cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
(400684) James Carmichael
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.
Review of evidence for adaptation to sperm competition in three major domesticates from Sperm competition as an under-appreciated factor in domestication
Creators: name: Ardern Hulme-Beaman
name: Searle, Jeremy B.
name: Stockley, Paula
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
subject: 60801 Animal Behaviour

description: Here we provide a brief review of evidence for sperm competition in dogs, cats and pigs. The evidence indicates that there are different levels of promiscuity between these domesticates and their wild counterparts. We further go on to illustrate that there is significant evidence that this promiscuity and changes in mating behaviour has resulted in adaptations that are likely associated with selective pressures for sperm competition in the domestic animals, but not in their wild counterparts.
Variation-preserving normalization unveils blind spots in gene expression profiling
Creators: name: Roca, Carlos P.
name: Gomes, Susana I. L.
name: Amorim, Mónica J. B.
name: Scott-Fordsmand, Janeck J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Populations and Evolution (q-bio.PE)
subject: Quantitative Methods (q-bio.QM)
subject: Applications (stat.AP)
subject: FOS: Biological sciences
subject: FOS: Computer and information sciences

description: RNA-Seq and gene expression microarrays provide comprehensive profiles of gene activity, but lack of reproducibility has hindered their application. A key challenge in the data analysis is the normalization of gene expression levels, which is currently performed following the implicit assumption that most genes are not differentially expressed. Here, we present a mathematical approach to normalization that makes no assumption of this sort. We have found that variation in gene expression is much larger than currently believed, and that it can be measured with available assays. Our results also explain, at least partially, the reproducibility problems encountered in transcriptomics studies. We expect that this improvement in detection will help efforts to realize the full potential of gene expression profiling, especially in analyses of cellular processes involving complex modulations of gene expression.
description: 92 pages, 15 figures, 2 tables, includes supplementary materials
Supplementary Material from Excision of the doubly methylated base N4,5-dimethylcytosine from DNA by Escherichia coli Nei and Fpg proteins.
Creators: name: Alexeeva, Marina
name: Prashanna Guragain
name: Tesfahun, Almaz N.
name: Miglė Tomkuvienė
name: Arshad, Aysha
name: Rūta Gerasimaitė
name: Audronė Rukšėnaitė
name: Giedrė Urbanavičiūtė
name: Bjørås, Magnar
name: Laerdahl, Jon K.
name: Klungland, Arne
name: Klimašauskas, Saulius
name: Bjelland, Svein
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology

description: Repair enzyme details and Supplementary Figures S1-S9
Gene-centric meta-analyses of 108 912 individuals confirm known body mass index loci and reveal three novel signals
Creators: name: Guo, Yiran
name: Keating, Brendan J.
name: Taylor, Kira C.
name: Hakonarson, Hakon
name: Lange, Leslie A.
name: Lanktree, Matthew B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Recent genetic association studies have made progress in uncovering components of the genetic architecture of the body mass index (BMI). We used the ITMAT-Broad-Candidate Gene Association Resource (CARe) (IBC) array comprising up to 49 320 single nucleotide polymorphisms (SNPs) across ∼2100 metabolic and cardiovascular-related loci to genotype up to 108 912 individuals of European ancestry (EA), African-Americans, Hispanics and East Asians, from 46 studies, to provide additional insight into SNPs underpinning BMI. We used a five-phase study design: Phase I focused on meta-analysis of EA studies providing individual level genotype data; Phase II performed a replication of cohorts providing summary level EA data; Phase III meta-analyzed results from the first two phases; associated SNPs from Phase III were used for replication in Phase IV; finally in Phase V, a multi-ethnic meta-analysis of all samples from four ethnicities was performed. At an array-wide significance (P < 2.40E-06), we identify novel BMI associations in loci translocase of outer mitochondrial membrane 40 homolog (yeast) - apolipoprotein E - apolipoprotein C-I (TOMM40-APOE-APOC1) (rs2075650, P = 2.95E-10), sterol regulatory element binding transcription factor 2 (SREBF2, rs5996074, P = 9.43E-07) and neurotrophic tyrosine kinase, receptor, type 2 [NTRK2, a brain-derived neurotrophic factor (BDNF) receptor gene, rs1211166, P = 1.04E-06] in the Phase IV meta-analysis. Of 10 loci with previous evidence for BMI association represented on the IBC array, eight were replicated, with the remaining two showing nominal significance. Conditional analyses revealed two independent BMI-associated signals in BDNF and melanocortin 4 receptor (MC4R) regions. Of the 11 array-wide significant SNPs, three are associated with gene expression levels in both primary B-cells and monocytes; with rs4788099 in SH2B adaptor protein 1 (SH2B1) notably being associated with the expression of multiple genes in cis. These multi-ethnic meta-analyses expand our knowledge of BMI genetics.
