cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Demographic characteristics, long-term health conditions and healthcare experiences of 6333 trans and non-binary adults in England: nationally representative evidence from the 2021 GP Patient Survey.
Creators: name: Saunders, Catherine L
name: Berner, Alison
name: Lund, Jenny
name: Mason, Amy M
name: Oakes-Monger, Tash
name: Roberts, Meg
name: Smith, Jack
name: Duschinsky, Robbie
Publisher: name: Apollo - University of Cambridge Repository
Year: 2023
Subjects: Health services research
1506
2474
1704
PRIMARY CARE
Quality in health care
HEALTH SERVICES ADMINISTRATION & MANAGEMENT

description: Peer reviewed: True
description: Acknowledgements: We would like to thank Roary Neat and all other members of the public involvement panel who contributed to this work.
description: OBJECTIVE: In order to address the lack of data on the health and healthcare needs of trans and non-binary adults, NHS England includes questions asking about both gender and trans status in its surveys to support quality improvement programmes.We used self-reported data from the GP Patient Survey to answer the research question: what are the demographic characteristics, health conditions and healthcare experiences of trans and non-binary adults in England? DESIGN/SETTING: Nationally representative, population-based cross-sectional survey in England with survey data collection from January to March 2021. PARTICIPANTS: 840 691 survey respondents including 6333 trans and non-binary adults. OUTCOMES: We calculated weighted descriptive statistics, and using logistic regression explored 15 long-term physical and mental health conditions, and 18 patient experience items, covering overall experience, access, communication and continuity. RESULTS: Trans and non-binary adults were younger, more likely to be from Asian, black, mixed or other ethnic groups and more likely to live in more deprived parts of the country. Age-specific patterns of long-term conditions were broadly similar among trans and non-binary adults compared with all other survey respondents, with some variation by condition. Overall, inequalities in long-term health conditions were largest for autism: OR (95% CI), 5.8 (5.0 to 6.6), dementia: 3.1 (2.5 to 3.9), learning disabilities: 2.8 (2.4 to 3.2) and mental health: 2.0 (1.9 to 2.2), with variation by age. In healthcare experience, disparities are much greater for interpersonal communication (OR for reporting a positive experience, range 0.4 to 0.7 across items) than access (OR range 0.8 to 1.2). Additionally, trans and non-binary adults report much higher preference for continuity 1.7 (1.6 to 1.8), with no evidence of any differences in being able to see or speak to a preferred general practitioner. CONCLUSION: This research adds up to date evidence about population demographics, health and healthcare needs to support healthcare improvement for trans and non-binary adults.
(1601) Bithia Swanwick
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.
Mucin Granule Intraluminal Organization in Living Mucous/Goblet Cells: ROLES OF PROTEIN POST-TRANSLATIONAL MODIFICATIONS AND SECRETION
Creators: name: Boucher, Richard C.
name: Perez-Vilar, Juan
name: Bertozzi, Carolyn R.
name: Mabolo, Raean
name: McVaugh, Cheryl T.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Recent studies suggest that the mucin granule lumen consists of a matrix meshwork embedded in a fluid phase. Secretory products can both diffuse, although very slowly, through the meshwork pores and interact noncovalently with the matrix. Using a green fluorescent protein-mucin fusion protein (SHGFP-MUC5AC/CK) as a FRAP (fluorescence recovery after photobleaching) probe, we have assessed in living mucous cells the relative importance of different protein post-translational modifications on the intragranular organization. Long term inhibition of mucin-type O-glycosylation, sialylation, or sulfation altered SHGFP-MUC5AC/CK characteristic diffusion time (t(1/2)), whereas all but sulfation diminished its mobile fraction. Reduction of protein disulfide bonds with tris(hydroxypropyl)phosphine resulted in virtually complete immobilization of the SHGFP-MUC5AC/CK intragranular pool. However, when activity of the vacuolar H+-ATPase was also inhibited, disulfide reduction decreased SHGFP-MUC5AC/CK t((1/2)) while diminishing its intraluminal concentration. Similar FRAP profiles were observed in granules that remained in the cells after the addition of a mucin secretagogue. Taken together these results suggest that: (a) the relative content of O-glycans and intragranular anionic groups is crucial for protein diffusion through the intragranular meshwork; (b) protein-protein, rather than carbohydrate-mediated, interactions are responsible for binding of SHGFP-MUC5AC/CK to the immobile fraction, although the degree of matrix O-glycosylation and sialylation affects such interactions; (c) intragranular organization does not depend on covalent multimerization of mucins or the presence of native disulfide bonds in the intragranular mucin/proteins, but rather on specific protein-mediated interactions that are important during the early stages of mucin matrix condensation; (d) alterations of the intragranular matrix precede granule discharge, which can be partial and, accordingly, does not necessarily involve the disappearance of the granule.
