cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
title: Knowledge management at the National Oceanography Centre: perspectives from an information specialist
Creators: name: Stephenson, Jane
Publisher: name: ASC 2010 - Theme session R
Year: 2024
Subjects: Ecosystem observation, processes and dynamics

description: No abstracts are to be cited without prior reference to the author.The National Oceanography Centre (NOC) is a newly established, national research organization, delivering world-class integrated marine science and technology from the coast to the deep ocean. Working in partnership with the UK marine research community, the NOC addresses key science challenges, including sea level change, the oceans’ role in climate change, predicting and simulating the behaviour of the oceans through computer modelling, development, the future of the Arctic Ocean, and long-term monitoring technologies. It is the UK’s leading institution for sea-level science, coastal and deep ocean research, and technology development. Its vision is to place UK marine science in a wider Earth system and socio-economic context, providing scientific knowledge that underpins policy development and wealth generation, and will aim to influence the European and global strategic research agenda. In this context, the National Oceanographic Library supports the mission of the organization and has developed and is developing strategies and processes to manage its knowledge and the knowledge needed to support the science. This includes managing research outputs, archives management, open access publishing, and knowledge transfer, desk-side training, bibliometrics, web delivery, collaborative work with data management, and access to published external information. This paper will present examples of these knowledge management strategies and processes, identifying strengths and challenges, as experienced within the National Oceanographic Centre.
The dopamine D1 receptor is expressed and induces CREB phosphorylation and MUC5AC expression in human airway epithelium
Creators: name: Matsuyama, Nao
name: Shibata, Sumire
name: Matoba, Atsuko
name: Kudo, Tada-Aki
name: Danielsson, Jennifer
name: Kohjitani, Atsushi
name: Masaki, Eiji
name: Emala, Charles W.
name: Mizuta, Kentaro
Publisher: name: Columbia University
Year: 2018
Subjects: Dopamine--Receptors
Epithelium
Biology
Anesthesiology

description: Background
Dopamine receptors comprise two subgroups, Gs protein-coupled “D1-like” receptors (D1, D5) and Gi-coupled “D2-like” receptors (D2, D3, D4). In airways, both dopamine D1 and D2 receptors are expressed on airway smooth muscle and regulate airway smooth muscle force. However, functional expression of the dopamine D1 receptor has never been identified on airway epithelium. Activation of Gs-coupled receptors stimulate adenylyl cyclase leading to cyclic AMP (cAMP) production, which is known to induce mucus overproduction through the cAMP response element binding protein (CREB) in airway epithelial cells. We questioned whether the dopamine D1 receptor is expressed on airway epithelium, and whether it promotes CREB phosphorylation and MUC5AC expression.

Methods
We evaluated the protein expression of the dopamine D1 receptor on native human airway epithelium and three sources of cultured human airway epithelial cells including primary cultured airway epithelial cells, the bronchial epithelial cell line (16HBE14o-), and the pulmonary mucoepidermoid carcinoma cell line (NCI-H292) using immunohistochemistry and immunoblotting. To characterize the stimulation of cAMP through the dopamine D1 receptor, 16HBE14o- cells and NCI-H292 cells were treated with dopamine or the dopamine D1 receptor agonists (SKF38393 or A68930) before cAMP measurements. The phosphorylation of CREB by A68930 in both 16HBE14o- and NCI-H292 cells was measured by immunoblot. The effect of dopamine or A68930 on the expression of MUC5AC mRNA and protein in NCI-H292 cells was evaluated by real-time PCR and immunofluorescence staining, respectively.

Results
The dopamine D1 receptor protein was detected in native human airway epithelium and three sources of cultured human airway epithelial cells. Dopamine or the dopamine D1-like receptor agonists stimulated cAMP production in 16HBE14o- cells and NCI-H292 cells, which was reversed by the selective dopamine D1-like receptor antagonists (SCH23390 or SCH39166). A68930 significantly increased phosphorylation of CREB in both 16HBE14o- and NCI-H292 cells, which was attenuated by the inhibitors of PKA (H89) and MEK (U0126). Expression of MUC5AC mRNA and protein were also increased by either dopamine or A68930 in NCI-H292 cells.

Conclusions
These results suggest that the activation of the dopamine D1 receptor on human airway epithelium could induce mucus overproduction, which could worsen airway obstructive symptoms.
A Group of Kiln Waste from Hardings Farm, Mill Green, Essex
Creators: name: M Meddens, Frank
name: Redknap, Mark
Publisher: name: Archaeology Data Service
Year: 2023

