cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Modelling Dependence in High Dimensions with Factor Copulas
Creators: name: Oh, Dong Hwan
name: Patton, Andrew J.
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Science Policy
subject: Mathematics
subject: FOS: Mathematics
subject: Biological Sciences
subject: Ecology
subject: FOS: Biological sciences
subject: Earth and Environmental Sciences
subject: Biotechnology

description: This paper presents flexible new models for the dependence structure, or copula, of economic variables based on a latent factor structure. The proposed models are particularly attractive for relatively high dimensional applications, involving fifty or more variables, and can be combined with semiparametric marginal distributions to obtain flexible multivariate distributions. Factor copulas generally lack a closed-form density, but we obtain analytical results for the implied tail dependence using extreme value theory, and we verify that simulation-based estimation using rank statistics is reliable even in high dimensions. We consider “scree” plots to aid the choice of the number of factors in the model. The model is applied to daily returns on all 100 constituents of the S&P 100 index, and we find significant evidence of tail dependence, heterogeneous dependence, and asymmetric dependence, with dependence being stronger in crashes than in booms. We also show that factor copula models provide superior estimates of some measures of systemic risk.
Molecular Characterization and Photoreactivity of Organic Aerosols Formed from Pyrolysis of Urban Materials during Fires at the Wildland–Urban Interface
Creators: name: Hopstock, Katherine S.
name: Nizkorodov, Sergey A.
name: Moschos, Vaios
name: Laskin, Alexander
name: Alvarado, Michael A.
name: Xie, Qiaorong
name: Surratt, Jason D.
name: Bililign, Solomon
Publisher: name: American Chemical Society (ACS)
Year: 2024

description: Fires at the wildland–urban interface (WUI) are increasing in magnitude and frequency, emitting organic aerosol (OA) with unknown composition and atmospheric impacts. In this study, we investigated the chemical composition of OA produced through the 600 °C pyrolysis of ten urban materials in nitrogen, which were subsequently aged under UV light for 2 h. The analysis utilized ultrahigh-performance liquid chromatography (UHPLC) separation, coupled with a photodiode array (PDA) detector and a high-resolution mass spectrometer (HRMS) for molecular characterization. Hierarchical clustering analysis demonstrated that lumber-derived OA was the most diverse and distinct in composition. Unaged and aged OA (for each urban material) did not significantly differ in chemical identities. Potential aromatic brown carbon (BrC) chromophores (based on their degree of unsaturation) constituted 13–42% of all assigned compounds. PDA chromatograms revealed multiple BrC chromophoric species that were either enhanced or degraded as a result of UV aging, providing insights into specific BrC chromophores responsible for photobleaching and photoenhancement of the overall absorption coefficient. Thirty-six BrC chromophores were identified across the ten OA types, and their structures were confirmed using reference standards. Components of plasticizers and resins, such as phthalic and terephthalic acids, were structurally confirmed in the samples. We present potential species for WUI fires as components of resins, epoxies, dyes, and adhesives commonly used in manufacturing urban materials. Photolysis did not significantly impact the chemical composition of OA emitted from the burning of specific WUI materials.
Incubation periods of viral gastroenteritis: A systematic review
Creators: name: Lee, R.M
name: Perl, T.M
name: Cummings, D.A.T
name: Lessler, J
name: Reich, N.G
name: Rudolph, K.E
name: Lee, R.A
Publisher: name: BioMed Central Ltd.
Year: 2013

description: Background: Accurate knowledge of incubation period is important to investigate and to control infectious diseases and their transmission, however statements of incubation period in the literature are often uncited, inconsistent, and/or not evidence based.Methods: In a systematic review of the literature on five enteric viruses of public health importance, we found 256 articles with incubation period estimates, including 33 with data for pooled analysis.Results: We fit a log-normal distribution to pooled data and found the median incubation period to be 4.5 days (95% CI 3.9-5.2 days) for astrovirus, 1.2 days (95% CI 1.1-1.2 days) for norovirus genogroups I and II, 1.7 days (95% CI 1.5-1.8 days) for sapovirus, and 2.0 days (95% CI 1.4-2.4 days) for rotavirus.Conclusions: Our estimates combine published data and provide sufficient quantitative detail to allow for these estimates to be used in a wide range of clinical and modeling applications. This can translate into improved prevention and control efforts in settings with transmission or the risk of transmission.
Low-boiling-point perfluorocarbon nanodroplets for adaptable ultrasound-induced blood-brain barrier opening.
Creators: name: Claire, Spitzlei
name: Durham Phillip, G
name: Anthony, Novell
name: Caroline, Denis
name: Dayton Paul, A
name: Erwan, Selingue
name: Jacob, Mattern A
name: Malika, Ouldali
name: Kelly, VanTreek
name: Benoit, Larrat
name: Ambre, Dauba
name: Nicolas, Tsapis
name: James, Tsuruta
name: Bautista, Kathlyne Jayne B.
name: Virginie, Papadopoulou
name: Laurène, Jourdain
name: Ana-Andreea, Arteni
name: Charles, Truillet
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2024

