cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 1 of Identification of intraoperative management strategies that have a differential effect on patients with reduced left ventricular ejection fraction: a retrospective cohort study
Creators: name: Maile, Michael D.
name: Mathis, Michael R.
name: Jewell, Elizabeth S.
name: Mentz, Graciela B.
name: Engoren, Milo C.
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy

description: Additional file 1: Supplemental Table 1. Interaction of intraoperative management and reduced left ventricular ejection fraction on the occurrence of the primary outcome. Supplemental Table 2. Multivariable logistic regressions showing effect of remifentanil on each outcome. Supplemental Table 3. Multivariable logistic regressions showing effect of fluid balance on each outcome.
Source Data: The mPFC DUSP1 mediates adolescent cocaine exposure-caused higher sensitivity to drug in adulthood
Creators: name: Fan, Yu
Publisher: name: figshare
Year: 2023
Subjects: Behavioural neuroscience

description: The source data for the manuscript" The mPFC DUSP1 mediates adolescent cocaine exposure-caused higher sensitivity to drug in adulthood".
Analytic derivation of electrostrictive tensors and their application to optical force density calculations
Creators: name: Sun, Wujiong
name: Wang, S. B.
name: Ng, Jack
name: Zhou, Lei
name: Chan, C. T.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Using multiple scattering theory, we derived for the first time analytical formulas for electrostrictive tensors for two dimensional metamaterial systems. The electrostrictive tensor terms are found to depend explicitly on the symmetry of the underlying lattice of the metamaterial and they also depend explicitly on the direction of a local effective wave vector. These analytical results enable us to calculate light induced body forces inside a composite system (metamaterial) using the Helmholtz stress tensor within the effective medium formalism in the sense that the fields used in the stress tensor are those obtained by solving the macroscopic Maxwell equation with the microstructure of the metamaterial replaced by an effective medium. Our results point to some fundamental questions of using an effective medium theory to determine optical force density. In particular, the fact that Helmholtz tensor carries electrostrictive terms that are explicitly symmetry dependent means that the standard effective medium parameters cannot give sufficient information to determine body force density, even though they can give the correct total force. A more challenging issue is that the electrostrictive terms are related to a local effective wave vector, and it is not always obtainable in systems with boundary reflections within the context of a standard effective medium approach.
description: 29 pages, 7 figures
Dephasing and dissipation in qubit thermodynamics
Creators: name: Pekola, J. P.
name: Masuyama, Y.
name: Nakamura, Y.
name: Bergli, J.
name: Galperin, Y. M.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We analyze the stochastic evolution and dephasing of a qubit within the quantum jump (QJ) approach. It allows one to treat individual realizations of inelastic processes, and in this way it provides solutions, for instance, to problems in quantum thermodynamics and distributions in statistical mechanics. As a solvable example, we study a qubit in the weak dissipation limit, and demonstrate that dephasing and relaxation render the Jarzynski and Crooks fluctuation relations (FRs) of non-equilibrium thermodynamics intact. On the contrary, the standard two-measurement protocol, taking into account only the fluctuations of the internal energy $U$, leads to deviations in FRs under the same conditions. We relate the average $\langle e^{-βU} \rangle $ (where $β$ is the inverse temperature) with the qubit's relaxation and dephasing rates, and discuss this relationship for different mechanisms of decoherence.
description: 9 pages
(502351) Catherine Vincent
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.
Additional file 3 of Frequent birth-and-death events throughout perforin-1 evolution
Creators: name: Araujo-Voces, Miguel
name: Quesada, Víctor
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 3 Perforin-1 loci in non-avian reptiles. PRF1 genes are depicted to scale with intron/exon boundaries (blue boxes). Pseudogenes are depicted in pink. Flanking genes may be cropped for ease of depiction.
Expanding the Chemical Diversity of Genetically Encoded Libraries
Creators: name: Bowers, A.A.
name: Haberman, V.A.
name: Iskandar, S.E.
Publisher: name: American Chemical Society
Year: 2020

