cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
G protein-coupled receptors as targets for transformative neuropsychiatric therapeutics
Creators: name: Roth B.L
name: Schmitz G.P
Publisher: name: NLM (Medline)
Year: 2023

description: G protein-coupled receptors (GPCRs) constitute the largest family of druggable genes in the human genome. Even though perhaps 30% of approved medications target GPCRs, they interact with only a small number of them. Here, we consider whether there might be new opportunities for transformative therapeutics for neuropsychiatric disorders by specifically targeting both known and understudied GPCRs. Using psychedelic drugs that target serotonin receptors as an example, we show how recent insights into the structure, function, signaling, and cell biology of these receptors have led to potentially novel therapeutics. We next focus on the possibility that nonpsychedelic 5-HT2A receptor agonists might prove to be safe and rapidly acting antidepressants. Finally, we examine understudied and orphan GPCRs using the MRGPR family of receptors as an example.
Cosmic acceleration in non-flat $f(T)$ cosmology
Creators: name: Capozziello, Salvatore
name: Luongo, Orlando
name: Pincak, Richard
name: Ravanpak, Arvin
Publisher: name: arXiv
Year: 2018
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We study $f(T)$ cosmological models inserting a non-vanishing spatial curvature and discuss its consequences on cosmological dynamics. To figure this out, a polynomial $f(T)$ model and a double torsion model are considered. We first analyze those models with cosmic data, employing the recent surveys of Union 2.1, baryonic acoustic oscillation and cosmic microwave background measurements. We then emphasize that the two popular $f(T)$ models enable the crossing of the phantom divide line due to dark torsion. Afterwards, we compute numerical bounds up to 3-$σ$ confidence level, emphasizing the fact that $Ω_{k0}$ turns out to be non-compatible with zero at least at 1$σ$. Moreover, we underline that, even increasing the accuracy, one cannot remove the degeneracy between our models and the $Λ$CDM paradigm. So that, we show that our treatments contain the concordance paradigm and we analyze the equation of state behaviors at different redshift domains. We also take into account gamma ray bursts and we describe the evolution of both the $f(T)$ models with high redshift data. We calibrate the gamma ray burst measurements through small redshift surveys of data and we thus compare the main differences between non-flat and flat $f(T)$ cosmology at different redshift ranges. We finally match the corresponding outcomes with small redshift bounds provided by cosmography. To do so, we analyze the deceleration parameters and their variations, proportional to the jerk term. Even though the two models well fit late-time data, we notice that the polynomial $f(T)$ approach provides an effective de-Sitter phase, whereas the second $f(T)$ framework shows analogous results compared with the $Λ$CDM predictions.
description: Accepted for publication in GRG
Tubipora serpens Linnaeus, 1758, spec. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1758
Subjects: Biodiversity
Taxonomy
Animalia
Cnidaria
Anthozoa
Alcyonacea
Tubiporidae
Tubipora
Tubipora serpens

description: Tubipora serpens [spec. nov.]
T. corallio repente filiformi subramoso: tubis rigidis cylindricis distantibus erectis.
Habitat in M. Mediterranei Conchis, Fucis & c.
description: Published as part of Linnaeus, Carolus, 1758, Systema Naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis, Stockholm :Laurentius Salvius on page 790, DOI: 10.5962/bhl.title.542, http://zenodo.org/record/3922206
Geometry, packing, and evolutionary paths to increased multicellular size
Creators: name: Jacobeen, Shane
name: Graba, Elyes C.
name: Brandys, Colin G.
name: Day, T. Cooper
name: Ratcliff, William C.
name: Yunker, Peter J.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Biological Physics (physics.bio-ph)
subject: Soft Condensed Matter (cond-mat.soft)
subject: FOS: Physical sciences

description: The evolutionary transition to multicellularity transformed life on earth, allowing for the evolution of large, complex organisms. While multicellularity can be strongly advantageous, its earliest stages bring unique physical challenges. Nascent multicellular organisms must contend with a novel constraint: intercellular stresses arising from cell-cell interactions that can limit multicellular size. Among the possible evolutionary routes to overcoming this size limit, two appear obvious: multicellular organisms can increase intercellular bond strength, allowing them to tolerate larger stresses, or, they can slow the rate of stress accumulation by altering their internal structure. Recent experiments demonstrated that multicellular 'snowflake yeast' readily find a solution to this problem via the latter route. By evolving more elongated cells, which decreases cellular packing fraction and thus the rate of internal stress accumulation during growth, snowflake yeast evolve to delay fracture and grow larger. However, it is unclear if snowflake yeast evolved large size along an optimal path, or if the observed path to large size was taken due to proximate biological reasons. Here, we examine the geometric efficiency of both strategies using a minimal model that was previously demonstrated to replicate many experimentally observed structural properties of snowflake yeast. We find that changing geometry is a far more efficient route to large size than evolving increased intercellular adhesion. In fact, increasing cellular aspect ratio is on average ~13 times more effective at increasing the number of cells in a cluster than increasing bond strength. These results suggest that geometrically-imposed physical constraints may have been a key early selective force guiding the emergence of multicellular complexity.
TRAJEDI: Trajectory Dissimilarity
Creators: name: Gharani, Pedram
name: Fernande, Kenrick
name: Raghu, Vineet
Publisher: name: arXiv
Year: 2018
Subjects: subject: Databases (cs.DB)
subject: FOS: Computer and information sciences