description: Low-boiling point perfluorocarbon nanodroplets (NDs) are valued as effective sonosensitive agents, encapsulating a liquid perfluorocarbon that would instantaneously vaporize at body temperature without the NDs shell. Those NDs have been explored for both therapeutic and diagnostic purposes. Here, phospholipid-shelled nanodroplets containing octafluoropropane (C3F8) or decafluorobutane (C4F10) formed by condensation of microbubbles were thoroughly characterized before blood-brain (BBB) permeabilization. Transmission electron microscopy (TEM) and cryo-TEM were employed to confirm droplet formation while providing high-resolution insights into the droplet surface and lipid arrangement assessed from electron density observation after condensation. The vaporization threshold of NDs was determined with a high-speed camera, and the frequency signal emitted by the freshly vaporized bubbles was analyzed using cavitation detection. C3F8 NDs exhibited vaporization at 0.3 MPa (f0 = 1.5 MHz, 50 cycles), and emitted signals at 2 f0 and 1.5 f0 from 0.45 MPa onwards (f0 = 1.5 MHz, 50 cycles), while broadband noise was measured starting from 0.55 MPa. NDs with the higher boiling point C4F10 vaporized at 1.15 MPa and emitted signals at 2 f0 from 0.65 MPa and 1.5 f0 from 0.9 MPa, while broadband noise was detected starting from 0.95 MPa. Both ND formulations were used to permeabilize the BBB in healthy mice using tailored ultrasound sequences, allowing for the identification of optimal applications for each NDs type. C3F8 NDs proved suitable and safe for permeabilizing a large area, potentially the entire brain, at low acoustic pressure. Meanwhile, C4F10 droplets facilitated very localized (400 μm isotropic) permeabilization at higher pressure. This study prompts a closer examination of the structural rearrangements occurring during the condensation of microbubbles into NDs and highlight the potential to tailor solutions for different brain pathologies by choosing the composition of the NDs and adjusting the ultrasound sequence.
Altering TET dioxygenase levels within physiological range affects DNA methylation dynamics of HEK293 cells
Creators: name: Grosser, Christian
name: Wagner, Nicholas
name: Grothaus, Katrin
name: Horsthemke, Bernhard
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Cancer
subject: Chemistry
subject: Science Policy
subject: Biological Sciences
subject: Earth and Environmental Sciences
subject: Molecular Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Cell Biology
subject: Biochemistry

description: The TET family of dioxygenases (TET1/2/3) can convert 5-methylcytosine (5 mC) into 5-hydroxymethylcytosine (5 hmC) and has been shown to be involved in active and passive DNA demethylation. Here, we demonstrate that altering TET dioxygenase levels within physiological range can affect DNA methylation dynamics of HEK293 cells. Overexpression of TET1 increased global 5 hmC levels and was accompanied by mild DNA demethylation of promoters, gene bodies and CpG islands. Conversely, the simultaneous knockdown of TET1, TET2, and TET3 led to decreased global 5 hmC levels and mild DNA hypermethylation of above-mentioned regions. The methylation changes observed in the overexpression and knockdown studies were mostly non-reciprocal and occurred with different preference depending on endogenous methylation and gene expression levels. Single-nucleotide 5 hmC profiling performed on a genome-wide scale revealed that TET1 overexpression induced 5 mC oxidation without a distribution bias among genetic elements and structures. Detailed analysis showed that this oxidation was related to endogenous 5 hmC levels. In addition, our results support the notion that the effects of TET1 overexpression on gene expression are generally unrelated to its catalytic activity.
Limiting regimes of turbulent horizontal convection. Part 2. Large Prandtl numbers
Creators: name: Passaggia, Pierre-Yves
name: Cohen, Nadia F.
name: Scotti, Alberto
Publisher: name: Cambridge University Press (CUP)
Year: 2024

