cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Generalized Spatial Modulation in Large-Scale Multiuser MIMO Systems
Creators: name: Narasimhan, T. Lakshmi
name: Raviteja, P.
name: Chockalingam, A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Information Theory (cs.IT)
subject: FOS: Computer and information sciences

description: Generalized spatial modulation (GSM) uses $n_t$ transmit antenna elements but fewer transmit radio frequency (RF) chains, $n_{rf}$. Spatial modulation (SM) and spatial multiplexing are special cases of GSM with $n_{rf}=1$ and $n_{rf}=n_t$, respectively. In GSM, in addition to conveying information bits through $n_{rf}$ conventional modulation symbols (for example, QAM), the indices of the $n_{rf}$ active transmit antennas also convey information bits. In this paper, we investigate {\em GSM for large-scale multiuser MIMO communications on the uplink}. Our contributions in this paper include: ($i$) an average bit error probability (ABEP) analysis for maximum-likelihood detection in multiuser GSM-MIMO on the uplink, where we derive an upper bound on the ABEP, and ($ii$) low-complexity algorithms for GSM-MIMO signal detection and channel estimation at the base station receiver based on message passing. The analytical upper bounds on the ABEP are found to be tight at moderate to high signal-to-noise ratios (SNR). The proposed receiver algorithms are found to scale very well in complexity while achieving near-optimal performance in large dimensions. Simulation results show that, for the same spectral efficiency, multiuser GSM-MIMO can outperform multiuser SM-MIMO as well as conventional multiuser MIMO, by about 2 to 9 dB at a bit error rate of $10^{-3}$. Such SNR gains in GSM-MIMO compared to SM-MIMO and conventional MIMO can be attributed to the fact that, because of a larger number of spatial index bits, GSM-MIMO can use a lower-order QAM alphabet which is more power efficient.
description: IEEE Trans. on Wireless Communications, accepted
BRCA1 Regulates the Interferon γ-mediated Apoptotic Response
Creators: name: Haber, Daniel A.
name: Quinn, Jennifer E.
name: Paul Harkin, D.
name: Pace, Amy
name: Andrews, Heather N.
name: Koller, Beverly
name: Mullan, Paul B.
name: Johnston, Patrick G.
name: McWilliams, Stewart
name: Sebelova, Sarka
name: Gilmore, Paula M.
name: McCabe, Nuala
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: BRCA1 is a tumor suppressor gene implicated in transcriptional regulation. We have generated cell lines with inducible expression of BRCA1 as a tool to identify downstream targets that may be important mediators of BRCA1 function. Oligonucleotide array-based expression profiling identified 11 previously described interferon regulated genes that were up-regulated following inducible expression of BRCA1. Northern blot analysis revealed that a subset of the identified targets including IRF-7, MxA, and ISG-54 were synergistically up-regulated by BRCA1 in the presence of interferon gamma (IFN-gamma) but not interferons alpha or beta. Importantly, IFN-gamma-mediated induction of IRF-7 and MxA was attenuated in the BRCA1 mutant cell line HCC1937, an effect that was rescued following reconstitution of exogenous wild type BRCA1 in these cells. Furthermore, reconstituted BRCA1 sensitized HCC1937 cells to IFN-gamma-induced apoptotic cell death. This study identifies BRCA1 as a component of the IFN-gamma-regulated signaling pathway and suggests that BRCA1 may play a role in the regulation of IFN-gamma-mediated apoptosis.
(1762) Charlotte Anglin Scarlett
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.
Supplementary Data from Herbarium specimens reveal substantial and unexpected variation in phenological sensitivity across the eastern United States
Creators: name: Park, Daniel S.
name: Breckheimer, Ian
name: Williams, Alex C.
name: Law, Edith
name: Ellison, Aaron M.
name: Davis, Charles C.
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: 60301 Animal Systematics and Taxonomy
subject: 60310 Plant Systematics and Taxonomy

description: Tables S2 - S4; Figures S1 - S3
On multiple zeta values of extremal height
Creators: name: Kaneko, Masanobu
name: Sakata, Mika
Publisher: name: arXiv
Year: 2015
Subjects: subject: Number Theory (math.NT)
subject: FOS: Mathematics

description: We give three identities involving multiple zeta values of height one and of maximal height; an explicit formula for the height-one multiple zeta values, a regularized sum formula, and a sum formula for the multiple zeta values of maximal height.
description: 8 pages
(1763) Robert Lawrence Scarlett
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.
title: Journal of Urban Mathematics Education, Vol 13 No 1B (2020): Special Issue - Addressing Racial Inequality
title: Special Issue - Addressing Racial Inequality
titleType: AlternativeTitle
Creators: name: Journal Of Urban Mathematics Education
Publisher: name: Journal of Urban Mathematics Education
Year: 2020

