cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Lead optimization, pharmacophore development and scaffold design of protein kinase CK2 inhibitors as potential COVID-19 therapeutics
Creators: name: Yadav, Siddharth
name: Ahamad, Shahzaib
name: Gupta, Dinesh
name: Mathur, Puniti
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 60506 Virology

description: Therapeutic agents being designed against COVID-19 have targeted either the virus directly or the host cellular machinery. A particularly attractive host target is the ubiquitous and constitutively active serine-threonine kinase, Protein kinase CK2 (CK2). CK2 enhances viral protein synthesis by inhibiting the sequestration of host translational machinery as stress granules and assists in viral egression via association with the N-protein at filopodial protrusions of the infected cell. CK2 inhibitors such as Silmitasertib have been proposed as possible therapeutic candidates in COVID-19 infections. The present study aims to optimize Silmitasertib, develop pharmacophore models and design unique scaffolds to modulate CK2. The lead optimization phase involved the generation of compounds structurally similar to Silmitasertib via bioisostere replacement followed by a multi-stage docking approach to identify drug-like candidates. Molecular dynamics (MD) simulations were performed for two promising candidates (ZINC-43206125 and PC-57664175) to estimate their binding stability and interaction. Top scoring candidates from the lead optimization phase were utilized to build ligand-based pharmacophore models. These models were then merged with structure-based pharmacophores (e-pharmacophores) to build a hybrid hypothesis. This hybrid hypothesis was validated against a decoy set and used to screen a diverse kinase inhibitors library to identify favored chemical features in the retrieved actives. These chemical features include; an anion, an aromatic ring and an H-bond acceptor. Based on the knowledge of these features; de-novo scaffold design was carried out which identified phenindiones, carboxylated steroids, macrocycles and peptides as novel scaffolds with the potential to modulate CK2. Communicated by Ramaswamy H. Sarma
Nanoscale $β$-Nuclear Magnetic Resonance Depth Imaging of Topological Insulators
Creators: name: Koumoulis, Dimitrios
name: Morris, Gerald D.
name: He, Liang
name: Kou, Xufeng
name: King, Danny
name: Wang, Dong
name: Hossain, Masrur D.
name: Wang, Kang L.
name: Fiete, Gregory A.
name: Kanatzidis, Mercouri G.
name: Bouchard, Louis-S.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Considerable evidence suggests that variations in the properties of topological insulators (TIs) at the nanoscale and at interfaces can strongly affect the physics of topological materials. Therefore, a detailed understanding of surface states and interface coupling is crucial to the search for and applications of new topological phases of matter. Currently, no methods can provide depth profiling near surfaces or at interfaces of topologically inequivalent materials. Such a method could advance the study of interactions. Herein we present a non-invasive depth-profiling technique based on $β$-NMR spectroscopy of radioactive $^8$Li$^+$ ions that can provide "one-dimensional imaging" in films of fixed thickness and generates nanoscale views of the electronic wavefunctions and magnetic order at topological surfaces and interfaces. By mapping the $^8$Li nuclear resonance near the surface and 10 nm deep into the bulk of pure and Cr-doped bismuth antimony telluride films, we provide signatures related to the TI properties and their topological non-trivial characteristics that affect the electron-nuclear hyperfine field, the metallic shift and magnetic order. These nanoscale variations in $β$-NMR parameters reflect the unconventional properties of the topological materials under study, and understanding the role of heterogeneities is expected to lead to the discovery of novel phenomena involving quantum materials.
description: 46 pages, 12 figures in Proc. Natl. Aca. Sci. USA (2015) Published online - early edition
Quantification of Flavin-containing Monooxygenases 1, 3, and 5 in Human Liver Microsomes by UPLC-MRM-Based Targeted Quantitative Proteomics and Its Application to the Study of Ontogeny
Creators: name: Thakker, Dhiren R.
name: Wang, Michael Zhuo
name: Chen, Yao
name: Zane, Nicole R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Flavin-containing monooxygenases (FMOs) have a significant role in the metabolism of small molecule pharmaceuticals. Among the five human FMOs, FMO1, FMO3, and FMO5 are the most relevant to hepatic drug metabolism. Although age-dependent hepatic protein expression, based on immunoquantification, has been reported previously for FMO1 and FMO3, there is very little information on hepatic FMO5 protein expression. To overcome the limitations of immunoquantification, an ultra-performance liquid chromatography (UPLC)-multiple reaction monitoring (MRM)-based targeted quantitative proteomic method was developed and optimized for the quantification of FMO1, FMO3, and FMO5 in human liver microsomes (HLM). A post-in silico product ion screening process was incorporated to verify LC-MRM detection of potential signature peptides before their synthesis. The developed method was validated by correlating marker substrate activity and protein expression in a panel of adult individual donor HLM (age 39–67 years). The mean (range) protein expression of FMO3 and FMO5 was 46 (26–65) pmol/mg HLM protein and 27 (11.5–49) pmol/mg HLM protein, respectively. To demonstrate quantification of FMO1, a panel of fetal individual donor HLM (gestational age 14–20 weeks) was analyzed. The mean (range) FMO1 protein expression was 7.0 (4.9–9.7) pmol/mg HLM protein. Furthermore, the ontogenetic protein expression of FMO5 was evaluated in fetal, pediatric, and adult HLM. The quantification of FMO proteins also was compared using two different calibration standards, recombinant proteins versus synthetic signature peptides, to assess the ratio between holoprotein versus total protein. In conclusion, a UPLC-MRM-based targeted quantitative proteomic method has been developed for the quantification of FMO enzymes in HLM.
Long-range properties of $1S$ bottomonium states
Creators: name: Brambilla, Nora
name: Krein, Gastão
name: Castellà, Jaume Tarrús
name: Vairo, Antonio
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: In the framework of weakly-coupled pNRQCD, we derive, first, an analytical expression for the chromo-polarizability of $1S$-bottomonium states in agreement with previous determinations. Then we use the QCD trace anomaly to obtain the two-pion production amplitude for the chromo-polarizability operator and match the result to a chiral effective field theory with $1S$-bottomonium states and pions as degrees-of-freedom. In this chiral effective field theory we compute some long-range properties of the $1S$ bottomonium generated by the pion coupling such as the leading chiral logarithm to the $1S$-bottomonium mass and the van der Waals potential between two $1S$-bottomonium states. Both results improve on previously known expressions.
description: 24 pages, 10 figures. Journal version
Leptogium tuckermanii C. W. Dodge 1933
Creators: name: Kitaura, Marcos J.
name: Bernardo, Caique M.
name: Koch, Natália M.
name: Rodrigues, Andressa S.
name: Torres, Jean-Marc
name: Barbosa, Thiago D.
name: Canêz, Luciana Da S.
name: Spielmann, Adriano A.
name: Honda, Neli K.
name: Fleig, Mariana
name: Lorenz, Aline P.
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Fungi
Ascomycota
Lecanoromycetes
Peltigerales
Collemataceae
Leptogium
Leptogium tuckermanii

