It has been observed that the Schr$\ddot{\rm{o}}$dinger equation can be reduced to an one dimensional hydrogen atom problem. Whereas, the quantized energy levels are exactly identical with that of an one dimensional quantum harmonic oscillator. Hence considering transitions, we have predicted the existence of a new kind of quanta, which will either be emitted or absorbed if the particles get excited or de-excited respectively.
description: 7 pages, No figure, To appear in Modern Physics Letter A
Ground state cooling of quantum systems via a one-shot measurement
Creators: name: Pyshkin, P. V.
name: Luo, Da-Wei
name: You, J. Q.
name: Wu, Lian-Ao
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We prove that there exists a family of quantum systems that can be cooled to their ground states by a one-shot projective measurement on the ancillas coupled to these systems. Consequently, this proof gives rise to the conditions for achieving the one-shot measurement ground-state cooling (OSMGSC). We also propose a general procedure for finding unitary propagators and corresponding Hamiltonians to realize such cooling by means of inverse engineering technique.
description: 5 pages, 4 figures
(1687) Henry Hawkins Turner
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Supplemental Methods.pdf from Molecular palaeontology illuminates the evolution of ecdysozoan vision
Creators: name: Fleming, James F.
name: Kristensen, Reinhardt Møbjerg
name: Sørensen, Martin Vinther
name: Tae-Yoon S. Park
name: Kazuharu Arakawa
name: Blaxter, Mark
name: Rebecchi, Lorena
name: Guidetti, Roberto
name: Williams, Tom A.
name: Roberts, Nicholas W.
name: Vinther, Jakob
name: Pisani, Davide
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: 40308 Palaeontology (incl. Palynology)
subject: FOS: Earth and related environmental sciences

description: A PDF file describing our methods in greater detail, alongside the new opsin family nomenclature
Metabolism of P2 Receptor Agonists in Human Airways: IMPLICATIONS FOR MUCOCILIARY CLEARANCE AND CYSTIC FIBROSIS
Creators: name: Picher, Maryse
name: Burch, Lauranell H.
name: Boucher, Richard C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Extracellular nucleotides are among the most potent mediators of mucociliary clearance (MCC) in human lungs. However, clinical trials revealed that aerosolized nucleotides provide only a transient improvement of MCC to patients diagnosed with cystic fibrosis (CF). In this study, we identified the mechanism that eliminates extracellular nucleotides from human airways. Polarized primary cultures of human bronchial epithelial cells were impermeable to extracellular nucleotides but rapidly dephosphorylated ATP into ADP, AMP, and adenosine. The half-life of a therapeutic ATP concentration (0.1 mm) was approximately 20 s within the periciliary liquid layer. The mucosal epithelial surface eliminated P2 receptor agonists (ATP = UTP > ADP > UDP) at 3-fold higher rates than the serosal surface. We also showed that mucosal (not serosal) ectoATPase activity increases toward areas most susceptible to airway obstruction (nose < bronchi << bronchioles). Bronchial cultures from patients with CF, primary ciliary dyskinesia, or alpha1-antitrypsin deficiency exhibited 3-fold higher mucosal (not serosal) ectoATPase activity than normal cultures. Time course experiments indicated that CF enhances ATP elimination and adenosine accumulation on the mucosal surface. Furthermore, nonspecific alkaline phosphatase was identified as the major regulator of airway nucleotide concentrations in CF, primary ciliary dyskinesia, and alpha1-antitrypsin deficiency. The ectoAT-Pase activity and mRNA expression of mucosally restricted nonspecific alkaline phosphatase were 3-fold higher on bronchial cultures from these patients than from healthy subjects. This study demonstrates that the duration of nucleotide-mediated MCC is limited by epithelial ectonucleotidases throughout human airways, with the efficiency of this mechanism enhanced in chronic inflammatory lung diseases, including CF.