description: The vast increase in our ability to obtain and store trajectory data necessitates trajectory analytics techniques to extract useful information from this data. Pair-wise distance functions are a foundation building block for common operations on trajectory datasets including constrained SELECT queries, k-nearest neighbors, and similarity and diversity algorithms. The accuracy and performance of these operations depend heavily on the speed and accuracy of the underlying trajectory distance function, which is in turn affected by trajectory calibration. Current methods either require calibrated data, or perform calibration of the entire relevant dataset first, which is expensive and time consuming for large datasets. We present TRAJEDI, a calibrationaware pair-wise distance calculation scheme that outperforms naive approaches while preserving accuracy. We also provide analyses of parameter tuning to trade-off between speed and accuracy. Our scheme is usable with any diversity, similarity or k-nearest neighbor algorithm.
G-Protein Peptidomimetics Stabilize GPCR Active State Conformations
Creators: name: Gumpper R.H
name: Roth B.L
Publisher: name: Elsevier Ltd
Year: 2021

description: Technologies stabilizing the active state of G protein-coupled receptors (GPCRs) represent potential breakthroughs for interrogating G protein activation. Camelid nanobodies have been used as a ‘one tool, one receptor’ paradigm. However, the development of G protein peptidomimetics, as discussed in Mannes et al. represent the opportunity to develop generically activating probes for many GPCRs.
Additional file 1 of Immunologic aspects of characteristics, diagnosis, and treatment of coronavirus disease 2019 (COVID-19)
Creators: name: Chang, Feng-Yee
name: Chen, Hsiang-Cheng
name: Chen, Pei-Jer
name: Ho, Mei-Shang
name: Hsieh, Shie-Liang
name: Lin, Jung-Chung
name: Liu, Fu-Tong
name: Sytwu, Huey-Kang
Publisher: name: figshare
Year: 2020
Subjects: subject: Immunology
subject: FOS: Clinical medicine

description: Additional file 1. Supplemental information.
Tubipora repens Linnaeus, 1758, spec. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1758
Subjects: Biodiversity
Taxonomy
Animalia
Cnidaria
Anthozoa
Alcyonacea
Tubiporidae
Tubipora
Tubipora repens

description: Tubipora repens [spec. nov.]
T. corallio repente filiformi dichotomo: tubis flexilibus cylindricis distantibus erectis. Fig. 5.
Amoen. acad. 2. p. 63.
Baeck. Actt. Stockh. 1746. t. 6. f. 3, 4?
Roes. ins. app. polyp. t. 73, 74, 75.
Schaeff. monogr. 1754. t. 1. f. 1, 2.
Habitat in Aquae dulcis Plantis, in Nymphaea & c. Minuta.
description: Published as part of Linnaeus, Carolus, 1758, Systema Naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis, Stockholm :Laurentius Salvius on page 790, DOI: 10.5962/bhl.title.542, http://zenodo.org/record/3922206
LASR-Guided Stellar Photometric Variability Subtraction: The Linear Algorithm For Significance Reduction
Creators: name: Ahlers, John P.
name: Barnes, Jason W.
name: Horvath, Sarah A.
name: Myers, Samuel A.
name: Hedman, Matthew M.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: We develop a technique for removing stellar variability in the light curves of $δ$-Scuti and similar stars. Our technique, which we name the Linear Algorithm for Significance Reduction (LASR), subtracts oscillations from a time series by minimizing their statistical significance in frequency space. We demonstrate that LASR can subtract variable signals of near-arbitrary complexity and can robustly handle close frequency pairs and overtone frequencies. We demonstrate that our algorithm performs an equivalent fit as prewhitening to the straightforward variable signal of KIC 9700322. We also show that LASR provides a better fit to seismic activity than prewhitening in the case of the complex $δ$-Scuti KOI-976.
description: 9 pages, 5 figures, accepted for publication in Astronomy & Astrophysics. Pseudocode and github link to code included in manuscript
Economic Evaluations, Economic Freedom, and Democratic Satisfaction in Africa
Creators: name: Memoli, Vincenzo
name: Quaranta, Mario
Publisher: name: Taylor & Francis
Year: 2018
Subjects: subject: Space Science
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: This article assesses the relationship between democratic satisfaction and micro and macroeconomic factors in Africa. Studies have shown that economic factors represent a cornerstone of the democratic process. However, research has rarely accounted for the effect of economic freedom on satisfaction with democracy, and its conditional role on the effect of citizens’ economic evaluations, particularly in the context of Africa where democracy is still developing. Using various rounds of the Afrobarometer, the article analyses the link between citizens’ evaluations of the economy and economic freedom with their satisfaction with democracy in 32 African countries between 2002 and 2013. First, the findings show that the openness of the economic context and positive economic evaluations are associated with an increase in democratic satisfaction. Second, economic freedom and economic evaluations appear to have a conditional association with democratic satisfaction. In fact, positive economic evaluations are a less important factor for democratic satisfaction in contexts that have a freer economy.
Interacting Topological Insulators with Synthetic Dimensions
Creators: name: Jian, Chao-Ming
name: Xu, Cenke
Publisher: name: arXiv
Year: 2018
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: Recent developments of experimental techniques have given us unprecedented opportunities of studying topological insulators in high dimensions, while some of the dimensions are "synthetic", in the sense that the effective lattice momenta along these synthetic dimensions are controllable periodic tuning parameters. In this work, we study interaction effects on topological insulators with synthetic dimensions. We show that although the free fermion band structure of high dimensional topological insulators can be precisely simulated with the "synthetic techniques", the generic interactions in these effective synthetic topological insulators are qualitatively different from the local interactions in ordinary condensed matter systems. And we show that these special but generic interactions have unexpected effects on topological insulators, namely they would change (or reduce) the classification of topological insulators differently from the previously extensively studied local interactions.
description: 9 pages and 3 figures
Reduced modeling of porous media convection in a minimal flow unit at large Rayleigh number
Creators: name: Wen, Baole
name: Chini, Gregory P.
Publisher: name: arXiv
Year: 2018
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: Direct numerical simulations (DNS) indicate that at large values of the Rayleigh number ($Ra$) convection in porous media self-organizes into narrowly-spaced columnar flows, with more complex spatiotemporal features being confined to boundary layers near the top and bottom walls. In this investigation of high-$Ra$ porous media convection in a minimal flow unit, two reduced modeling strategies are proposed that exploit these specific flow characteristics. Both approaches utilize the idea of decomposition since the flow exhibits different dynamics in different regions of the domain: small-scale cellular motions generally are localized within the thermal and vorticity boundary layers near the upper and lower walls, while in the interior, the flow exhibits persistent large-scale structures and only a few low (horizontal) wavenumber Fourier modes are active. Accordingly, in the first strategy, the domain is decomposed into two near-wall regions and one interior region. Our results confirm that suppressing the interior high-wavenumber modes has negligible impact on the essential structural features and transport properties of the flow. In the second strategy, a hybrid reduced model is constructed by using Galerkin projection onto a fully \emph{a priori} eigenbasis drawn from energy stability and upper bound theory, thereby extending the model reduction strategy developed by Chini \emph{et al.} (\emph{Physica~D}, vol. 240, 2011, pp. 241--248) to large $Ra$. The results indicate that the near-wall upper-bound eigenmodes can economically represent the small-scale rolls within the exquisitely-thin thermal boundary layers. Relative to DNS, the hybrid algorithm enables over an order-of-magnitude increase in computational efficiency with only a modest loss of accuracy.
Causal propagation of constraints in bimetric relativity in standard 3+1 form
Creators: name: Kocic, Mikica
Publisher: name: arXiv
Year: 2018
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The goal of this work was to investigate the propagation of the constraints in the ghost-free bimetric theory where the evolution equations are in standard 3+1 form. It is established that the constraints evolve according to a first-order symmetric hyperbolic system whose characteristic cone consists of the null cones of the two metrics. Consequently, the constraint evolution equations are well-posed, and the constraints stably propagate.
description: 17 pages, 3 figures
Gene expression changes following chronic antipsychotic exposure in single cells from mouse striatum
Creators: name: Hultman R
name: Sekle S
name: Stuber G.D
name: Sullivan P.F
name: Abrantes A
name: Giusti-Rodriguez P
name: Ancalade N.E
name: Basiri M.L
Publisher: name: Springer Nature
Year: 2022