Polaritons are Not Weakly Interacting: Direct Measurement of the Polariton-Polariton Interaction Strength
Creators: name: Sun, Yongbao
name: Yoon, Yoseob
name: Steger, Mark
name: Liu, Gangqiang
name: Pfeiffer, Loren N.
name: West, Ken
name: Snoke, David W.
name: Nelson, Keith A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Exciton-polaritons in a microcavity are composite two-dimensional bosonic quasiparticles, arising from the strong coupling between confined light modes in a resonant planar optical cavity and excitonic transitions, typically using excitons in semiconductor quantum wells (QWs) placed at the antinodes of the same cavity. Quantum phenomena such as Bose-Einstein condensation (BEC), quantized vortices, and macroscopic quantum states have been reported at temperatures from tens of Kelvin up to room temperatures, and polaritonic devices such as spin switches \cite{Amo2010} and optical transistors have also been reported. Many of these effects of exciton-polaritons depend crucially on the polariton-polariton interaction strength. Despite the importance of this parameter, it has been difficult to make an accurate experimental measurement, mostly because of the difficulty of determining the absolute densities of polaritons and bare excitons. Here we report the direct measurement of the polariton-polariton interaction strength in a very high-Q microcavity structure. By allowing polaritons to propagate over 40 $μ$m to the center of a laser-generated annular trap, we are able to separate the polariton-polariton interactions from polariton-exciton interactions. The interaction strength is deduced from the energy renormalization of the polariton dispersion as the polariton density is increased, using the polariton condensation as a benchmark for the density. We find that the interaction strength is about two orders of magnitude larger than previous theoretical estimates, putting polaritons squarely into the strongly-interacting regime. When there is a condensate, we see a sharp transition to a different dependence of the renormalization on the density, which is evidence of many-body effects.
description: 27 pages, 14 figures
Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network
Creators: name: Lange, Leslie
name: Ziv, Elad
name: Zonderman, Alan B.
name: Li, Jin
name: Loos, Ruth J.F.
name: Nalls, Michael A.
name: Thomson, Cynthia
name: van Rooij, Frank J.A.
name: Rasmussen-Torvik, Laura
name: Singleton, Andrew B.
name: Gottesman, Omri
name: Schick, Ursula M.
name: Ruderfer, Douglas M.
name: Okada, Yukinori
name: Keller, Margaux F.
name: Yanek, Lisa R.
name: Evans, Michele
name: Bottinger, Erwin P.
name: Ganesh, Santhi
name: Hakonarson, Hakon
name: Handsaker, Robert
name: Papanicolaou, George
name: Linderman, Michael D.
name: Meng, Yan
name: McCarroll, Steven
name: Tang, Hua
name: Keating, Brendan
name: Sleiman, Patrick M.A.
name: Kubo, Michiaki
name: Lu, Yingchang
name: Chen, Zhao
name: Qayyum, Rehan
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Laboratory red blood cell (RBC) measurements are clinically important, heritable and differ among ethnic groups. To identify genetic variants that contribute to RBC phenotypes in African Americans (AAs), we conducted a genome-wide association study in up to ∼16 500 AAs. The alpha-globin locus on chromosome 16pter [lead SNP rs13335629 in ITFG3 gene; P < 1E−13 for hemoglobin (Hgb), RBC count, mean corpuscular volume (MCV), MCH and MCHC] and the G6PD locus on Xq28 [lead SNP rs1050828; P < 1E − 13 for Hgb, hematocrit (Hct), MCV, RBC count and red cell distribution width (RDW)] were each associated with multiple RBC traits. At the alpha-globin region, both the common African 3.7 kb deletion and common single nucleotide polymorphisms (SNPs) appear to contribute independently to RBC phenotypes among AAs. In the 2p21 region, we identified a novel variant of PRKCE distinctly associated with Hct in AAs. In a genome-wide admixture mapping scan, local European ancestry at the 6p22 region containing HFE and LRRC16A was associated with higher Hgb. LRRC16A has been previously associated with the platelet count and mean platelet volume in AAs, but not with Hgb. Finally, we extended to AAs the findings of association of erythrocyte traits with several loci previously reported in Europeans and/or Asians, including CD164 and HBS1L-MYB. In summary, this large-scale genome-wide analysis in AAs has extended the importance of several RBC-associated genetic loci to AAs and identified allelic heterogeneity and pleiotropy at several previously known genetic loci associated with blood cell traits in AAs.
Proof of the Wilf-Zeilberger Conjecture for Mixed Hypergeometric Terms
Creators: name: Chen, Shaoshi
name: Koutschan, Christoph
Publisher: name: arXiv
Year: 2015
Subjects: subject: Combinatorics (math.CO)
subject: Symbolic Computation (cs.SC)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences
subject: 33C70, 33F10

description: In 1992, Wilf and Zeilberger conjectured that a hypergeometric term in several discrete and continuous variables is holonomic if and only if it is proper. Strictly speaking the conjecture does not hold, but it is true when reformulated properly: Payne proved a piecewise interpretation in 1997, and independently, Abramov and Petkovsek in 2002 proved a conjugate interpretation. Both results address the pure discrete case of the conjecture. In this paper we extend their work to hypergeometric terms in several discrete and continuous variables and prove the conjugate interpretation of the Wilf-Zeilberger conjecture in this mixed setting.
description: 20 pages, 1 figure
(400685) Grace Henderson
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.