Molecular Cloning, Genomic Structure, and Expression Analysis of MUC20, a Novel Mucin Protein, Up-regulated in Injured Kidney
Creators: name: Nanayama, Toyomichi
name: Saito, Yutaka
name: Yamasaki, Yoshiki
name: Waga, Iwao
name: Sun, Hong Wei
name: Alcorta, David A.
name: Higuchi, Toshio
name: Yamamoto, Tadashi
name: Li, Huiping
name: Nakamura, Motonao
name: Orita, Takuya
name: Jennette, J. Charles
name: Nakanishi, Setsuko
name: Watanabe, Hirotaka
name: Falk, Ronald J.
name: Katsuya, Ken
name: Yamamoto, Yoshihisa
name: Munger, William
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Immunoglobulin A nephropathy (IgAN) is the most common primary glomerulonephritis in the world. Here, we identify a cDNA encoding a novel mucin protein, shown previously to be up-regulated in IgAN patients, from a human kidney cDNA library. This protein contains a mucin tandem repeat of 19 amino acids consisting of many threonine, serine, and proline residues and likely to be extensively O-glycosylated; thus, this gene was classified in the mucin family and named MUC20. The human MUC20 gene contains at least four exons and is localized close to MUC4 on chromosome 3q29. We found variations in repeat numbers in the mucin tandem domain, suggesting polymorphism of this region. Northern blot and reverse transcription-PCR analyses revealed that human MUC20 mRNA was expressed most highly in kidney and moderately in placenta, colon, lung, prostate, and liver. Immunohistochemical analysis of human kidney revealed that MUC20 protein was localized in the proximal tubules. Immunoblotting analysis of MUC20 proteins produced in Madin-Darby canine kidney and HEK293 cells indicated the localization of MUC20 protein in a membrane fraction and extensive posttranslational modification. Immunoelectron microscopy of MUC20-producing Madin-Darby canine kidney cells demonstrated that MUC20 protein was localized on the plasma membrane. Expression of MUC20 mRNA in a human kidney cell line was up-regulated by tumor necrosis factor-alpha, phorbol 12-myristate 13-acetate, or lipopolysaccharide. Two species of MUC20 mRNA (hMUC20-L and hMUC20-S), resulting from alternative transcription, were identified in human tissue, whereas only one variant was observed in mouse tissues. Mouse MUC20 mRNA was expressed in the epithelial cells of proximal tubules, and the expression increased dramatically with the progression of lupus nephritis in the kidney of MRL/MpJ-lpr/lpr mice. Moreover, the expression of mouse MUC20 was augmented in renal tissues acutely injured by cisplatin or unilateral ureteral obstruction. These characteristics suggest that the production of MUC20 is correlated with development and progression of IgAN and other renal injuries.
Supplementary Methods from Snap-jaw morphology is specialized for high-speed power amplification in the Dracula ant, Mystrium camillae.
Creators: name: Larabee, Fredrick J.
name: Smith, Adrian A.
name: Suarez, Andrew V.
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 110601 Biomechanics
subject: FOS: Health sciences
subject: 60801 Animal Behaviour

description: Detailed methods and data supporting the main text
Molecular Mapping of the Thrombin-Heparin Cofactor II Complex
Creators: name: Whinna, Herbert C.
name: Leung, Lawrence L.K.
name: Gentry, Holly R.
name: Myles, Timothy
name: Church, Frank C.
name: Fortenberry, Yolanda M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: We used 55 Ala-scanned recombinant thrombin molecules to define residues important for inhibition by the serine protease inhibitor (serpin) heparin cofactor II (HCII) in the absence and presence of glycosaminoglycans. We verified the importance of numerous basic residues in anion-binding exosite-1 (exosite-1) and found 4 additional residues, Gln24, Lys65, His66, and Tyr71 (using the thrombin numbering system), that were resistant to HCII inhibition with and without glycosaminoglycans. Inhibition rate constants for these exosite-1 (Q24A, K65A, H66A, Y71A) thrombin mutants (0.02-0.38 x 10(8) m(-1) min(-1) for HCII-heparin when compared with 2.36 x 10(8) m(-1) min(-1) with wild-type thrombin and 0.03-0.53 x 10(8) m(-1) min(-1) for HCII-dermatan sulfate when compared with 5.23 x 10(8) m(-1) min(-1) with wild-type thrombin) confirmed that the structural integrity of thrombin exosite-1 is critical for optimal HCII-thrombin interactions in the presence of glycosaminoglycans. However, our results are also consistent for HCII-glycosaminoglycan-thrombin ternary complex formation. Ten residues surrounding the active site of thrombin were implicated in HCII interactions. Four mutants (Asp51, Lys52, Lys145/Thr147/Trp148, Asp234) showed normal increased rates of inhibition by HCII-glycosaminoglycans, whereas four mutants (Trp50, Glu202, Glu229, Arg233) remained resistant to inhibition by HCII with glycosaminoglycans. Using 11 exosite-2 thrombin mutants with 20 different mutated residues, we saw no major perturbations of HCII-glycosaminoglycan inhibition reactions. Collectively, our results support a "double bridge" mechanism for HCII inhibition of thrombin in the presence of glycosaminoglycans, which relies in part on ternary complex formation but is primarily dominated by an allosteric process involving contact of the "hirudin-like" domain of HCII with thrombin exosite-1.