Constraining the radio-loud fraction of quasars at z>5.5
Creators: name: Bañados, E.
name: Venemans, B. P.
name: Morganson, E.
name: Hodge, J.
name: Decarli, R.
name: Walter, F.
name: Stern, D.
name: Schlafly, E.
name: Farina, E. P.
name: Greiner, J.
name: Chambers, K. C.
name: Fan, X.
name: Rix, H-W.
name: Burgett, W. S.
name: Draper, P. W.
name: Flewelling, J.
name: Kaiser, N.
name: Metcalfe, N.
name: Morgan, J. S.
name: Tonry, J. L.
name: Wainscoat, R. J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Radio-loud Active Galactic Nuclei at z~2-4 are typically located in dense environments and their host galaxies are among the most massive systems at those redshifts, providing key insights for galaxy evolution. Finding radio-loud quasars at the highest accessible redshifts (z~6) is important to study their properties and environments at even earlier cosmic time. They would also serve as background sources for radio surveys intended to study the intergalactic medium beyond the epoch of reionization in HI 21 cm absorption. Currently, only five radio-loud ($R=f_{ν,5{\rm GHz}}/f_{ν,4400Å}>10$) quasars are known at z~6. In this paper we search for 5.5 < z < 7.2 quasars by cross-matching the optical Pan-STARRS1 and radio FIRST surveys. The radio information allows identification of quasars missed by typical color-based selections. While we find no good 6.4 < z <7.2 quasar candidates at the sensitivities of these surveys, we discover two new radio-loud quasars at z~6. Furthermore, we identify two additional z~6 radio-loud quasars which were not previously known to be radio-loud, nearly doubling the current z~6 sample. We show the importance of having infrared photometry for z>5.5 quasars to robustly classify them as radio-quiet or radio-loud. Based on this, we reclassify the quasar J0203+0012 (z=5.72), previously considered radio-loud, to be radio-quiet. Using the available data in the literature, we constrain the radio-loud fraction of quasars at z~6, using the Kaplan--Meier estimator, to be $8.1^{+5.0}_{-3.2}\%$. This result is consistent with there being no evolution of the radio-loud fraction with redshift, in contrast to what has been suggested by some studies at lower redshifts.
description: Accepted for publication in ApJ. 3 Figures. 3 Tables
NFFA-Europe Pilot - D17.2 - Terms of Reference of the Dissemination Plan
Creators: name: Carsughi, Flavio
Publisher: name: Zenodo
Year: 2021

description: The present deliverable regards the Terms of References of the Dissemination Plan (DP) of the NFFA-Europe Pilot project. The DP paves the way on one hand to disseminate the results obtained within the NFFA-Europe Pilot project to the proper target scientific communities and on the other one to reach new scientific communities. This double objective ensures efficiency as well as flexibility through the number of measures considered.
description: WP17 - Communication and dissemination
Multiple Conformations of Phosphodiesterase-5: IMPLICATIONS FOR ENZYME FUNCTION AND DRUG DEVELOPMENT
Creators: name: Zoraghi, Roya
name: Ke, Hengming
name: Liu, Yudong
name: Lin, Guiting
name: Huai, Qing
name: Xin, Zhongcheng
name: Corbin, Jackie D.
name: Cai, Jiwen
name: Francis, Sharron H.
name: Robinson, Howard
name: Wang, Huanchen
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Phosphodiesterase-5 (PDE5) is the target for sildenafil, vardenafil, and tadalafil, which are drugs for treatment of erectile dysfunction and pulmonary hypertension. We report here the crystal structures of a fully active catalytic domain of unliganded PDE5A1 and its complexes with sildenafil or icarisid II. These structures together with the PDE5A1-isobutyl-1-methylxanthine complex show that the H-loop ( residues 660-683) at the active site of PDE5A1 has four different conformations and migrates 7-35 angstrom upon inhibitor binding. In addition, the conformation of sildenafil reported herein differs significantly from those in the previous structures of chimerically hybridized or almost inactive PDE5. Mutagenesis and kinetic analyses confirm that the H-loop is particularly important for substrate recognition and that invariant Gly(659), which immediately precedes the H-loop, is critical for optimal substrate affinity and catalytic activity.
Figure S6k from Expansion in geographical and morphological space drives continued lineage diversification in a global passerine radiation.