description: The power of ribosomes has increasingly been harnessed for the synthesis and selection of molecular libraries. Technologies, such as phage display, yeast display, and mRNA display, effectively couple genotype to phenotype for the molecular evolution of high affinity epitopes for many therapeutic targets. Genetic code expansion is central to the success of these technologies, allowing researchers to surpass the intrinsic capabilities of the ribosome and access new, genetically encoded materials for these selections. Here, we review techniques for the chemical expansion of genetically encoded libraries, their abilities and limits, and opportunities for further development. Importantly, we also discuss methods and metrics used to assess the efficiency of modification and library diversity with these new techniques.
Additional file 4 of Frequent birth-and-death events throughout perforin-1 evolution
Creators: name: Araujo-Voces, Miguel
name: Quesada, Víctor
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 4 Perforin-1 loci in birds. PRF1 genes are depicted to scale with intron/exon boundaries (blue boxes). Pseudogenes are depicted in pink. Flanking genes may be cropped for ease of depiction.
(502343) Arthur Evelyn Carey
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.
(502345) Theodora Edgington
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.
Additional file 2 of Identification of intraoperative management strategies that have a differential effect on patients with reduced left ventricular ejection fraction: a retrospective cohort study
Creators: name: Maile, Michael D.
name: Mathis, Michael R.
name: Jewell, Elizabeth S.
name: Mentz, Graciela B.
name: Engoren, Milo C.
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy

description: Additional file 2: Supplemental Fig. 1. Assignment of surgical risk category based on the incidence of the primary outcome for each surgical type. The surgical risk categories are displayed using distinct colors as defined in the figure legend. High-risk surgery consisted of acute care and trauma surgery. Moderate-risk surgery consisted of thoracic, vascular, otolaryngology, and neurosurgery. Low-risk surgery consisted of urology and gynecology, general surgery, orthopedics, and plastic surgery.
Thiopeptides Induce Proteasome-Independent Activation of Cellular Mitophagy
Creators: name: Schmalstig, A.A.
name: Wang, X.
name: Emanuele, M.J.
name: Bowers, A.A.
name: Bird, K.E.
name: Braunstein, M.
name: Murcia, S.
name: Xander, C.
Publisher: name: American Chemical Society
Year: 2020

description: Thiopeptide antibiotics are emerging clinical candidates that exhibit potent antibacterial activity against a variety of intracellular pathogens, including Mycobacterium tuberculosis (Mtb). Many thiopeptides directly inhibit bacterial growth by disrupting protein synthesis. However, recent work has shown that one thiopeptide, thiostrepton (TSR), can also induce autophagy in infected macrophages, which has the potential to be exploited for host-directed therapies against intracellular pathogens, such as Mtb. To better define the therapeutic potential of this class of antibiotics, we studied the host-directed effects of a suite of natural thiopeptides that spans five structurally diverse thiopeptide classes, as well as several analogs. We discovered that thiopeptides as a class induce selective autophagic removal of mitochondria, known as mitophagy. This activity is independent of other biological activities, such as proteasome inhibition or antibiotic activity. We also find that many thiopeptides exhibit potent activity against intracellular Mtb in macrophage infection models. However, the thiopeptide-induced mitophagy occurs outside of pathogen-containing autophagosomes and does not appear to contribute to thiopeptide control of intracellular Mtb. These results expand basic understanding of thiopeptide biology and provide key guidance for the development of new thiopeptide antibiotics and host-directed therapeutics.
(502346) Henrietta [dau. of Alfred Southby] Crowdy
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.
Therapeutic impact of thymoquninone to alleviate ischemic brain injury via Nrf2/HO-1 pathway
Creators: name: Amin, Nashwa
name: Du, Xiaoxue
name: Chen, Shijia
name: Ren, Qiannan
name: Hussien, Azhar B.
name: Botchway, Benson O.A.
name: Hu, Zhiying
name: Fang, Marong
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Physiology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine

description: Introduction: Reactive oxygen species (ROS)-mediated inflammation plays a crucial role in ischemic brain injury. Therefore, the activation of the nuclear erythroid 2 related protein and heme-oxygenase-1 (Nrf2/HO-1) pathway by thymoquinone (TQ) could ameliorate ischemic brain damage. Areas covered: The photo-thrombotic method was employed to assess the impact of TQ in attenuating ischemic brain damage in C57BL/6 J mice and thy1-YFP-16 transgenic mice. In vitro study of TQ efficiency to attenuate the oxygen-glucose deprivation/reoxygenation (OGD/R) induced cell death by fluorescence-activated cell sorting (FACs) analysis was also analyzed. The protein expression levels of Nrf2/HO-1, inflammatory, and apoptotic were evaluated by immunofluorescence and western blot techniques. Besides, mRNA expression level of inducible nitric oxide synthase (iNOS), proto-oncogene (c-MYC), proto-oncogene (c-FOS), 5-hydroxytryptamine receptors (5-HT), and autophagy-related 5 (Atg5) were evaluated by RT-qPCR. The dendritic spine density of YFP slices was determined by confocal microscope. Results: Our in vivo and in vitro results indicated that TQ significantly mitigates brain damage and motor dysfunction after ischemic stroke. These observations coincided with curtailed cell death, inflammation, oxidative stress, apoptosis, and autophagy. Most importantly, Nrf2/HO-1 signaling pathway activation by TQ was vital in the modulation of the above processes. Lastly, we found TQ to have minimal toxicity in liver tissue. Conclusion: Our study gives credence to TQ as a promising intervention therapy for cerebral ischemia that decreases inflammation, oxidative stress, and neuronal cell death via the Nrf2/HO-1 pathway, along with modulation of apoptotic and autophagic processes.
Discovery and Characterization of Peptide Inhibitors for Calcium and Integrin Binding Protein 1
Creators: name: Bowers, A.A.
name: Bogart, J.W.
name: Cholensky, S.H.
name: Haberman, V.A.
name: Pearce, K.H.
name: Godoy, A.S.
name: Frye, S.V.
name: Leisner, T.M.
name: Parise, L.V.
name: Larson, J.E.
name: Puhl, A.C.
name: Norris-Drouin, J.L.
name: Parise, L.V.
Publisher: name: American Chemical Society
Year: 2020