description: This special issue is a response from the Editorial Board. Our purpose is to spark ideas and and foster thoughtful discussion. Both of articles are reprinted with permisison from the copyright holders.
description: When One Lacks Will, They Denounce . . ....1–4 Black Lives Matter in Teaching Mathematics for Social Justice...5–11 Mathematics Literacy, Identity Resilience, and Opportunity Sixty Years Since Brown v. Board...12–37
Cellular Response to an Antisense-mediated Shift of Bcl-x Pre-mRNA Splicing and Antineoplastic Agents
Creators: name: Mercatante, Danielle R.
name: Kole, Ryszard
name: Mohler, James L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: Overexpression of Bcl-xL, an anti-apoptotic member of the Bcl-2 family, negatively correlates with the sensitivity of various cancers to chemotherapeutic agents. We show here that high levels of expression of Bcl-xL promoted apoptosis of cells treated with an antisense oligonucleotide (5'Bcl-x AS) that shifts the splicing pattern of Bcl-x pre-mRNA from the anti-apoptotic variant, Bcl-xL, to the pro-apoptotic variant, Bcl-xS. This surprising finding illustrates the advantage of antisense-induced modulation of alternative splicing versus down-regulation of targeted genes. It also suggests a specificity of the oligonucleotide effects since non-cancerous cells with low levels of Bcl-xL should resist the treatment. 5'Bcl-x AS sensitized cells to several antineoplastic agents and radiation and was effective in promoting apoptosis of MCF-7/ADR cells, a breast cancer cell line resistant to doxorubicin via overexpression of the mdr1 gene. Efficacy of 5'Bcl-x AS combined with chemotherapeutic agents in the PC3 prostate cancer cell line may be translated to clinical prostate cancer since recurrent prostate cancer tissue samples expressed higher levels of Bcl-xL than benign prostate tissue. Treatment with 5'Bcl-x AS may enhance the efficacy of standard anti-cancer regimens and should be explored, especially in recurrent prostate cancer.
Supplementary information from Drivers of spatio-temporal patterns of salinity in Spanish rivers: a nationwide assessment.
Creators: name: Estévez, Edurne
name: Rodríguez-Castillo, Tamara
name: González-Ferreras, Alexia María
name: Cañedo-Argüelles, Miguel
name: Barquín, José
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Environmental Science
subject: Ecology
subject: FOS: Biological sciences

description: S1. Environmental variables calculated to explain spatial patterns of salinity.
Active optical frequency standards using cold atoms: perspectives and challenges
Creators: name: Kazakov, Georgy A.
name: Schumm, Thorsten
Publisher: name: arXiv
Year: 2015
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: Optics (physics.optics)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We consider various approaches to the creation of a high-stability active optical frequency standard, where the atomic ensemble itself produces a highly stable and accurate frequency signal. The short-time frequency stability of such standards may overcome the stability of lasers stabilized to macroscopic cavities which are used as local oscillators in the modern optical frequency standard systems. The main idea is to create a "superradiant" laser operating deep in the bad cavity regime, where the decay rate of the cavity field significantly exceeds the decoherence rate of the lasing transition. Two main approaches towards the realization of an active optical frequency standard have been proposed already: the optical lattice laser, and the atomic beam laser. We consider these and some alternative approaches, and discuss the parameters for atomic ensembles necessary to attain the metrology relevant level of short-time frequency stability, and various effects and main challenges critical for practical implementations.
description: 5 pages, 5 figures
Figure S2 from Drivers of spatio-temporal patterns of salinity in Spanish rivers: a nationwide assessment.
Creators: name: Estévez, Edurne
name: Rodríguez-Castillo, Tamara
name: González-Ferreras, Alexia María
name: Cañedo-Argüelles, Miguel
name: Barquín, José
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Environmental Science
subject: Ecology
subject: FOS: Biological sciences

description: Observed versus predicted conductivity values for training (a) and testing (b) sets in the spatial Random Forest model.
Entanglement like properties in Spin-Orbit Coupled Ultra Cold Atom and violation of Bell like Inequality
Creators: name: Kumar, Rahul
name: Ghosh, Sankalpa
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We show that the general quantum state of synthetically spin-orbit coupled ultra cold bosonic atom whose condensate was experimentally created recently ( Y. J. Lin {\it et al.}, Nature, {\bf 471}, 83, (2011)), shows entanglement between motional degrees of freedom ( momentum) and internal degrees of freedom (hyperfine spin). We demonstrate the violation of Bell-like inequality (CHSH) for such states that provides a unique opportunity to verify fundamental principle like quantum non-contextuality for commutating observables which are not spatially separated. We analyze in detail the Rabi oscillation executed by such atom-laser system and how that influneces quantities like entanglement entropy, violation of Bell like Inequality etc. We also discuss the implication of our result in testing the quantum non-contextuality and Bell's Inequality vioaltion by macroscopic quantum object like Bose-Einstein Condensate of ultra cold atoms.
description: Latex file with 4 pdf figures
Mathematics Literacy, Identity Resilience, and Opportunity Sixty Years Since Brown v. Board
Creators: name: Leonard, Jacqueline
name: Walker, Erica N.
name: Bloom, Victoria R.
name: Joseph, Nicole M.
Publisher: name: Journal of Urban Mathematics Education
Year: 2020