Creators: name: Kennedy, Jonathan D.
name: Borregaard, Michael K.
name: Marki, Petter Z.
name: Machac, Antonin
name: Fjeldså, Jon
name: Rahbek, Carsten
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: Why diversification rates vary so extensively across the tree of life remains an important yet unresolved issue in biology. Two prominent and potentially independent factors proposed to explain these trends reflect the capacity of lineages to expand into new areas of (i) geographical or (ii) ecological space. Here, we present the first global assessment of how diversification rates vary as a consequence of geographical and ecological expansion, studying these trends among 15 speciose passerine families (together approximately 750 species) using phylogenetic path analysis. We find that relative slowdowns in diversification rates characterize families that have accumulated large numbers of co-occurring species (at the 1° scale) within restricted geographical areas. Conversely, more constant diversification through time is prevalent among families in which species show limited range overlap. Relative co-occurrence is itself also a strong predictor of ecological divergence (here approximated by morphological divergence among species); however, once the relationship between co-occurrence and diversification rates have been accounted for, increased ecological divergence is an additional explanatory factor accounting for why some lineages continue to diversify towards the present. We conclude that opportunities for prolonged diversification are predominantly determined by continued geographical range expansion and to a lesser degree by ecological divergence among lineages.
Predictions for Neutrinoless Double-Beta Decay in the 3+1 Sterile Neutrino Scenario
Creators: name: Giunti, C.
name: Zavanin, E. M.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: We present accurate predictions of the effective Majorana mass $|m_{ββ}|$ in neutrinoless double-$β$ decay in the standard case of $3ν$ mixing and in the case of 3+1 neutrino mixing indicated by the reactor, Gallium and LSND anomalies. We have taken into account the uncertainties of the neutrino mixing parameters determined by oscillation experiments. It is shown that the predictions for $|m_{ββ}|$ in the cases of $3ν$ and 3+1 mixing are quite different, in agreement with previous discussions in the literature, and that future measurements of neutrinoless double-$β$ decay and of the effective light neutrino mass in $β$ decay or the total mass of the three lightest neutrinos in cosmological experiments may distinguish the $3ν$ and 3+1 cases if the mass ordering is determined by oscillation experiments. We also present a relatively simple method to determine the minimum value of $|m_{ββ}|$ in the general case of $N$-neutrino mixing.
description: 14 pages; final version published in JHEP 1507 (2015) 171
(1597) Henry Mitchell-Dawson
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.
Understanding the Photoluminescence Quenching of Liquid Exfoliated WS2 Monolayers.
Creators: name: Li, Zhaojun
name: Rashvand, Farnia
name: Bretscher, Hope
name: Szydłowska, Beata M
name: Xiao, James
name: Backes, Claudia
name: Rao, Akshay
Publisher: name: Apollo - University of Cambridge Repository
Year: 2022

description: Monolayer transition metal dichalcogenides (TMDs) are being investigated as active materials in optoelectronic devices due to their strong excitonic effects. While mechanical exfoliation (ME) of monolayer TMDs is limited to small areas, these materials can also be exfoliated from their parent layered materials via high-volume liquid phase exfoliation (LPE). However, it is currently considered that LPE-synthesized materials show poor optoelectronic performance compared to ME materials, such as poor photoluminescence quantum efficiencies (PLQEs). Here we evaluate the photophysical properties of monolayer-enriched LPE WS2 dispersions via steady-state and time-resolved optical spectroscopy and benchmark these materials against untreated and chemically treated ME WS2 monolayers. We show that the LPE materials show features of high-quality semiconducting materials such as very small Stokes shift, smaller photoluminescence line widths, and longer exciton lifetimes than ME WS2. We reveal that the energy transfer between the direct-gap monolayers and in-direct gap few-layers in LPE WS2 dispersions is a major reason for their quenched PL. Our results suggest that LPE TMDs are not inherently highly defective and could have a high potential for optoelectronic device applications if improved strategies to purify the LPE materials and reduce aggregation could be implemented.