Tagging Spallation Backgrounds with Showers in Water-Cherenkov Detectors
Creators: name: Li, Shirley Weishi
name: Beacom, John F.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: High Energy Physics - Experiment (hep-ex)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Cosmic-ray muons and especially their secondaries break apart nuclei ("spallation") and produce fast neutrons and beta-decay isotopes, which are backgrounds for low-energy experiments. In Super-Kamiokande, these beta decays are the dominant background in 6--18 MeV, relevant for solar neutrinos and the diffuse supernova neutrino background. In a previous paper, we showed that these spallation isotopes are produced primarily in showers, instead of in isolation. This explains an empirical spatial correlation between a peak in the muon Cherenkov light profile and the spallation decay, which Super-Kamiokande used to develop a new spallation cut. However, the muon light profiles that Super-Kamiokande measured are grossly inconsistent with shower physics. We show how to resolve this discrepancy and how to reconstruct accurate profiles of muons and their showers from their Cherenkov light. We propose a new spallation cut based on these improved profiles and quantify its effects. Our results can significantly benefit low-energy studies in Super-Kamiokande, and will be especially important for detectors at shallower depths, like the proposed Hyper-Kamiokande.
description: 17 pages, 11 figures, comments are welcome; minor changes; version accepted for publication in Phys. Rev. D
Gene-centric meta-analyses for central adiposity traits in up to 57 412 individuals of European descent confirm known loci and reveal several novel associations
Creators: name: Beitelshees, Amber
name: Padmanabhan, Sandosh
name: Peters, Annette
name: Barnes, Michael R.
name: O'Connell, Jeffrey R.
name: Karczewski, Konrad J
name: Monda, Keri L.
name: Bauer, Florianne
name: Lamonte, Michael J.
name: Guo, Yiran
name: Peter, Inga
name: Shaffer, Jonathan
name: Boer, Jolanda M.A.
name: Gong, Yan
name: Elbers, Clara C.
name: Gieger, Christian
name: Burke, Gregory
name: Lanktree, Matthew B.
name: Cooper-Dehoff, Rhonda M.
name: Heard-Costa, Nancy
name: Mcdonough, Caitrin
name: Gorski, Mathias
name: Onland-Moret, N. Charlotte
name: Berenson, Gerald S.
name: Chen, Wei
name: Yoneyama, Sachiko
name: Cade, Brian
name: Baumert, Jens
name: Ordovas, Jose
name: Johnson, Toby
name: Nelson, Christopher P.
name: Gaunt, Tom R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Waist circumference (WC) and waist-to-hip ratio (WHR) are surrogate measures of central adiposity that are associated with adverse cardiovascular events, type 2 diabetes and cancer independent of body mass index (BMI). WC and WHR are highly heritable with multiple susceptibility loci identified to date. We assessed the association between SNPs and BMI-adjusted WC and WHR and unadjusted WC in up to 57 412 individuals of European descent from 22 cohorts collaborating with the NHLBI's Candidate Gene Association Resource (CARe) project. The study population consisted of women and men aged 20–80 years. Study participants were genotyped using the ITMAT/Broad/CARE array, which includes ∼50 000 cosmopolitan tagged SNPs across ∼2100 cardiovascular-related genes. Each trait was modeled as a function of age, study site and principal components to control for population stratification, and we conducted a fixed-effects meta-analysis. No new loci for WC were observed. For WHR analyses, three novel loci were significantly associated (P < 2.4 × 10−6). Previously unreported rs2811337-G near TMCC1 was associated with increased WHR (β ± SE, 0.048 ± 0.008, P = 7.7 × 10−9) as was rs7302703-G in HOXC10 (β = 0.044 ± 0.008, P = 2.9 × 10−7) and rs936108-C in PEMT (β = 0.035 ± 0.007, P = 1.9 × 10−6). Sex-stratified analyses revealed two additional novel signals among females only, rs12076073-A in SHC1 (β = 0.10 ± 0.02, P = 1.9 × 10−6) and rs1037575-A in ATBDB4 (β = 0.046 ± 0.01, P = 2.2 × 10−6), supporting an already established sexual dimorphism of central adiposity-related genetic variants. Functional analysis using ENCODE and eQTL databases revealed that several of these loci are in regulatory regions or regions with differential expression in adipose tissue.