description: Medieval Ceramics: Journal of the Medieval Ceramics Research Group, 16, 11-44
description: Late 13th/14th-century Mill Green ware has been recognised on an increasing number of sites in south-east England. This paper presents a group of kiln waste from Harding's Farm, near Mill Green (Essex). A large part of the assemblage is composed of squat jugs with plain or carinated necks, decorated with geometric or 'vine scroll' designs in white slip. Courseware cooking pots and, to a lesser degree, bowls were also produced for local markets; unusual forms include culinary stamps and cauldrons. The dating of this ware, and the distribution, which is concentrated in south Essex, London and its environs, and north Kent, are also discussed in the light of recent finds.
Asymmetric velocity anisotropies in remnants of collisionless mergers
Creators: name: Sparre, Martin
name: Hansen, Steen H.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Dark matter haloes in cosmological N-body simulations are affected by processes such as mergers, accretion and the gravitational interaction with baryonic matter. Typically the analysis of dark matter haloes is performed in spherical or elliptical bins and the velocity distributions are often assumed to be constant within those bins. However, the velocity anisotropy, which describes differences between the radial and tangential velocity dispersion, has recently been show to have a strong dependence on direction in the triaxial halos formed in cosmological simulations. In this study we derive properties of particles in cones parallel or perpendicular to the collision axis of merger remnants. We find that the velocity anisotropy has a strong dependence on direction. The finding that the direction-dependence of the velocity anisotropy of a halo depends on the merger history, explains the existence of such trends in cosmological simulations. It also explains why a large diversity is seen in the velocity anisotropy profiles in the outer parts of high-resolution simulations of cosmological haloes.
description: 19 pages, 15 figures, Resubmitted to JCAP after referee comments
Symmetries of N=4 supersymmetric CP(n) mechanics
Creators: name: Bellucci, S.
name: Kozyrev, N.
name: Krivonos, S.
name: Sutulin, A.
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We explicitly constructed the generators of $SU(n+1)$ group which commute with the supercharges of N=4 supersymmetric $\mathbb{CP}^n$ mechanics in the background U(n) gauge fields. The corresponding Hamiltonian can be represented as a direct sum of two Casimir operators: one Casimir operator on $SU(n+1)$ group contains our bosonic and fermionic coordinates and momenta, while the second one, on the SU(1,n) group, is constructed from isospin degrees of freedom only.
description: 10 pages, PACS numbers: 11.30.Pb, 03.65.-w; minor changes in Introduction, references added
Almost commuting unitary matrices related to time reversal
Creators: name: Loring, Terry A.
name: Sørensen, Adam P. W.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Operator Algebras (math.OA)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Mathematics
subject: FOS: Physical sciences

description: The behavior of fermionic systems depends on the geometry of the system and the symmetry class of the Hamiltonian and observables. Almost commuting matrices arise from band-projected position observables in such systems. One expects the mathematical behavior of almost commuting Hermitian matrices to depend on two factors. One factor will be the approximate polynomial relations satisfied by the matrices. The other factor is what algebra the matrices are in, either the matrices over A for A the real numbers, A the complex numbers or A the algebra of quaternions. There are potential obstructions keeping k-tuples of almost commuting operators from being close to a commuting k-tuple. We consider two-dimensional geometries and so this obstruction lives in KO_{-2}(A). This obstruction corresponds to either the Chern number or spin Chern number in physics. We show that if this obstruction is the trivial element in K-theory then the approximation by commuting matrices is possible.
description: 33 pages, 2 figures. In version 2 some formulas have been corrected and some proofs have been rewritten to improve the exposition
Relativistic Corrections to the Exclusive Decays of C-even Bottomonia into S-wave Charmonium Pairs
Creators: name: Sang, Wen-Long
name: Rashidin, Reyima
name: Kim, U-Rae
name: Lee, Jungil
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Within the nonrelativistic quantum chromodynamics (NRQCD) factorization formalism, we compute the relativistic corrections to the exclusive decays of bottomonia with even charge conjugation parity into $S$-wave charmonium pairs at leading order in the strong coupling constant. Relativistic corrections are resummed for a class of color-singlet contributions to all orders in the charm-quark velocity $v_c$ in the charmonium rest frame. Almost every process that we consider in this work has negative relativistic corrections ranging from -20 to -35,%. Among the various processes, the relativistic corrections of the next-to-leading order in $v_c$ to the decay rate for $χ_{b2}\to η_c(mS)+η_c(nS)$ with $m,$ $n=1$ or 2 are very large. In every case, the resummation of the relativistic corrections enhances the rate in comparison with the next-to-leading-order results. We compare our results with available predictions based on the NRQCD factorization formalism. The NRQCD predictions are significantly smaller than those based on the light-cone formalism by an or two orders of magnitudes.
description: 20 pages, 1 figure. Typos corrected, published version
Additional file 1: of Cyclin-dependent kinase 5 acts as a promising biomarker in clear cell Renal Cell Carcinoma
Creators: name: Zhu, Liangsong
name: Ding, Rong
name: Zhang, Jianping
name: Zhang, Jin
name: Lin, Zongming
Publisher: name: figshare
Year: 2019
Subjects: subject: Space Science
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer

description: Figure S1. The mRNA expression of specific gene after LSD1 inhibition in ccRCC cell lines (RNA-seq data). Figure S2. Representative images of IHC staining of CDK5 and p21. Bar 100um. Figure S3. The comparation of overall survival rate of CHPH patients with others. Table S1. Patients’ information of the fresh samples. Age (range 42–72 years old). (DOCX 9 kb)
title: Using systematic review methodology to build an evidence-base for marine and fisheries policy
Creators: name: Pullin, Andrew S.
Publisher: name: ASC 2010 - Theme session R
Year: 2024
Subjects: Ecosystem observation, processes and dynamics

description: No abstracts are to be cited without prior reference to the author.There are a number of areas of environmental management, such as marine sciences and fisheries, where considerable evidence has been accumulated that might inform policy decisions. However, in policy areas where conflicting views are held by different stakeholders, fragments of evidence can be used to obfuscate the true picture and inhibit progress toward consensus solutions. Systematic review is a rigorous methodology designed to maximize transparency and minimize bias in developing an evidence base on questions of concern to policy and practice. The systematic review process is partly social and partly scientific and can be used to build consensus for action to address specific problems or contribute to strategic policy frameworks to address broad societal goals (such as sustainability of fish stocks). This talk will introduce the concept of systematic review and provide some examples of the how this methodology could be used to address marine policy issues.
title: Knowledge management in fisheries science and policy: from databases to real people
Creators: name: Scott, Alister
name: Lock, John
Publisher: name: ASC 2010 - Theme session R
Year: 2024
Subjects: Ecosystem observation, processes and dynamics

description: No abstracts are to be cited without prior reference to the author.The need to manage knowledge better grows all the time, as the amount of knowledge in the world continues to increase and the need for that knowledge to inform related decisions becomes ever clearer. These simple statements hold as much truth and challenge for the field of marine fisheries as any other field: the science is complex and expensive, the amount of knowledge is growing all the time, and the consequences for stakeholders are serious. And yet the term knowledge management can sound scary—complicated, specialized, arcane. By contrast, it is our conviction that it does not need to be. A set of simple ideas and approaches can help you rapidly assess how well you are acquiring, sharing, and using knowledge in your organization, and where you might go next. This talk will outline the findings of extensive research and consulting within the MariFish ERA-Net. We will outline the main barriers to knowledge management, a range of common mistakes made by those wanting to start managing knowledge better, and will finish by outlining nine Golden Rules of Knowledge Management. The aim of the talk is to dispel fears, build confidence, and offer simple ideas and tools.
Standardized patients in psychiatry – the best way to learn clinical skills?
Creators: name: Himmelbauer, Monika
name: Seitz, Tamara
name: Seidman, Charles
name: Löffler-Stastka, Henriette
Publisher: name: Columbia University
Year: 2018
Subjects: Medical education
Psychiatry--Study and teaching
Physician and patient
Communication in medicine

description: Background
                Standardized patients (SP) have been successfully utilized in medical education to train students’ communication skills. At the Medical University of Vienna communication training with SPs in psychiatry is a mandatory part of the curriculum. In the training, the SP plays the role of four different patients suffering from depression/suicidal tendencies, somatoform disorder, anxiety disorder, or borderline disorder while the student attempts to gather the patient’s medical history. Both the instructor and SP then give the student constructive feedback afterwards.

                Method
                The aim of the study was to evaluate the quality of the SP’s roleplay and feedback, using a self-created questionnaire. Additionally, we wanted to gauge the differences between the students’ and teachers’ evaluations of the SP’s role playing performance and feedback.

                Results
                The questionnaire was completed by 529 students and 29 teachers who attended the training. Overall, both students and teachers evaluated the SPs’ performance and feedback very well. In comparison to the responses given by the teachers, more students reported that the “SP overacted” while fewer students believed that the “SP could be a real patient”. The feedback given by the SP was evaluated similarly by students and teachers, suggesting that students are able to recognize the quality of constructive feedback. Furthermore, the SP’s quality of roleplaying was evaluated as the poorest while playing the psychiatric disorder “depression/suicidal tendencies.”

                Conclusions
                Our study showed that students and teachers appreciate SPs’ competence of role play and of giving feedback. However, further studies should be performed to figure out why both students and teachers alike evaluated the played psychiatric disorder “depression/suicidal tendencies” to be the worst.
Evaluation of a flipped classroom approach to learning introductory epidemiology
Creators: name: Shiau, Stephanie
name: Kahn, Linda G.
name: Platt, Jonathan
name: Li, Chihua
name: Guzman, Jason T.
name: Kornhauser, Zachary G.
name: Keyes, Katherine M.
name: Martins, Silvia S.
Publisher: name: Columbia University
Year: 2018
Subjects: Medical education
Epidemiology
Flipped classrooms
Educational technology
Public health

description: Background
                Although the flipped classroom model has been widely adopted in medical education, reports on its use in graduate-level public health programs are limited. This study describes the design, implementation, and evaluation of a flipped classroom redesign of an introductory epidemiology course and compares it to a traditional model.