Connection between inner jet kinematics and broadband flux variability in the BL Lac object S5 0716+714
Creators: name: Rani, B.
name: Krichbaum, T. P.
name: Marscher, A. P.
name: Hodgson, J. A.
name: Fuhrmann, L.
name: Angelakis, E.
name: Britzen, S.
name: Zensus, J. A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We present a high-frequency very long baseline interferometry (VLBI) kinematical study of the BL Lac object S5 0716+714 over the time period of September 2008 to October 2010. The aim of the study is to investigate the relation of the jet kinematics to the observed broadband flux variability. We find significant non-radial motions in the jet outflow of the source. In the radial direction, the highest measured apparent speed is \sim37 c, which is exceptionally high, especially for a BL Lac object. Patterns in the jet flow reveal a roughly stationary feature \sim0.15 mas downstream of the core. The long-term fits to the component trajectories reveal acceleration in the sub-mas region of the jet. The measured brightness temperature, T_{B}, follows a continuous trend of decline with distance, T_B \propto r_{jet}^{-(2.36\pm0.41)}, which suggests a gradient in Doppler factor along the jet axis. Our analysis suggest that a moving disturbance (or a shock wave) from the base of the jet produces the high-energy (optical to γ-ray) variations upstream of the 7 mm core, and then later causes an outburst in the core. Repetitive optical/γ-ray flares and the curved trajectories of the associated components suggest that the shock front propagates along a bent trajectory or helical path. Sharper γ-ray flares could be related to the passage of moving disturbances through the stationary feature. Our analysis suggests that the γ-ray and radio emission regions have different Doppler factors.
description: 12 pages, 8 figures, accepted for publication in A&A
Figure S6l from Expansion in geographical and morphological space drives continued lineage diversification in a global passerine radiation.
Creators: name: Kennedy, Jonathan D.
name: Borregaard, Michael K.
name: Marki, Petter Z.
name: Machac, Antonin
name: Fjeldså, Jon
name: Rahbek, Carsten
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: Why diversification rates vary so extensively across the tree of life remains an important yet unresolved issue in biology. Two prominent and potentially independent factors proposed to explain these trends reflect the capacity of lineages to expand into new areas of (i) geographical or (ii) ecological space. Here, we present the first global assessment of how diversification rates vary as a consequence of geographical and ecological expansion, studying these trends among 15 speciose passerine families (together approximately 750 species) using phylogenetic path analysis. We find that relative slowdowns in diversification rates characterize families that have accumulated large numbers of co-occurring species (at the 1° scale) within restricted geographical areas. Conversely, more constant diversification through time is prevalent among families in which species show limited range overlap. Relative co-occurrence is itself also a strong predictor of ecological divergence (here approximated by morphological divergence among species); however, once the relationship between co-occurrence and diversification rates have been accounted for, increased ecological divergence is an additional explanatory factor accounting for why some lineages continue to diversify towards the present. We conclude that opportunities for prolonged diversification are predominantly determined by continued geographical range expansion and to a lesser degree by ecological divergence among lineages.
(1599) Charles Wicksteed
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.
Figure S6i from Expansion in geographical and morphological space drives continued lineage diversification in a global passerine radiation
Creators: name: Kennedy, Jonathan D.
name: Borregaard, Michael K.
name: Marki, Petter Z.
name: Machac, Antonin
name: Fjeldså, Jon
name: Rahbek, Carsten
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: Why diversification rates vary so extensively across the tree of life remains an important yet unresolved issue in biology. Two prominent and potentially independent factors proposed to explain these trends reflect the capacity of lineages to expand into new areas of (i) geographical or (ii) ecological space. Here, we present the first global assessment of how diversification rates vary as a consequence of geographical and ecological expansion, studying these trends among 15 speciose passerine families (together approximately 750 species) using phylogenetic path analysis. We find that relative slowdowns in diversification rates characterize families that have accumulated large numbers of co-occurring species (at the 1° scale) within restricted geographical areas. Conversely, more constant diversification through time is prevalent among families in which species show limited range overlap. Relative co-occurrence is itself also a strong predictor of ecological divergence (here approximated by morphological divergence among species); however, once the relationship between co-occurrence and diversification rates have been accounted for, increased ecological divergence is an additional explanatory factor accounting for why some lineages continue to diversify towards the present. We conclude that opportunities for prolonged diversification are predominantly determined by continued geographical range expansion and to a lesser degree by ecological divergence among lineages.
Nonlinear Low-to-High Frequency Energy Cascades in Diatomic Granular Crystals
Creators: name: Kim, E.
name: Chaunsali, R.
name: Xu, H.
name: Jaworski, J.
name: Yang, J.
name: Kevrekidis, P.
name: Vakakis, A. F.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Other Condensed Matter (cond-mat.other)
subject: FOS: Physical sciences

description: We study wave propagation in strongly nonlinear 1D diatomic granular crystals under an impact load. Depending on the mass ratio of the `light' to `heavy' beads, this system exhibits rich wave dynamics from highly localized traveling waves to highly dispersive waves featuring strong attenuation. We experimentally demonstrate the nonlinear resonant and anti-resonant interactions of particles and verify that the nonlinear resonance results in strong wave attenuation, leading to highly efficient nonlinear energy cascading without relying on material damping. In this process, mechanical energy is transferred from low to high frequencies, while propagating waves emerge in both ordered and chaotic waveforms via a distinctive spatial cascading. This energy transfer mechanism from lower to higher frequencies and wavenumbers is of particular significance towards the design of novel nonlinear acoustic metamaterials with inherently passive energy redistribution properties.