description: Schizophrenia is an idiopathic psychiatric disorder with a high degree of polygenicity. Evidence from genetics, single-cell transcriptomics, and pharmacological studies suggest an important, but untested, overlap between genes involved in the etiology of schizophrenia and the cellular mechanisms of action of antipsychotics. To directly compare genes with antipsychotic-induced differential expression to genes involved in schizophrenia, we applied single-cell RNA-sequencing to striatal samples from male C57BL/6 J mice chronically exposed to a typical antipsychotic (haloperidol), an atypical antipsychotic (olanzapine), or placebo. We identified differentially expressed genes in three cell populations identified from the single-cell RNA-sequencing (medium spiny neurons [MSNs], microglia, and astrocytes) and applied multiple analysis pipelines to contextualize these findings, including comparison to GWAS results for schizophrenia. In MSNs in particular, differential expression analysis showed that there was a larger share of differentially expressed genes (DEGs) from mice treated with olanzapine compared with haloperidol. DEGs were enriched in loci implicated by genetic studies of schizophrenia, and we highlighted nine genes with convergent evidence. Pathway analyses of gene expression in MSNs highlighted neuron/synapse development, alternative splicing, and mitochondrial function as particularly engaged by antipsychotics. In microglia, we identified pathways involved in microglial activation and inflammation as part of the antipsychotic response. In conclusion, single-cell RNA sequencing may provide important insights into antipsychotic mechanisms of action and links to findings from psychiatric genomic studies.
Tubipora arenosa Linnaeus, 1758, spec. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1758
Subjects: Biodiversity
Taxonomy
Animalia
Cnidaria
Anthozoa
Alcyonacea
Tubiporidae
Tubipora
Tubipora arenosa

description: Tubipora arenosa [spec. nov.]
T. corallio tophoso poris adsperso, intus cellulis concamerato.
Ellis corall. 90. t. 36. Tubularia arenosa anglica.
Habitat in O Europaeo, srequens inter Angliam & Belgium. J. F. Gronovius.
Animal videtur Nereis esse.
description: Published as part of Linnaeus, Carolus, 1758, Systema Naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis, Stockholm :Laurentius Salvius on page 790, DOI: 10.5962/bhl.title.542, http://zenodo.org/record/3922206
Additional file 1: of Coverage of azithromycin mass treatment for trachoma elimination in Northwestern Ethiopia: a community based cross-sectional study
Creators: name: Zelalem Tilahun
name: Teferi Fenta
Publisher: name: figshare
Year: 2018
Subjects: subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics

description: Questionnaires used in the survey. (PDF 37 kb)
General anaesthesia during infancy reduces white matter micro-organisation in developing rhesus monkeys
Creators: name: Hu, X
name: Caudill, G
name: Sanchez, M
name: Alexander, A.L
name: Howell, B.R
name: Noel, J
name: Kuitchoua, K.I
name: Vlasova, R.M
name: Styner, M
name: Young, J.T
name: Paule, M.G
name: Coe, C.L
name: Lubach, G.R
name: Niethammer, M
name: Morin, E
name: Knickmeyer, R.C
name: Shi, Y
Publisher: name: Elsevier Ltd
Year: 2021

description: Background: Non-human primates are commonly used in neuroimaging research for which general anaesthesia or sedation is typically required for data acquisition. In this analysis, the cumulative effects of exposure to ketamine, Telazol® (tiletamine and zolazepam), and the inhaled anaesthetic isoflurane on early brain development were evaluated in two independent cohorts of typically developing rhesus macaques. Methods: Diffusion MRI scans were analysed from 43 rhesus macaques (20 females and 23 males) at either 12 or 18 months of age from two separate primate colonies. Results: Significant, widespread reductions in fractional anisotropy with corresponding increased axial, mean, and radial diffusivity were observed across the brain as a result of repeated anaesthesia exposures. These effects were dose dependent and remained after accounting for age and sex at time of exposure in a generalised linear model. Decreases of up to 40% in fractional anisotropy were detected in some brain regions. Conclusions: Multiple exposures to commonly used anaesthetics were associated with marked changes in white matter microstructure. This study is amongst the first to examine clinically relevant anaesthesia exposures on the developing primate brain. It will be important to examine if, or to what degree, the maturing brain can recover from these white matter changes.
Generalizability of the REDUCE-IT trial and cardiovascular outcomes associated with hypertriglyceridemia among patients potentially eligible for icosapent ethyl therapy: An analysis of the REduction of Atherothrombosis for Continued Health (REACH) registry
Creators: name: Smith, Jr., S.C
name: Ohman, E.M
name: Wilson, P.W.F
name: Picard, F
name: Bhatt, D.L
name: Steg, P.G
name: Elbez, Y
name: Goto, S
name: Ducrocq, G
name: Eagle, K.A
Publisher: name: Elsevier Ireland Ltd
Year: 2021

description: Background: The REDUCE-IT (Reduction of Cardiovascular Events with Icosapent Ethyl–Intervention Trial) trial demonstrated that high-dose icosapent-ethyl reduced the risk of ischemic events in statin-treated patients with elevated triglycerides (TG) and either atherosclerotic cardiovascular disease (ASCVD) or diabetes plus at least one risk factor. Methods and results: Using data from REACH (Reduction of Atherothrombosis for Continued Health), a large international registry of outpatients with or at risk of ASCVD, we evaluated the proportion of patients potentially eligible for enrolment in REDUCE-IT and compared their outcomes to those excluded because of low TG. Among 62,464 patients with either ASCVD or diabetes enrolled in the REACH Registry, 1036/8418 (12.3%) patients in primary prevention and 6049/54046 (11.2%) patients in secondary prevention (11.3% overall) would have been eligible for inclusion in REDUCE-IT. Compared with patients excluded for low TG level, adjusted risk of the primary composite outcome of cardiovascular death, non-fatal myocardial infarction (MI), non-fatal stroke, unstable angina, or coronary revascularization was higher in the REDUCE-IT eligible group (HR:1.06, 95%CI:1.00–1.13, p = 0.04). In addition, unstable angina, non-fatal MI, percutaneous coronary intervention and coronary artery bypass grafting were also more frequent in the REDUCE-IT eligible group (HR:1.17, 95%CI:1.07–1.27, p < 0.001; HR:1.25, 95%CI:1.07–1.45, p < 0.001; HR:1.42, 95%CI:1.27–1.57, p < 0.001; HR:1.43, 95%CI:1.19–1.71, p < 0.001, respectively), whereas the adjusted risk of non-fatal stroke was lower (HR:0.64, 95%CI:0.54–0.75, p < 0.001). Conclusion: In this large international registry of patients with or at high-risk of ASCVD, 11.3% met the REDUCE-IT trial selection criteria. REDUCE-IT eligible patients were found to be at higher risk of cardiac atherothrombotic events, but at lower risk of stroke than trial-ineligible patients with lower TG.
Additional file 10 of Prognostic perspectives of PD-L1 combined with tumor-infiltrating lymphocytes, Epstein-Barr virus, and microsatellite instability in gastric carcinomas
Creators: name: Choi, Euno
name: Chang, Mee Soo
name: Byeon, Sun-ju
name: Jin, Heejin
name: Jung, Kyeong Cheon
name: Kim, Haeryoung
name: Lee, Kook Lae
name: Kim, Won
name: Park, Jin Hyun
name: Kim, Ki Hwan
name: Kim, Jin-Soo
name: Choi, In Sil
name: Han, Dong-Seok
name: Ahn, Hye Seong
name: Heo, Seung Chul
Publisher: name: figshare
Year: 2020
Subjects: subject: Immunology
subject: FOS: Clinical medicine