description: Calcium and integrin binding protein 1 (CIB1) is an EF-hand-containing, small intracellular protein that has recently been implicated in cancer cell survival and proliferation. In particular, CIB1 depletion significantly impairs tumor growth in triple-negative breast cancer (TNBC). Thus, CIB1 is a potentially attractive target for cancer chemotherapy that has yet to be validated by a chemical probe. To produce a probe molecule to the CIB1 helix 10 (H10) pocket and demonstrate that it is a viable target for molecular intervention, we employed random peptide phage display to screen and select CIB1-binding peptides. The top peptide sequence selected, UNC10245092, was produced synthetically, and binding to CIB1 was confirmed by isothermal titration calorimetry (ITC) and a time-resolved fluorescence resonance energy transfer (TR-FRET) assay. Both assays showed that the peptide bound to CIB1 with low nanomolar affinity. CIB1 was cocrystallized with UNC10245092, and the 2.1 Å resolution structure revealed that the peptide binds as an α-helix in the H10 pocket, displacing the CIB1 C-terminal H10 helix and causing conformational changes in H7 and H8. UNC10245092 was further derivatized with a C-terminal Tat-derived cell penetrating peptide (CPP) to demonstrate its effects on TNBC cells in culture, which are consistent with results of CIB1 depletion. These studies provide a first-in-class chemical tool for CIB1 inhibition in cell culture and validate the CIB1 H10 pocket for future probe and drug discovery efforts.
Additional file 2 of Frequent birth-and-death events throughout perforin-1 evolution
Creators: name: Araujo-Voces, Miguel
name: Quesada, Víctor
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2 Perforin-1 loci in mammalian species. PRF1 genes are depicted to scale with intron/exon boundaries (blue boxes). Pseudogenes are depicted in pink. Flanking genes may be cropped for ease of depiction.
Additional file 5 of Frequent birth-and-death events throughout perforin-1 evolution
Creators: name: Araujo-Voces, Miguel
name: Quesada, Víctor
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 5 Perforin-1 loci in amphibians. PRF1 genes are depicted to scale with intron/exon boundaries (blue boxes). Pseudogenes are depicted in pink. Flanking genes may be cropped for ease of depiction.
Entropic uncertainty relation in de Sitter space
Creators: name: Jia, Lijuan
name: Tian, Zehua
name: Jing, Jiliang
Publisher: name: arXiv
Year: 2015
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The uncertainty principle restricts our ability to simultaneously predict the measurement outcomes of two incompatible observables of a quantum particle. However, this uncertainty could be reduced and quantified by a new Entropic Uncertainty Relation (EUR). By the open quantum system approach, we explore how the nature of de Sitter space affects the EUR. When the quantum memory $A$ freely falls in the de Sitter space, we demonstrate that the entropic uncertainty acquires an increase resulting from a thermal bath with the Gibbons-Hawking temperature. And for the static case, we find that the temperature coming from both the intrinsic thermal nature of the de Sitter space and the Unruh effect associated with the proper acceleration of $A$ also brings effect on entropic uncertainty, and the higher temperature, the greater uncertainty and the quicker the uncertainty reaches the maxima value. And finally the possible mechanism behind this phenomenon is also explored.
description: 17 pages, 5 figures
(502338) Elizabeth Styles
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.
(502342) Ranulph Vincent
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.
Additional file 6 of Frequent birth-and-death events throughout perforin-1 evolution
Creators: name: Araujo-Voces, Miguel
name: Quesada, Víctor
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 6 Perforin-1 loci in teleosts. PRF1 genes are depicted to scale with intron/exon boundaries (blue boxes). Pseudogenes are depicted in pink. Genes with names containing hcX belong to the c2PRF1 family. Flanking genes may be cropped for ease of depiction.
Additional file 1 of Acupuncture attenuates comorbid anxiety- and depressive-like behaviors of atopic dermatitis through modulating neuroadaptation in the brain reward circuit in mice
Creators: name: Yeom, Mijung
name: Ahn, Sora
name: Jang, Sun-Young
name: Jang, Jae-Hwan
name: Lee, Youngrye
name: Hahm, Dae-Hyun
name: Park, Hi-Joon
Publisher: name: figshare
Year: 2022
Subjects: subject: Biochemistry
subject: Medicine
subject: Neuroscience
subject: Sociology
subject: FOS: Sociology
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1: Fig. S1. Representative images of hematoxylin and eosin–stained skin sections from each experimental group of mice on day 11. NOR untreated control group, MC903 MC903-induced atopic dermatitis group, pAP MC903- and preventive acupuncture-treated group, tAP MC903- and therapeutic acupuncture-treated group, CP MC903- and acupuncture at control point (non-acupoint)-treated group. Magnification, ×100. Fig. S2. Representative activity tracks in the open field test (OFT, top) and elevated plus maze (EPM, bottom). NOR untreated control group, MC903 MC903-induced atopic dermatitis group, pAP MC903- and preventive acupuncture-treated group, tAP MC903- and therapeutic acupuncture-treated group, CP MC903- and acupuncture at control point (non-acupoint)-treated group. Fig. S3. Representative immunoblots of plasticity-related (A, C, and E; pCREB, ΔFosB and BDNF) and DA-related (B, D, and F; TH, D1AR and pDARPP-32) proteins in the brain reward regions. NOR untreated control group, MC903 MC903-induced atopic dermatitis group, pAP MC903- and preventive acupuncture-treated group, tAP MC903- and therapeutic acupuncture-treated group, CP MC903- and acupuncture at control point (non-acupoint)-treated group. CREB cyclic AMP-response element binding protein, pCREB phospho-Ser133 CREB, BDNF brain-derived neurotrophic factor, TH tyrosine hydroxylase, D1AR dopamine D1 receptor, DARPP-32 dopamine- and cAMP-regulated phosphoprotein of 32 kDa, pDARPP-32 phospho-Thr34 DARPP-32. Fig. S4. Correlations between clinical symptom of atopic dermatitis and psychological distress. A Heatmap of the correlation matrix comparing the clinical symptoms of atopic dermatitis (skin lesion severity and scratching behavior) and psychological distress (anxiety-like/depression-like behavior). Color represents the Spearman’s correlation coefficient. *** p < 0.001. B Scatterplots depicting the association between pairs. The linear model describing the relationship is depicted as a solid line with a 95% confidence interval (CI), as indicated by dashed lines. EPM elevated plus maze, OFT open-field test, TST tail suspension test. NOR untreated control group, MC903 MC903-induced atopic dermatitis group, pAP MC903- and preventive acupuncture-treated group, tAP MC903- and therapeutic acupuncture-treated group, CP MC903- and acupuncture at control point (non-acupoint)-treated group.
Interception of the Bycroft-Gowland Intermediate in the Enzymatic Macrocyclization of Thiopeptides
Creators: name: Houk, K.N.
name: Kramer, N.J.
name: Bleich, R.M.
name: Bogart, J.W.
name: Nair, S.K.
name: Bowers, A.A.
name: Williamson, R.T.
name: Schroeder, F.C.
name: Catlin, D.S.
name: Turlik, A.
Publisher: name: American Chemical Society
Year: 2020