MutL-catalyzed ATP Hydrolysis Is Required at a Post-UvrD Loading Step in Methyl-directed Mismatch Repair
Creators: name: Matson, Steven W.
name: Robertson, Adam B.
name: Pattishall, Steven R.
name: Gibbons, Erin A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Methyl-directed mismatch repair is a coordinated process that ensures replication fidelity and genome integrity by resolving base pair mismatches and insertion/deletion loops. This post-replicative event involves the activities of several proteins, many of which appear to be regulated by MutL. MutL interacts with and modulates the activities of MutS, MutH, UvrD, and perhaps other proteins. The purified protein catalyzes a slow ATP hydrolysis reaction that is essential for its role in mismatch repair. However, the role of the ATP hydrolysis reaction is not understood. We have begun to address this issue using two point mutants: MutL-E29A, which binds nucleotide but does not catalyze ATP hydrolysis, and MutL-D58A, which does not bind nucleotide. As expected, both mutants failed to complement the loss of MutL in genetic assays. Purified MutL-E29A protein interacted with MutS and stimulated the MutH-catalyzed nicking reaction in a mismatch-dependent manner. Importantly, MutL-E29A stimulated the loading of UvrD on model substrates. In fact, stimulation of UvrD-catalyzed unwinding was more robust with MutL-E29A than the wild-type protein. MutL-D58A, on the other hand, did not interact with MutS, stimulate MutH-catalyzed nicking, or stimulate the loading of UvrD. We conclude that ATP-bound MutL is required for the incision steps associated with mismatch repair and that ATP hydrolysis by MutL is required for a step in the mismatch repair pathway subsequent to the loading of UvrD and may serve to regulate helicase loading.
Nephrocan, a Novel Member of the Small Leucine-rich Repeat Protein Family, Is an Inhibitor of Transforming Growth Factor-β Signaling
Creators: name: Parisuthiman, Duenpim
name: Hanai, Jun Ichi
name: Sukhatme, Vikas P.
name: Mochida, Yoshiyuki
name: Yamauchi, Mitsuo
name: Kaku, Masaru
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: In a search of new, small leucine-rich repeat proteoglycan/protein (SLRP) family members, a novel gene, nephrocan (NPN), has been identified. The gene consists of three exons, and based on the deduced amino acid sequence, NPN has 17 leucine-rich repeat motifs and unique cysteine-rich clusters both in the N and C termini, indicating that this gene belongs to a new class of SLRP family. NPN mRNA was predominantly expressed in kidney in adult mice, and during mouse embryogenesis, the expression was markedly increased in 11-day-old embryos at a time when early kidney development takes place. In the adult mouse kidney, NPN protein was located in distal tubules and collecting ducts. When NPN was overexpressed in cell culture, the protein was detected in the cultured medium, and upon treatment with N-glycosidase F, the molecular mass was lowered by approximately 14 kDa, indicating that NPN is a secreted N-glycosylated protein. Furthermore, transforming growth factor-beta (TGF-beta)-responsive 3TP promoter luciferase activity was down-regulated, and TGF-beta-induced Smad3 phosphorylation was also inhibited by NPN, suggesting that NPN suppresses TGF-beta/Smad signaling. Taken together, NPN is a novel member of the SLRP family that may play important roles in kidney development and pathophysiology by functioning as an endogenous inhibitor of TGF-beta signaling.
Figure S6j from Expansion in geographical and morphological space drives continued lineage diversification in a global passerine radiation
Creators: name: Kennedy, Jonathan D.
name: Borregaard, Michael K.
name: Marki, Petter Z.
name: Machac, Antonin
name: Fjeldså, Jon
name: Rahbek, Carsten
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: Why diversification rates vary so extensively across the tree of life remains an important yet unresolved issue in biology. Two prominent and potentially independent factors proposed to explain these trends reflect the capacity of lineages to expand into new areas of (i) geographical or (ii) ecological space. Here, we present the first global assessment of how diversification rates vary as a consequence of geographical and ecological expansion, studying these trends among 15 speciose passerine families (together approximately 750 species) using phylogenetic path analysis. We find that relative slowdowns in diversification rates characterize families that have accumulated large numbers of co-occurring species (at the 1° scale) within restricted geographical areas. Conversely, more constant diversification through time is prevalent among families in which species show limited range overlap. Relative co-occurrence is itself also a strong predictor of ecological divergence (here approximated by morphological divergence among species); however, once the relationship between co-occurrence and diversification rates have been accounted for, increased ecological divergence is an additional explanatory factor accounting for why some lineages continue to diversify towards the present. We conclude that opportunities for prolonged diversification are predominantly determined by continued geographical range expansion and to a lesser degree by ecological divergence among lineages.