description: Additional file 10: Supplemental Table 5. Comparison of Clinicopathologic Characteristics, and Statuses of PD-L1, FOXP3+, and PD-1+ According to the Density of CD8+ TILs in the Entire Cohort (N = 514)
Additional file 1: of DS1/OsEMF1 interacts with OsARF11 to control rice architecture by regulation of brassinosteroid signaling
Creators: name: X. Liu
name: C. Yang
name: R. Miao
name: C. Zhou
name: P. Cao
name: J. Lan
name: X. Zhu
name: C. Mou
name: Y. Huang
name: S. Liu
name: Y. Tian
name: T. Nguyen
name: L. Jiang
name: J. Wan
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Table S1 Comparison of agronomic traits between WT and ds1. Table S2 Primers used in mapping. Table S3 Primers used in real-time PCR and vector construction. Figure S1 Relative expression levels of cell wall synthesis-related genes (CESA6, IRX10L, GT8, UGA4e, and CSLF6) and cell expansion-related genes, Exp1, ExpA8, ExpA10, ExpA17, ExpA30, ExpB2, ExpB3, ExpB5, and ExpB12. Figure S2 Alignment amino acid sequences of DS1 and AtEMF1. (DOC 1088 kb)
Generalizing trial evidence to target populations in non-nested designs: Applications to AIDS clinical trials
Creators: name: Li F
name: Buchanan A.L
name: Cole S.R
Publisher: name: John Wiley and Sons Inc
Year: 2022

description: Comparative effectiveness evidence from randomized trials may not be directly generalizable to a target population of substantive interest when, as in most cases, trial participants are not randomly sampled from the target population. Motivated by the need to generalize evidence from two trials conducted in the AIDS Clinical Trials Group (ACTG), we consider weighting, regression and doubly robust estimators to estimate the causal effects of HIV interventions in a specified population of people living with HIV in the USA. We focus on a non-nested trial design and discuss strategies for both point and variance estimation of the target population average treatment effect. Specifically in the generalizability context, we demonstrate both analytically and empirically that estimating the known propensity score in trials does not increase the variance for each of the weighting, regression and doubly robust estimators. We apply these methods to generalize the average treatment effects from two ACTG trials to specified target populations and operationalize key practical considerations. Finally, we report on a simulation study that investigates the finite-sample operating characteristics of the generalizability estimators and their sandwich variance estimators.
Vanilla oroana Dodson
Creators: name: Damián-Parizaca, Alexander
name: Karremans, Adam P.
name: Mitidieri-Rivera-Rivera, Nicole
name: Cameron, Kenneth M.
Publisher: name: Zenodo
Year: 2025
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Liliopsida
Asparagales
Orchidaceae
Vanilla
Vanilla oroana

description: 18.Vanilla oroanaDodson (Dodson 2003: 210)
Fig. 2 H
Type.
ECUADOR – El Oro • 3.7 km N of junction of old and new roads from Piñas to Santa Rosa, 12 km west of Piñas; 1400 m; 19 Apr. 1989; Dodson, Williams, Dressler, Whitten & Embree 17951; holotype: MO! (ex RPSC) [MO 6777486]; isotypes: AMES! [AMES 00287585], K! [K 001551030], SEL! [SEL 003524], QCNE! [QCNE 10821].
Notes.
Soto-Arenas’s notes at AMO suggest that he was in the process of describing this species, maintaining the same epithet as “ Dodson ex Soto-Arenas, ” but for an unknown reason, did not effectively publish his manuscript. It appears that he intended to publish the name alongside with Vanilla espondae Soto-Arenas, including an extensive description and illustration.
description: Published as part of Damián-Parizaca, Alexander, Karremans, Adam P., Mitidieri-Rivera-Rivera, Nicole & Cameron, Kenneth M., 2025, Towards a monograph of membranaceous Vanillas: a nomenclatural revision of Vanilla subgen. Vanilla (Vanilloideae, Orchidaceae), pp. 111-121 in Plant Ecology and Evolution 158 (1) on pages 111-121, DOI: 10.5091/plecevo.140667
A Quantitative Meta-Analysis and Qualitative Meta-Synthesis of Aged Care Residents' Experiences of Autonomy, Being Controlled, and Optimal Functioning
Creators: name: Bradshaw, Emma L
name: Anderson, Joel
name: Banday, Ma AJ
name: Basarkod, Geetanjali
name: Daliri-Ngametua, Rafaan
name: Ferber, Kelly A
name: Henry, Dylan
name: Ryan, Richard M
Publisher: name: La Trobe
Year: 2024
Subjects: classificationCode: 320210
subject: Geriatrics and gerontology
classificationCode: 4203
subject: Health services and systems
classificationCode: 42
subject: Health sciences
subject: FOS: Health sciences