description: Leptogium tuckermanii C.W. Dodge (1933: 436).
 Type not traced:— CUBA. Monte Verde: C. Wright 56.
Description: Dodge (1933).
 Notes: Leptogium tuckermanii is characterized by the mineral gray to darker color, smooth surface, apothecia 0.5–0.9 mm diam. with constrict base, margin of apothecia smooth and pale, and amphithecia with pseudoparaplectenchymatous cortex (Dodge 1933).
Until now, the holotype C. Wright 56 was not found, but the specimen C. Wright 15 from the same locality is in FH herbarium and is the strongest candidate for the neotype. We do not know whether the collection date is the same for both vouchers, since Dodge (1933) did not specify when C. Wright 56 was collected. C. Wright 15 was collected on 1 April 1861.
 Leptogium tuckermanii differs from L. cochleatum by the type of upper surface. Leptogium tuckermanii has smooth upper surface and L. cochleatum has distinctly striate upper surface.
 Leptogium moluccanum var. denticulatum can be confused with L. tuckermanii, but the first has apothecia with bluish margin and circular wrinkles and L. tuckermanii has apothecia with pale and smooth margins.
Distribution in Brazil: Paraná (Osorio 1977); Mato Grosso do Sul, in Ponta Porã (Osorio 1992); and Rio Grande do Sul (Spielmann 2006).
description: Published as part of Kitaura, Marcos J., Bernardo, Caique M., Koch, Natália M., Rodrigues, Andressa S., Torres, Jean-Marc, Barbosa, Thiago D., Canêz, Luciana Da S., Spielmann, Adriano A., Honda, Neli K., Fleig, Mariana & Lorenz, Aline P., 2019, Leptogium (Collemataceae, Peltigerales) from Mato Grosso do Sul state, Brazil: nine new records, three new taxa and a key for the species, pp. 127-146 in Phytotaxa 399 (2) on page 142, DOI: 10.11646/phytotaxa.399.2.3, http://zenodo.org/record/13714341
Design, synthesis, molecular modeling, DFT, ADME and biological evaluation studies of some new 1,3,4-oxadiazole linked benzimidazoles as anticancer agents and aromatase inhibitors
Creators: name: Çevik, Ulviye Acar
name: Celik, Ismail
name: Işık, Ayşen
name: Ahmad, Iqrar
name: Patel, Harun
name: Özkay, Yusuf
name: Kaplancıklı, Zafer Asım
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Cancer

