cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 12 of Optimal experimental designs for estimating genetic and non-genetic effects underlying infectious disease transmission
Creators: name: Pooley, Christopher
name: Marion, Glenn
name: Bishop, Stephen
name: Doeschl-Wilson, Andrea
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Additional file 12: Fig. S9. Partitioning contributions to the SD of SNP effects. Description: Figure 6 in the paper shows the result of sequentially adding residuals, group effects and a fixed effect to the basic SNP-only model. Here, we present the corresponding results assuming only 100 individuals.
(3943) William Auld
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.
Primate-specific Melanoma Antigen-A11 Regulates Isoform-specific Human Progesterone Receptor-B Transactivation
Creators: name: Su, Shifeng
name: Yuan, Lingwen
name: Minges, John T.
name: Young, Steven L.
name: Grossman, Gail
name: Blackwelder, Amanda J.
name: Wilson, Elizabeth M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Progesterone acting through the progesterone receptor (PR) and its coregulators prepares the human endometrium for receptivity to embryo implantation and maintains pregnancy. The menstrual cycle-dependent expression of melanoma antigen-A11 (MAGE-11) in the mid-secretory human endometrium suggested a novel function in human PR signaling. Here we show that MAGE-11 is an isoform-specific coregulator responsible for the greater transcriptional activity of human PR-B relative to PR-A. PR was recruited to progesterone response regions of progesterone-regulated FK506-binding protein 5 (FKBP5) immunophilin and small Ras family G protein cell growth inhibitor RASD1 genes. Expression of MAGE-11 lentivirus shRNA in human endometrial Ishikawa cells expressing PR-B showed that MAGE-11 is required for isoform-specific PR-B up-regulation of FKBP5. In contrast, MAGE-11 was not required for progesterone up-regulation of RASD1 in endometrial cells expressing the PR-A/B heterodimer. Target gene specificity of PR-B depended on the synergistic actions of MAGE-11 and p300 mediated by the unique PR-B NH2-terminal 110LLXXVLXXLL119 motif that interacts with the MAGE-11 F-box region in a phosphorylation- and ubiquitinylation-dependent manner. A progesterone-dependent mechanism is proposed in which MAGE-11 and p300 increase PR-B up-regulation of the FKBP5 gene. MAGE-11 down-regulates PR-B, similar to the effects of progesterone, and interacts with FKBP5 to stabilize a complex with PR-B. We conclude that the coregulator function of MAGE-11 extends to isoform-specific regulation of PR-B during the cyclic development of the human endometrium.
Host Genetic Variation Impacts SARS-CoV-2 Vaccination Response in the Diversity Outbred Mouse Population
Creators: name: Dillard, Jacob A.
name: Taft-Benz, Sharon
name: Pardo-Manuel de Villena, Fernando
name: Hock, Pablo
name: Madden, Emily A.
name: Ferris, Martin T.
name: Hampton, Brea K.
name: Cruz Cisneros, Marta C.
name: Parotti, Breantié
name: Anderson, Elizabeth J.
name: Bell, Timothy A.
name: Sarkar, Sanjay
name: Baric, Ralph S.
name: Heise, Mark T.
name: West, Ande
name: Dinnon, Kenneth H.
name: Baxter, Victoria K.
name: Leist, Sarah R.
name: Shaw, Ginger D.
name: Blanchard, Matthew
Publisher: name: MDPI
Year: 2024

description: The COVID-19 pandemic led to the rapid and worldwide development of highly effective vaccines against SARS-CoV-2. However, there is significant individual-to-individual variation in vaccine efficacy due to factors including viral variants, host age, immune status, environmental and host genetic factors. Understanding those determinants driving this variation may inform the development of more broadly protective vaccine strategies. While host genetic factors are known to impact vaccine efficacy for respiratory pathogens such as influenza and tuberculosis, the impact of host genetic variation on vaccine efficacy against COVID-19 is not well understood. To model the impact of host genetic variation on SARS-CoV-2 vaccine efficacy, while controlling for the impact of non-genetic factors, we used the Diversity Outbred (DO) mouse model. We found that DO mice immunized against SARS-CoV-2 exhibited high levels of variation in vaccine-induced neutralizing antibody responses. While the majority of the vaccinated mice were protected from virus-induced disease, similar to human populations, we observed vaccine breakthrough in a subset of mice. Importantly, we found that this variation in neutralizing antibody, virus-induced disease, and viral titer is heritable, indicating that the DO serves as a useful model system for studying the contribution of genetic variation of both vaccines and disease outcomes.
A Combinatorial Approach to Voiculescu's Bi-Free Partial Transforms
Creators: name: Skoufranis, Paul
Publisher: name: arXiv
Year: 2015
Subjects: subject: Operator Algebras (math.OA)
subject: Probability (math.PR)
subject: FOS: Mathematics
subject: 46L54, 46L53