View FImP Miracle (by Scale Invariance) $\acute{\rm a}$ $\rm la$ Self-interaction
Creators: name: Kang, Zhaofeng
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Combining feebly interacting massive particle (FIMP) dark matter (DM) with scale invariance (SI) leads to extremely light FIMP (thus the FImP) with FImP miracle, i.e., the mass and relic generations of FImP DM share the same dynamics. In this paper we show that due to the lightness of FImP, it, especially for a scalar FImP, can easily accommodate large DM self-interaction. For a fermionic FImP, such as the sterile neutrino, self-interaction additionally requires a mediator which is another FImP, a scalar boson with mass either much lighter or heavier than the FImP DM. DM self-interaction opens a new window to observe FImP (miracle), which does not leave traces in the conventional DM searches. As an example, FImP can account for the offsets between the centroid of DM halo and stars of galaxies recently observed in the galaxy cluster Abel 3827.
description: references updated; 9 pages no figures
Single Spin Optically Detected Magnetic Resonance with E-Band Microwave Resonators
Creators: name: Aslam, Nabeel
name: Pfender, Matthias
name: Stöhr, Rainer
name: Neumann, Philipp
name: Scheffler, Marc
name: Sumiya, Hitoshi
name: Abe, Hiroshi
name: Onoda, Shinobu
name: Ohshima, Takeshi
name: Isoya, Junichi
name: Wrachtrup, Jörg
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Magnetic resonance with ensembles of electron spins is nowadays performed in frequency ranges up to 240 GHz and in corresponding magnetic fields of up to 10 T. However, experiments with single electron and nuclear spins so far only reach into frequency ranges of several 10 GHz, where existing coplanar waveguide structures for microwave (MW) delivery are compatible with single spin readout techniques (e.g. electrical or optical readout). Here, we explore the frequency range up to 90 GHz, respectively magnetic fields of up to $\approx 3\,$T for single spin magnetic resonance in conjunction with optical spin readout. To this end, we develop MW resonators with optical single spin access. In our case, rectangular E-band waveguides guarantee low-loss supply of microwaves to the resonators. Three dimensional cavities, as well as coplanar waveguide resonators enhance MW fields by spatial and spectral confinement with a MW efficiency of $1.36\,\mathrm{mT/\sqrt{W}}$. We utilize single NV centers as hosts for optically accessible spins, and show, that their properties regarding optical spin readout known from smaller fields (<0.65 T) are retained up to fields of 3 T. In addition, we demonstrate coherent control of single nuclear spins under these conditions. Furthermore, our results extend the applicable magnetic field range of a single spin magnetic field sensor. Regarding spin based quantum registers, high fields lead to a purer product basis of electron and nuclear spins, which promises improved spin lifetimes. For example, during continuous single-shot readout the $^{14}$N nuclear spin shows second-long longitudinal relaxation times.