Farm and Nonfarm Investment in Commercial Beef Breeding Herds: Incentives and Consequences of the Tax Law
Creators: name: Harrison, Virden L.
name: Woods, W. Fred
name: Harrison, Virden L.
name: Woods, W. Fred
Publisher: name: Unknown
Year: 1972
Subjects: subject: Agricultural Finance
subject: Demand and Price Analysis
subject: Financial Economics
subject: Livestock Production/Industries
subject: Research Methods/ Statistical Methods
subject: Nonfarm investment
subject: Tax shelters
subject: Beef cow herds
subject: Farm tax law
subject: Capital gains
subject: Investment incentives
subject: Simulation

description: This report examines the incentives and consequences of investment by farmers and nonfarmers in commercial beef breeding herds. It investigates the profitability of investment in beef cow herds with and without the special tax provisions of capital gains, net operating loss carryover, income averaging, and offsetting nonfarm incomes with farm losses. A computer simulator was used to budget the operations over a 15-year period using several levels of product and input prices. Results indicated that there is no economic incentive for nonfarm investments in commercial beef cow herds through management companies without the special provisions of capital gains and offsetting nonfarm income with farm losses. Even with current provisions of the tax law, nonfarm investment in beef cow herds is not profitable unless the investor is at or above the 50 percent tax bracket. Implications for various sectors of society as a result of nonfarm investment in beef breeding herds are discussed.
Significant contributions of Albrecht's $A$ term to non-resonant Raman scattering processes
Creators: name: Gong, Zu-Yong
name: Tian, Guangjun
name: Duan, Sai
name: Luo, Yi
Publisher: name: arXiv
Year: 2015
Subjects: subject: Optics (physics.optics)
subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: The Raman intensity can be well described by the famous Albrecht equation that consists of A and B terms. It is well known that the contribution from Albrecht's A term can be neglected without loss of accuracy for far off-resonant Raman scattering processes. However, as demonstrated in this study, we have found that this widely accepted long-standing assumption fails drastically for totally symmetric vibration modes of molecules in general off-resonant Raman scattering. Perturbed first principles calculations for water molecule show that strong constructive interference between the A and B terms occurs for the Raman intensity of the symmetric O-H stretching mode, which can account for about 40% of the total intensity. Meanwhile, a minor destructive interference is found for the angle bending mode. The state to state mapping between the Albrecht's theory and the perturbation theory allows us to verify the accuracy of the widely employed perturbation method for the dynamic/resonant Raman intensities. The model calculations rationalized from water molecule with the bending mode show that the perturbation method is a good approximation only when the absolute energy difference between the first excited state and the incident light is more than five times of the vibrational energy in ground state.
description: 6 pages, 4 figures, revised version extended to full article
Changes in the Lysosomal Proteome Under Stressed Conditions
Creators: name: O'Connor, Kaela
Publisher: name: Université d'Ottawa / University of Ottawa
Year: 2022
Subjects: Lysosome
Autophagy
ALS
Stress

description: Autophagy is a critical cellular process that is implicated in a vast array of human diseases, including amyotrophic lateral sclerosis (ALS). The targets of this degradative mechanism are frequently altered depending upon the inducing condition, however exactly how these targets change has rarely been explored on a proteomic level. To assess the targets of autophagy, this project analyzed the proteome of lysosomes collected by immunoprecipitation from cells undergoing starvation or recovering from oxidative stress. Oxidative stress induces stress granule formation and is frequently used as a cellular model for ALS. Our results show that while lysosomes from these two conditions retain a similar array of traditionally lysosomal proteins, they nevertheless display substantial differences indicating that their autophagic targets differ. Using Ingenuity Pathway Analysis (IPA) as well as gene ontology (GO) term analysis, the purine biosynthesis pathway was identified as being significantly enriched in lysosomes collected from sodium arsenite treated cells. The enrichment of the purine biosynthesis pathway was heavily dependent on ATG7, indicating these proteins localized to the lysosome primarily through macroautophagy. IMPDH2, the rate-limiting enzyme for guanylate production in the purine biosynthesis pathway drew particular attention due to its significant enrichment in sodium arsenite lysosomes, and its partial dependence on ATG7. Due to this discovery, and the presence of KFERQ-like sequences within the protein, our data suggests that IMPDH2 may localize to the lysosome through both macroautophagy and chaperone-mediated autophagy. Furthermore, numerous ALS-linked proteins were identified to be enriched in sodium arsenite lysosomes including SOD1, DCTN1, PFN1, TUBA4A, SQSTM1, VCP, CHMP2B, TDP-43, VAPB and TMEM106B. Their presence within the lysosome strengthens arguments that autophagy plays a key role in ALS. Overall, this project confirms the changing substrates of autophagy depending on the environmental condition and highlights the purine biosynthesis pathway as being involved in the cellular response to oxidative stress.