description: In this paper, we present a combinatorial approach to the 2-variable bi-free partial $S$- and $T$-transforms recently discovered by Voiculescu. This approach produces an alternate definition of said transforms using $(\ell, r)$-cumulants.
title: Sous-sols des maisons d'habitation
Creators: name: Crocker, C. R.
Publisher: name: Conseil national de recherches du Canada. Division des recherches en construction
Year: 1962
Subjects: subject: Basements and foundations
valueUri: urn:ircsubjects:IRC0320
subject: Sous-sol et fondations
valueUri: urn:ircsubjects:IRC0320
subject: basements
subject: sous sol (bâtiment)
subject: damp proofings
subject: protection contre l'humidité
subject: paintwork
subject: peinture (revêtement)
subject: floor coverings
subject: revêtement de sol
subject: wall coverings
subject: revêtement mural

description: Le présent Digeste traite des techniques qu'on doit employer durant la construction pour que les sous-sols restent secs. Il traite également de la procédure à suivre pour finir les murs et les parquets des sous-sols.
Mariner transposons are widespread genetic parasites in the genome of hydrothermal invertebrates
Creators: name: CASSE, Nathalie
name: PRADIER, Elisabeth
name: DEMATTEI, Marie-Véronique
name: BIGOT, Yves
name: LAULIER, Marc
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2002

Abstract
Probing Structural Selectivity of Synthetic Heparin Binding to Stabilin Protein Receptors
Creators: name: Harris, Edward N.
name: Liu, Jian
name: Gopalakrishnan, Sandhya
name: Xu, Yongmei
name: Pempe, Elizabeth H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: As one of the most widely used drugs worldwide, heparin is an essential anticoagulant required for surgery, dialysis, treatment of thrombosis, cancer, and general circulatory management. Stabilin-2 is a scavenger clearance receptor with high expression in the sinusoidal endothelium of liver. It is believed that Stabilin-2 is the primary receptor for the clearance of unfractionated and low molecular weight heparins in the liver. Here, we identify the modifications and length of the heparin polymer that are required for binding and endocytosis by both human Stabilin receptors: Stabilin-2 and its homolog Stabilin-1 (also found in liver endothelium). Using enzymatically synthesized 35S-labeled heparan sulfate oligomers, we identified that sulfation of the 3-OH position of N-sulfated glucosamine (GlcNS) is the most beneficial modification for binding and endocytosis via both Stabilin receptors. In addition, our data suggest that a decasaccharide is the minimal size for binding to the Stabilin receptors. These findings define the physical parameters of the heparin structure required for efficient clearance from blood circulation. These results will also aid in the design of synthetic heparins with desired clearance rates.
Protein Kinase Cα Phosphorylates a Novel Argininosuccinate Synthase Site at Serine 328 during Calcium-dependent Stimulation of Endothelial Nitric-oxide Synthase in Vascular Endothelial Cells
Creators: name: Corbin, Karen D.
name: Eichler, Duane C.
name: Pendleton, Laura C.
name: Haines, Ricci J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Endothelial nitric-oxide synthase (eNOS) utilizes l-arginine as its principal substrate, converting it to l-citrulline and nitric oxide (NO). l-Citrulline is recycled to l-arginine by two enzymes, argininosuccinate synthase (AS) and argininosuccinate lyase, providing the substrate arginine for eNOS and NO production in endothelial cells. Together, these three enzymes, eNOS, AS, and argininosuccinate lyase, make up the citrulline-NO cycle. Although AS catalyzes the rate-limiting step in NO production, little is known about the regulation of AS in endothelial cells beyond the level of transcription. In this study, we showed that AS Ser-328 phosphorylation was coordinately regulated with eNOS Ser-1179 phosphorylation when bovine aortic endothelial cells were stimulated by either a calcium ionophore or thapsigargin to produce NO. Furthermore, using in vitro kinase assay, kinase inhibition studies, as well as protein kinase Cα (PKCα) knockdown experiments, we demonstrate that the calcium-dependent phosphorylation of AS Ser-328 is mediated by PKCα. Collectively, these findings suggest that phosphorylation of AS at Ser-328 is regulated in accordance with the calcium-dependent regulation of eNOS under conditions that promote NO production and are in keeping with the rate-limiting role of AS in the citrulline-NO cycle of vascular endothelial cells.
First record of the marbled crab Pachygrapsus marmoratus (Fabricius, 1787) on the coast of Calvados (Bay of Seine, English Channel)
Creators: name: PEZY, Jean-Philippe
name: DAUVIN, Jean-Claude
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2015