description: Breast cancer is the most frequent female cancer and second cause of cancer-related deaths among women around the world. Two thirds of breast cancer patients have hormone-dependent tumors, which is very likely be treated with hormonal therapy. Aromatase is involved in the biosynthesis of estrogen thus a critical target for breast cancer. In this study, in order to identify new aromatase enzyme inhibitors, a series of benzimidazole-1,3,4-oxadiazole derivatives were synthesized and characterized by 1H NMR, 13C NMR, and MS spectra analyses. In the in vitro anticancer assay, all the compounds tested anticancer activities using MTT-based assay against five cancer cell lines (MCF-7, A549, HeLa, C6, and HepG2). Among them, compound 5a exhibited the most potent activity with IC50 values of 5.165 ± 0.211 μM and 5.995 ± 0.264 μM against MCF-7 and HepG2 cell lines. Compound 5a was included in the BrdU test to determine the DNA synthesis inhibition effects for both cell types. Furthermore, compound 5c was also found to be more effective than doxorubicin on the HeLa cell line. The selectivity of anticancer activity was evaluated in NIH3T3 cell line. In vitro, enzymatic inhibition assays of aromatase enzyme were performed for compound 5a acting on the MCF-7 cell line. For compound 5a, in silico molecular docking and dynamics simulations against aromatase enzyme was performed to determine possible protein-ligand interactions and stability. DFT study was performed to evaluate the quantum mechanical and electronic properties of compound 5a. Finally, the theoretical ADME properties of the potential aromatase inhibitor compound 5a were analyzed by calculations. Communicated by Ramaswamy H. Sarma
The role of public-private partnerships in the discovery and development of a pan-serotype antiviral to prevent and treat dengue
Creators: name: van Loock, Marnix
Publisher: name: Zenodo
Year: 2023
Subjects: AViDD
Antiviral Drug Discovery
Antiviral Drug Discovery Open Science Forum
AViDD Open Science Forum
Open Science Forum
open science

description: This is Marnix Van Loock's presentation at the monthly [virtual] Antiviral Drug Discovery (AViDD) Open Science Forum on 2023-07-19. Their talk centers on the role of public-private partnerships in the discovery and development of a pan-serotype antiviral to prevent and treat dengue. Included is a copy of the Nature publication with the preclinical data of clinical candidate JNJ-1802.

 You can find a recording of their talk on the AViDD Open Science Forum Youtube page.
A randomized controlled trial on the effect of the VIPP-SD in parents of school-aged twins: A replication of the preschooler twin study
Creators: name: Runze, Jana
name: Bakermans-Kranenburg, Marian
name: Oosterman, Mirjam
name: van IJzendoorn, Marinus
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Psychiatry and Psychology
subject: Medicine and Health Sciences
subject: Child Psychology
subject: Social and Behavioral Sciences
subject: Psychology
subject: FOS: Psychology

description: Addendum to our original pre-registration
Structural and Functional Evaluation of Clinically Relevant Inhibitors of Steroidogenic Cytochrome P450 17A1
Creators: name: Aubé, Jeffrey
name: Scott, Emily E.
name: Petrunak, Elyse M.
name: Rogers, Steven A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: Human steroidogenic cytochrome P450 17A1 (CYP17A1) is a bifunctional enzyme that performs both hydroxylation and lyase reactions, with the latter required to generate androgens that fuel prostate cancer proliferation. The steroid abiraterone, the active form of the only CYP17A1 inhibitor approved by the Food and Drug Administration, binds the catalytic heme iron, nonselectively impeding both reactions and ultimately causing undesirable corticosteroid imbalance. Some nonsteroidal inhibitors reportedly inhibit the lyase reaction more than the preceding hydroxylase reaction, which would be clinically advantageous, but the mechanism is not understood. Thus, the nonsteroidal inhibitors seviteronel and orteronel and the steroidal inhibitors abiraterone and galeterone were compared with respect to their binding modes and hydroxylase versus lyase inhibition. Binding studies and X-ray structures of CYP17A1 with nonsteroidal inhibitors reveal coordination to the heme iron like the steroidal inhibitors. (S)-seviteronel binds similarly to both observed CYP17A1 conformations. However, (S)-orteronel and (R)-orteronel bind to distinct CYP17A1 conformations that differ in a region implicated in ligand entry/exit and the presence of a peripheral ligand. To reconcile these binding modes with enzyme function, side-by-side enzymatic analysis was undertaken and revealed that neither the nonsteroidal seviteronel nor the (S)-orteronel inhibitors demonstrated significant lyase selectivity, but the less potent (R)-orteronel was 8- to 11-fold selective for lyase inhibition. While active-site iron coordination is consistent with competitive inhibition, conformational selection for binding of some inhibitors and the differential presence of a peripheral ligand molecule suggest the possibility of CYP17A1 functional modulation by features outside the active site.
Descriptor-free QSAR: effectiveness in screening for putative inhibitors of FGFR1
Creators: name: Joel, I. Y.
name: Sulaimon, L. A.
name: Idris, M. O.
name: Adigun, T. O.
name: Adisa, R. A.
name: Ademoye, T. A.
name: Ogunleye, M. O.
name: Olaniyi, T. O.
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Pharmacology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences

description: The long short-term memory (LSTM) algorithm has provided solutions to the limitations of the descriptors-utilizing QSAR models in drug design. However, the direct application of LSTM remains scarce. The effectiveness of a descriptor-free QSAR (LSTM-SM) in modeling the FGFR1 inhibitors dataset while comparing with two conventional QSAR using descriptors (126 bits Morgan fingerprint and 2 D descriptors respectively) as a baseline model was investigated in this study. The validated descriptor-free QSAR model was thereafter used to screen for active FGFR1 inhibitors in the ChemDiv database and subjected to molecular docking, induced-fit docking, QM-MM optimization, and molecular dynamics simulations to filter for compounds with high binding affinity and suggest the putative mechanism of inhibition and specificity. The LSTM-SM model performed better than conventional QSAR; having accuracy, specificity, and sensitivity of 0.92, model loss of 0.025, and AUC of 0.95. Fifteen thousand compounds were predicted as actives from the ChemDiv database and four compounds were finally selected. Of the four, two showed putatively effective binding interactions with key active site residues. Molecular dynamics simulations on these compounds in complex with the receptor further give insight into the conformational dynamics of each compound bounded to the receptor. The complexes formed are stable and exhibit a similar degree of compactness. Our findings predicted the advent of self-feature extracting machine learning algorithms of compounds, and have provided the possibility of better predictive model quality that is not necessarily limited by compound descriptors. The putative FGFR1 inhibitors, with their mechanism of inhibition and specificity, were elucidated using this approach Communicated by Ramaswamy H. Sarma
Searching the Web: Pilot
Creators: name: Shepherdson, Peter
name: Eythórsdóttir, Karítas
name: Kolbeinsdottir, Una
name: Gylfason, Gunnar
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Cognitive Psychology
subject: Social and Behavioral Sciences
subject: Psychology
subject: FOS: Psychology

description: A replication of Fisher et al.'s (2015) Experiment 2b, as a pilot for our subsequently planned experiment. See attached document for more information.
Magnetospherically driven optical and radio aurorae at the end of the stellar main sequence
Creators: name: Hallinan, G.
name: Littlefair, S. P.
name: Cotter, G.
name: Bourke, S.
name: Harding, L. K.
name: Pineda, J. S.
name: Butler, R. P.
name: Golden, A.
name: Basri, G.
name: Doyle, J. G.
name: Kao, M. M.
name: Berdyugina, S. V.
name: Kuznetsov, A.
name: Rupen, M. P.
name: Antonova, A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Aurorae are detected from all the magnetized planets in our Solar System, including Earth. They are powered by magnetospheric current systems that lead to the precipitation of energetic electrons into the high-latitude regions of the upper atmosphere. In the case of the gas-giant planets, these aurorae include highly polarized radio emission at kilohertz and megahertz frequencies produced by the precipitating electrons, as well as continuum and line emission in the infrared, optical, ultraviolet and X-ray parts of the spectrum, associated with the collisional excitation and heating of the hydrogen-dominated atmosphere. Here we report simultaneous radio and optical spectroscopic observations of an object at the end of the stellar main sequence, located right at the boundary between stars and brown dwarfs, from which we have detected radio and optical auroral emissions both powered by magnetospheric currents. Whereas the magnetic activity of stars like our Sun is powered by processes that occur in their lower atmospheres, these aurorae are powered by processes originating much further out in the magnetosphere of the dwarf star that couple energy into the lower atmosphere. The dissipated power is at least four orders of magnitude larger than what is produced in the Jovian magnetosphere, revealing aurorae to be a potentially ubiquitous signature of large-scale magnetospheres that can scale to luminosities far greater than those observed in our Solar System. These magnetospheric current systems may also play a part in powering some of the weather phenomena reported on brown dwarfs.
description: Accepted for publication in the 30 July 2015 issue of Nature. 27 pages, 2 figures, 2 extended data figures
The pharmacogenomics of drug resistance to protein kinase inhibitors
Creators: name: Gillis, Nancy K.
name: McLeod, Howard L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Dysregulation of growth factor cell signaling is a major driver of most human cancers. This has led to development of numerous drugs targeting protein kinases, with demonstrated efficacy in the treatment of a wide spectrum of cancers. Despite their high initial response rates and survival benefits, the majority of patients eventually develop resistance to these targeted therapies. This review article discusses examples of established mechanisms of drug resistance to anticancer therapies, including drug target mutations or gene amplifications, emergence of alternate signaling pathways, and pharmacokinetic variation. This reveals a role for pharmacogenomic analysis to identify and monitor for resistance, with possible therapeutic strategies to combat chemoresistance.
An in silico molecular modeling approach of halolactone derivatives as potential inhibitors for human immunodeficiency virus type-1 reverse transcriptase enzyme
Creators: name: da Costa, Ana Paula Lima
name: Cardoso, Fábio José Bonfim
name: de Molfetta, Fábio Alberto
Publisher: name: Taylor & Francis
Year: 2022
Subjects: subject: Biochemistry
subject: Medicine
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Computational Biology