description: In this chapter, the authors use Black Feminist Thought (BFT) to examine the mathematics education and the educational attainment of African American females in a matrilineal line that spans five generations. A cross analysis of school experiences, from a maternal great-great-grandmother to her great-great-granddaughter, reveal a portrait of segregation, desegregation, and resegregation. The impact of these educational contexts on the mathematics literacy and mathematics identity of four African American women and the hope and promise of a young girl in the class of 2026 are also presented. From sharecropper schools in Mississippi to prestigious universities in the eastern United States, the challenges and successes of one family’s struggle to obtain mathematics literacy and the American dream are discussed through the historical lens of Brown v. Board of Education. Using this historical context, the specific experiences of these five family members encourage a dialogue about a larger narrative—the mathematics attainment of all Black children.
description: Journal of Urban Mathematics Education, Vol 13 No 1B (2020): Special Issue - Addressing Racial Inequality
(1765) Thomas Rowland Scarlett
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.
Black Lives Matter in Teaching Mathematics for Social Justice
Creators: name: Leonard, Jacqueline
Publisher: name: Journal of Urban Mathematics Education
Year: 2020

description: Prior to becoming a mathematics educator, I was a teacher in Prince George’s County, Maryland. Because of the success I experienced with culturally relevant pedagogy (CRP), it became part of my research agenda along with teaching mathematics for social justice (TMfSJ). Databases like 23andme and Ancestry can be used as a context for CRP and TMfSJ. Data related to education, occupation, military service, and voting records can be accessed online. Our ancestors’ experiences can shape our identity and serve as powerful tools for contextualizing mathematics. The stories and counterstories of African Americans can be problematized to show Black lives matter.
description: Journal of Urban Mathematics Education, Vol 13 No 1B (2020): Special Issue - Addressing Racial Inequality
Characterization of a Heparan Sulfate Octasaccharide That Binds to Herpes Simplex Virus Type 1 Glycoprotein D
Creators: name: Raska, Christina S.
name: Linhardt, Robert J.
name: Marshall Pope, R.
name: Eisenberg, Roselyn J.
name: Liu, Jian
name: Sasisekharan, Ram
name: Shriver, Zach
name: Yoshida, Keiichi
name: Copeland, Ronald J.
name: Thorp, Suzanne C.
name: Cohen, Gary
name: Duncan, Michael B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: Herpes simplex virus type 1 utilizes cell surface heparan sulfate as receptors to infect target cells. The unique heparan sulfate saccharide sequence offers the binding site for viral envelope proteins and plays critical roles in assisting viral infections. A specific 3-O-sulfated heparan sulfate is known to facilitate the entry of herpes simplex virus 1 into cells. The 3-O-sulfated heparan sulfate is generated by the heparan sulfate d-glucosaminyl-3-O-sulfotransferase isoform 3 (3-OST-3), and it provides binding sites for viral glycoprotein D (gD). Here, we report the purification and structural characterization of an oligosaccharide that binds to gD. The isolated gD-binding site is an octasaccharide, and has a binding affinity to gD around 18 microm, as determined by affinity coelectrophoresis. The octasaccharide was prepared and purified from a heparan sulfate oligosaccharide library that was modified by purified 3-OST-3 enzyme. The molecular mass of the isolated octasaccharide was determined using both nanoelectrospray ionization mass spectrometry and matrix-assisted laser desorption/ionization mass spectrometry. The results from the sequence analysis suggest that the structure of the octasaccharide is a heptasulfated octasaccharide. The proposed structure of the octasaccharide is DeltaUA-GlcNS-IdoUA2S-GlcNAc-UA2S-GlcNS-IdoUA2S-GlcNH(2)3S6S. Given that the binding of 3-O-sulfated heparan sulfate to gD can mediate viral entry, our results provide structural information about heparan sulfate-assisted viral entry.
Harrington's principle over higher order arithmetic
Creators: name: Cheng, Yong
name: Schindler, Ralf
Publisher: name: arXiv
Year: 2015
Subjects: subject: Logic (math.LO)
subject: FOS: Mathematics

description: Let $Z_2$, $Z_3$, and $Z_4$ denote $2^{\rm nd}$, $3^{\rm rd}$, and $4^{\rm th}$ order arithmetic, respectively. We let Harrington's Principle, {\sf HP}, denote the statement that there is a real $x$ such that every $x$--admissible ordinal is a cardinal in $L$. The known proofs of Harrington's theorem "$Det(Σ_1^1)$ implies $0^{\sharp}$ exists" are done in two steps: first show that $Det(Σ_1^1)$ implies {\sf HP}, and then show that {\sf HP} implies $0^{\sharp}$ exists. The first step is provable in $Z_2$. In this paper we show that $Z_2 \, + \, {\sf HP}$ is equiconsistent with ${\sf ZFC}$ and that $Z_3\, + \, {\sf HP}$ is equiconsistent with ${\sf ZFC} \, +$ there exists a remarkable cardinal. As a corollary, $Z_3\, + \, {\sf HP}$ does not imply $0^{\sharp}$ exists, whereas $Z_4\, + \, {\sf HP}$ does. We also study strengthenings of Harrington's Principle over $2^{\rm nd}$ and $3^{\rm rd}$ order arithmetic.
description: 13 pages, to appear in JSL Volume 80,Issue 2 (June 2015)
When One Lacks Will, They Denounce . . .
Creators: name: Capraro, Robert M.
name: Chang, Jonas
Publisher: name: Journal of Urban Mathematics Education
Year: 2020