                Methods
                One hundred fifty Masters-level students enrolled in an introductory epidemiology course with a traditional format (in-person lecture and discussion section, at-home assignment; 2015, N = 72) and a flipped classroom format (at-home lecture, in-person discussion section and assignment; 2016, N = 78). Using mixed methods, we compared student characteristics, examination scores, and end-of-course evaluations of the 2016 flipped classroom format and the 2015 traditional format. Data on the flipped classroom format, including pre- and post-course surveys, open-ended questions, self-reports of section leader teaching practices, and classroom observations, were evaluated.

                Results
                There were no statistically significant differences in examination scores or students’ assessment of the course between 2015 (traditional) and 2016 (flipped). In 2016, 57.1% (36) of respondents to the end-of-course evaluation found watching video lectures at home to have a positive impact on their time management. Open-ended survey responses indicated a number of strengths of the flipped classroom approach, including the freedom to watch pre-recorded lectures at any time and the ability of section leaders to clarify targeted concepts. Suggestions for improvement focused on ways to increase regular interaction with lecturers.

                Conclusions
                There was no significant difference in students’ performance on quantitative assessments comparing the traditional format to the flipped classroom format. The flipped format did allow for greater flexibility and applied learning opportunities at home and during discussion sections.
Exact solutions of a Flat Full Causal Bulk viscous FRW cosmological model through factorization
Creators: name: Cornejo-Pérez, O.
name: Belinchón, J. A.
Publisher: name: arXiv
Year: 2012
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We study the classical flat full causal bulk viscous FRW cosmological model through the factorization method. The method shows that there exists a relationship between the viscosity parameter $s$ and the parameter $γ$ entering the equations of state of the model. Also, the factorization method allows to find some new exact parametric solutions for different values of the viscous parameter $s$. Special attention is given to the well known case $s=1/2$, for which the cosmological model admits scaling symmetries. Furthermore, some exact parametric solutions for $s=1/2$ are obtained through the Lie group method.
description: 18 pas. RevTeX4. New solutions. arXiv admin note: text overlap with arXiv:gr-qc/0107004 by other authors
The Imported Pottery from Fast Castle, Near Dunbar, Scotland
Creators: name: Haggarty, George R
name: Jennings, Sarah
Publisher: name: Archaeology Data Service
Year: 2023