description: Thiopeptides are a broad class of macrocyclic, heavily modified peptide natural products that are unified by the presence of a substituted, nitrogen-containing heterocycle core. Early work indicated that this core might be fashioned from two dehydroalanines by an enzyme-catalyzed aza-[4 + 2] cycloaddition to give a cyclic-hemiaminal intermediate. This common intermediate could then follow a reductive path toward a dehydropiperidine, as in the thiopeptide thiostrepton, or an aromatization path to yield the pyridine groups observed in many other thiopeptides. Although several of the enzymes proposed to perform this cycloaddition have been reconstituted, only pyridine products have been isolated and any hemiaminal intermediates have yet to be observed. Here, we identify the conditions and substrates that decouple the cycloaddition from subsequent steps and allow interception and characterization of this long hypothesized intermediate. Transition state modeling indicates that the key amide-iminol tautomerization is the major hurdle in an otherwise energetically favorable cycloaddition. An anionic model suggests that deprotonation and polarization of this amide bond by TbtD removes this barrier and provides a sufficient driving force for facile (stepwise) cycloaddition. This work provides evidence for a mechanistic link between disparate cyclases in thiopeptide biosynthesis.
CropBASE-EU populated with UC historic data
Creators: name: Azam-Ali, Sayed
Publisher: name: Zenodo
Year: 2023

description: CropBASE-EU aims at collating historical and RADIANT data related to the value chain of Underutilised Crops (UCs). Further technical refinements are done to the ‘database’ which henceforth is referred to as the `Knowledge Base’ for EU underutilised crops and the ‘ecosystem of apps’ to enhance the collaborative data collection for both historical and RADIANT data within Task 1.4.
Additional file 1 of The feasibility of collecting the physiotherapy outcomes airway clearance, physical activity and fitness for the Australian Cystic Fibrosis Data Registry
Creators: name: Potter, Angela
name: Singh, Ben
name: Scutter, Emily
name: Maher, Carol
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Science Policy
subject: Sociology
subject: FOS: Sociology

description: Additional file 1. Summary of field notes taken from the physiotherapist during data collection. The physiotherapist took notes related to patient recruitment, staff availability, time available, willingness to participate, completing surveys, completing fitness test, and time taken to enter patient data. ACT: airway clearance techniques; PA: physical activity.
Exploring the Post-translational Enzymology of PaaA by mRNA Display
Creators: name: Fleming, S.R.
name: Suga, H.
name: Himes, P.M.
name: Goto, Y.
name: Bowers, A.A.
name: Ghodge, S.V.
Publisher: name: American Chemical Society
Year: 2020

description: PaaA is a RiPP enzyme that catalyzes the transformation of two glutamic acid residues within a substrate peptide into the bicyclic core of Pantocin A. Here, for the first time, we use mRNA display techniques to understand RiPP enzyme-substrate interactions to illuminate PaaA substrate recognition. Additionally, our data revealed insights into the enzymatic timing of glutamic acid modification. The technique developed is quite sensitive and a significant advancement over current RiPP studies and opens the door to enzyme modified mRNA display libraries for natural product-like inhibitor pans.
(502335) John Moxon Clabon
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.
Dehydroamino acids: chemical multi-tools for late-stage diversification
Creators: name: Bogart, J.W.
name: Bowers, A.A.
Publisher: name: Royal Society of Chemistry
Year: 2019