description: Robert M. Capraro, the editor-in-cheif of the Journal of Urban Mathematics Education, and Jonas Chang, copyeditor for JUME, introduce this special issue of the journal. Through discussion of the events that prompted the Black Lives Matter protests of Summer 2020 and the responses of several national organizations and corporations, they argues that the journal and its members must do more than simply denounce systemic racism and violence; math educators must additionally use their privelage and influence to support the message of the protests and consider in what ways they can more effectively support the mathematics achievement, considered a powerful equalizer of society, of Black and Brown children.
description: Journal of Urban Mathematics Education, Vol 13 No 1B (2020): Special Issue - Addressing Racial Inequality
D1.9 Agricultural Research Data Index Tool (ARDIT)
Creators: name: Ayesa
name: Idener
name: University Of Parma
Publisher: name: Zenodo
Year: 2022
Subjects: AGRICORE H2020

description: The Agricultural Research Data Index Tool (ARDIT) is a platform created in the framework of the AGRICORE Project to index characterisations of datasets that can be used for the analysis and research of the agri-food chain. These characterisations of datasets (or dataset catalogues) can be incorporated by registered users through web-based forms built on the basis of the AGRICORE-DCAT 2.0 ontology, which allows characterisation down to the level of the variables contained in each dataset. The aim of this document is to explain what ARDIT is, how it has been constructed, how it works and its importance within the AGRICORE project. For this purpose, a detailed description of its architecture is provided together with annexes that include user manuals for operating the platform and characterising agricultural datasets. This document is organised as follows: The introduction section presents how ARDIT fits into the AGRICORE suite and its data flow in combination with the data warehouse. The second section outlines the requirements (functional and nonfunctional) defined for the ARDIT tool. The third section presents the architecture of the tool, distinguishing the front-end from the back-end. It also introduces the format of the different requests including the built-in security configuration. The fourth section shows the development process of the tool, including its links with the development of the underlying AGRICORE-DCAT 2.0 ontology, as well as decisions related to the graphical interface and workflow. The fifth section presents the plan for the future governance of the tool, comprising both the IT maintenance part and the editing and enhancement of existing characterisations and those that may be added in the future. The sixth section summarises the conclusions of the document.
Critical Role of the Pleckstrin Homology and Cysteine-rich Domains in Vav Signaling and Transforming Activity
Creators: name: Der, Channing J.
name: Palmby, Todd R.
name: Abe, Karon
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: Vav family proteins are members of the Dbl family of guanine nucleotide exchange factors and activators of Rho family small GTPases. In addition to the Dbl homology (DH) domain important for guanine nucleotide exchange factor catalytic function, all Dbl family proteins contain an adjacent pleckstrin homology (PH) domain that serves to regulate DH domain activity. Although the role of the PH domain in Vav function has been evaluated extensively, its precise role and whether it serves a distinct role in different Vav proteins remain unresolved. Additionally, the precise role of an adjacent cysteine-rich domain (CRD) in regulating DH domain function is also unclear. In this study, we evaluated the contribution of these putative protein-protein or protein-lipid interaction domains to Vav signaling and transforming activity. In contrast to previous observations, we found that the PH domain is critical for Vav transforming activity. Similarly, the CRD was also essential and served a function distinct from that of the PH domain. Although mutation of either domain reduced Vav membrane association, addition of plasma membrane targeting sequences to either the CRD or PH domain mutant proteins did not restore Vav transforming activity. This result contrasts with other Dbl family proteins, where a membrane targeting sequence alone was sufficient to restore the loss of function caused by mutation of the PH domain. Furthermore, green fluorescent protein fusion proteins containing the PH domain or CRD, or both, failed to target to the plasma membrane, suggesting that these two domains also serve regulatory functions independent of promoting membrane localization. Finally, we found that phosphatidylinositol 3-kinase activation may promote Vav membrane association via phosphatidylinositol 3,4,5-triphosphate binding to the PH domain.
Figure S1 from Drivers of spatio-temporal patterns of salinity in Spanish rivers: a nationwide assessment.
Creators: name: Estévez, Edurne
name: Rodríguez-Castillo, Tamara
name: González-Ferreras, Alexia María
name: Cañedo-Argüelles, Miguel
name: Barquín, José
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Environmental Science
subject: Ecology
subject: FOS: Biological sciences