description: Medieval Ceramics: Journal of the Medieval Ceramics Research Group, 16, 45-54
description: Fast Castle is situated on the coast 17 km (12 miles) east of Dunbar. During the late 15th and early 16th centuries the castle was used as the principal residence of Sir Patrick Home, the 4th son of Sir Alexander Home who headed a family of great power and prestige, for whom a Lordship was created in 1473. The castle was sufficiently important for Margaret Tudor to stay there in 1503, on her way north for her marriage to James IV. The excavation of a large pit, or quarry, in the courtyard of the Castle yielded a significant group of imported pottery and a range of locally produced wares. The wide range of 15th- and 16th-century imported pottery is very unusual in a Scottish context; with the independent dating evidence deriving from coins and documents, this is an exceptional assemblage for this area. This report deals primarily with the imports from the castle: vessels from Germany, the Low Countries, France, Italy and the Iberian Peninsula. The detailed examination of the local wares will form the basis of a future report
From Maximal Entropy Random Walk to quantum thermodynamics
Creators: name: Duda, Jarek
Publisher: name: arXiv
Year: 2011
Subjects: subject: Quantum Physics (quant-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: Surprisingly the looking natural random walk leading to Brownian motion occurs to be often biased in a very subtle way: usually refers to only approximate fulfillment of thermodynamical principles like maximizing uncertainty. Recently, a new philosophy of stochastic modeling was introduced, which by being mathematically similar to euclidean path integrals, finally fulfills these principles exactly. Their local behavior is usually similar, but may lead to completely different global properties. In contrast to Brownian motion leading to nearly uniform stationary density, this recent approach turns out in agreement with having strong localization properties thermodynamical predictions of quantum mechanics, like thermalizing to dynamical equilibrium state having probability density as the quantum ground state: squares of coordinates of the lowest energy eigenvector of the Bose-Hubbard Hamiltonian for single particle in discrete case, or of the standard Schrodinger operator while including potential and making infinitesimal limit. It also provides a natural intuition of the amplitudes' squares relating to probabilities. The present paper gathers, formalizes and extends these results. There are also introduced and discussed some new generalizations, like considering multiple particles with thermodynamical analogue of Pauli exclusion principle or time dependent cases, which allowed to introduce thermodynamical analogues of momentum operator, Ehrenfest equation and Heisenberg uncertainty principle.
description: 60 pages, 19 figures
Testing the minimum variance method for estimating large-scale velocity moments
Creators: name: Agarwal, Shankar
name: Feldman, Hume A.
name: Watkins, Richard
Publisher: name: arXiv
Year: 2012
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: The estimation and analysis of large-scale bulk flow moments of peculiar velocity surveys is complicated by non-spherical survey geometry, the non-uniform sampling of the matter velocity field by the survey objects and the typically large measurement errors of the measured line-of-sight velocities. Previously, we have developed an optimal `minimum variance' (MV) weighting scheme for using peculiar velocity data to estimate bulk flow moments for idealized, dense and isotropic surveys with Gaussian radial distributions, that avoids many of these complications. These moments are designed to be easy to interpret and are comparable between surveys. In this paper, we test the robustness of our MV estimators using numerical simulations. Using MV weights, we estimate the bulk flow moments for various mock catalogues extracted from the LasDamas and the Horizon Run numerical simulations and compare these estimates to the moments calculated directly from the simulation boxes. We show that the MV estimators are unbiased and negligibly affected by non-linear flows.
description: 11 pages, 8 figures, 2 tables, updated to match version accepted by MNRAS
Nuclear Activity In Isolated Galaxies
Creators: name: Hernandez-Ibarra, Francisco
name: Dultzin, Deborah
name: Krongold, Yair
name: Del Olmo, Ascencion
name: Perea, Jaime
name: Gonzalez, Jesus
Publisher: name: arXiv
Year: 2012
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present a spectroscopic study of the incidence of AGN nuclear activity in two samples of isolated galaxies (Karachentseva, V.E. & Varela, J.). Our results show that the incidence of non-thermal nuclear activity is about 43% and 31% for galaxies with emission lines and for the total sample 40% and 27% respectively. For the first time we have a large number of bona-fide isolated galaxies (513 objects), with statistically significant number of all types. We find a clear relation between bulge mass and the incidence of nuclear activity in the sample with emission lines. This relation becomes flatter when we take into account the complete sample with no emission line galaxies. A large fraction (~70%) of elliptical galaxies or early type spirals have an active galactic nucleus and ~70% of them are LINERs. Only 3% of the AGN show the presence of broad lines (a not a single one can be classified as type 1 AGN). This is a remarkable result which is completely at odds with the unified model even if we consider warped or clumpy tori. Finally, we interpret the large fraction of AGN in isolated galaxies as the result of secular evolution of their supermasive black holes.
description: 7 figures, 7 tables
Juggling Jakobakannen
Creators: name: Clevis, Hemmy
Publisher: name: Archaeology Data Service
Year: 2023

description: Medieval Ceramics: Journal of the Medieval Ceramics Research Group, 16, 55-64
description: Only rarely does an archaeologist have the good fortune to work with large numbers of finds of a single type. This study deals with the analysis of Jacobakan jugs and loosely related forms from well-stratified contexts in the Netherlands, notably the castles of Hattem, Roozendaal and De Voorst. By measuring these according to a number of set parameters, and plotting the dimensions on a triangular graph, it is demonstrated that most of the various types can be differentiated.
Continuum extrapolation of $B_K$ with staggered fermions
Creators: name: Lee, Weonjong
name: Jang, Yong-Chull
name: Kim, Hyung-Jin
name: Kim, Jangho
name: Kim, Kwangwoo
name: Yoon, Boram
name: Bae, Taegil
name: Jung, Chulwoo
name: Kim, Jongjeong
name: Sharpe, Stephen R.
name: Collaboration, SWME
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We report on recent progress in the calculation of $B_K$ using HYP-smeared staggered fermions on the MILC asqtad lattices. Our main focus is on the continuum extrapolation, which is done using (up to) four different lattice spacings---$a\approx$ 0.12, 0.09, 0.06 and 0.045 fm. Since Lattice 2010, we have reduced the statistical errors on the $a\approx 0.09\;$fm lattices by a factor of $\sim 3$, and roughly doubled the size of the $a\approx0.045\;$fm ensemble. We find that these improvements have a very significant impact on the continuum extrapolation, with the $a\approx 0.12\;$fm data lying outside the range of applicability of simple functional forms. Hence we use only the three smallest lattice spacings to perform the extrapolation, finding $\hat{B}_K = B_K(\text{RGI}) = 0.725 \pm 0.004(\text{stat}) \pm 0.038(\text{sys}) $. This value is consistent with our published value from 2010 (based the three coarsest lattice spacings), but has smaller errors.
description: 7 pages, 6 figures, references updated
Higgs anomalous couplings, FCNC and LFV decays
Creators: name: Sarica, Ulascan
Publisher: name: Zenodo
Year: 2019

description: An overview of searches for the lepton flavor violating decays of the Higgs boson, and for flavor changing neutral currents in Hqt couplings are presented from the ATLAS. In addition, different approaches on the Higgs anomalous couplings to vector bosons from the two experiments are presented.
Information, Branding, Certification, and Consumer Willingness to Pay for High-Iron Pearl Millet: Evidence from Experimental Auctions in Maharashtra, India
Creators: name: A. Banerji
name: Birol, Ekin
name: Bhuskhana Karandikar
name: Jeevant Rampal
Publisher: name: Gates Open Research
Year: 2019