description: A unique specimen of the decapod Pachygrapsus marmoratus, the marbled crab, was reported for the first time in August 2014 from the intertidal zone on the Calvados coast (western part of the Bay of Seine, Eastern English Channel). However, information is still insufficient to ascertain the origin and mode of introduction of this species into the Eastern English Channel. Among the different hypotheses, the presence of the marbled crab could be related to shipping traffic, while the occurrence of mild winters in the Bay of Seine over several years could provide favorable conditions for the permanent establishment of this Mediterranean species. Supplementary records will be necessary to confirm that this species is becoming established in the Bay of Seine, such as already observed along the western coast of the Cotentin peninsula (western English Channel).
Additional file 13 of Optimal experimental designs for estimating genetic and non-genetic effects underlying infectious disease transmission
Creators: name: Pooley, Christopher
name: Marion, Glenn
name: Bishop, Stephen
name: Doeschl-Wilson, Andrea
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Additional file 13: Fig. S10. Design replication. Description: Investigates how the reduction in precision when incorporating group effects can be moderated by means of design replication (that is repeating the same basic designs in Fig. 2 several times).
title: Fire in buildings
Creators: name: Shorter, G. W.
Publisher: name: National Research Council of Canada. Division of Building Research
Year: 1962
Subjects: subject: Fire
valueUri: urn:ircsubjects:IRC0400
subject: Incendie
valueUri: urn:ircsubjects:IRC0400
subject: combustion
subject: fire spread
subject: développement du feu
subject: combustibility
subject: combustibilité
subject: flammability
subject: inflammabilité
subject: fire compartments
subject: compartiment coupe feu

description: The main purpose of this Digest is to discuss principles and features of effective fire protection. Although fire, and in particular fire in buildings, is an extremely complex subject, the designer can, with some knowledge of the basic principles involved, give rational consideration to the fire protection features of buildings.
Protein Modification by Deamidation Indicates Variations in Joint Extracellular Matrix Turnover
Creators: name: McCudden, Christopher R.
name: Bolognesi, Michael
name: Stabler, Thomas V.
name: Kraus, Virginia B.
name: Jordan, Joanne M.
name: Renner, Jordan B.
name: Catterall, Jonathan B.
name: Zura, Robert
name: Hsueh, Ming F.
name: Feng, Sheng
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: As extracellular proteins age, they undergo and accumulate nonenzymatic post-translational modifications that cannot be repaired. We hypothesized that these could be used to systemically monitor loss of extracellular matrix due to chronic arthritic diseases such as osteoarthritis (OA). To test this, we predicted sites of deamidation in cartilage oligomeric matrix protein (COMP) and confirmed, by mass spectroscopy, the presence of deamidated (Asp64) and native (Asn64) COMP epitopes (mean 0.95% deamidated COMP (D-COMP) relative to native COMP) in cartilage. An Asp64, D-COMP-specific ELISA was developed using a newly created monoclonal antibody 6-1A12. In a joint replacement study, serum D-COMP (p = 0.017), but not total COMP (p = 0.5), declined significantly after replacement demonstrating a joint tissue source for D-COMP. In analyses of 450 participants from the Johnston County Osteoarthritis Project controlled for age, gender, and race, D-COMP was associated with radiographic hip (p < 0.0001) but not knee (p = 0.95) OA severity. In contrast, total COMP was associated with radiographic knee (p < 0.0001) but not hip (p = 0.47) OA severity. D-COMP was higher in soluble proteins extracted from hip cartilage proximal to OA lesions compared with remote from lesions (p = 0.007) or lesional and remote OA knee (p < 0.01) cartilage. Total COMP in cartilage did not vary by joint site or proximity to the lesion. This study demonstrates the presence of D-COMP in articular cartilage and the systemic circulation, and to our knowledge, it is the first biomarker to show specificity for a particular joint site. We believe that enrichment of deamidated epitope in hip OA cartilage indicates a lesser repair response of hip OA compared with knee OA cartilage.
Tail abnormalities in thornback ray Raja clavata (Chondrichthyes: Rajidae) from the coast of Syria (eastern Mediterranean)
Creators: name: CAPAPÉ, Christian
name: ALI, Malek
name: SAAD, Adib
name: REYNAUD, Christian
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2015

description: Three specimens of thornback ray Raja clavata Linnaeus, 1758 presenting tail abnormalities were captured off the Syrian coast. A first specimen was a juvenile male with an ecaudated tail reduced to a stump like structure. The two other specimens, an adult male and an adult female, showed abnormalities of the tail essentially constituted by lack of dorsal and caudal fins. The three specimens were described in the present note, and it appears that these tail abnormalities did not affect their development and they reached similar parameters and swimming activities than the normal ones.
(3944) Mary MacDonald
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.
GÉNÉTIQUE DES POPULATIONS DE SPHAEROMA SERRATUM (F.). IX.- Étude des populations des îles anglo-normandes de Jersey et de Guernesey
Creators: name: BOCQUET, Charles
name: LEJUEZ, Robert
name: TEISSIER, Georges
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 1969

description: The polychromatism of the populations of Sphaeroma serratum, collected on the coasts of Jersey and Guernesey, was observed after 18 representative samples gathering 22 770 individuals. The populations from Jersey and Guernesey are rather different from one another, and the whole largely differ from those of the western Cotentin. The albicans rate obviously becomes lower and lower from the coasts of the Cotentin to Guernesey, by Jersey; the discretum rate correlati- vely becomes higher and higher. The lunulatum and the signatum are particularly abundant at Guernesey while the ornatum and the “rouges” (rubrum-{-aurantiacum, luteum being absent) are very numerous at Jersey. These various mutants show intermediate or lower frequencies on the western coast of the Cotentin.
CHORDODASYS RIEDLI GEN. NOV., SPEC. NOV. A MACRODASYOID GASTROTRICH WITH A CHORDOID ORGAN
Creators: name: SCHÖPFER-STERRER, Christiane
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 1969