description: Boxplots of water conductivity measured in river reaches in good and poor ecological status in each river typology. The mean conductivity (± the standard error) for each typology is indicated in brackets.
(1760) James Williams Scarlett
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.
DDB Accumulates at DNA Damage Sites Immediately after UV Irradiation and Directly Stimulates Nucleotide Excision Repair
Creators: name: Sancar, Aziz
name: Matsunaga, Tsukasa
name: Mori, Toshio
name: Morioka, Hiroshi
name: Kawashima, Aki
name: Nikaido, Osamu
name: Wakasugi, Mitsuo
name: Linn, Stuart
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: Damaged DNA-binding protein, DDB, is a heterodimer of p127 and p48 with a high specificity for binding to several types of DNA damage. Mutations in the p48 gene that cause the loss of DDB activity were found in a subset of xeroderma pigmentosum complementation group E (XP-E) patients and have linked to the deficiency in global genomic repair of cyclobutane pyrimidine dimers (CPDs) in these cells. Here we show that with a highly defined system of purified repair factors, DDB can greatly stimulate the excision reaction reconstituted with XPA, RPA, XPC.HR23B, TFIIH, XPF.ERCC1 and XPG, up to 17-fold for CPDs and approximately 2-fold for (6-4) photoproducts (6-4PPs), indicating that no additional factor is required for the stimulation by DDB. Transfection of the p48 cDNA into an SV40-transformed human cell line, WI38VA13, was found to enhance DDB activity and the in vivo removal of CPDs and 6-4PPs. Furthermore, the combined technique of recently developed micropore UV irradiation and immunostaining revealed that p48 (probably in the form of DDB heterodimer) accumulates at locally damaged DNA sites immediately after UV irradiation, and this accumulation is also observed in XP-A and XP-C cells expressing exogenous p48. These results suggest that DDB can rapidly translocate to the damaged DNA sites independent of functional XPA and XPC proteins and directly enhance the excision reaction by core repair factors.
Figure S2 from Drivers of spatio-temporal patterns of salinity in Spanish rivers: a nationwide assessment
Creators: name: Estévez, Edurne
name: Rodríguez-Castillo, Tamara
name: González-Ferreras, Alexia María
name: Cañedo-Argüelles, Miguel
name: Barquín, José
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Environmental Science
subject: Ecology
subject: FOS: Biological sciences

description: Observed versus predicted conductivity values for training (a) and testing (b) sets in the spatial Random Forest model.
Capillary and winding transitions in a confined cholesteric liquid crystal
Creators: name: Heras, Daniel de las
name: Velasco, Enrique
name: Martínez-Ratón, Yuri
Publisher: name: arXiv
Year: 2015
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: We consider a Lebwohl-Lasher model of chiral particles confined in a planar cell (slit pore) with different boundary conditions, and solve it using mean-field theory. The phase behaviour of the system with respect to temperature and pore width is studied. Two phenomena are observed: (i) an isotropic-cholesteric transition which exhibits an oscillatory structure with respect to pore width, and (ii) an infinite set of winding transitions caused by commensuration effects between cholesteric pitch and pore width. The latter transitions have been predicted and analysed by other authors for cholesterics confined in a fixed pore and subject to an external field promoting the uniaxial nematic phase; here we induce winding transitions solely from geometry by changing the pore width at zero external field (a setup recently explored in Atomic-Force Microscopy experiments). In contrast with previous studies, we obtain the phase diagrams in the temperature vs pore width plane, including the isotropic-cholesteric transition, the winding transitions and their complex relationship. In particular, the structure of winding transitions terminates at the capillary isotropic-cholesteric transition via triple points where the confined isotropic phase coexists with two cholesterics with different helix indices. For symmetric and asymmetric monostable plate anchorings the phase diagram are qualitatively similar.
description: 9 pages, 5 figures, accepted in Soft Matter
Near-field speckle-scanning-based x-ray imaging
Creators: name: Berujon, Sebastien
name: Ziegler, Eric
Publisher: name: arXiv
Year: 2015
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: The x-ray near-field speckle-scanning concept is an approach recently introduced to obtain absorption, phase, and dark-field images of a sample. In this paper, we present ways of recovering from a sample its ultrasmall-angle x-ray scattering distribution using numerical deconvolution. We also show how to access the 2D phase gradient signal from random step scans, the latter having the potential to elude the flat-field correction error. Each feature is explained theoretically and demonstrated experimentally at a synchrotron x-ray facility.
description: 8 figures, 9 pages
Supplementary information from Drivers of spatio-temporal patterns of salinity in Spanish rivers: a nationwide assessment
Creators: name: Estévez, Edurne
name: Rodríguez-Castillo, Tamara
name: González-Ferreras, Alexia María
name: Cañedo-Argüelles, Miguel
name: Barquín, José
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Environmental Science
subject: Ecology
subject: FOS: Biological sciences

description: S1. Environmental variables calculated to explain spatial patterns of salinity.
Die Gerling Sternwarte (Gerling Astronomical Observatory)
Creators: name: Schrimpf, Andreas
Publisher: name: arXiv
Year: 2015
Subjects: subject: History and Philosophy of Physics (physics.hist-ph)
subject: FOS: Physical sciences