description: Information, Branding, Certification, and Consumer Willingness to Pay for High-Iron Pearl Millet: Evidence from Experimental Auctions in Maharashtra, India
Elevated polygenic burden for autism is associated with differential DNA methylation at birth
Creators: name: Hannon, Eilis
name: Schendel, Diana
name: Ladd-Acosta, Christine
name: Grove, Jakob
name: Hansen, Christine S.
name: Andrews, Shan V.
name: Hougaard, David M.
name: Bresnahan, Michaeline
name: Mors, Ole
name: Hollegaard, Mads V.
name: Bækvad-Hansen, Marie
name: Hornig, Mady
name: Mortensen, Preben B.
name: Børglum, Anders D.
name: Werge, Thomas
name: Pedersen, Marianne G.
name: Nordentoft, Merete
name: Buxbaum, Joseph
name: Daniele Fallin, M.
name: Bybjerg-Grauholm, Jonas
name: Reichenberg, Abraham
name: Mill, Jonathan
Publisher: name: Columbia University
Year: 2018
Subjects: subject: DNA--Methylation
subject: Autism spectrum disorders
subject: Genetics
subject: FOS: Biological sciences
subject: Human genome

description: Background
                Autism spectrum disorder (ASD) is a severe neurodevelopmental disorder characterized by deficits in social communication and restricted, repetitive behaviors, interests, or activities. The etiology of ASD involves both inherited and environmental risk factors, with epigenetic processes hypothesized as one mechanism by which both genetic and non-genetic variation influence gene regulation and pathogenesis. The aim of this study was to identify DNA methylation biomarkers of ASD detectable at birth.

                Methods
                We quantified neonatal methylomic variation in 1263 infants—of whom ~ 50% went on to subsequently develop ASD—using DNA isolated from archived blood spots taken shortly after birth. We used matched genotype data from the same individuals to examine the molecular consequences of ASD-associated genetic risk variants, identifying methylomic variation associated with elevated polygenic burden for ASD. In addition, we performed DNA methylation quantitative trait loci (mQTL) mapping to prioritize target genes from ASD GWAS findings.

                Results
                We identified robust epigenetic signatures of gestational age and prenatal tobacco exposure, confirming the utility of DNA methylation data generated from neonatal blood spots. Although we did not identify specific loci showing robust differences in neonatal DNA methylation associated with later ASD, there was a significant association between increased polygenic burden for autism and methylomic variation at specific loci. Each unit of elevated ASD polygenic risk score was associated with a mean increase in DNA methylation of − 0.14% at two CpG sites located proximal to a robust GWAS signal for ASD on chromosome 8.

                Conclusions
                This study is the largest analysis of DNA methylation in ASD undertaken and the first to integrate genetic and epigenetic variation at birth. We demonstrate the utility of using a polygenic risk score to identify molecular variation associated with disease, and of using mQTL to refine the functional and regulatory variation associated with ASD risk variants.
Electron temperature in electrically isolated Si double quantum dots
Creators: name: Rossi, A.
name: Ferrus, T.
name: Williams, D. A.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Charge-based quantum computation can be attained through reliable control of single electrons in lead-less quantum systems. Single-charge transitions in electrically-isolated double quantum dots (DQD) realised in phosphorus-doped silicon can be detected via capacitively coupled single-electron tunnelling devices. By means of time-resolved measurements of the detector's conductance, we investigate the dots' occupancy statistics in temperature. We observe a significant reduction of the effective electron temperature in the DQD as compared to the temperature in the detector's leads. This sets promises to make isolated DQDs suitable platforms for long-coherence quantum computation.
description: 4 pages, 3 figures
Additional file 2 of MAPK14 over-expression is a transcriptomic feature of polycythemia vera and correlates with adverse clinical outcomes
Creators: name: Guo, Chao
name: Gao, Ya-yue
name: Ju, Qian-qian
name: Wang, Min
name: Zhang, Chun-xia
name: Gong, Ming
name: Li, Zhen-ling
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 2: Figure S2. The value of scale independence (left) and mean connectivity (right) to identify the soft threshold in the following network analysis.
Psychotropic medication use among patients with celiac disease
Creators: name: Zylberberg, Haley M.
name: Ludvigsson, Jonas F.
name: Green, Peter H. R.
name: Lebwohl, Benjamin
Publisher: name: Columbia University
Year: 2018
Subjects: Psychotropic drugs
Celiac disease
Psychiatric disorders
Epidemiology

description: Background
                Celiac disease is a multi-system disorder with manifestations that may result in psychiatric disorders. We assessed the prevalence of medication use to treat psychiatric disorders in celiac disease patients.