Pheromone-regulated Sumoylation of Transcription Factors That Mediate the Invasive to Mating Developmental Switch in Yeast
Creators: name: Wang, Yuqi
name: Dohlman, Henrik G.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: A fundamental question in biology is how different signaling pathways use common signaling proteins to attain different developmental outcomes. The yeast transcription factor Ste12 is required in at least two distinct signaling processes, each regulated by many of the same protein kinases. Whereas Ste12-Ste12 homodimers promote transcription of genes required for mating, Ste12-Tec1 heterodimers activate genes required for invasive growth. We report that Ste12 and Tec1 undergo covalent modification by the ubiquitin-related modifier SUMO. Stimulation by mating pheromone promotes sumoylation of Ste12 and diminishes the sumoylation of Tec1. In the absence of sumoylation Tec1 is more rapidly degraded. We propose that pheromone-regulated sumoylation of Ste12 and Tec1 promotes a developmental switch from the invasive to the mating differentiation program.
Effective interactions between fluid membranes
Creators: name: Lu, Bing-Sui
name: Podgornik, Rudolf
Publisher: name: arXiv
Year: 2015
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Biological Physics (physics.bio-ph)
subject: FOS: Physical sciences

description: A self-consistent theory is proposed for the general problem of interacting undulating fluid membranes subject to the constraint that they do not interpenetrate. We implement the steric constraint via an exact functional integral representation, and through the use of a saddle-point approximation transform it into a novel effective steric potential. The steric potential is found to consist of two contributions: one generated by zero mode fluctuations of the membranes, and the other by thermal bending fluctuations. For membranes of cross-sectional area $S$, we find that the bending fluctuation part scales with the inter-membrane separation $d$ as $d^{-2}$ for $d \ll \sqrt{S}$, but crosses over to $d^{-4}$ scaling for $d \gg \sqrt{S}$, whereas the zero mode part of the steric potential always scales as $d^{-2}$. For membranes interacting exclusively via the steric potential, we obtain closed-form expressions for the effective interaction potential and for the rms undulation amplitude $σ$, which becomes small at low temperatures $T$ and/or large bending stiffnesses $κ$. Moreover, $σ$ scales as $d$ for $d \ll \sqrt{S}$, but saturates at $\sqrt{k_{\rm B} T S/κ}$ for $d \gg \sqrt{S}$. In addition, using variational Gaussian theory, we apply our self-consistent treatment to study inter-membrane interactions subject to three different types of potential: (i)~the Moreira-Netz potential for a pair of strongly charged membranes with an intervening solution of multivalent counterions, (ii)~an attractive square well, (iii)~the Morse potential, and (iv)~a combination of hydration and van der Waals interactions.
description: 17 pages, 7 figures
Probing the Functional Link between Androgen Receptor Coactivator and Ligand-binding Sites in Prostate Cancer and Androgen Insensitivity
Creators: name: French, Frank S.
name: He, Bin
name: Faggart, Jonathan L.
name: Minges, John T.
name: Hnat, Andrew T.
name: Wilson, Elizabeth M.
name: Gampe Jr., Robert T.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: The androgen receptor (AR) is a ligand-activated transcription factor required for male sex development and virilization and contributes to prostate cancer initiation and progression. High affinity androgen binding triggers conformational changes required for AR transactivation. Here we characterized naturally occurring AR gene mutations in the region of activation function 2 (AF2) that decrease or increase AR transcriptional activity by altering the region bounded by AF2 and the ligand binding pocket without affecting equilibrium androgen binding affinity. In the androgen insensitivity syndrome, germ line AR mutations increase the androgen dissociation rate and reduce AR FXXLF motif binding and the recruitment of steroid receptor coactivator (SRC)/p160 coactivator LXXLL motifs. In prostate cancer, somatic AR mutations in AF2 or near the bound ligand slow androgen dissociation and increase AR stabilization and coactivator recruitment. Crystal structures of the AR ligand binding domain bound to R1881 and FXXLF or LXXLL motif peptide indicate the mutations are proximal to the AF2 bound peptide, adjacent to the ligand pocket, or in a putative ligand gateway. The results suggest a bidirectional structural relay between bound ligand and coactivator that establishes AR functional potency in vivo.