description: Chordodasys represents a new genus of the Macrodasyoid gastrotrichsfrom clean coarse sand in 41 m depth, off Beaufort (North Carolina). The main difference between Chordodasys and the other genera of the family Dactylopodaliidae (to which it is placed provisionally) is the loricated dorsal body surface and the presence of a chordoid organ in the tail region, which has not been described as yetwithintheAschelminthes.
Charge transfer and hybrid ferroelectricity in (YFeO$_{3}$)$_{n}$/(YTiO$_{3}$)$_{n}$ magnetic superlattices
Creators: name: Zhang, Huimin
name: Weng, Yakui
name: Yao, Xiaoyan
name: Dong, Shuai
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Interfaces in oxide heterostructures always provide a fertile ground for emergent properties. Charge transfer from a high energy band to a low energy opponent is naturally expected, as occurring in semiconductor $p$-$n$ junctions. In this study, several exceptional physical phenomena have been predicted in (YFeO$_3$)$_n$/(YTiO$_3$)$_n$ superlattices. First, the charge transfer between these Mott insulators is in opposite to the intuitive band alignment scenario. Second, hybrid ferroelectricity with a moderate polarization is generated in the $n=2$ magnetic superlattice. Furthermore, the ferroelectric-type distortion can persist even if the ($AB$O$_3$)$_2$/($AB$'O$_3$)$_2$ system turns to be metallic, rending possible metallic ferroelectricity.
description: 6 pages, 4 figures
RAD51 Protein ATP Cap Regulates Nucleoprotein Filament Stability
Creators: name: Amunugama, Ravindra
name: Forties, Robert A.
name: He, Yujiong
name: Shim, Kang Sup
name: Willcox, Smaranda
name: Luo, Yu
name: Fishel, Richard
name: Griffith, Jack
name: Bundschuh, Ralf
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: RAD51 mediates homologous recombination by forming an active DNA nucleoprotein filament (NPF). A conserved aspartate that forms a salt bridge with the ATP γ-phosphate is found at the nucleotide-binding interface between RAD51 subunits of the NPF known as the ATP cap. The salt bridge accounts for the nonphysiological cation(s) required to fully activate the RAD51 NPF. In contrast, RecA homologs and most RAD51 paralogs contain a conserved lysine at the analogous structural position. We demonstrate that substitution of human RAD51(Asp-316) with lysine (HsRAD51(D316K)) decreases NPF turnover and facilitates considerably improved recombinase functions. Structural analysis shows that archaebacterial Methanococcus voltae RadA(D302K) (MvRAD51(D302K)) and HsRAD51(D316K) form extended active NPFs without salt. These studies suggest that the HsRAD51(Asp-316) salt bridge may function as a conformational sensor that enhances turnover at the expense of recombinase activity.
Mott Quantum Criticality in the Anisotropic 2D Hubbard Model
Creators: name: Lenz, Benjamin
name: Manmana, Salvatore R.
name: Pruschke, Thomas
name: Assaad, Fakher F.
name: Raczkowski, Marcin
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We present evidence for Mott quantum criticality in an anisotropic two-dimensional system of coupled Hubbard chains at half-filling. In this scenario emerging from variational cluster approximation and cluster dynamical mean-field theory, the interchain hopping $t_{\perp}$ acts as a control parameter driving the second-order critical end point $T_c$ of the metal-insulator transition down to zero at $t_{\perp}^{c}/t\simeq 0.2$. Below $t_{\perp}^{c}$, the volume of the hole and electron Fermi pockets of a compensated metal vanishes continuously at the Mott transition. Above $t_{\perp}^{c}$, the volume reduction of the pockets is cut off by a first-order transition. We discuss the relevance of our findings to a putative quantum critical point in layered organic conductors, whose location remains elusive so far.
description: 4+ pages, plus supplemental material; v3: final version
First record of the lesser amberjack Seriola fasciata (Teleostei: Carangidae) in Syrian coasts
Creators: name: JAWAD, Laith
name: MTAWEJ, Amjad
name: IBRAHIM, Amir
name: HASSAN, Mohamed
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2015

description: The first record of one fish species from the Mediterranean coasts of Syria is reported: the lesser amberjack Seriola fasciata. The specimen was caught in the Syrian waters during an ichthyologic survey on the 19th October 2013. The captured specimen is a juvenile individual of 141 mm in standard length. Several factors may explain the presence of this species in the Syrian waters.
The Euclid-Mullin graph
Creators: name: Booker, Andrew R.
name: Irvine, Sean A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Number Theory (math.NT)
subject: FOS: Mathematics