description: 7 pages, 4 figures
Computing maximal autarkies with few and simple oracle queries
Creators: name: Kullmann, Oliver
name: Marques-Silva, Joao
Publisher: name: arXiv
Year: 2015
Subjects: subject: Logic in Computer Science (cs.LO)
subject: Discrete Mathematics (cs.DM)
subject: Data Structures and Algorithms (cs.DS)
subject: FOS: Computer and information sciences
subject: F.2.2; G.2.1
subject: 68R99 (Primary) 03B05, 05D99 (Secondary)

description: We consider the algorithmic task of computing a maximal autarky for a clause-set F, i.e., a partial assignment which satisfies every clause of F it touches, and where this property is destroyed by adding any non-empty set of further assignments. We employ SAT solvers as oracles, using various capabilities. Using the standard SAT oracle, log_2(n(F)) oracle calls suffice, where n(F) is the number of variables, but the drawback is that (translated) cardinality constraints are employed, which makes this approach less efficient in practice. Using an extended SAT oracle, motivated by the capabilities of modern SAT solvers, we show how to compute maximal autarkies with 2 n(F)^{1/2} simpler oracle calls. This novel algorithm combines the previous two main approaches, based on the autarky-resolution duality and on SAT translations.
description: 18 pages; second version with editorial changes, to appear in LNCS for Theory and Applications of Satisfiability Testing - SAT 2015
NMR Solution Structure of the Focal Adhesion Targeting Domain of Focal Adhesion Kinase in Complex with a Paxillin LD Peptide: EVIDENCE FOR A TWO-SITE BINDING MODEL
Creators: name: London, Robert E.
name: Gao, Guanghua
name: DeRose, Eugene F.
name: Campbell, Sharon L.
name: Schaller, Michael D.
name: Scheswohl, Danielle M.
name: Prutzman, Kirk C.
name: King, Michelle L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase that is regulated by integrins. Upon activation, FAK generates signals that modulate crucial cell functions, including cell proliferation, migration, and survival. The C-terminal focal adhesion targeting (FAT) sequence mediates localization of FAK to discrete regions in the cell called focal adhesions. Several binding partners for the FAT domain of FAK have been identified, including paxillin. We have determined the solution structure of the avian FAT domain in complex with a peptide mimicking the LD2 motif of paxillin by NMR spectroscopy. The FAT domain retains a similar fold to that found in the unliganded form when complexed to the paxillin-derived LD2 peptide, an antiparallel four-helix bundle. However, noticeable conformational changes were observed upon the LD2 peptide binding, especially the position of helix 4. Multiple lines of evidence, including the results obtained from isothermal titration calorimetry, intermolecular nuclear Overhauser effects, mutagenesis, and protection from paramagnetic line broadening, support the existence of two distinct paxillin-binding sites on the opposite faces of the FAT domain. The structure of the FAT domain-LD2 complex was modeled using the program HADDOCK based on our solution structure of the LD2-bound FAT domain and mutagenesis data. Our model of the FAT domain-LD2 complex provides insight into the molecular basis of FAK-paxillin binding interactions, which will aid in understanding the role of paxillin in FAK targeting and signaling.
Non-homologous End Joining Requires That the DNA-PK Complex Undergo an Autophosphorylation-dependent Rearrangement at DNA Ends
Creators: name: Lees-Miller, Susan P.
name: Ramsden, Dale A.
name: Ding, Qi
name: Meek, Katheryn
name: Reddy, Yeturu V.R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Repair of chromosome breaks by non-homologous end joining requires the XRCC4-ligase IV complex, Ku, and the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). DNA-PKcs must also retain kinase activity and undergo autophosphorylation at six closely linked sites (ABCDE sites). We describe here an end-joining assay using only purified components that reflects cellular requirements for both Ku and kinase-active DNA-PKcs and investigate the mechanistic basis for these requirements. A need for DNA-PKcs autophosphorylation is sufficient to explain the requirement for kinase activity, in part because autophosphorylation is generally required for end-joining factors to access DNA ends. However, DNA-PKcs with all six ABCDE autophosphorylation sites mutated to alanine allows access to ends through autophosphorylation of other sites, yet our in vitro end-joining assay still reflects the defectiveness of this mutant in cellular end joining. In contrast, mutation of ABCDE sites to aspartate, a phosphorylation mimic, supports high levels of end joining that is now independent of kinase activity. This is likely because DNA-PKcs with aspartate substitutions at ABCDE sites allow access to DNA ends while retaining affinity for Ku-bound ends and stabilizing recruitment of the XRCC4-ligase IV complex. Autophosphorylation at ABCDE sites thus apparently directs a rearrangement of the DNA-PK complex that ensures access to broken ends and joining steps are coupled together within a synaptic complex, making repair more accurate.