description: Acquired Immune Deficiency Syndrome (AIDS) is an infectious disease caused by Human Immunodeficiency Virus (HIV) infection and its replication requires the Reverse Transcriptase (RT) enzyme. RT plays a key role in the HIV life cycle, making it one of the most important targets for designing new drugs. Thus, in order to increase therapeutic options against AIDS, halolactone derivatives (D-halolactone) that have been showed as potential non-nucleoside inhibitors of the RT enzyme were studied. In the present work, a series of D-halolactone were investigated by molecular modeling studies, combining Three-dimensional Quantitative Structure-Activity Relationship (3 D-QSAR), molecular docking and Molecular Dynamics (MD) techniques, to understand the molecular characteristics that promote biological activity. The internal and external validation parameters indicated that the 3 D-QSAR model has good predictive capacity and statistical significance. Contour maps provided useful information on the structural characteristics of compounds for anti-HIV-1 activity. The docking results showed that D-halolactone present good complementarity by the RT allosteric site. In MD simulations it was observed that the formation of enzyme-ligand complexes were favorable, and from the free energy decomposition it was found that Leu100, Val106, Tyr181, Try188, and Trp229 are key residues for stabilization in the enzymatic site. Thus, the results showed that the proposed models can be used to design promising HIV-1 RT inhibitors. Communicated by Ramaswamy H. Sarma
Modelling the chemistry of star forming filaments - H$_2$ and CO chemistry
Creators: name: Seifried, D.
name: Walch, S.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We present simulations of star forming filaments incorporating on of the largest chemical network used to date on-the-fly in a 3D-MHD simulation. The network contains 37 chemical species and about 300 selected reaction rates. For this we use the newly developed package KROME (Grassi et al. 2014). We combine the KROME package with an algorithm which allows us to calculate the column density and attenuation of the interstellar radiation field necessary to properly model heating and ionisation rates. Our results demonstrate the feasibility of using such a complex chemical network in 3D-MHD simulations on modern supercomputers. We perform simulations with different strengths of the interstellar radiation field and the cosmic ray ionisation rate. We find that towards the centre of the filaments there is gradual conversion of hydrogen from H to H$_2$ as well as of C$^+$ over C to CO. Moreover, we find a decrease of the dust temperature towards the centre of the filaments in agreement with recent HERSCHEL observations.
description: 6 pages + 6 pages online material, 6 figures, accepted by MNRAS Letters
AMENDMENT Are pregnant women’s childhood maltreatment experiences associated with their sympathetic nervous system responses to infant cues?
Creators: name: Speck, Bailey
name: crowell, sheila
name: Raby, Lee
name: Kaliush, Parisa
name: Conradt, Elisabeth
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Developmental Psychology
subject: Social and Behavioral Sciences
subject: Psychology
subject: FOS: Psychology