description: Christian Ludwig Gerling's 1817 appointment as Professor for Mathematics, Physics and Astronomy resulted in the foundation of the Mathematical and Physical Institute of the Philipps University. In 1838, Gerling moved onto new premises in the main building of the former Dörnberger Hof in Renthof Street where the Philipps University's astronomical observatory was installed in the upper part of the old tower in 1841. The most important device at that time was a transit instrument which served to measure the transit times of stars in the meridian. Precise alignment required the use of a meridian stone, an artificial point of reference exactly north of and at about four kilometers' distance from the observatory. The scientists observed planets and their moons, the asteroids that were only discovered at the beginning of the 19th century, and some fainter stars in order to improve stellar charts. The Gerling Observatory is the first place in Hesse, where positions of asteroids were read.
description: 6 pages, 3 figures, in German
Table S1 from Drivers of spatio-temporal patterns of salinity in Spanish rivers: a nationwide assessment.
Creators: name: Estévez, Edurne
name: Rodríguez-Castillo, Tamara
name: González-Ferreras, Alexia María
name: Cañedo-Argüelles, Miguel
name: Barquín, José
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Environmental Science
subject: Ecology
subject: FOS: Biological sciences

description: River typologies according to the Spanish Royal Decree, RD 817/2015, on water policy and number of river reaches in good and poor status in each river typology with water conductivity measures considered in this study. *SAICA = Automatic Water Quality Information System
title: Primary Human Colon Epithelial Cells (pHCoEpiCs) Do Express the Shiga Toxin (Stx) Receptor Glycosphingolipids Gb3Cer and Gb4Cer and Are Largely Refractory but Not Resistant towards Stx
Creators: name: Detzner, Johanna
name: Püttmann, Charlotte
name: Pohlentz, Gottfried
name: Humpf, Hans-Ulrich
name: Mellmann, Alexander
name: Karch, Helge
name: Müthing, Johannes
Publisher: name: University of Muenster, Institutional Repository MIAMI
Year: 2023
Subjects: subject: 610 Medicine and health

description: Shiga toxin (Stx) is released by enterohemorrhagic Escherichia coli (EHEC) into the human intestinal lumen and transferred across the colon epithelium to the circulation. Stx-mediated damage of human kidney and brain endothelial cells and renal epithelial cells is a renowned feature, while the sensitivity of the human colon epithelium towards Stx and the decoration with the Stx receptor glycosphingolipids (GSLs) globotriaosylceramide (Gb3Cer, Galα1-4Galβ1-4Glcβ1-1Cer) and globotetraosylceramide (Gb4Cer, GalNAcβ1-3Galα1-4Galβ1-4Glcβ1-1Cer) is a matter of debate. Structural analysis of the globo-series GSLs of serum-free cultivated primary human colon epithelial cells (pHCoEpiCs) revealed Gb4Cer as the major neutral GSL with Cer (d18:1, C16:0), Cer (d18:1, C22:1/C22:0) and Cer (d18:1, C24:2/C24:1) accompanied by minor Gb3Cer with Cer (d18:1, C16:0) and Cer (d18:1, C24:1) as the dominant lipoforms. Gb3Cer and Gb4Cer co-distributed with cholesterol and sphingomyelin to detergent-resistant membranes (DRMs) used as microdomain analogs. Exposure to increasing Stx concentrations indicated only a slight cell-damaging effect at the highest toxin concentration of 1 µg/mL for Stx1a and Stx2a, whereas a significant effect was detected for Stx2e. Considerable Stx refractiveness of pHCoEpiCs that correlated with the rather low cellular content of the high-affinity Stx-receptor Gb3Cer renders the human colon epithelium questionable as a major target of Stx1a and Stx2a.
description: Finanziert durch den Open-Access-Publikationsfonds der Westfälischen Wilhelms-Universität Münster (WWU Münster).
Visualizing clonal evolution with clevRvis
Creators: name: Sandmann, Sarah
name: Inserte, Clara
name: Varghese, Julian
Publisher: name: F1000 Research Limited
Year: 2023