Scaling limit for a long-range divisible sandpile
Creators: name: Frómeta, Susana
name: Jara, Milton
Publisher: name: arXiv
Year: 2015
Subjects: subject: Analysis of PDEs (math.AP)
subject: Probability (math.PR)
subject: FOS: Mathematics
subject: 60K35, 31C20, 35R35

description: We study the scaling limit of a divisible sandpile model associated to a truncated $α$-stable random walk. We prove that the limiting distribution is related to an obstacle problem for a truncated fractional Laplacian. We also provide, as a fundamental tool, precise asymptotic expansions for the corresponding rescaled discrete Green's functions. In particular, the convergence rate of these Green's functions to its continuous counterpart is derived.
description: 45 pages
Cancer Risks for MLH 1 and MSH 2 Mutation Carriers
Creators: name: Gunawardena, Shanaka R.
name: Gallinger, Steve
name: Casey, Graham
name: Thibodeau, Stephen N.
name: Gattas, Michael
name: Lindor, Noralane M.
name: Clendenning, Mark
name: Baron, John A.
name: James, Paul A.
name: Parry, Susan
name: Giles, Graham G.
name: Antill, Yoland C.
name: Boussioutas, Alex
name: Marchand, Loic Le
name: Win, Aung K.
name: Leggett, Barbara A.
name: Dowty, James G.
name: Buchanan, Daniel D.
name: Haile, Robert W.
name: Newcomb, Polly A.
name: Young, Graeme P.
name: Goldblatt, Jack
name: Young, Joanne P.
name: Jenkins, Mark A.
name: Macrae, Finlay A.
name: Hopper, John L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: We studied 17,576 members of 166 MLH1 and 224 MSH2 mutation-carrying families from the Colon Cancer Family Registry. Average cumulative risks of colorectal cancer (CRC), endometrial cancer (EC) and other cancers for carriers were estimated using modified segregation analysis conditioned on ascertainment criteria. Heterogeneity in risks was investigated using a polygenic risk modifier. Average CRC cumulative risks to age 70 years (95% confidence intervals) for MLH1 and MSH2 mutation carriers, respectively, were estimated to be 34% (25%-50%) and 47% (36%-60%) for male carriers and 36% (25%-51%) and 37% (27%-50%) for female carriers. Corresponding EC risks were 18% (9.1%-34%) and 30% (18%-45%). A high level of CRC risk heterogeneity was observed (p<0.001), with cumulative risks to age 70 years estimated to follow U-shaped distributions. For example 17% of male MSH2 mutation carriers have estimated lifetime risks of 0-10% while 18% have risks of 90-100%. Therefore, average risks are similar for the two genes but there is so much individual variation about the average that large proportions of carriers have either very low or very high lifetime cancer risks. Our estimates of CRC and EC cumulative risks for MLH1 and MSH2 mutation carriers are the most precise currently available.
Founder Mutation in RSPH4A Identified in Patients of Hispanic Descent with Primary Ciliary Dyskinesia
Creators: name: Knowles, Michael R.
name: Collins, Francis S.
name: Leigh, Margaret W.
name: Dell, Sharon D.
name: Hazucha, Milan
name: Carson, Johnny L.
name: Zariwala, Maimoona A.
name: Armstrong, Michael C.
name: Davis, Stephanie D.
name: Daniels, M. Leigh Anne
name: Eriksson, Maria
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Primary ciliary dyskinesia (PCD) is a rare, autosomal recessive, genetically heterogeneous disorder characterized by ciliary dysfunction resulting in chronic oto-sino-pulmonary disease, respiratory distress in term neonates, laterality (situs) defects, and bronchiectasis. Diagnosis has traditionally relied on ciliary ultrastructural abnormalities seen by electron microscopy. Mutations in radial spoke head proteins occur in PCD patients with central apparatus defects. Advances in genetic testing have been crucial in addressing the diagnostic challenge. Here, we describe a novel splice-site mutation (c.921+3_6delAAGT) in RSPH4A, which leads to a premature translation termination signal in nine subjects with PCD (seven families). Loss-of-function was confirmed with quantitative ciliary ultrastructural analysis, measurement of ciliary beat frequency and waveform, and transcript analysis. All nine individuals carrying c.921+3_6delAAGT splice-site mutation in RSPH4A were Hispanic with ancestry tracing to Puerto Rico. This mutation is a founder mutation and a common cause of PCD without situs abnormalities in patients of Puerto Rican descent.