description: α,β-Dehydroamino acids (dhAAs) are noncanonical amino acids that are found in a wide array of natural products and can be easily installed into peptides and proteins. dhAAs exhibit remarkable synthetic flexibility, readily undergoing a number of reactions, such as polar and single-electron additions, transition metal catalyzed cross-couplings, and cycloadditions. Because of the relatively mild conditions required for many of these reactions, dhAAs are increasingly being used as orthogonal chemical handles for late-stage modification of biomolecules. Still, only a fraction of the chemical reactivity of dhAAs has been exploited in such biorthogonal applications. Herein, we provide an overview of the broad spectrum of chemical reactivity of dhAAs, with special emphasis on recent efforts to adapt such transformations for biomolecules such as natural products, peptides, and proteins. We also discuss examples of enzymes from natural product biosynthetic pathways that have been found to catalyze many similar reactions; these enzymes provide mild, regio- and stereoselective, biocatalytic alternatives for future development. We anticipate that the continued investigation of the innate reactivity of dhAAs will furnish a diverse portfolio dhAA-based chemistries for use in chemical biology and drug discovery.
Additional file 7 of Frequent birth-and-death events throughout perforin-1 evolution
Creators: name: Araujo-Voces, Miguel
name: Quesada, Víctor
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 7 Perforin-1 loci in cartilaginous fishes. PRF1 genes are depicted to scale with intron/exon boundaries (blue boxes). Pseudogenes are depicted in pink. Flanking genes may be cropped for ease of depiction.
(502337) George Badrick
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.
Additional file 1 of Mental health workers’ perspectives on peer support in high-, middle- and low income settings: a focus group study
Creators: name: Krumm, Silvia
name: Haun, Maria
name: Hiller, Selina
name: Charles, Ashleigh
name: Kalha, Jasmine
name: Niwemuhwezi, Jackie
name: Nixdorf, Rebecca
name: Puschner, Bernd
name: Ryan, Grace
name: Shamba, Donat
name: Epstein, Paula Garber
name: Moran, Galia
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Science Policy

description: Additional file 1.
Inter-Modular Linkers play a crucial role in governing the biosynthesis of non-ribosomal peptides
Creators: name: Shank, E.A.
name: Isayev, O.
name: Farag, S.
name: Tropsha, A.
name: Bleich, R.M.
name: Bowers, A.A.
Publisher: name: Oxford University Press
Year: 2019

description: Motivation: Non-ribosomal peptide synthetases (NRPSs) are modular enzymatic machines that catalyze the ribosome-independent production of structurally complex small peptides, many of which have important clinical applications as antibiotics, antifungals and anti-cancer agents. Several groups have tried to expand natural product diversity by intermixing different NRPS modules to create synthetic peptides. This approach has not been as successful as anticipated, suggesting that these modules are not fully interchangeable. Results: We explored whether Inter-Modular Linkers (IMLs) impact the ability of NRPS modules to communicate during the synthesis of NRPs. We developed a parser to extract 39 804 IMLs from both well annotated and putative NRPS biosynthetic gene clusters from 39 232 bacterial genomes and established the first IMLs database. We analyzed these IMLs and identified a striking relationship between IMLs and the amino acid substrates of their adjacent modules. More than 92% of the identified IMLs connect modules that activate a particular pair of substrates, suggesting that significant specificity is embedded within these sequences. We therefore propose that incorporating the correct IML is critical when attempting combinatorial biosynthesis of novel NRPS. Availability and implementation: The IMLs database as well as the NRPS-Parser have been made available on the web at https://nrps-linker.unc.edu. The entire source code of the project is hosted in GitHub repository (https://github.com/SWFarag/nrps-linker). Supplementary information: Supplementary data are available at Bioinformatics online.
Additional file 2 of Mental health workers’ perspectives on peer support in high-, middle- and low income settings: a focus group study
Creators: name: Krumm, Silvia
name: Haun, Maria
name: Hiller, Selina
name: Charles, Ashleigh
name: Kalha, Jasmine
name: Niwemuhwezi, Jackie
name: Nixdorf, Rebecca
name: Puschner, Bernd
name: Ryan, Grace
name: Shamba, Donat
name: Epstein, Paula Garber
name: Moran, Galia
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Science Policy

description: Additional file 2.
van der Waals coefficients for positronium interactions with atoms
Creators: name: Swann, A. R.
name: Ludlow, J. A.
name: Gribakin, G. F.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: The random-phase approximation with exchange (RPAE) is used with a $B$-spline basis to compute dynamic dipole polarizabilities of noble-gas atoms and several other closed-shell atoms (Be, Mg, Ca, Zn, Sr, Cd, and Ba). From these, values of the van der Waals $C_6$ constants for positronium interactions with these atoms are determined and compared with existing data. Our best predictions of $C_6$ for Ps--noble-gas pairs are expected to be accurate to within 1%, and to within a few per cent for the alkaline earths. We also used accurate dynamic dipole polarizabilities from the literature to compute the $C_6$ coefficients for the alkali-metal atoms. Implications of increased $C_6$ values for Ps scattering from more polarizable atoms are discussed.
description: 6 pages, submitted to Physical Review A
(502341) Gustavus Alfred Sneyd
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.
(502332) Charles Kent
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.
Mapping the sites of the lipoprotein lipase (LPL)–angiopoietin-like protein 4 (ANGPTL4) interaction provides mechanistic insight into LPL inhibition
Creators: name: Gutgsell, A.R.
name: Neher, S.B.
name: Bowers, A.A.
name: Ghodge, S.V.
Publisher: name: American Society for Biochemistry and Molecular Biology Inc.
Year: 2019