description: Background and Objectives: The poor mental health of adults living in aged care needs addressing. Improvements to nutrition and exercise are important, but mental health requires a psychological approach. Self-determination theory finds that autonomy is essential to wellbeing while experiences of being controlled undermine it. A review of existing quantitative data could underscore the importance of autonomy in aged care, and a review of the qualitative literature could inform ways to promote autonomy and avoid control. Testing these possibilities was the objective of this research. Research Design and Methods: We conducted a mixed-methods systematic review of studies investigating autonomy, control, and indices of optimal functioning in aged care settings. The search identified 30 eligible reports (19 quantitative, 11 qualitative), including 141 quantitative effect sizes, 84 qualitative data items, and N = 2,668. Quantitative effects were pooled using three-level meta-analytic structural equation models, and the qualitative data were meta-synthesized using a grounded theory approach. Results: As predicted, the meta-analysis showed a positive effect of aged care residents' autonomy and their wellness, r = 0.33 [95% CI: 0.27, 0.39], and a negative effect of control, r = -0.16 [95% CI: -0.27, -0.06]. The meta-synthesis revealed seven primary and three sub-themes describing the nuanced ways autonomy, control, and help seeking are manifest in residential aged care settings. Discussion and Implications: The results suggest that autonomy should be supported, and unnecessary external control should be minimized in residential aged care, and we discuss ways the sector could strive for both aims.
Millepora celiulosa Linnaeus, 1758, spec. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1758
Subjects: Biodiversity
Taxonomy
Animalia
Cnidaria
Hydrozoa
Anthoathecata
Milleporidae
Millepora
Millepora celiulosa

description: Millepora celiulosa [spec. nov.]
M. corallio membranaceo contorto-reticulato.
Hort cliff. 480. Millepora membranacea rigida cellulosa connata labyrinthiformis.
Bauh. hist 3. p. 809. Eschara.
Raj. angl 3. p. 31. n. 1. Eschara retiformis.
Bonan. kirch. t. 286. f. 10.
Rumph. amb. 6. p. 247. t. 87. f. 5. Reticulum marinum.
Ginann. adriat. 9. t. 4. f. 9.
Ellis corall. 71. t. 30. f. H, a. Eschara foliacea millepora lapidea extremitatibus hinc inde irregulariter coalescentibus, utraque superficie ex cellulis ovatis constans.
Habitat in M. Numidico, Mediterraneo.
Membrana lapidea, alba, campanulato-turbinata, varie complicata, perforata foraminibus ovatis inaequalibus in quincuncem; supra punctata; subtus laevis.
description: Published as part of Linnaeus, Carolus, 1758, Systema Naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis, Stockholm :Laurentius Salvius on pages 790-791, DOI: 10.5962/bhl.title.542, http://zenodo.org/record/3922206
Additional file 4 of Earth microbial co-occurrence network reveals interconnection pattern across microbiomes
Creators: name: Ma, Bin
name: Wang, Yiling
name: Ye, Shudi
name: Liu, Shan
name: Stirling, Erinne
name: Gilbert, Jack A.
name: Faust, Karoline
name: Knight, Rob
name: Jansson, Janet K.
name: Cardona, Cesar
name: Röttjers, Lisa
name: Xu, Jianming
Publisher: name: figshare
Year: 2020
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Biotechnology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences

description: Fig. S1. The degree distribution of Earth microbial co-occurrence network. Fig. S2. The relative abundance of vertices in 8 modules of the Earth microbial co-occurrence network. Fig. S3. The co-occurrence across 8 modules of the Earth microbial co-occurrence network. Fig. S4. The distribution of vertices from subnetworks for 14 environmental types among 8 dominant modules. Fig. S5. Relationships between proportions of generalist edge, specialist edge linking generalist vertex pair, and specialist edge linking specialist vertex pair. Fig. S6. Relationship between edge number and generalist edge, specialist edge linking generalist vertex pair, and specialist edge linking specialist vertex pair. Fig. S7. Taxon profiles of generalist edge linked vertices in subnetworks of 12 environments inferred from trimmed datasets. Fig. S8. Taxon profiles of specialist edge linking generalist vertex pair linked vertices in subnetworks of 12 environments inferred from trimmed datasets. Fig. S9. Taxon profiles of specialist edge linking specialist vertex pair linked vertices in subnetworks of 12 environments inferred from trimmed datasets.
Additional file 5: of Public involvement in health research systems: a governance framework
Creators: name: Miller, Fiona
name: Patton, Sarah
name: Dobrow, Mark
name: Berta, Whitney
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Immunology
subject: FOS: Clinical medicine
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: Science Policy
subject: Computational Biology

description: Conceptualising patient and public involvement [1, 4, 6, 15, 16, 38, 41â 48, 51, 56, 61â 63, 81]. (DOCX 17 kb)
Additional file 4: of Public involvement in health research systems: a governance framework
Creators: name: Miller, Fiona
name: Patton, Sarah
name: Dobrow, Mark
name: Berta, Whitney
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Molecular Biology
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Developmental Biology
subject: Cancer
subject: Science Policy
subject: Computational Biology

description: List of included policy reports by jurisdiction. (DOCX 16 kb)
Additional file 2 of 2D-DIGE based proteome analysis of wheat-Thinopyrum intermedium 7XL/7DS translocation line under drought stress
Creators: name: Lu, Fengkun
name: Duan, Wenjing
name: Cui, Yue
name: Zhang, Junwei
name: Zhu, Dong
name: Zhang, Ming
name: Yan, Yueming
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Plant Biology

description: Additional file 2.
Millepora lichenoides Linnaeus, 1758, spec. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1758
Subjects: Biodiversity
Taxonomy
Animalia
Cnidaria
Hydrozoa
Anthoathecata
Milleporidae
Millepora
Millepora lichenoides