Supplementary Material from Excision of the doubly methylated base N4,5-dimethylcytosine from DNA by Escherichia coli Nei and Fpg proteins
Creators: name: Alexeeva, Marina
name: Prashanna Guragain
name: Tesfahun, Almaz N.
name: Miglė Tomkuvienė
name: Arshad, Aysha
name: Rūta Gerasimaitė
name: Audronė Rukšėnaitė
name: Giedrė Urbanavičiūtė
name: Bjørås, Magnar
name: Laerdahl, Jon K.
name: Klungland, Arne
name: Klimašauskas, Saulius
name: Bjelland, Svein
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology

description: Repair enzyme details and Supplementary Figures S1-S9
The Equivalence Principle in a Quantum World
Creators: name: Bjerrum-Bohr, N. E. J.
name: Donoghue, John F.
name: El-Menoufi, Basem Kamal
name: Holstein, Barry R.
name: Planté, Ludovic
name: Vanhove, Pierre
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We show how modern methods can be applied to quantum gravity at low energy. We test how quantum corrections challenge the classical framework behind the Equivalence Principle, for instance through introduction of non-locality from quantum physics, embodied in the Uncertainty Principle. When the energy is small we now have the tools to address this conflict explicitly. Despite the violation of some classical concepts, the EP continues to provide the core of the quantum gravity framework through the symmetry - general coordinate invariance - that is used to organize the effective field theory.
description: 5 pages, Honorable Mention in the Gravity Research Foundation Essay Competition 2015
(400686) Harriet C Lyell
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.
Toxicity of pyrrolizidine alkaloids from Echium vulgare for honeybee larvae from Nursing protects honeybee larvae from secondary metabolites of pollen.
Creators: name: Lucchetti, Matteo A.
name: Kilchenmann, Verena
name: Glauser, Gaetan
name: Praz, Christophe
name: Kast, Christina
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Environmental Science
subject: Ecology
subject: FOS: Biological sciences
subject: Plant Biology

description: Extraction and purification of pyrrolizidine alkaloids from Echium vulgare, toxicity for honeybee larvae and estimation of the median lethal doses.
Kohlschütter-Tönz Syndrome: Mutations in ROGDI and Evidence of Genetic Heterogeneity
Creators: name: Houlden, Henry
name: Schossig, Anna
name: Hardy, John
name: Wimmer, Katharina
name: Tennison, Michael
name: Hayes, Ian
name: Hernandez, Dena
name: Hall, Roger
name: Paisán-Ruiz, Coro
name: Bast, Thomas
name: Lo, Chien-Ning
name: Tucci, Arianna
name: Palmeri, Silvia
name: Fawcett, Katherine
name: Tzschach, Andreas
name: Wolf, Nicole I.
name: Kara, Eleanna
name: Hordijk, Roel
name: Zschocke, Johannes
name: Singleton, Andrew
name: Raskin, Salmo
name: Hennig, Corina
name: Hennekam, Raoul
name: Plagnol, Vincent
name: Musumeci, Sebastiano
name: Donnai, Dian
name: Malandrini, Alessandro
name: Shorvon, Simon
name: Mefford, Heather
name: Eichler, Evan E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Kohlschütter–Tönz syndrome (KTS) is a rare autosomal recessive disorder characterized by amelogenesis imperfecta, psychomotor delay or regression and seizures starting early in childhood. KTS was established as a distinct clinical entity after the first report by Kohlschütter in 1974, and to date, only a total of 20 pedigrees have been reported. The genetic etiology of KTS remained elusive until recently when mutations in ROGDI were independently identified in three unrelated families and in five likely related Druze families. Herein, we report a clinical and genetic study of 10 KTS families. By using a combination of whole exome sequencing, linkage analysis, and Sanger sequencing, we identify novel homozygous or compound heterozygous ROGDI mutations in five families, all presenting with a typical KTS phenotype. The other families, mostly presenting with additional atypical features, were negative for ROGDI mutations, suggesting genetic heterogeneity of atypical forms of the disease.
Anatomy of the $ρ$ resonance from lattice QCD at the physical point
Creators: name: Sun, Wei
name: Alexandru, Andrei
name: Chen, Ying
name: Draper, Terrence
name: Liu, Zhaofeng
name: Yang, Yi-Bo
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: We propose a strategy to access the $q\bar{q}$ component of the $ρ$ resonance in lattice QCD. Through a mixed action formalism (overlap valence on domain wall sea), the energy of the $q\bar{q}$ component is derived at different valence quark masses, and shows a linear dependence on $m_π^2$. The slope is determined to be $c_1=0.505(3)\,{\rm GeV}^{-1}$, from which the valence $πρ$ sigma term is extracted to be $σ_{πρ}^{(\rm val)}=9.82(6)$ MeV using the Feynman-Hellman theorem. At the physical pion mass, the mass of the $q\bar{q}$ component is interpolated to be $m_ρ=775.9\pm 6.0\pm 1.8$ MeV, which is close to the $ρ$ resonance mass. We also obtain the leptonic decay constant of the $q\bar{q}$ component to be $f_{ρ^-}=208.5\pm 5.5\pm 0.9$ MeV, which can be compared with the experimental value $f_ρ^{\rm exp}\approx 221$ MeV through the relation $f_ρ^{\rm exp}=\sqrt{Z_ρ}f_{ρ^\pm} $ with $Z_ρ\approx 1.13$ being the on-shell wavefunction renormalization of $ρ$ owing to the $ρ-π$ interaction. We emphasize that $m_ρ$ and $f_ρ$ of the $q\bar{q}$ component, which are obtained for the first time from QCD, can be taken as the input parameters of $ρ$ in effective field theory studies where $ρ$ acts as a fundamental degree of freedom.
description: 7 pages, 4 figures. Considerably modified, more discussions, matching to the published version
(400682) David Lyell
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.