description: Description This is an amendment to the pre-registration associated with the project entitled: "Are pregnant women’s childhood maltreatment experiences associated with their sympathetic nervous system responses to infant cues?" osf.io/sg9qm.
Development of Open-Set Word Recognition in Children: Speech-Shaped Noise and Two-Talker Speech Maskers
Creators: name: Leibold, Lori J.
name: Corbin, Nicole E.
name: Bonino, Angela Yarnell
name: Buss, Emily
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: The goal of this study was to establish the developmental trajectories for children’s open-set recognition of monosyllabic words in each of two maskers: two-talker speech and speech-shaped noise.
Comparing models of the periodic variations in spin-down and beam-width for PSR B1828-11
Creators: name: Ashton, G.
name: Jones, D. I.
name: Prix, R.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We build a framework using tools from Bayesian data analysis to evaluate models explaining the periodic variations in spin-down and beam-width of PSR B1828-11. The available data consists of the time averaged spin-down rate, which displays a distinctive double-peaked modulation, and measurements of the beam-width. Two concepts exist in the literature that are capable of explaining these variations; we formulate predictive models from these and quantitatively compare them. The first concept is phenomenological and stipulates that the magnetosphere undergoes periodic switching between two meta-stable states as first suggested by Lyne et al. The second concept, precession, was first considered as a candidate for the modulation of B1828-11 by Stairs et al.. We quantitatively compare models built from these concepts using a Bayesian odds-ratio. Because the phenomenological switching model itself was informed by this data in the first place, it is difficult to specify appropriate parameter-space priors that can be trusted for an unbiased model comparison. Therefore we first perform a parameter estimation using the spin-down data, and then use the resulting posterior distributions as priors for model comparison on the beam-width data. We find that a precession model with a simple circular Gaussian beam geometry fails to appropriately describe the data, while allowing for a more general beam geometry provides a good fit to the data. The resulting odds between the precession model (with a general beam geometry) and the switching model are estimated as $10^{2.7 \pm 0.5}$ in favour of the precession model.
description: 20 pages, 15 figures; removed incorrect factor of (2\pi) from equation (15), allowed for arbitrary braking index, and revised prior ranges; overall conclusions unchanged
Hard X-ray Morphological and Spectral Studies of The Galactic Center Molecular Cloud Sgr B2: Constraining Past Sgr A* Flaring Activity
Creators: name: Zhang, Shuo
name: Hailey, Charles J.
name: Mori, Kaya
name: Clavel, Maïca
name: Terrier, Régis
name: Ponti, Gabriele
name: Goldwurm, Andrea
name: Bauer, Franz E.
name: Boggs, Steven E.
name: Craig, William W.
name: Christensen, Finn E.
name: Harrison, Fiona A.
name: Hong, Jaesub
name: Nynka, Melania
name: Stern, Daniel
name: Soldi, Simona
name: Tomsick, John A.
name: Zhang, William W.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Galactic Center (GC) molecular cloud Sgr B2 is the best manifestation of an X-ray reflection nebula (XRN) reprocessing a past giant outburst from the supermassive black hole Sgr A*. Alternatively, Sgr B2 could be illuminated by low-energy cosmic ray electrons (LECRe) or protons (LECRp). In 2013, NuSTAR for the first time resolved Sgr B2 hard X-ray emission on sub-arcminute scales. Two prominent features are detected above 10 keV - a newly emerging cloud G0.66-0.13 and the central 90" radius region containing two compact cores Sgr B2(M) and Sgr B2(N) surrounded by diffuse emission. It is inconclusive whether the remaining level of Sgr B2 emission is still decreasing or has reached a constant background level. A decreasing Fe K$α$ emission can be best explained by XRN while a constant background emission can be best explained by LECRp. In the XRN scenario, the 3-79 keV Sgr B2 spectrum can well constrain the past Sgr A* outburst, resulting in an outburst spectrum with a peak luminosity of $L_{3-79\rm~keV} \sim 5\times10^{38} \rm~erg~s^{-1}$ derived from the maximum Compton-scattered continuum and the Fe K$α$ emission consistently. The XRN scenario is preferred by the fast variability of G0.66-0.13, which could be a molecular clump located in the Sgr B2 envelope reflecting the same Sgr A* outburst. In the LECRp scenario, we derived the required CR ion power $dW/dt=(1-4)\times10^{39}\rm~erg~s^{-1}$ and the CR ionization rate $ζ_{H}=(6-10)\times 10^{-15}\rm~H^{-1}~s^{-1}$. The Sgr B2 background level X-ray emission will be a powerful tool to constrain GC CR population.
description: 17 pages, 6 figures, submitted to ApJ
Effects of Self-Generated Noise on Estimates of Detection Threshold in Quiet for School-Age Children and Adults
Creators: name: Leibold, Lori J.
name: Grose, John H.
name: Hall, Joseph W.
name: Buss, Emily
name: Porter, Heather L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Detection thresholds in quiet become adult-like earlier in childhood for high than low frequencies. When adults listen for sounds near threshold, they tend to engage in behaviors that reduce physiologic noise (e.g., quiet breathing), which is predominantly low frequency. Children may not suppress self-generated noise to the same extent as adults, such that low-frequency self-generated noise elevates thresholds in the associated frequency regions. This possibility was evaluated by measuring noise levels in the ear canal simultaneous with adaptive threshold estimation.
Harmonising the human biobanking consent process: an Irish experience
Creators: name: O'Sullivan, Lydia
name: Carroll, Tomás
name: Cooper, Sarah
name: Cullen, Ann
name: Gorman, Laura
name: McCann, Billy
name: Mee, Blánaid
name: Miller, Nicola
name: Murphy, Verena
name: Murray, Máiréad
name: O’Leary, Jackie
name: O’Toole, Sharon
name: Snapes, Emma
name: Bracken, Suzanne
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Medicine and Health Sciences

description: This project aimed to develop a suite of resources for health research biobanks in Ireland, via robust and meaningful patient engagement, which are accessible, GDPR/HRR-compliant and could be used nationally, including a PIL/ICF template.
Electrically Evoked Auditory Event-Related Responses in Patients with Auditory Brainstem Implants: Morphological Characteristics, Test–Retest Reliability, Effects of Stimulation Level, and Association with Auditory Detection
Creators: name: Ewend, Matthew
name: He, Shuman
name: Henderson, Lillian
name: Buchman, Craig A.
name: McFayden, Tyler C.
name: Teagle, Holly F. B.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: This study aimed to 1) characterize morphological characteristics of the electrically-evoked cortical auditory event-related potentials (eERP) and explore the potential association between onset eERP morphology and auditory vs non-auditory stimulation; 2) assess test-retest reliability of onset eERPs; 3) investigate effects of stimulation level on onset eERPs; and 4) explore the feasibility of using the onset eERP to estimate the lowest stimulation level that can be detected for individual stimulating electrodes in patients with auditory brainstem implants (ABIs).
A Comparison of MIMO Techniques in Downlink Millimeter Wave Cellular Networks with Hybrid Beamforming
Creators: name: Kulkarni, Mandar N.
name: Ghosh, Amitava
name: Andrews, Jeffrey G.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Information Theory (cs.IT)
subject: FOS: Computer and information sciences