description: Accurate reconstruction of clonal evolution is essential for the application of precision oncology. It allows for the early detection of newly developing, highly aggressive subclones that might be resistant to therapy and can potentially lead to relapse. However, analysis is characterized by challenges: Often, data on only few time points are available. As a consequence, clonal evolution is incomplete, lacking information on a tumor's development over time and its response to therapy. Furthermore, bi-allelic events, which are considered of high relevance with respect to many cancers, cannot be depicted properly.
 To address these challenges, we developed clevRvis – an R/Bioconductor package providing a wide set of innovative visualization techniques for clonal evolution in R. Three different representations are available: shark plots (graph-based), dolphin plots (fish plot-like) and plaice plots (allele-aware). Phylogeny-aware color coding is available by default. Plots are generated on the basis of a seaObject, optionally containing automatically interpolated time points and/or estimated therapy effect. Alternative trees, determined on the basis of the user-defined cancer cell fractions, can be explored interactively. A shiny interface allows for user-friendly analysis.
 Concluding, clevRvis provides novel techniques for visualizing clonal evolution, contributing to a better understanding of a tumor's development.
New insights on the Galactic Bulge Initial Mass Function
Creators: name: Calamida, A.
name: Sahu, K. C.
name: Casertano, S.
name: Anderson, J.
name: Cassisi, S.
name: Gennaro, M.
name: Cignoni, M.
name: Brown, T. M.
name: Kains, N.
name: Ferguson, H.
name: Livio, M.
name: Bond, H. E.
name: Buonanno, R.
name: Clarkson, W.
name: Ferraro, I.
name: Pietrinferni, A.
name: Salaris, M.
name: Valenti, J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We have derived the Galactic bulge initial mass function of the SWEEPS field in the mass range 0.15 $< M/M_{\odot}
description: 13 pages, 8 figures, accepted for publication on ApJ
Dependence of Selective Gene Activation on the Androgen Receptor NH 2 - and COOH-terminal Interaction
Creators: name: Wilson, Elizabeth M.
name: Lee, Lori W.
name: He, Bin
name: Minges, John T.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: The agonist-induced androgen receptor NH(2)- and COOH-terminal (N/C) interaction is mediated by the FXXLF and WXXLF NH(2)-terminal motifs. Here we demonstrate that agonist-dependent transactivation of prostate-specific antigen (PSA) and probasin enhancer/promoter regions requires the N/C interaction, whereas the sex-limited protein gene and mouse mammary tumor virus long terminal repeat do not. Transactivation of PSA and probasin response regions also depends on activation function 1 (AF1) in the NH(2)-terminal region but can be increased by binding an overexpressed p160 coactivator to activation function 2 (AF2) in the ligand binding domain. The dependence of the PSA and probasin enhancer/promoters on the N/C interaction for transactivation allowed us to demonstrate that in the presence of androgen, the WXXLF motif with the sequence (433)WHTLF(437) contributes as an inhibitor to AR transactivation. We further show that like the FXXLF and LXXLL motifs, the WXXLF motif interacts in the presence of androgen with AF2 in the ligand binding domain. Sequence comparisons among species indicate greater conservation of the FXXLF motif compared with the WXXLF motif, paralleling the functional significance of these binding motifs. The data provide evidence for promoter-specific differences in the requirement for the androgen receptor N/C interaction and in the contributions of AF1 and AF2 in androgen-induced gene regulation.
Figure S3 from Drivers of spatio-temporal patterns of salinity in Spanish rivers: a nationwide assessment.
Creators: name: Estévez, Edurne
name: Rodríguez-Castillo, Tamara
name: González-Ferreras, Alexia María
name: Cañedo-Argüelles, Miguel
name: Barquín, José
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Environmental Science
subject: Ecology
subject: FOS: Biological sciences

description: Partial dependence plots showing the fitted functions for the most important environmental factors driving spatial water salinity patterns (MN = in the draining catchment to the river reach, LC = in the hillslopes adjacent to the river reach). Codes according to Table S2: (a) MN_PRE, (b) MN_AGR, (c) LC_TEM, (d) MN_CON, (e) ELE, (f) MN_HAR.
D2.1 Data Warehouse (DWH) for agriculture policy impact assessment data management
Creators: name: Ayesa
name: Idener
Publisher: name: Zenodo
Year: 2021
Subjects: AGRICORE H2020

description: This document provides a detailed description of the role and functioning of the DWH within the AGRICORE project architecture, as a fundamental component for the storage, processing and exchange of data. By providing an extensive list of requirements necessary to fulfil the modularity and distributed architecture principles of the project, a complete guide to the architecture defined as the solution and to the tools and technologies selected to build the DWH, and descriptions of how the DWH and the ARDIT indexer will be connected for data ingestion. Finally, a deployment plan is defined and divided into several separate phases, increasing in each of them the features, functionalities and capabilities of the DWH.
ReproSNP: phenotype-specific variant filtering and exploration based on UK biobank data
Creators: name: Ogoniak, Lynn
name: Varghese, Julian
name: Busch, Alexander S.
name: Sandmann, Sarah
Publisher: name: F1000 Research Limited
Year: 2023