description: We introduce the Euclid-Mullin graph, which encodes all instances of Euclid's proof of the infinitude of primes. We investigate structural properties of the graph both theoretically and numerically; in particular, we prove that it is not a tree.
description: 24 pages, 2 figures, to appear in Journal of Number Theory
Contamination of copper, zinc, cadmium and lead in fish species captured from Bali Strait, Indonesia, and potential risks to human health
Creators: name: RUAENY, Tities Alhaq
name: HARIYANTO, Sucipto
name: SOEGIANTO, Agoes
Publisher: name: Station Biologique de Roscoff (SBR)
Year: 2015

description: The objectives of this study were to measure the concentrations of copper, zinc, cadmium and lead in the tissues of fish species captured from Strait of Bali, Indonesia, to evaluate their mean level in relation to the maximum residual limit for human consumption, to estimate the weekly intake, and to compare it with the provisional tolerable weekly intake (PTWI). The concentrations of copper, zinc, cadmium and lead in all fish ranged from 0.72-2.22, 3.36-13.16, 0.005-0.026, and 1.50-2.48 mg.kg-1 respectively. The level of Pb in all fish exceeds the permissible limit for human consumption, whereas the one of Cu, Zn and Cd did not exceed the permissible limit for human consumption. The estimated weekly intakes of Cu, Zn, and Cd were below the recommended values of PTWI. However, the weekly intake of Pb was higher than the PTWI values.
Reconstitution of the Very Short Patch Repair Pathway from Escherichia coli
Creators: name: Matsone, Steven W.
name: Robertson, Adam B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: The Escherichia coli very short patch (VSP) repair pathway corrects thymidine-guanine mismatches that result from spontaneous hydrolytic deamination damage of 5-methyl cytosine. The VSP repair pathway requires the Vsr endonuclease, DNA polymerase I, a DNA ligase, MutS, and MutL to function at peak efficiency. The biochemical roles of most of these proteins in the VSP repair pathway have been studied extensively. However, these proteins have not been studied together in the context of VSP repair in an in vitro system. Using purified components of the VSP repair system in a reconstitution reaction, we have begun to develop an understanding of the role played by each of these proteins in the VSP repair pathway and have gained insights into their interactions. In this report we demonstrate an in vitro reconstitution of the VSP repair pathway using a plasmid DNA substrate. Surprisingly, the repair track length can be modulated by the concentration of DNA ligase. We propose roles for MutL and MutS in coordination of this repair pathway.
On one-parameter Koopman groups
Creators: name: ter Elst, A. F. M.
name: Lemanczyk, M.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Dynamical Systems (math.DS)
subject: Functional Analysis (math.FA)
subject: FOS: Mathematics
subject: 37A10, 47D03