Toxicity of pyrrolizidine alkaloids from Echium vulgare for honeybee larvae from Nursing protects honeybee larvae from secondary metabolites of pollen
Creators: name: Lucchetti, Matteo A.
name: Kilchenmann, Verena
name: Glauser, Gaetan
name: Praz, Christophe
name: Kast, Christina
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Environmental Science
subject: Ecology
subject: FOS: Biological sciences
subject: Plant Biology

description: Extraction and purification of pyrrolizidine alkaloids from Echium vulgare, toxicity for honeybee larvae and estimation of the median lethal doses.
(400678) Charles Lyell
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.
Mutations in CCDC 39 and CCDC 40 are the Major Cause of Primary Ciliary Dyskinesia with Axonemal Disorganization and Absent Inner Dynein Arms
Creators: name: Scambler, Peter J.
name: Lucas, Jane S.
name: Shoemark, Amelia
name: Forouhan, Mitra
name: Jaspers, Martine
name: Leigh, Margaret W.
name: Taylor-Cox, Theresa
name: Goggin, Patricia
name: Daniels, M. Leigh Anne
name: O'Callaghan, Christopher
name: Chung, Eddie M.K.
name: Jackson, Claire
name: Schmidts, Miriam
name: Knowles, Michael R.
name: Zariwala, Maimoona A.
name: Olbrich, Heike
name: Jorissen, Mark
name: Dixit, Abhijit
name: Dewar, Ann
name: Antony, Dinu
name: Wilson, Robert
name: Becker-Heck, Anita
name: Onoufriadis, Alexandros
name: Noone, Peadar G.
name: Loges, Niki T.
name: Rosenfeld, Margaret
name: Emes, Richard D.
name: Wolf, Whitney E.
name: Ferkol, Thomas W.
name: Rutman, Andrew
name: Hogg, Claire
name: Sagel, Scott D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Primary ciliary dyskinesia (PCD) is a genetically heterogeneous disorder caused by cilia and sperm dysmotility. About 12% of cases show perturbed 9+2 microtubule cilia structure and inner dynein arm (IDA) loss, historically termed ‘radial spoke defect’. We sequenced CCDC39 and CCDC40 in 54 ‘radial spoke defect’ families, as these are the two genes identified so far to cause this defect. We discovered biallelic mutations in a remarkable 69% (37/54) of families, including identification of 25 (19 novel) mutant alleles (12 in CCDC39 and 13 in CCDC40). All the mutations were nonsense, splice and frameshift predicting early protein truncation, which suggests this defect is caused by ‘null’ alleles conferring complete protein loss. Most families (73%; 27/37) had homozygous mutations, including families from outbred populations. A major putative hotspot mutation was identified, CCDC40 c.248delC, as well as several other possible hotspot mutations. Together, these findings highlight the key role of CCDC39 and CCDC40 in PCD with axonemal disorganisation and IDA loss, and these genes represent major candidates for genetic testing in families affected by this ciliary phenotype. We show that radial spoke structures are largely intact in these patients and propose this ciliary ultrastructural abnormality be referred to as ‘IDA and nexin-dynein regulatory complex (N-DRC) defect’, rather than ‘radial spoke defect’.
Table S1. List of species involved in the analysis with their geographic distribution and their fire adaptations. from A biogeographic perspective on the evolution of fire syndromes in pine trees (Pinus: Pinaceae).
Creators: name: Badik, Kevin J.
name: Jahner, Joshua P.
name: Wilson, Joseph S.
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: This Table provides all of the biogeographic data and fire adaptation information for all of the Pine species included in the analysis. Some Pine species exhibit multiple different fire adaptations, these are all included in the table.
Quartic double solids with icosahedral symmetry
Creators: name: Cheltsov, Ivan
name: Przyjalkowski, Victor
name: Shramov, Constantin
Publisher: name: arXiv
Year: 2015
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14E07, 14J45, 14E08

description: We study quartic double solids admitting icosahedral symmetry.
description: 19 pages
Maternal risk factors for prematurity related neonatal mortality among preterm neonates admitted to Neonatal Intensive Care Unit of selected referral Hospitals in Addis Ababa, Ethiopia
Creators: name: Dirreba Gemeda
Publisher: name: Zenodo
Year: 2017

description: Background: The neonatal period is considered high risk period in terms of mortality. Globally, approximately 15 million infants are born prematurely each year, which is more than one tenth of all newborn infants. Mortality due to complications of prematurity is the leading cause of neonatal and children under five age death. Little is known about specific maternal risk factors for prematurity related neonate mortality. Objective: The aim of the proposed study was to identify risk factors for prematurity related neonate mortality.