description: Millepora lichenoides [spec. nov.]
M. ramosissima plana: supra scabra porosa, subtus glabra, lateribus dilatatis.
Habitat.
Rami ramosissimi in plano, facie Lichenis sruticulosi s. foliacei. Ramuli filiformes, teretiusculi, subcomplanati, supra scabri, subtus glabri, lateribus den- tato-serratis. Pori inter scabritiem superiorem vix manifesti.
description: Published as part of Linnaeus, Carolus, 1758, Systema Naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis, Stockholm :Laurentius Salvius on page 791, DOI: 10.5962/bhl.title.542, http://zenodo.org/record/3922206
Dietary Transitions and Health Outcomes in Four Populations – Systematic Review
Creators: name: Pressler, Mariel
name: Devinsky, Julie
name: Duster, Miranda
name: Lee, Joyce H.
name: Glick, Courtney S.
name: Wiener, Samson
name: Laze, Juliane
name: Friedman, Daniel
name: Roberts, Timothy
name: Devinsky, Orrin
Publisher: name: PRIME
Year: 2025
Subjects: classificationCode: 321004
subject: Nutritional science
classificationCode: 420208
subject: Nutritional epidemiology

description: AbstractImportance: Non-communicable chronic diseases (NCDs) such as obesity, type 2 diabetes, heart disease, and cancer were rare among non-westernpopulationswith traditional diets and lifestyles. Aspopulationstransitionedtoward industrialized diets and lifestyles, NCDs developed.Objective: We performed asystematicliteraturereviewto examine the effects ofdietand lifestyletransitionson NCDs.Evidence review: We identified 22populationsthat underwent a nutritiontransition, eleven of which had sufficient data. Of these, we chosefourpopulationswith diverse geographies, diets and lifestyles who underwent adietaryand lifestyletransitionand explored the relationship betweendietarychanges andhealthoutcomes. We excludedpopulationswith features overlapping with selectedpopulationsor with complicating factors such as inadequate data, subgroups, and different study methodologies over different periods. The selectedpopulationswere Yemenite Jews, Tokelauans, Tanushimaru Japanese, and Maasai. We alsoreviewtransitiondata from seven excludedpopulations(Pima, Navajo, Aboriginal Australians, South African Natal Indians and Zulu speakers, Inuit, and Hadza) to assess for bias.Findings: The threegroupsthat replaced saturated fats (SFA) from animal (Yemenite Jews, Maasai) or plants (Tokelau) with refined carbohydrates had negativehealthoutcomes(e.g., increased obesity, diabetes, heart disease). Yemenites reduced SFA consumption by >40% post-transitionbut men's BMI increased 19% and diabetes increased ~40-fold. Tokelauans reduced fat, dramatically reduced SFA, and increased sugar intake: obesity and diabetes rose. The Tanushimaruanstransitionedto more fats and less carbohydrates and used more anti-hypertensive medications; stroke and breast cancer declined while heart disease was stable. The Maasaitransitionedto lower fat, SFA and higher carbohydrates and had increased BMI and diabetes. Similar patterns were observed in the seven otherpopulations.Conclusion: The nutrient category most strongly associated with negativehealthoutcomes- especially obesity and diabetes - was sugar (increased 600-650% in Yemenite Jews and Tokelauans) and refined carbohydrates (among Maasai, total carbohydrates increased 39% in men and 362% in women), while increased calories was less strongly associated with these disorders. Across 11populations, NCDs were associated with increased refined carbohydrates more than increased calories, reduced activity or other factors, but cannot be attributed to SFA or total fat consumption.
Generation of Mature DENVs via Genetic Modification and Directed Evolution
Creators: name: Meganck R.M
name: de Silva A.M
name: Dong S
name: Baric R.S
name: Adams L.E
name: Mallory M.L
name: Tse L.V
name: White L.J
name: Jadi R
Publisher: name: American Society for Microbiology
Year: 2022

description: Maturation of dengue viruses (DENVs) alters the structure, immunity, and infectivity of the virion and highly mature particles represent the dominant form in vivo. The production of highly mature virions principally relies on the structure and function of the viral premature membrane protein (prM) and its cleavage by the host protease furin. We redeveloped a reliable clonal cell line (VF1) which produces single-round mature DENVs without the need for DENV reverse genetics. More importantly, using protein engineering and directed evolution of the prM cleavage site, we engineered genetically stable mature DENVs in all serotypes independent of cell or host, usually with minimal impact on viral yield. Using these complementary strategies to regulate maturation, we demonstrate that the resulting mature DENVs are antigenically distinct from their isogenic partially mature forms. Given the clinical importance of mature DENVs in immunity, our study provides reliable strategies and reagents for the production of stable, high-titer mature DENVs for DENV antibody neutralization and vaccination immunity studies. Biologically, our data from directed evolution across host species reveals distinct maturation-dependent selective pressures between mammalian and insect cells, verifying the substrate preference between mammalian and insect furin, while hinting at an evolutionary equilibrium of DENV prM cleavage site between its host and vector in nature.
Additional file 3: of Public involvement in health research systems: a governance framework
Creators: name: Miller, Fiona
name: Patton, Sarah
name: Dobrow, Mark
name: Berta, Whitney
Publisher: name: figshare
Year: 2018
Subjects: Medicine
Developmental Biology
Cancer
Science Policy
Computational Biology

description: List of included journal papers. (DOCX 20 kb)
Genetic changes associated with relapse in favorable histology Wilms tumor: A Children's Oncology Group AREN03B2 study
Creators: name: Yap, K.L
name: Ramirez, N.C
name: Fernandez, C.V
name: Renfro, L.A
name: Aris, S
name: Perlman, E.J
name: Phung, Q.H
name: Jones, C.D
name: Gadd, S
name: Mullen, E.A
name: Hoadley, K.A
name: Huff, V
name: Skol, A.D
Publisher: name: Cell Press
Year: 2022