                Methods
                We conducted a cross-sectional study of patients undergoing esophagogastroduodenoscopy over 9-years at a celiac disease referral center. We compared the prevalence of psychotropic medication use among celiac disease patients (n = 1293) to a control group (n = 1401) with abdominal pain or reflux.

                Results
                Among all patients the mean age was 48.4 years, most were female (69.5%), and 22.7% used any psychotropic medication. There was no difference between overall psychotropic medication use among celiac disease patients and controls (23.9% vs 21.8%, OR 1.16; 95% CI 0.96–1.39, p = 0.12). However, those with celiac disease were more likely to use antidepressants on univariate (16.4% vs 13.4%, p = 0.03) and multivariate analysis (OR 1.28; 95% CI 1.03–1.59; p = 0.03). Use of psychotropic medications was not associated with disease duration or mode of presentation of celiac disease.

                Conclusions
                Celiac disease patients use psychotropic medications at similar rates as those with other gastrointestinal diseases, though subgroup analysis suggests they may use more antidepressants. Future studies should investigate whether celiac disease is associated with mood disorders that are not treated with medications.
Additional file 3 of MAPK14 over-expression is a transcriptomic feature of polycythemia vera and correlates with adverse clinical outcomes
Creators: name: Guo, Chao
name: Gao, Ya-yue
name: Ju, Qian-qian
name: Wang, Min
name: Zhang, Chun-xia
name: Gong, Ming
name: Li, Zhen-ling
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 3: Figure S3. The cluster dendrogram (upper) and gene co-expressed modules (lower), in which the height of branches represented the distance of Euclidean.
Additional file 4 of MAPK14 over-expression is a transcriptomic feature of polycythemia vera and correlates with adverse clinical outcomes
Creators: name: Guo, Chao
name: Gao, Ya-yue
name: Ju, Qian-qian
name: Wang, Min
name: Zhang, Chun-xia
name: Gong, Ming
name: Li, Zhen-ling
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 4: Figure S4. The topological overlap heatmap for 400 randomly selected genes.
Extinction probabilities for a distylous plant population modeled by an inhomogeneous random walk on the positive quadrant
Creators: name: Lafitte-Godillon, Pauline
name: Raschel, Kilian
name: Tran, Viet Chi
Publisher: name: arXiv
Year: 2012
Subjects: subject: Probability (math.PR)
subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics

description: In this paper, we study a flower population in which self-reproduction is not permitted. Individuals are diploid, {that is, each cell contains two sets of chromosomes}, and {distylous, that is, two alleles, A and a, can be found at the considered locus S}. Pollen and ovules of flowers with the same genotype at locus S cannot mate. This prevents the pollen of a given flower to fecundate its {own} stigmata. Only genotypes AA and Aa can be maintained in the population, so that the latter can be described by a random walk in the positive quadrant whose components are the number of individuals of each genotype. This random walk is not homogeneous and its transitions depend on the location of the process. We are interested in the computation of the extinction probabilities, {as} extinction happens when one of the axis is reached by the process. These extinction probabilities, which depend on the initial condition, satisfy a doubly-indexed recurrence equation that cannot be solved directly. {Our contribution is twofold : on the one hand, we obtain an explicit, though intricate, solution through the study of the PDE solved by the associated generating function. On the other hand, we provide numerical results comparing stochastic and deterministic approximations of the extinction probabilities.
description: 23 pages
Spectral properties of matrices arising from primal-dual interior-point methods for convex quadratic programs
Creators: name: Moulding, Erin
Publisher: name: University of British Columbia
Year: 2012

description: The solution of convex quadratic programs using primal-dual interior-point methods has at its core the solution of a series of linear systems, which are in practice commonly reduced by block Gaussian elimination from the original unsymmetric block 3-by-3 formulation to either a block 2-by-2 saddle-point matrix or a block 1-by-1 normal equations form. The 3-by-3 formulation can also be symmetrized with a similarity transformation if a symmetric solver is to be used. We examine whether this practice of reduction is beneficial for the solver. For each of these formulations we find analytical results for the following spectral properties: the inertia, condition number, conditions for nonsingularity, and bounds on the eigenvalues. While the reduced systems become increasingly ill-conditioned throughout the iterations except in special cases, the 3-by-3 formulations remain nonsingular and well-conditioned with only mild assumptions on the problem; with regularization the assumptions are further simplified. Numerical examples are used to support the analytical results. We conclude that the 3-by-3 formulations, unsymmetric or symmetric, unregularized or regularized, have superior spectral properties that support their use in practice.
Additional file 5 of MAPK14 over-expression is a transcriptomic feature of polycythemia vera and correlates with adverse clinical outcomes
Creators: name: Guo, Chao
name: Gao, Ya-yue
name: Ju, Qian-qian
name: Wang, Min
name: Zhang, Chun-xia
name: Gong, Ming
name: Li, Zhen-ling
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 5: Figure S5. The module eigengene adjacency heatmap (lower), which indicated the relationship between distinct co-expression modules. The results of module clustering were shown in the upper part.
Cell Division and the Presence of a Growth Factor
Creators: name: Gross, Lou
name: Beals, Monica
name: Harrell, Susan
Publisher: name: QUBES Educational Resources
Year: 2019