description: We characterize Koopman one-parameter $C_0$-groups in the class of all unitary one-parameter $C_0$-groups on $L_2(X)$ as those that preserve $L_\infty(X)$ and for which the infinitesimal generator is a derivation on the bounded functions in its domain.
Regulation of Class I Major Histocompatibility Complex (MHC) by Nucleotide-binding Domain, Leucine-rich Repeat-containing (NLR) Proteins
Creators: name: Ting, Jenny P.Y.
name: Robbins, Gregory R.
name: Zhang, Lu
name: Brickey, W. June
name: Truax, Agnieszka D.
name: Davis, Beckley K.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Most of the nucleotide-binding domain, leucine-rich repeat (NLR) proteins regulate responses to microbial and damage-associated products. Class II transactivator (CIITA) has a distinct function as the master regulator of class II major histocompatibility complex (MHC-II) transcription. Recently, human NLRC5 was found to regulate MHC-I in cell lines; however, a host of conflicting positive and negative functions has been attributed to this protein. To address the function of NLRC5 in a physiologic setting, we generated an Nlrc5−/− strain that contains a deletion in the exon that encodes the nucleotide-binding domain. We have not detected a role for this protein in cytokine induction by pathogen-associated molecular patterns and viruses. However, Nlrc5−/− cells showed a dramatic decrease of classical (H-2K) and nonclassical (Tla) MHC-I expression by T/B lymphocytes, natural killer (NK) cells, and myeloid-monocytic lineages. As a comparison, CIITA did not affect mouse MHC-I expression. Nlrc5−/− splenocytes and bone marrow-derived macrophages were able to up-regulate MHC-I in response to IFN-γ; however, the absolute levels of MHC-I expression were significantly lower than WT controls. Chromatin immunoprecipitation of IFN-γ-treated cells indicates that Nlrc5 reduced the silencing H3K27me3 histone modification, but did not affect the activating AcH3 modification on a MHC-I promoter. In summary, we conclude that Nlrc5 is important in the regulation of MHC-I expression by reducing H3K27me3 on MHC-I promoter and joins CIITA as an NLR subfamily that controls MHC gene transcription.
Coupled Landau-Zener-Stuckelberg Quantum Dot Interferometers
Creators: name: Gallego-Marcos, Fernando
name: Sánchez, Rafael
name: Platero, Gloria
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We investigate the interplay between long-range and direct photon-assisted transport in a triple quantum dot chain where local ac voltages are applied to the outer dots. We propose the phase difference between the two ac voltages as an external parameter, which can be easily tuned to manipulate the current characteristics. For gate voltages in phase opposition we find quantum destructive interferences analogous to the interferences in closed-loop undriven triple dots. As the voltages oscillate in phase, interferences between multiple paths give rise to dark states. Those totally cancel the current, and could be experimentally resolved.
description: 6 pages, 4 figures
Extracting the Redox Orbitals in Li Battery Materials with High-Resolution X-Ray Compton Scattering Spectroscopy
Creators: name: Suzuki, K.
name: Barbiellini, B.
name: Orikasa, Y.
name: Go, N.
name: Sakurai, H.
name: Kaprzyk, S.
name: Itou, M.
name: Yamamoto, K.
name: Uchimoto, Y.
name: Wang, Yung Jui
name: Hafiz, H.
name: Bansil, A.
name: Sakurai, Y.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We present an incisive spectroscopic technique for directly probing redox orbitals based on bulk electron momentum density measurements via high-resolution x-ray Compton scattering. Application of our method to spinel LixMn2O4, a lithium ion battery cathode material, is discussed. The orbital involved in the lithium insertion and extraction process is shown to mainly be the oxygen 2p orbital. Moreover, the manganese 3d states are shown to experience spatial delocalization involving 0.16 electrons per Mn site during the battery operation. Our analysis provides a clear understanding of the fundamental redox process involved in the working of a lithium ion battery.
description: 24 pages, 3 figures
Regulation of the Subcellular Localization of the G-protein Subunit Regulator GPSM3 through Direct Association with 14-3-3 Protein
Creators: name: Siderovski, David P.
name: Laroche, Geneviève
name: Duncan, Joseph A.
name: Giguère, Patrick M.
name: Oestreich, Emily A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: G-protein signaling modulator-3 (GPSM3), also known as G18 or AGS4, is a member of the Gαi/o-Loco (GoLoco) motif containing proteins. GPSM3 acts through its two GoLoco motifs to exert GDP dissociation inhibitor activity over Gαi subunits; recently revealed is the existence of an additional regulatory site within GPSM3 directed toward monomeric Gβ subunits during their biosynthesis. Here, using in silico and proteomic approaches, we have found that GPSM3 also interacts directly with numerous members of the 14-3-3 protein family. This interaction is dependent on GPSM3 phosphorylation, creating a mode II consensus 14-3-3 binding site. 14-3-3 binding to the N-terminal disordered region of GPSM3 confers stabilization from protein degradation. The complex of GPSM3 and 14-3-3 is exclusively cytoplasmic, and both moieties mutually control their exclusion from the nucleus. Phosphorylation of GPSM3 by a proline-directed serine/threonine kinase and the resultant association of 14-3-3 is the first description of post-translational regulation of GPSM3 subcellular localization, a process that likely regulates important spatio-temporal aspects of G-protein-coupled receptor signaling modulation by GPSM3.
Additional file 14 of Optimal experimental designs for estimating genetic and non-genetic effects underlying infectious disease transmission
Creators: name: Pooley, Christopher
name: Marion, Glenn
name: Bishop, Stephen
name: Doeschl-Wilson, Andrea
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Additional file 14: Fig. S11. Figure S11 investigates the addition of a single large fixed effect with elements in the design matrix X set in such a way as to give a certain degree of correlation with the SNP.
Automated weighing by sequential inference in dynamic environments
Creators: name: Martin, A. D.
name: Molteno, T. C. A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: We demonstrate sequential mass inference of a suspended bag of milk powder from simulated measurements of the vertical force component at the pivot while the bag is being filled. We compare the predictions of various sequential inference methods both with and without a physics model to capture the system dynamics. We find that non-augmented and augmented-state unscented Kalman filters (UKFs) in conjunction with a physics model of a pendulum of varying mass and length provide rapid and accurate predictions of the milk powder mass as a function of time. The UKFs outperform the other method tested - a particle filter. Moreover, inference methods which incorporate a physics model outperform equivalent algorithms which do not.
description: 5 pages, 7 figures. Copyright IEEE (2015)
Additional file 15 of Optimal experimental designs for estimating genetic and non-genetic effects underlying infectious disease transmission
Creators: name: Pooley, Christopher
name: Marion, Glenn
name: Bishop, Stephen
name: Doeschl-Wilson, Andrea
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Biotechnology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Additional file 15: Rather than defining the proportions of genotypes in the seeder and contact populations, we consider the case in which individual genotypes are randomly allocated with A allele having frequency p, assuming Hardy-Weinberg equilibrium. Fig. S12. Precision estimates for the SNP parameters with random genotype allocation.
Assortativity and leadership emergence from anti-preferential attachment in heterogeneous networks
Creators: name: Sendiña-Nadal, I.
name: Danziger, M. M.
name: Wang, Z.
name: Havlin, S.
name: Boccaletti, S.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Social and Information Networks (cs.SI)
subject: Adaptation and Self-Organizing Systems (nlin.AO)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: Many real-world networks exhibit degree-assortativity, with nodes of similar degree more likely to link to one another. Particularly in social networks, the contribution to the total assortativity varies with degree, featuring a distinctive peak slightly past the average degree. The way traditional models imprint assortativity on top of pre-defined topologies is via degree-preserving link permutations, which however destroy the particular graph's hierarchical traits of clustering. Here, we propose the first generative model which creates heterogeneous networks with scale-free-like properties and tunable realistic assortativity. In our approach, two distinct populations of nodes are added to an initial network seed: one (the followers) that abides by usual preferential rules, and one (the potential leaders) connecting via anti-preferential attachments, i.e. selecting lower degree nodes for their initial links. The latter nodes come to develop a higher average degree, and convert eventually into the final hubs. Examining the evolution of links in Facebook, we present empirical validation for the connection between the initial anti-preferential attachment and long term high degree. Thus, our work sheds new light on the structure and evolution of social networks.
The scabini in historiographical perspective
Creators: name: Hicklin, Alice
Publisher: name: Freie Universität Berlin
Year: 2020
Subjects: subject: scabini
subject: 900 Geschichte und Geografie::900 Geschichte::900 Geschichte und Geografie