Ziggurat fringes are self-similar
Creators: name: Chowdhury, Subhadip
Publisher: name: arXiv
Year: 2015
Subjects: subject: Geometric Topology (math.GT)
subject: Dynamical Systems (math.DS)
subject: Group Theory (math.GR)
subject: FOS: Mathematics
subject: 37E45 (Primary)

description: We give explicit formulae for fringe lengths of the Calegari-Walker Ziggurats -- i.e. graphs of extremal rotation numbers associated to positive words in free groups. These formulae reveal (partial) integral projective self-similarity in ziggurat fringes, which are low-dimensional projections of characteristic polyhedra on the bounded cohomology of free groups. This explains phenomena observed experimentally by Gordenko and Calegari-Walker.
description: 20 pages, 8 figures
Figure S6k from Expansion in geographical and morphological space drives continued lineage diversification in a global passerine radiation
Creators: name: Kennedy, Jonathan D.
name: Borregaard, Michael K.
name: Marki, Petter Z.
name: Machac, Antonin
name: Fjeldså, Jon
name: Rahbek, Carsten
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: Why diversification rates vary so extensively across the tree of life remains an important yet unresolved issue in biology. Two prominent and potentially independent factors proposed to explain these trends reflect the capacity of lineages to expand into new areas of (i) geographical or (ii) ecological space. Here, we present the first global assessment of how diversification rates vary as a consequence of geographical and ecological expansion, studying these trends among 15 speciose passerine families (together approximately 750 species) using phylogenetic path analysis. We find that relative slowdowns in diversification rates characterize families that have accumulated large numbers of co-occurring species (at the 1° scale) within restricted geographical areas. Conversely, more constant diversification through time is prevalent among families in which species show limited range overlap. Relative co-occurrence is itself also a strong predictor of ecological divergence (here approximated by morphological divergence among species); however, once the relationship between co-occurrence and diversification rates have been accounted for, increased ecological divergence is an additional explanatory factor accounting for why some lineages continue to diversify towards the present. We conclude that opportunities for prolonged diversification are predominantly determined by continued geographical range expansion and to a lesser degree by ecological divergence among lineages.
Legal Professionals' Perceptions of Marriage Contracts
Creators: name: Houston, Claire
name: Nicolyn Charlot
name: Joel, Samantha
Publisher: name: Open Science Framework
Year: 2023
Subjects: subject: Social and Behavioral Sciences
subject: Psychology
subject: FOS: Psychology
subject: Law
subject: FOS: Law
subject: Social Psychology
subject: Family Law

description: To reduce the burden on the justice system and better support lawyers drafting marriage contracts and the people entering into them, we need a better understanding of how these contracts are functioning and how they can be improved. In this study, we survey and interview family law lawyers to get their insights into current issues surrounding marriage agreements, and promising steps forward for the justice system.
(1600) John Wicksteed
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.
Appendix A from Evolution of non-kin cooperation: social assortment by cooperative phenotype in guppies.
Creators: name: Brask, Josefine Bohr
name: Croft, Darren P.
name: Edenbrow, Mathew
name: James, Richard
name: Bleakley, Bronwyn H.
name: Indar W. Ramnarine
name: Heathcote, Robert J. P.
name: Tyler, Charles R.
name: Hamilton, Patrick B.
name: Dabelsteen, Torben
name: Safi K. Darden
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: 60801 Animal Behaviour

description: Schematic drawing of test tank
The two D6R4 type invariants and their higher order generalisation
Creators: name: Bossard, Guillaume
name: Verschinin, Valentin
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We show that there are two distinct classes of D6R4 type supersymmetry invariants in maximal supergravity. The second class includes a coupling in F2D4R4 that generalises to 1/8 BPS protected F2kD4R4 couplings. We work out the supersymmetry constraints on the corresponding threshold functions, and argue that the functions in the second class satisfy to homogeneous differential equations for arbitrary k>0, such that the corresponding exact threshold functions in type II string theory should be proportional to Eisenstein series, which we identify. This analysis explains in particular that the exact D6R4 threshold function is the sum of an Eisenstein function and a solution to an inhomogeneous Poisson equation in string theory.
description: 53 pages