description: This module introduces exponential growth, the Michaelis-Menten, and Lineweaver-Burk equations in the context of understanding how growth factors influence cell division. It is intended for an introductory biology audience.
Search for leptonic decays of W' bosons in pp collisions at sqrt(s) = 7 TeV
Creators: name: CMS Collaboration
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: A search for a new heavy gauge boson W' decaying to an electron or muon, plus a low mass neutrino, is presented. This study uses data corresponding to an integrated luminosity of 5.0 inverse femtobarns, collected using the CMS detector in pp collisions at a centre-of-mass energy of 7 TeV at the LHC. Events containing a single electron or muon and missing transverse momentum are analyzed. No significant excess of events above the standard model expectation is found in the transverse mass distribution of the lepton-neutrino system, and upper limits for cross sections above different transverse mass thresholds are presented. Mass exclusion limits at 95% CL for a range of W' models are determined, including a limit of 2.5 TeV for right-handed W' bosons with standard-model-like couplings and limits of 2.43--2.63 TeV for left-handed W' bosons, taking into account their interference with the standard model W boson. Exclusion limits have also been set on Kaluza--Klein W[KK] states in the framework of split universal extra dimensions.
description: Submitted to the Journal of High Energy Physics
Sine-square deformation of free fermion systems in one and higher dimensions
Creators: name: Maruyama, Isao
name: Katsura, Hosho
name: Hikihara, Toshiya
Publisher: name: arXiv
Year: 2011
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Quantum Gases (cond-mat.quant-gas)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We study free fermion systems with the sine-square deformation (SSD), in which the energy scale of local Hamiltonians is modified according to the scaling function f(x)=sin^2[π(x-1/2)/L], where x is the position of the local Hamiltonian and L is the length of the system in the x direction. It has been revealed that when applied to one-dimensional critical systems the SSD realizes the translationally-invariant ground state which is the same as that of the uniform periodic system. In this paper, we propose a simple theory to explain how the SSD maintains the translational invariance in the ground-state wave function. In particular, for a certain one-dimensional system with SSD, it is shown that the ground state is exactly identical with the Fermi sea of the uniform periodic chain. We also apply the SSD to two-dimensional systems and show that the SSD is able to suppress the boundary modulations from the open edges extremely well, demonstrating that the SSD works in any dimensions and in any directions.
description: 9 pages, 6 figures. v2: accepted version
Optomechanical superpositions via nested interferometry
Creators: name: Pepper, Brian
name: Ghobadi, Roohollah
name: Jeffrey, Evan
name: Simon, Christoph
name: Bouwmeester, Dirk
Publisher: name: arXiv
Year: 2011
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We present a scheme for achieving macroscopic quantum superpositions in optomechanical systems by using single photon postselection and detecting them with nested interferometers. This method relieves many of the challenges associated with previous optical schemes for measuring macroscopic superpositions, and only requires the devices to be in the weak coupling regime. It requires only small improvements on currently achievable device parameters, and allows observation of decoherence on a timescale unconstrained by the system's optical decay time. Prospects for observing novel decoherence mechanisms are discussed.
description: 5 pages, 3 figures
Additional file 6 of MAPK14 over-expression is a transcriptomic feature of polycythemia vera and correlates with adverse clinical outcomes
Creators: name: Guo, Chao
name: Gao, Ya-yue
name: Ju, Qian-qian
name: Wang, Min
name: Zhang, Chun-xia
name: Gong, Ming
name: Li, Zhen-ling
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Additional file 6: Figure S6. The dotplot of GSEA results associating with MAPK14 expression. The size of dots represented the count of genes involved in the corresponding pathways. While the color of dots correlated with the -log10(adjusted p value).
Proof of Consistency of Nonlinear Massive Gravity in the Stuckelberg Formulation
Creators: name: Hassan, S. F.
name: Schmidt-May, Angnis
name: von Strauss, Mikael
Publisher: name: arXiv
Year: 2012
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We address some recent concerns about the absence of the Boulware-Deser ghost in the Stuckelberg formulation of nonlinear massive gravity. First we provide general arguments for why any ghost analysis in the Stuckelberg formulation has to agree with existing consistency proofs that have been carried out without using Stuckelberg fields. We then demonstrate the absence of the ghost at the completely nonlinear level in the Stuckelberg formulation of the minimal massive gravity action. The constraint that removes the ghost field and the associated secondary constraint that eliminates its conjugate momentum are computed explicitly, confirming the consistency of the theory in the Stuckelberg formulation.
description: v1: Latex, 11 pages, v2: a comment added