NFFA-Europe Pilot - D15.2 - Image Registration Procedures
Creators: name: Dwivedi, Jagrati
name: Van Malderen, Stijn
name: Vidar Falch, Ken
name: Garrevoet, Jan
name: Keller, Thomas F.
Publisher: name: Zenodo
Year: 2022

description: Image registration procedure for correlative Nano-Spectroscopy and Nano-Diffraction experiments. Detailed description of the python-based GUI script and validation using different modalities of microscopic imaging. Automated identification of isolated nanoparticles for analysis at selected nano-lab instruments and focused X-ray beamlines.
description: WP15 - Correlative Nano-Spectroscopy and Nano-Diffraction
Overexpression of Collagenase 1 (MMP-1) Is Mediated by the ERK Pathway in Invasive Melanoma Cells: ROLE OFBRAFMUTATION AND FIBROBLAST GROWTH FACTOR SIGNALING
Creators: name: Benbow, Ulrike
name: Shields, Janiel M.
name: Wyatt, Colby A.
name: Slingluff Jr., Craig L.
name: Brinckerhoff, Constance E.
name: Der, Channing J.
name: Huntington, Jonathan T.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Melanoma progresses as a multistep process where the thickness of the lesion and depth of tumor invasion are the best prognostic indicators of clinical outcome. Degradation of the interstitial collagens in the extracellular matrix is an integral component of tumor invasion and metastasis, and much of this degradation is mediated by collagenase-1 (MMP-1), a member of the matrix metalloproteinase (MMP) family. MMP-1 levels increase during melanoma progression where they are associated with shorter disease-free survival. The Ras/Raf/MEK/ERK mitogen-activated protein kinase (MAPK) pathway is a major regulator of melanoma cell proliferation. Recently, BRAF has been identified as a common site of activating mutations, and, although many reports focus on its growth-promoting effects, this pathway has also been implicated in progression toward metastatic disease. In this study, we describe four melanoma cell lines that produce high levels of MMP-1 constitutively. In each cell line the Ras/Raf/MEK/ERK pathway is constitutively active and is the dominant pathway driving the production of MMP-1. Activation of this pathway arises due to either an activating mutation in BRAF (three cell lines) or autocrine fibroblast growth factor signaling (one cell line). Furthermore, blocking MEK/ERK activity inhibits melanoma cell proliferation and abrogates collagen degradation, thus decreasing their metastatic potential. Importantly, this inhibition of invasive behavior can occur in the absence of any detectable changes in cell proliferation and survival. Thus, constitutive activation of this MAPK pathway not only promotes the increased proliferation of melanoma cells but is also important for the acquisition of an invasive phenotype.
(1685) Edward G Ramsbottom
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
p68RacGAP Is a Novel GTPase-activating Protein That Interacts with Vascular Endothelial Zinc Finger-1 and Modulates Endothelial Cell Capillary Formation
Creators: name: Wennerberg, Krister
name: Kedar, Vishram
name: Aitsebaomo, Julius
name: Der, Channing J.
name: Moser, Martin
name: Patterson, Cam
name: Zhang, Chunlian
name: Zeng, Guo Qing
name: Kingsley-Kallesen, Michelle L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: The endothelium is required for maintenance of vascular integrity and homeostasis during vascular development and in adulthood. However, little is known about the coordinated interplay between transcription factors and signaling molecules that regulate endothelial cell-dependent transcriptional events. Vascular endothelial zinc finger-1 (Vezf1) is a zinc finger-containing transcription factor that is specifically expressed within the endothelium during vascular development. We have previously shown that Vezf1 potently activates transcription of the endothelin-1 promoter. We now report the identification of p68RacGAP, a novel Vezf1-interacting 68-kDa RhoGAP domain-containing protein. p68RacGAP mRNA is highly expressed in vascular endothelial cells by Northern blot analysis, and immunohistochemical staining of adult mouse tissues identified p68RacGAP in endothelial cells, vascular smooth muscle cells, and epithelial cells in vivo. Rac1 and Vezf1 both bind avidly to p68RacGAP, suggesting that p68RacGAP is not only a GTPase-activating protein for Rac1 but that p68RacGAP may also be part of the protein complex that binds to and modulates Vezf1 transcriptional activity. Functionally p68RacGAP specifically activates the GTPase activity of Rac1 in vivo but not Cdc42 or RhoA. In addition, p68RacGAP potently inhibits Vezf1/DB1-mediated transcriptional activation of the human endothelin-1 promoter and modulates endothelial cell capillary tube formation. Taken together, these data suggest that p68RacGAP is a multifunctional regulatory protein that has a Rac1-specific GTPase-activating activity, regulates transcriptional activity of the endothelin-1 promoter, and is involved in the signal transduction pathway that regulates endothelial cell capillary tube formation during angiogenesis.