description: Large antenna arrays will be needed in future millimeter wave (mmWave) cellular networks, enabling a large number of different possible antenna architectures and multiple-input multiple-output (MIMO) techniques. It is still unclear which MIMO technique is most desirable as a function of different network parameters. This paper, therefore, compares the coverage and rate performance of hybrid beamforming enabled multi-user (MU) MIMO and single-user spatial multiplexing (SM) with single-user analog beamforming (SU-BF). A stochastic geometry model for coverage and rate analysis is proposed for MU-MIMO mmWave cellular networks, taking into account important mmWave-specific hardware constraints for hybrid analog/digital precoders and combiners, and a blockage-dependent channel model which is sparse in angular domain. The analytical results highlight the coverage, rate and power consumption tradeoffs in multiuser mmWave networks. With perfect channel state information at the transmitter and round robin scheduling, MU-MIMO is usually a better choice than SM or SU-BF in mmWave cellular networks. This observation, however, neglects any overhead due to channel acquisition or computational complexity. Incorporating the impact of such overheads, our results can be re-interpreted so as to quantify the minimum allowable efficiency of MU-MIMO to provide higher rates than SM or SU-BF.
description: submitted to IEEE Transactions on Communications, under minor revision
Masked Speech Perception Thresholds in Infants, Children, and Adults
Creators: name: Bonino, Angela Yarnell
name: Buss, Emily
name: Leibold, Lori J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: The primary goal of this study was to compare infants' susceptibility to making produced by a two-talker speech and a speech-shaped noise masker. It is well documented that school-age children experience more difficulty recognizing speech embedded in two-talker speech than spectrally matched noise, a result attributed to immaturity in the ability to segregate target from masker speech, and/or to selectively attend to the target while disregarding the perceptually similar speech masker. However, findings from infant psychophysical studies suggest that infants are susceptible to auditory masking even when target and competing sounds are acoustically distinct.
Masking Period Patterns and Forward Masking for Speech-Shaped Noise: Age-Related Effects
Creators: name: Porter, Heather L.
name: Griz, Silvana
name: Menezes, Denise C.
name: Grose, John H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: The purpose of this study was to assess age-related changes in temporal resolution in listeners with relatively normal audiograms. The hypothesis was that increased susceptibility to non-simultaneous masking contributes to the hearing difficulties experienced by older listeners in complex fluctuating backgrounds.
In silico bioprospecting of antiviral compounds from marine fungi and mushroom for rapid development of nutraceuticals against SARS-CoV-2
Creators: name: Srivastav, Amit Kumar
name: Jaiswal, Jyoti
name: Kumar, Umesh
Publisher: name: Taylor & Francis
Year: 2021
Subjects: subject: Medicine
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: Ecology
subject: FOS: Biological sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) affects human respiratory function that causes COVID-19 disease. COVID-19 has spread rapidly all over the world and became a pandemic within no time. Therefore, it is the need of hour to screen potential lead candidates from natural resources like edible mushrooms and marine fungi. These natural resources are very less explored till now and known to be the source for many medicinal compounds with several health benefits. These medicinal compounds can be easily exploited for the faster development of nutraceuticals for controlling SARS-CoV-2 infections. Our Insilico research suggests, bioactive compounds originating from mushroom and marine fungi shows strong potential to interact with ACE2 receptor or main protease of SARS-CoV-2, showing the inhibition activity towards the enzymatic protease. We performed a series of Insilico studies for the validation of our results, which includes Molecular docking, drug likeness property investigation by Swiss ADME tools, MD simulation, and thermodynamically stable free binding energy calculation. Overall, these results suggest that Ganodermadiol and Heliantriol F bioactive compounds originating from edible mushroom has strong potential to be developed as low-cost nutraceutical against SARS-CoV-2 viral infection. The drug candidate isolated from marine fungi and edible mushroom are highly unexplored for the development of potential alternative drug against SARS-CoV-2 virus with minimum side effects. Though our in silico studies of these compounds are showing a promising results against SARS-CoV-2 main protease and ACE2 receptor binding domain, the effectiveness of these bioactive compounds should be further validated by proper clinical trials. Communicated by Ramaswamy H. Sarma
Temporal Response Properties of the Auditory Nerve in Implanted Children with Auditory Neuropathy Spectrum Disorder and Implanted Children with Sensorineural Hearing Loss
Creators: name: He, Shuman
name: Mulherin, Stephen
name: Abbas, Paul J.
name: McFayden, Tyler C.
name: Doyle, Danielle V.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: This study aimed to 1) characterize temporal response properties of the auditory nerve in implanted children with auditory neuropathy spectrum disorder (ANSD); and 2) compare results recorded in implanted children with ANSD with those measured in implanted children with sensorineural hearing loss (SNHL).
Discrete Solitons and Vortices in Anisotropic Hexagonal and Honeycomb Lattices
Creators: name: Hoq, Q. E.
name: Kevrekidis, P. G.
name: Bishop, A. R.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Pattern Formation and Solitons (nlin.PS)
subject: FOS: Physical sciences