description: Cardiovascular disease has been the leading cause of death throughout the world for nearly 2 decades. Hypertriglyceridemia affects more than one-third of the population in the United States and is an independent risk factor for cardiovascular disease. Despite the frequency of hypertriglyceridemia, treatment options are primarily limited to diet and exercise. Lipoprotein lipase (LPL) is an enzyme responsible for clearing triglycerides from circulation, and its activity alone can directly control plasma triglyceride concentrations. Therefore, LPL is a good target for triglyceride-lowering therapeutics. One approach for treating hypertriglyceridemia may be to increase the amount of enzymatically active LPL by preventing its inhibition by angiopoietin-like protein 4 (ANGPTL4). However, little is known about how these two proteins interact. Therefore, we used hydrogen– deuterium exchange MS to identify potential binding sites between LPL and ANGPTL4. We validated sites predicted to be located at the protein–protein interface by using chimeric variants of LPL and an LPL peptide mimetic. We found that ANGPTL4 binds LPL near the active site at the lid domain and a nearby -helix. Lipase lid domains cover the active site to control both enzyme activation and substrate specificity. Our findings suggest that ANGPTL4 specifically inhibits LPL by binding the lid domain, which could prevent substrate catalysis at the active site. The structural details of the LPL–ANGPTL4 interaction uncovered here may inform the development of therapeutics targeted to disrupt this interaction for the management of hypertriglyceridemia.
MT2 to the Rescue -- Searching for Sleptons in Compressed Spectra at the LHC
Creators: name: Han, Zhenyu
name: Liu, Yandong
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: We propose a novel method for probing sleptons in compressed spectra at hadron colliders. The process under study is slepton pair production in R-parity conserving supersymmetry, where the slepton decays to a neutralino LSP of mass close to the slepton mass. In order to pass the trigger and obtain large missing energy, an energetic mono-jet is required. Both leptons need to be detected in order to suppress large standard model backgrounds with one charged lepton. We study variables that can be used to distinguish the signal from the remaining major backgrounds, which include tt, WW+jet, Z+jet, and single top production. We find that the dilepton MT2, bound by the mass difference, can be used as an upper bound to efficiently reduce the backgrounds. It is estimated that sleptons with masses up to about 150 GeV can be discovered at the 14 TeV LHC with 100/fb integrated luminosity.
description: 12 pages, 6 figures
Additional file 3 of Mental health workers’ perspectives on peer support in high-, middle- and low income settings: a focus group study
Creators: name: Krumm, Silvia
name: Haun, Maria
name: Hiller, Selina
name: Charles, Ashleigh
name: Kalha, Jasmine
name: Niwemuhwezi, Jackie
name: Nixdorf, Rebecca
name: Puschner, Bernd
name: Ryan, Grace
name: Shamba, Donat
name: Epstein, Paula Garber
name: Moran, Galia
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: Science Policy

description: Additional file 3.
Thiopeptide Pyridine Synthase TbtD Catalyzes an Intermolecular Formal Aza-Diels-Alder Reaction
Creators: name: Bogart, J.W.
name: Bowers, A.A.
Publisher: name: American Chemical Society
Year: 2019