Peroxisome Proliferator-activated Receptor γ Induces a Phenotypic Switch from Activated to Quiescent Hepatic Stellate Cells
Creators: name: Wang, Jiaohong
name: Rippe, Richard A.
name: Hazra, Saswati
name: Chatterjee, V. Krishna K.
name: Xiong, Shigang
name: Tsukamoto, Hidekazu
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Depletion of peroxisome proliferator-activated receptor gamma (PPARgamma) accompanies myofibroblastic transdifferentiation of hepatic stellate cells (HSC), the primary cellular event underlying liver fibrogenesis. The treatment of activated HSC in vitro or in vivo with synthetic PPARgamma ligands suppresses the fibrogenic activity of HSC. However, it is uncertain whether PPARgamma is indeed a molecular target of this effect, because the ligands are also known to have receptor-independent actions. To test this question, the present study examined the effects of forced expression of PPARgamma via an adenoviral vector on morphologic and biochemical features of culture-activated HSC. The vector-mediated expression of PPARgamma itself is sufficient to reverse the morphology of activated HSC to the quiescent phenotype with retracted cytoplasm, prominent dendritic processes, reduced stress fibers, and accumulation of retinyl palmitate. These effects are abrogated by concomitant expression of a dominant negative mutant of PPARgamma that prevents transactivation of but not binding to the PPAR response element. PPARgamma expression also inhibits the activation markers such as the expression of alpha-smooth muscle actin, type I collagen, and transforming growth factor beta1; DNA synthesis; and JunD binding to the activator protein-1 (AP-1) site and AP-1 promoter activity. Inhibited JunD activity by PPARgamma is not due to reduced JunD expression or JNK activity or to a competition for p300. But it is due to a JunD-PPARgamma interaction as demonstrated by co-immunoprecipitation and glutathione S-transferase pull-down analysis. Further, the use of deletion constructs reveals that the DNA binding region of PPARgamma is the JunD interaction domain. In summary, our results demonstrate that the restoration of PPARgamma reverses the activated HSC to the quiescent phenotype and suppresses AP-1 activity via a physical interaction between PPARgamma and JunD.
Processing and Transport of Matrix γ-Carboxyglutamic Acid Protein and Bone Morphogenetic Protein-2 in Cultured Human Vascular Smooth Muscle Cells: EVIDENCE FOR AN UPTAKE MECHANISM FOR SERUM FETUIN
Creators: name: Wajih, Nadeem
name: Hutson, Susan M.
name: Wallin, Reidar
name: Borras, Terete
name: Xue, Wei
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Matrix gamma-carboxyglutamic acid protein (MGP) is a member of the vitamin K-dependent protein family with unique structural and physical properties. MGP has been shown to be an inhibitor of arterial wall and cartilage calcification. One inhibitory mechanism is thought to be binding of bone morphogenetic protein-2. Binding has been shown to be dependent upon the vitamin K-dependent gamma-carboxylation modification of MGP. Since MGP is an insoluble matrix protein, this work has focused on intracellular processing and transport of MGP to become an extracellular binding protein for bone morphogenetic protein-2. Human vascular smooth muscle cells (VSMCs) were infected with an adenovirus carrying the MGP construct, which produced non-gamma-carboxylated MGP and fully gamma-carboxylated MGP. Both forms of MGP were found in the cytosolic and microsomal fractions obtained from the cells by differential centrifugation. The crude microsomal fraction was shown to contain an additional, more acidic Ser-phosphorylated form of MGP believed to be the product of Golgi casein kinase. The data suggest that phosphorylation of MGP dictates different transport routes for MGP in VSMCs. A proteomic approach failed to identify a larger soluble precursor of MGP or an intracellular carrier protein for MGP. Evidence is presented for a receptor-mediated uptake mechanism for fetuin by cultured human VSMCs. Fetuin, shown by mass spectrometry not to contain MGP, was found to be recognized by anti-MGP antibodies. Fetuin uptake and secretion by proliferating and differentiating cells at sites of calcification in the arterial wall may represent an additional protective mechanism against arterial calcification.