description: The introduction of the scabini, men who served as judgement finders, has long been connected to judicial reform enacted by Charlemagne. By the thirteenth century, the term scabini had become synonymous with legal culture and courts from Norway to Hungary and beyond. This article will trace the scabini from historiographical debates over their provenance, to their introduction under Charlemagne, why and how this change was enacted, their duties and the impact of the reform on terminology and the writing of documentary texts. This touches on keystones of changing historiographical perspectives of the Carolingians: from nineteenth‐century views of a ‘Germanic’ past that privileged collective judgement to twentieth‐century emphasis on the written word as a mode of governance and the relationship between Charlemagne and the aristocracy, and recent attention to the function of capitularies in tenth‐century western Europe. It will explore the alleged disappearance of the scabini, a development that is connected in scholarship to nothing less significant than debates concerning the feudal revolution, before considering areas for future study.
Growth of Wide-Bandgap Monolayer Molybdenum Disulfide for a Highly Sensitive Micro-Displacement Sensor
Creators: name: Huang, Jiahai
name: Wu, Yizhang
name: Hao, Huimin
name: Wang, Shaopeng
Publisher: name: MDPI
Year: 2024

description: Two-dimensional (2D) piezoelectric semiconductor materials are garnering significant attention in applications such as intelligent sensing and energy harvesting due to their exceptional physical and chemical properties. Among these, molybdenum disulfide (MoS2), a 2D wide-bandgap semiconductor, exhibits piezoelectricity in odd-layered structures due to the absence of an inversion symmetry center. In this study, we present a straightforward chemical vapor deposition (CVD) technique to synthesize monolayer MoS2 on a Si/SiO2 substrate, achieving a lateral size of approximately 50 µm. Second-harmonic generation (SHG) characterization confirms the non-centrosymmetric crystal structure of the wide-bandgap MoS2, indicative of its piezoelectric properties. We successfully transferred the triangular MoS2 to a polyethylene terephthalate (PET) flexible substrate using a wet-transfer method and developed a wide-bandgap MoS2-based micro-displacement sensor employing maskless lithography and hot evaporation techniques. Our testing revealed a piezoelectric response current of 5.12 nA in the sensor under a strain of 0.003% along the armchair direction of the monolayer MoS2. Furthermore, the sensor exhibited a near-linear relationship between the piezoelectric response current and the strain within a displacement range of 40–100 µm, with a calculated response sensitivity of 1.154 µA/%. This research introduces a novel micro-displacement sensor, offering potential for advanced surface texture sensing in various applications.
Light‐Promoted Organocatalysis with N‐Heterocyclic Carbenes
Creators: name: Mavroskoufis, Andreas
name: Jakob, Michael
name: Hopkinson, Matthew N.
Publisher: name: Freie Universität Berlin
Year: 2020
Subjects: subject: N-Heterocyclic carbenes
subject: organocatalysis
subject: photochemistry
subject: photoredox catalysis
subject: single electron transfer
subject: 500 Naturwissenschaften und Mathematik::540 Chemie::540 Chemie und zugeordnete Wissenschaften

description: The combination of N‐heterocyclic carbene (NHC)‐organocatalysis with photochemical activation can lead to unprecedented reaction pathways not observed without light. A selection of dual catalytic systems merging NHCs with photoredox catalysis, for example, have leveraged the ability of NHCs to stabilize intermediate radical species and facilitate single electron transfer events. Furthermore, NHCs can transiently modulate the photochemical properties of a substrate and enable direct absorption of otherwise photoinactive organic compounds. In this Concept article, the recent advances in this rapidly developing field are summarized. For each transformation, a particular focus is placed on the mechanistic aspects of the process while key features that highlight the synthetic potential of the light mediated NHC organocatalysis are presented.
New constraints on the formation of lunar mafic impact melt breccias from S‐Se‐Te and highly siderophile elements
Creators: name: Gleißne, Philipp
name: Becker, Harry
Publisher: name: Freie Universität Berlin
Year: 2020
Subjects: subject: highly siderophile elements
subject: S‐Se‐Te
subject: 500 Naturwissenschaften und Mathematik::550 Geowissenschaften, Geologie::551 Geologie, Hydrologie, Meteorologie