description: Thiopeptide pyridine synthases catalyze a multistep reaction involving a unique and nonspontaneous intramolecular aza-[4 + 2] cycloaddition between two dehydroalanines to forge a trisubstituted pyridine core. We discovered that the in vitro activity of pyridine synthases from the thiocillin and thiomuracin pathways are significantly enhanced by general base catalysis and that this broadly expands the enzymes substrate tolerance. Remarkably, TbtD is competent to perform an intermolecular cyclization in addition to its cognate intramolecular reaction, underscoring its versatility as a biocatalyst. These data provide evidence that pyridine synthases use a two-site substrate recognition model to engage and process their substrates.
(502333) William Ingham Whittaker
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.
Using entanglement to discern phases in the disordered one-dimensional Bose-Hubbard model
Creators: name: Goldsborough, Andrew M.
name: Römer, Rudolf A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: We perform a matrix product state based density matrix renormalisation group analysis of the phases for the disordered one-dimensional Bose-Hubbard model. For particle densities N/L = 1, 1/2 and 2 we show that it is possible to obtain a full phase diagram using only the entanglement properties, which come "for free" when performing an update. We confirm the presence of Mott insulating, superfluid and Bose glass phases when N/L = 1 and 1/2 (without the Mott insulator) as found in previous studies. For the N/L = 2 system we find a double lobed superfluid phase with possible reentrance.
description: 6 pages, 4 figures
Additional file 1 of Medical decision-making in hospices from the viewpoint of physicians: results from two qualitative studies
Creators: name: Walker, Andreas
name: Breitsameter, Christof
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Science Policy

description: Additional file 1: Table1. Overview of the course of studies/data sources.
Flexizyme-Enabled Benchtop Biosynthesis of Thiopeptides
Creators: name: Kirkpatrick, C.L.
name: Hicks, L.M.
name: Fleming, S.R.
name: Vinogradov, A.A.
name: Bowers, A.A.
name: Suga, H.
name: Goto, Y.
name: Bartges, T.E.
Publisher: name: American Chemical Society
Year: 2019

description: Thiopeptides are natural antibiotics that are fashioned from short peptides by multiple layers of post-translational modification. Their biosynthesis, in particular the pyridine synthases that form the macrocyclic antibiotic core, has attracted intensive research but is complicated by the challenges of reconstituting multiple-pathway enzymes. By combining select RiPP enzymes with cell free expression and flexizyme-based codon reprogramming, we have developed a benchtop biosynthesis of thiopeptide scaffolds. This strategy side-steps several challenges related to the investigation of thiopeptide enzymes and allows access to analytical quantities of new thiopeptide analogs. We further demonstrate that this strategy can be used to validate the activity of new pyridine synthases without the need to reconstitute the cognate prior pathway enzymes.
Additional file 2 of Medical decision-making in hospices from the viewpoint of physicians: results from two qualitative studies
Creators: name: Walker, Andreas
name: Breitsameter, Christof
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Science Policy

description: Additional file 2: Table 2. Sampling of the studies regarding physicians working in hospices.
The multifaceted impact of US trade policy on financial markets
Creators: name: Boer, Lukas
name: Menkhoff, Lukas
name: Rieth, Malte
Publisher: name: Humboldt-Universität zu Berlin
Year: 2022
Subjects: subject: 330 Wirtschaft

description: We study the multifaceted effects of trade policy shocks on financial markets using a structural vector autoregression identified via event day heteroskedasticity. We find that restrictive US trade policy shocks affect US and international stock prices heterogeneously, but generally negatively. They increase market uncertainty, lower US interest rates, and lead to an appreciation of the US dollar. The effects are significant for several weeks or quarters. Decomposing the trade policy shocks further suggests that trade policy uncertainty dominates tariff level effects. Chinese trade policy shocks against the United States further hurt US stocks.
Additional file 3 of Medical decision-making in hospices from the viewpoint of physicians: results from two qualitative studies
Creators: name: Walker, Andreas
name: Breitsameter, Christof
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Science Policy

description: Additional file 3. Interview guide for physicians: Study "Decisions in Hospices".
The substrate lends a hand
Creators: name: Bowers, A.A.
Publisher: name: Nature Publishing Group
Year: 2018

description: Duramycin is a small post-translationally modified peptide with antibody-like affinity for phosphatidylethanolamine. As it turns out, the same functionality that is essential for duramycin activity helps to catalyze the formation of its conformationally constrained and compact polycyclic architecture.
Additional file 4 of Medical decision-making in hospices from the viewpoint of physicians: results from two qualitative studies
Creators: name: Walker, Andreas
name: Breitsameter, Christof
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Developmental Biology
subject: Science Policy

description: Additional file 4. Interview guide for physicians: Study "On 'dying well'. Actor constellations, normative patterns, differences in perspective".