Rat Long Chain Acyl-CoA Synthetase 5, but Not 1, 2, 3, or 4, Complements Escherichia coli fadD
Creators: name: Li, Lei O.
name: Caviglia, Jorge M.
name: Coleman, Rosalind A.
name: Wang, Shuli
name: Lewin, Tal M.
name: DiRusso, Concetta C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2004

description: Long chain fatty acids are converted to acyl-CoAs by acyl-CoA synthetase (fatty acid CoA ligase: AMP forming, E.C. 6.2.1.3; ACS). Escherichia coli has a single ACS, FadD, that is essential for growth when fatty acids are the sole carbon and energy source. Rodents have five ACS isoforms that differ in substrate specificity, tissue expression, and subcellular localization and are believed to channel fatty acids toward distinct metabolic pathways. We expressed rat ACS isoforms 1-5 in an E. coli strain that lacked FadD. All rat ACS isoforms were expressed in E. coli fadD or fadDfadR and had ACS specific activities that were 1.6-20-fold higher than the wild type control strain expressing FadD. In the fadD background, the rat ACS isoforms 1, 2, 3, 4 and 5 oxidized [(14)C]oleate at 5 to 25% of the wild type levels, but only ACS5 restored growth on oleate as the sole carbon source. To ensure that enzymes of beta-oxidation were not limiting, assays of ACS activity, beta-oxidation, fatty acid transport, and phospholipid synthesis were also examined in a fadD fadR strain, thereby eliminating FadR repression of the transporter FadL and the enzymes of beta-oxidation. In this strain, fatty acid transport levels were low but detectable for ACS1, 2, 3, and 4 and were nearly 50% of wild type levels for ACS5. Despite increases in beta-oxidation, only ACS5 transformants were able to grow on oleate. These studies show that although ACS isoforms 1-4 variably supported moderate transport activity, beta-oxidation, and phospholipid synthesis and although their in vitro specific activities were greater than that of chromosomally encoded FadD, they were unable to substitute functionally for FadD regarding growth. Thus, membrane composition and protein-protein interactions may be critical in reconstituting bacterial ACS function.
Condensate formation in a zero-range process with random site capacities
Creators: name: Gupta, Shamik
name: Barma, Mustansir
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We study the effect of quenched disorder on the zero-range process (ZRP), a system of interacting particles undergoing biased hopping on a one-dimensional periodic lattice, with the disorder entering through random capacities of sites. In the usual ZRP, sites can accommodate an arbitrary number of particles, and for a class of hopping rates and high enough density, the steady state exhibits a condensate which holds a finite fraction of the total number of particles. The sites of the disordered zero-range process considered here have finite capacities chosen randomly from the Pareto distribution. From the exact steady state measure of the model, we identify the conditions for condensate formation, in terms of parameters that involve both interactions (through the hop rates) and randomness (through the distribution of the site capacities). Our predictions are supported by results obtained from a direct numerical sampling of the steady state and from Monte Carlo simulations. Our study reveals that for a given realization of disorder, the condensate can relocate on the subset of sites with largest capacities. We also study sample-to-sample variation of the critical density required to observe condensation, and show that the corresponding distribution obeys scaling, and has a Gaussian or a Levy-stable form depending on the values of the relevant parameters.
description: Contribution to the JStatMech Special Issue dedicated to the Galileo Galilei Institute, Florence Workshop "Advances in nonequilibrium statistical mechanics",v2: close to the published version