description: Over the last decade, sequencing of primary tumors has clarified the genetic underpinnings of Wilms tumor but has not affected therapy, outcome, or toxicity. We now sharpen our focus on relapse samples from the umbrella AREN03B2 study. We show that over 40% of relapse samples contain mutations in SIX1 or genes of the MYCN network, drivers of progenitor proliferation. Not previously seen in large studies of primary Wilms tumors, DIS3 and TERT are now identified as recurrently mutated. The analysis of primary-relapse tumor pairs suggests that 11p15 loss of heterozygosity (and other copy number changes) and mutations in WT1 and MLLT1 typically occur early, but mutations in SIX1, MYCN, and WTX are late developments in some individuals. Most strikingly, 75% of relapse samples had gain of 1q, providing strong conceptual support for studying circulating tumor DNA in clinical trials to better detect 1q gain earlier and monitor response.
Additional file 1: of Public involvement in health research systems: a governance framework
Creators: name: Miller, Fiona
name: Patton, Sarah
name: Dobrow, Mark
name: Berta, Whitney
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: Developmental Biology
subject: Cancer
subject: Science Policy
subject: Computational Biology

description: Search terms. (DOCX 32 kb)
Additional file 2: of Public involvement in health research systems: a governance framework
Creators: name: Miller, Fiona
name: Patton, Sarah
name: Dobrow, Mark
name: Berta, Whitney
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Developmental Biology
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: List of key organisations included in environmental scan by jurisdiction. (DOCX 21 kb)
Genetic comorbidity between major depression and cardio-metabolic traits, stratified by age at onset of major depression
Creators: name: Adams M.J
name: Campbell A
name: Hottenga J.J
name: Milaneschi Y
name: Jones I
name: Dannlowski U
name: Pistis G
name: Deary I.J
name: Kutalik Z
name: Air T.M
name: Ripke S
name: Boomsma D.I
name: Hodgson K
name: Whitfield J.B
name: Blackwood D.H.R
name: Hagenaars S.P
name: de Geus E.J.C
name: Hamilton S.P
name: Ising M
name: Czamara D
name: Arolt V
name: Breen G
name: Baune B.T
name: McIntosh A.M
name: Wray N.R
name: Porteous D.J
name: Lewis C.M
name: Sullivan P.F
name: Shyn S.I
name: Padmanabhan S
name: Owen M.J
name: Martin N.G
name: Domschke K
name: Penninx B.W.J.H
name: Traylor M
name: Howard D.M
name: Jones L
name: Cearns M
name: Preisig M
name: Coleman J.R.I
name: Andlauer T.F.M
name: Choi S.W
name: Hickie I.B
name: Hayward C
name: Mueller-Myhsok B
name: Binder E.B
name: Lucae S
name: Gaspar H
Publisher: name: John Wiley and Sons Inc.
Year: 2020

description: It is imperative to understand the specific and shared etiologies of major depression and cardio-metabolic disease, as both traits are frequently comorbid and each represents a major burden to society. This study examined whether there is a genetic association between major depression and cardio-metabolic traits and if this association is stratified by age at onset for major depression. Polygenic risk scores analysis and linkage disequilibrium score regression was performed to examine whether differences in shared genetic etiology exist between depression case control status (N cases = 40,940, N controls = 67,532), earlier (N = 15,844), and later onset depression (N = 15,800) with body mass index, coronary artery disease, stroke, and type 2 diabetes in 11 data sets from the Psychiatric Genomics Consortium, Generation Scotland, and UK Biobank. All cardio-metabolic polygenic risk scores were associated with depression status. Significant genetic correlations were found between depression and body mass index, coronary artery disease, and type 2 diabetes. Higher polygenic risk for body mass index, coronary artery disease, and type 2 diabetes was associated with both early and later onset depression, while higher polygenic risk for stroke was associated with later onset depression only. Significant genetic correlations were found between body mass index and later onset depression, and between coronary artery disease and both early and late onset depression. The phenotypic associations between major depression and cardio-metabolic traits may partly reflect their overlapping genetic etiology irrespective of the age depression first presents.
Millepora damicornis Linnaeus, 1758, spec. nov.
Creators: name: Linnaeus, Carolus
Publisher: name: Laurentius Salvius
Year: 1758
Subjects: Biodiversity
Taxonomy
Animalia
Cnidaria
Hydrozoa
Anthoathecata
Milleporidae
Millepora
Millepora damicornis

description: Millepora damicornis [spec. nov.]
M. ramosa scabra, poris sparsis immersis.
Gvalt. test. t 104. Madrepora candida ramosa damae cornua referens, foraminibus rotundis in superficie insignita.
Rumph. amb. 6. t. 86. f. 3. Lithodendron littoreum.
Bauh. hist. 3. p. 846. Corallium asperum candicans adulterinum.
Habitat in O. Asiatico.
Rami ramosi, breves, punctis subscabri. Pori sparsi, impressi, patentes interiori margine, fundo obtusi.
description: Published as part of Linnaeus, Carolus, 1758, Systema Naturae per regna tria naturae: secundum classes, ordines, genera, species, cum characteribus, differentiis, synonymis, locis, Stockholm :Laurentius Salvius on page 791, DOI: 10.5962/bhl.title.542, http://zenodo.org/record/3922206