Prioritization of Genetic Variants in the microRNA Regulome as Functional Candidates in Genome-Wide Association Studies
Creators: name: Selitsky, Sara
name: Bulik-Sullivan, Brendan
name: Sethupathy, Praveen
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Comprehensive analyses of results from genome-wide association studies (GWAS) have demonstrated that complex disease/trait-associated loci are enriched in gene regulatory regions of the genome. The search for causal regulatory variation has focused primarily on transcriptional elements, such as promoters and enhancers. microRNAs (miRNAs) are now widely appreciated as critical posttranscriptional regulators of gene expression and are thought to impart stability to biological systems. Naturally occurring genetic variation in the miRNA regulome is likely an important contributor to phenotypic variation in the human population. However, the extent to which polymorphic miRNA-mediated gene regulation underlies GWAS signals remains unclear. In this study, we have developed the most comprehensive bioinformatic analysis pipeline to date for cataloging and prioritizing variants in the miRNA regulome as functional candidates in GWAS. We highlight specific findings, including a variant in the promoter of the miRNA let-7 that may contribute to human height variation. We also provide a discussion of how our approach can be expanded in the future. Overall, we believe that the results of this study will be valuable for researchers interested in determining whether GWAS signals implicate the miRNA regulome in their disease/trait of interest.
Table S1. List of species involved in the analysis with their geographic distribution and their fire adaptations. from A biogeographic perspective on the evolution of fire syndromes in pine trees (Pinus: Pinaceae)
Creators: name: Badik, Kevin J.
name: Jahner, Joshua P.
name: Wilson, Joseph S.
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: This Table provides all of the biogeographic data and fire adaptation information for all of the Pine species included in the analysis. Some Pine species exhibit multiple different fire adaptations, these are all included in the table.
Wrinkling reveals a new isometry of pressurized elastic shells
Creators: name: Vella, Dominic
name: Ebrahimi, Hamid
name: Vaziri, Ashkan
name: Davidovitch, Benny
Publisher: name: arXiv
Year: 2015
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We consider the point indentation of a pressurized, spherical elastic shell. Previously it was shown that such shells wrinkle once the indentation reaches a threshold value. Here, we study the behaviour of this system beyond the onset of instability. We show that rather than simply approaching the classical `mirror-buckled' shape, the wrinkled shell approaches a new, universal shape that reflects a nontrivial type of isometry. For a given indentation depth, this ``asymptotic isometry", which is only made possible by wrinkling, is reached in the doubly asymptotic limit of weak pressure and vanishing shell thickness.
description: 6 pages main text plus 14 pages of supplementary information
Discovery and Functional Assessment of Gene Variants in the Vascular Endothelial Growth Factor Pathway
Creators: name: Skol, Andrew D.
name: Glubb, Dylan
name: Etheridge, Amy S.
name: Duan, Shiwei
name: Di Rienzo, Anna
name: Evans, Patrick
name: Gamazon, Eric R.
name: Berenguer-Llergo, Antoni
name: Paré-Brunet, Laia
name: Innocenti, Federico
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Angiogenesis is a host-mediated mechanism in disease pathophysiology. The vascular endothelial growth factor (VEGF) pathway is a major determinant of angiogenesis, and a comprehensive annotation of the functional variation in this pathway is essential to understand the genetic basis of angiogenesis-related diseases. We assessed the allelic heterogeneity of gene expression, population specificity of cis expression quantitative trait loci (eQTLs), and eQTL function in luciferase assays in CEU and YRI HapMap lymphoblastoid cell lines (LCLs) in 23 resequenced genes. Among 356 cis-eQTLs, 155 and 174 were unique to CEU and YRI, respectively, and 27 were shared between CEU and YRI. Two cis-eQTLs provided mechanistic evidence for two GWAS findings. Five eQTLs were tested for function in luciferase assays and the effect of two KRAS variants was concordant with the eQTL effect. Two eQTLs found in each of PRKCE, PIK3C2A, and MAP2K6, could predict 44, 37 and 45% of the variance in gene expression, respectively. This is the first analysis focusing on the pattern of functional genetic variation of the VEGF pathway genes in CEU and YRI populations and providing mechanistic evidence for genetic association studies of diseases for which angiogenesis plays a pathophysiologic role.