description: Mass fractions of the siderophile volatile elements S, Se, and Te were determined together with highly siderophile elements (HSE) and osmium isotope ratios in multiple aliquots of five lunar mafic impact melt breccias. The impactites were sampled from presumably Imbrium‐related ejecta deposits at the Apollo 14, 15, and 16 landing sites. As in many mafic impact melt breccias, all studied impactites display fractionated siderophile element patterns characteristic of differentiated metal, interpreted to reflect metal‐rich impactor material from the core of a differentiated planetesimal. The compositional record of Fra Mauro crystalline matrix breccias and recent constraints on the time of their formation suggest that the admixture of this differentiated metal component to the Procellarum KREEP Terrane occurred before the Imbrium basin was formed. The impact melt rock portion of dimict breccia 61015 displays fractionations of HSE like other mafic impact melt breccias, but CI chondrite‐like ratios of S, Se, Te, and Ir. Preservation of these contrasting impactor signatures in a single impactite sample demonstrates mixing of differentiated metal and CI chondrite‐like impactor material and their homogenization in an impact melt sheet. Correlations of highly siderophile element ratios between impactites from different Apollo landing sites suggest that siderophile element inventories of many lunar impactites were affected by similar mixing processes. Mass fractions and ratios of S, Se, and Te in other mafic impact melt breccias closely resemble those of pristine mafic target rocks.
Regulator of G-protein Signaling-21 (RGS21) Is an Inhibitor of Bitter Gustatory Signaling Found in Lingual and Airway Epithelia
Creators: name: Arshavsky, Vadim Y.
name: Cohen, Staci P.
name: Bosch Jr., Dustin E.
name: Willard, Francis S.
name: Garland, Alaina L.
name: Siderovski, David P.
name: Buckley, Brian K.
name: Kimple, Adam J.
name: Kosloffs, Mickey
name: Cheng, Gang
name: Radhakrishna, Harish
name: Brown, Michael D.
name: Tarran, Robert
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: The gustatory system detects tastants and transmits signals to the brain regarding ingested substances and nutrients. Although tastant receptors and taste signaling pathways have been identified, little is known about their regulation. Because bitter, sweet, and umami taste receptors are G protein-coupled receptors (GPCRs), we hypothesized that regulators of G protein signaling (RGS) proteins may be involved. The recent cloning of RGS21 from taste bud cells has implicated this protein in the regulation of taste signaling; however, the exact role of RGS21 has not been precisely defined. Here, we sought to determine the role of RGS21 in tastant responsiveness. Biochemical analyses confirmed in silico predictions that RGS21 acts as a GTPase-accelerating protein (GAP) for multiple G protein α subunits, including adenylyl cyclase-inhibitory (Gαi) subunits and those thought to be involved in tastant signal transduction. Using a combination of in situ hybridization, RT-PCR, immunohistochemistry, and immunofluorescence, we demonstrate that RGS21 is not only endogenously expressed in mouse taste buds but also in lung airway epithelial cells, which have previously been shown to express components of the taste signaling cascade. Furthermore, as shown by reverse transcription-PCR, the immortalized human airway cell line 16HBE was found to express transcripts for tastant receptors, RGS21, and downstream taste signaling components. Over- and underexpression of RGS21 in 16HBE cells confirmed that RGS21 acts to oppose bitter tastant signaling to cAMP and calcium second messenger changes. Our data collectively suggests that RGS21 modulates bitter taste signal transduction.
Resolving Holliday Junctions with Escherichia coli UvrD Helicase
Creators: name: Compton, Sarah A.
name: Carter, Annamarie S.
name: Matson, Steven W.
name: Tahmaseb, Kambiz
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: The Escherichia coli UvrD helicase is known to function in the mismatch repair and nucleotide excision repair pathways and has also been suggested to have roles in recombination and replication restart. The primary intermediate DNA structure in these two processes is the Holliday junction. UvrD has been shown to unwind a variety of substrates including partial duplex DNA, nicked DNA, forked DNA structures, blunt duplex DNA and RNA-DNA hybrids. Here, we demonstrate that UvrD also catalyzes the robust unwinding of Holliday junction substrates. To characterize this unwinding reaction we have employed steady-state helicase assays, pre-steady-state rapid quench helicase assays, DNaseI footprinting, and electron microscopy. We conclude that UvrD binds initially to the junction compared with binding one of the blunt ends of the four-way junction to initiate unwinding and resolves the synthetic substrate into two double-stranded fork structures. We suggest that UvrD, along with its mismatch repair partners, MutS and MutL, may utilize its ability to unwind Holliday junctions directly in the prevention of homeologous recombination. UvrD may also be involved in the resolution of stalled replication forks by unwinding the Holliday junction intermediate to allow bypass of the blockage.