description: In the present work, we consider the self-focusing discrete nonlinear Schrodinger equation on hexagonal and honeycomb lattice geometries. Our emphasis is on the study of the effects of anisotropy, motivated by the tunability afforded in recent optical and atomic physics experiments. We find that important classes of solutions, such as the so-called discrete vortices, undergo destabilizing bifurcations as the relevant anisotropy control parameter is varied. We quantify these bifurcations by means of explicit analytical calculations of the solutions, as well as of their spectral linearization eigenvalues. Finally, we corroborate the relevant stability picture through direct numerical computations. In the latter, we observe the prototypical manifestation of these instabilities to be the spontaneous rearrangement of the solution, for larger values of the coupling, into localized waveforms typically centered over fewer sites than the original unstable structure. For weak coupling, the instability appears to result in a robust breathing of the relevant waveforms.
description: 26 pages, 17 figures
An exploratory study of the impact of digital technologies on adolescent mental health during the COVID-19 pandemic in the United Kingdom
Creators: name: Metherell, Thomas
name: Ghai, Sakshi
name: Orben, Amy
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Social and Behavioral Sciences
subject: Psychology
subject: FOS: Psychology
subject: adolescents
subject: COVID-19
subject: digital
subject: mental health
subject: SNS
subject: social media
subject: United Kingdom
subject: wellbeing

description: Public health measures relating to the COVID-19 pandemic in the United Kingdom have led to dramatically increased reliance on digital technologies for everyday tasks. Despite this, the overall impacts of these technologies on mental health remain unclear, particularly in adolescents. By using data from the Understanding Society COVID-19 study of a national representative sample of 10-15 year olds (N = 1,432) and potentially also of those respondents over 15 years (N = 12,876), we intend to explore the interactions between technology use and mental health indicators. We will subsequently test any relations of interest using inferential statistics and longitudinal modelling.
Spatial Release From Masking in Children: Effects of Simulated Unilateral Hearing Loss
Creators: name: Corbin, Nicole E.
name: Leibold, Lori J.
name: Buss, Emily
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: The purpose of this study was twofold: 1) to determine the effect of an acute simulated unilateral hearing loss on children’s spatial release from masking in two-talker speech and speech-shaped noise, and 2) to develop a procedure to be used in future studies that will assess spatial release from masking in children who have permanent unilateral hearing loss. There were three main predictions. First, spatial release from masking was expected to be larger in two-talker speech than speech-shaped noise. Second, simulated unilateral hearing loss was expected to worsen performance in all listening conditions, but particularly in the spatially separated two-talker speech masker. Third, spatial release from masking was expected to be smaller for children than for adults in the two-talker masker.
Common core, overlaps, and differences: subcommunity practices in open science.
Creators: name: Schneider, Jürgen
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Education

description: This project starts with the notion that “Not all open science practices are relevant for all research projects - but for no project open science is irrelevant.” Which open science practices researchers can adopt is determined first and foremost by the nature of the research project itself (e.g., the research interest, design, etc.). This may differ also within disciplines and research paradigms. The scientific landscape is still very heterogeneous in the applicability of open science practices. It is still unclear what typical applications of open science practices are possible in research. Which open science practices are relevant for all subcommunities and their research projects? Which open science practices differ significantly between subcommunities? How many subcommunities are there and by which profiles of open science practices are they characterized? Answers to these questions support the work of policymakers, scientific societies, research funders, and the researchers themselves. In an exploratory study, we generate data-driven profiles regarding the use of open science practices to answer these questions.
Youth Experiencing Homelessness, Technology, and Health
Creators: name: Lal, Shalini
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Medicine and Health Sciences
subject: Social and Behavioral Sciences
subject: access
subject: adolescent
subject: cellular phone
subject: digital health
subject: ehealth
subject: equity
subject: health services
subject: homeless
subject: internet
subject: technology
subject: telehealth
subject: telemedicine
subject: young adult
subject: youth

description: We are conducting a series of scoping reviews on the subject of youth experiencing homelessness and technology in relation to their health. These address the topics of: 1) access and use of technology by youth experiencing homelessness, 2) technology-based health interventions for youth experiencing homelessness and 3) the use of technology-based interventions to address mental health issues among youth experiencing homelessness.
Features of apps, digital games and e-books which influence joint media engagement (JME) between adults and children aged 2 to 7 years: a systematic review
Creators: name: Mathers, Sandra
name: Hodgkiss, Alex
name: Kolancali, Pinar
name: Booton, Sophie
name: Singh, Daniela
name: Eynon, Rebecca
name: Murphy, Victoria
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Education
subject: Social and Behavioral Sciences
subject: Apps
subject: Digital technology
subject: E-books
subject: Joint Media Engagement
subject: Meta-analysis
subject: Oral language
subject: Parent-child interaction
subject: Psychology
subject: FOS: Psychology
subject: Systematic review

description: This is a pre-registration of a systematic review protocol. The review will synthesise empirical studies which have examined joint media engagement (JME) between adults and children aged 2-7 years. Specifically, it aims to examine the features of apps, digital games or e-books which influence JME, with a focus on the adult-child interactions which support child learning across all domains, but with a particular focus on oral language. The full protocol is detailed in the attached document.