Large circulant graphs of fixed diameter and arbitrary degree
Creators: name: Bevan, David
name: Erskine, Grahame
name: Lewis, Robert
Publisher: name: arXiv
Year: 2015
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: 05C25, 05C35

description: We consider the degree-diameter problem for undirected and directed circulant graphs. To date, attempts to generate families of large circulant graphs of arbitrary degree for a given diameter have concentrated mainly on the diameter 2 case. We present a direct product construction yielding improved bounds for small diameters and introduce a new general technique for "stitching" together circulant graphs which enables us to improve the current best known asymptotic orders for every diameter. As an application, we use our constructions in the directed case to obtain upper bounds on the minimum size of a subset $A$ of a cyclic group of order $n$ such that the $k$-fold sumset $kA$ is equal to the whole group. We also present a revised table of largest known circulant graphs of small degree and diameter.
description: 17 pages, 3 tables, 1 figure. Updates to reflect referees' comments, revised tables and add journal ref
Entropy Production of Doubly Stochastic Quantum Channels
Creators: name: Müller-Hermes, Alexander
name: Franca, Daniel Stilck
name: Wolf, Michael M.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We study the entropy increase of quantum systems evolving under primitive, doubly stochastic Markovian noise and thus converging to the maximally mixed state. This entropy increase can be quantified by a logarithmic-Sobolev constant of the Liouvillian generating the noise. We prove a universal lower bound on this constant that stays invariant under taking tensor-powers. Our methods involve a new comparison method to relate logarithmic-Sobolev constants of different Liouvillians and a technique to compute logarithmic-Sobolev inequalities of Liouvillians with eigenvectors forming a projective representation of a finite abelian group. Our bounds improve upon similar results established before and as an application we prove an upper bound on continuous-time quantum capacities. In the last part of this work we study entropy production estimates of discrete-time doubly-stochastic quantum channels by extending the framework of discrete-time logarithmic-Sobolev inequalities to the quantum case.
description: 24 pages
Fitting Laguerre tessellation approximations to tomographic image data
Creators: name: Spettl, Aaron
name: Brereton, Tim
name: Duan, Qibin
name: Werz, Thomas
name: Krill, Carl E.
name: Kroese, Dirk P.
name: Schmidt, Volker
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Computation (stat.CO)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: The analysis of polycrystalline materials benefits greatly from accurate quantitative descriptions of their grain structures. Laguerre tessellations approximate such grain structures very well. However, it is a quite challenging problem to fit a Laguerre tessellation to tomographic data, as a high-dimensional optimization problem with many local minima must be solved. In this paper, we formulate a version of this optimization problem that can be solved quickly using the cross-entropy method, a robust stochastic optimization technique that can avoid becoming trapped in local minima. We demonstrate the effectiveness of our approach by applying it to both artificially generated and experimentally produced tomographic data.
description: 27 pages, 10 figures, 2 tables
(400680) George Lyell
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 Information from Hijacking DNA methyltransferase transition state analogues to produce chemical scaffolds for PRMTs inhibitors.
Creators: name: Halby, Ludovic
name: Marechal, Nils
name: Pechalrieu, Dany
name: Cura, Vincent
name: Don-Marc Franchini
name: Faux, Céline
name: Fréderic Alby
name: Troffer-Charlier, Nathalie
name: Srikanth Kudithipudi
name: Jeltsch, Albert
name: Aouadi, Wahiba
name: Decroly, Etienne
name: Guillemot, Jean-Claude
name: Page, Patrick
name: Ferroud, Clotilde
name: Bonnefond, Luc
name: Guianvarc'h, Dominique
name: Cavarelli, Jean
name: Arimondo, Paola B.
Publisher: name: The Royal Society
Year: 2018
Subjects: Biochemistry

description: NMR attribution, complementary Materials & Methods and Biological results
Coherent control of bond making: The performance of rationally phase-shaped femtosecond laser pulses
Creators: name: Levin, Liat
name: Skomorowski, Wojciech
name: Kosloff, Ronnie
name: Koch, Christiane P.
name: Amitay, Zohar
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: The first step in the coherent control of a photoinduced binary reaction is bond making or photoassociation. We have recently demonstrated coherent control of bond making in multi-photon femtosecond photoassociation of hot magnesium atoms, using linearly chirped pulses [Levin et al., arXiv:1411.1542]. The detected yield of photoassociated magnesium dimers was enhanced by positively chirped pulses which is explained theoretically by a combination of purification and chirp-dependent Raman transitions. The yield could be further enhanced by pulse optimization resulting in pulses with an effective linear chirp and a sub-pulse structure, where the latter allows for exploiting vibrational coherences. Here, we systematically explore the efficiency of phase-shaped pulses for the coherent control of bond making, employing a parametrization of the spectral phases in the form of cosine functions. We find up to an order of magnitude enhancement of the yield compared to the unshaped transform-limited pulse. The highly performing pulses all display an overall temporally increasing instantaneous frequency and are composed of several overlapping sub-pulses. The time delay between the first two sub-pulses almost perfectly fits the vibrational frequency of the generated intermediate wavepacket.These findings are in agreement with chirp-dependent Raman transitions and exploitation of vibrational dynamics as underlying control mechanisms.