description: The UK Biobank (UKB) provides phenotype and genotype data from over 500,000 participants. It is an extremely valuable resource for the analysis of genetically as- sociated diseases, especially those that are rare and/or have very heterogeneous and complex phenotypes. However, undiagnosed cases may be present in the UKB cohort. One example is male infertility: About 7% of men worldwide are estimated to be affected. For a large proportion, the medical cause remains unknown (60-70%). However, only 0.25% of male UKB participants report diagnosed infertility, indicating a high dark rate in the UKB cohort. To address this constraint, we developed the R Shiny application ReproSNP. Two cohorts, potentially infertile vs supposed fertile, are available. Additionally, a selection of phenotypes is provided, which allows for inter- active definition of further subgroups. Comparing two subgroups, users can identify and explore candidate variants (based on whole exome sequencing) to validate or exclude them for further research. Visual and tabular output, including statistical tests, is automatically generated, providing easy and intuitive handling also for non- bioinformaticians. Concluding, ReproSNP enables a previously impractical analysis and exploration of infertility-associated variants. The integration of additional phe- notypes for research in various medical fields will target a broad range of scientists and clinicians.
(1757) James Brown
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.
Dual Inhibition of Focal Adhesion Kinase and Epidermal Growth Factor Receptor Pathways Cooperatively Induces Death Receptor-mediated Apoptosis in Human Breast Cancer Cells
Creators: name: Golubovskaya, Vita
name: Cance, William
name: Xu, Li Hui
name: Beviglia, Lucia
name: Shelton Earp III, H.
name: Craven, Rolf
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: The focal adhesion kinase (FAK) and epidermal growth factor receptor (EGFR) are protein-tyrosine kinases that are overexpressed and activated in human breast cancer. To determine the role of EGFR and FAK survival signaling in breast cancer, EGFR was stably overexpressed in BT474 breast cancer cells, and each signaling pathway was specifically targeted for inhibition. FAK and EGFR constitutively co-immunoprecipitated in EGFR-overexpressing BT474 cells. In low EGFR-expressing BT474-pcDNA3 vector control cells, inhibition of FAK by the FAK C-terminal domain caused detachment and apoptosis via pathways involving activation of caspase-3 and -8, cleavage of poly(ADP-ribose) polymerase, and caspase-3-dependent degradation of AKT. This apoptosis could be rescued by the dominant-negative Fas-associated death domain, indicating involvement of the death receptor pathway. EGFR overexpression did not inhibit detachment induced by the FAK C-terminal domain, but did suppress apoptosis, activating AKT and ERK1/2 survival pathways and inhibiting cleavage of FAK, caspase-3 and -8, and poly(ADP-ribose) polymerase. Furthermore, this protective effect of EGFR signaling was reversed by EGFR kinase inhibition with AG1478. In addition, inhibition of FAK and EGFR in another breast cancer cell line (BT20) endogenously overexpressing these kinases also induced apoptosis via the same mechanism as in the EGFR-overexpressing BT474 cells. The results of this study indicate that dual inhibition of FAK and EGFR signaling pathways can cooperatively enhance apoptosis in breast cancers.
Evaluating the Specificity of Antisense Oligonucleotide Conjugates: A DNA ARRAY ANALYSIS
Creators: name: Shaw, Barbara Ramsay
name: Fisher, Michael H.
name: Fisher, Anna Astriab
name: Juliano, Rudolph L.
name: Ye, Dongjiu
name: Sergueev, Dimitri S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: Antisense oligonucleotides are potentially powerful tools for selective control of cellular and viral gene expression. Crucial to successful application of this approach is the specificity of the oligonucleotide for the chosen RNA target. Here we apply DNA array technology to examine the specificity of antisense oligonucleotide treatments. The molecules used in these studies consisted of phosphorothioate oligomers linked to the Antennapedia (Ant) delivery peptide. The antisense oligonucleotide component was complementary to a site flanking the AUG of the MDR1 message, which codes for P-glycoprotein, a membrane ATPase associated with multidrug resistance in tumor cells. Using a DNA array of 2059 genes, we analyzed cellular responses to molecules comprised of Ant peptide-oligonucleotide conjugates, as well as to the Ant peptide alone. Besides the expected reduction in MDR1 message level, 37 other genes (approximately 2% of those tested) showed changes of comparable magnitude. The validity of the array results was confirmed for selected genes using Northern blots to assess messenger RNA levels. These results suggest that studies using antisense oligonucleotide technology to modulate gene expression need to be interpreted with caution.
Evidence That Inhibition of p44/42 Mitogen-activated Protein Kinase Signaling Is a Factor in Proteasome Inhibitor-mediated Apoptosis
Creators: name: Shi, Yue Y.
name: Small, George W.
name: Orlowski, Robert Z.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: The proteasome is emerging as a target for cancer therapy because small molecule inhibitors of its catalytic activity induce apoptosis in both in vitro and in vivo models of human malignancies and are proving to have efficacy in early clinical trials. To further elucidate the mechanism of action of these inhibitors, their impact on signaling through the p44/42 mitogen-activated protein kinase (MAPK) pathway was studied. Proteasome inhibition with either carbobenzoxy-leucyl-leucyl-phenylalaninal or lactacystin led to a loss of dually phosphorylated, activated p44/42 MAPK in A1N4-myc human mammary and MDA-MB-231 breast carcinoma cells in a dose- and time-dependent fashion. This correlated with an induction of the dual specificity MAPK phosphatases (MKP)-1 and -2, and blockade of MKP induction using either actinomycin D or Ro-31-8220 significantly decreased loss of activated p44/42 MAPK. Inhibition of p44/42 MAPK signaling by use of the MAPK kinase inhibitors PD 98059 or U0126, or by use of a dominant negative MAPK construct, enhanced proteasome inhibitor-mediated apoptosis. Conversely, activation of MAPK by epidermal growth factor, or use of a mutant MAPK resistant to MKP-mediated dephosphorylation, inhibited apoptosis. These studies support a role for inactivation of signaling through the p44/42 MAPK pathway in proteasome inhibitor-mediated apoptosis.