description:  Horizontal convection at large Rayleigh and Prandtl numbers is studied experimentally in a regime up to seven orders of magnitude larger in terms of Rayleigh numbers than previously achieved. To reach Rayleigh numbers up to 10^17, the horizontal density gradient is generated using differential solutal convection by a differential input of salt and fresh water controlled by diffusion in a novel experiment in which the zero-net mass flux of water is ensured through permeable membranes. This set-up allows us to accurately measure the Nusselt number in solutal convection by carefully controlling the amount of salt water exchanged through the membranes. Combined measurements of density and velocity across more than five orders of magnitude in Rayleigh numbers show that the flow transitions from the Beardsley & Festa (J. Phys. Oceanogr., vol. 2, issue 4, 1972, pp. 444–455), Shishkina & Wagner (Phys. Rev. Lett. , vol. 116, issue 2, 2016, 024302) regime to the Chiu-Webster et al. (J. Fluid Mech., vol. 611, 2008, pp. 395–426) regime and frames the present results within the scope of Shishkina et al. (Geophys. Res. Lett. , vol. 43, issue 3, 2016, pp. 1219–1225), and the theory of Part 1 (Passaggia & Scotti, vol. 997, 2024, J. Fluid Mech., A5). In particular, we show that, even for large Prandtl numbers, the circulation eventually clusters underneath the forcing horizontal boundary, leaving a stratified core without motion. Finally, the previous regime diagrams (Hughes & Griffiths, Annu. Rev. Fluid Mech., vol. 40, 2008, pp. 185–208; Shishkina et al., Geophys. Res. Lett., vol. 43, issue 3, 2016, pp. 1219–1225) are extended by combining the present results at high Prandtl numbers, the results at low Prandtl numbers of Part 1, together with previous results from the literature. This work sets a new picture of the transition landscape of horizontal convection over six orders of magnitude in Prandtl number and sixteen orders of magnitude in Rayleigh number.
Structured models of infectious disease: Inference with discrete data
Creators: name: Klepac, P
name: Lessler, J
name: Metcalf, C.J.E
name: Bjørnstad, O.N
name: Grenfell, B.T
name: Morice, A
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: The usage of structured population models can make substantial contributions to public health, particularly for infections where clinical outcomes vary over age. There are three theoretical challenges in implementing such analyses: (i) developing an appropriate framework that models both demographic and epidemiological transitions; (ii) parameterizing the framework, where parameters may be based on data ranging from the biological course of infection, basic patterns of human demography, specific characteristics of population growth, and details of vaccination regimes implemented; (iii) evaluating public health strategies in the face of changing human demography. We illustrate the general approach by developing a model of rubella in Costa Rica. The demographic profile of this infection is a crucial aspect of its public health impact, and we use a transient perturbation analysis to explore the impact of changing human demography on immunization strategies implemented.
A Shot in the Dark. Jacques Closeau Did It Again!
Creators: name: Toledo, Michel
Publisher: name: Zenodo
Year: 2011

description: This essay explores A Shot in the Dark from a narrative and symbolic perspective, focusing on Jacques Closeau as a disruptor of traditional social structures. Through a critical lens on Blake Edwards’ cinematic style and Peter Sellers’ performance, the essay emphasizes how chaos, love, and clumsiness become tools to dismantle a society rooted in hypocrisy. Closeau’s eccentric viewpoint allows him to uncover hidden truths and force other characters to confront their contradictions. The film is approached not merely as a comedy but as a subtle critique of the established order and the forced belonging to rigid social systems.
Bayesian Variable Selection on Model Spaces Constrained by Heredity Conditions
Creators: name: Taylor-Rodriguez, Daniel
name: Womack, Andrew
name: Bliznyuk, Nikolay
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental 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: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Plant Biology

description: This article investigates Bayesian variable selection when there is a hierarchical dependence structure on the inclusion of predictors in the model. In particular, we study the type of dependence found in polynomial response surfaces of orders two and higher, whose model spaces are required to satisfy weak or strong heredity conditions. These conditions restrict the inclusion of higher-order terms depending upon the inclusion of lower-order parent terms. We develop classes of priors on the model space, investigate their theoretical and finite sample properties, and provide a Metropolis–Hastings algorithm for searching the space of models. The tools proposed allow fast and thorough exploration of model spaces that account for hierarchical polynomial structure in the predictors and provide control of the inclusion of false positives in high posterior probability models.
Lysibia tenax TOWNES 1983
Creators: name: Riedel
name: Pénigot
name: Schwarz
name: Diller
name: Johansson
name: Japoshvili, G.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Ichneumonidae
Lysibia
Lysibia tenax

description: Lysibia tenax TOWNES, 1983
M a t e r i a l e x a m i n e d: Trap 4: 1♀ 20.iv.-5.v.; trap 7: 1♁ 5-20.v., 1♀ 21.ix.-5.x., 2♀♀ 5- 19.x.
D i s t r i b u t i o n: Holarctic, new record for Georgia and the Caucasus region.
description: Published as part of Riedel, Pénigot, Schwarz, Diller, Johansson & Japoshvili, G., 2023, Darwin wasps (Hymenoptera, Ichneumonidae) of the Kintrishi National Park, Sakartvelo (Georgia), with descriptions of six new species, pp. 61-153 in Linzer biologische Beiträge 55 (1) on page 123, DOI: 10.5281/zenodo.10788481
Evidence for antigenic seniority in influenza A (H3N2) antibody responses in southern China
Creators: name: Guan, Y
name: Zhu, H
name: Riley, S
name: Wang, S
name: Cummings, D.A.T
name: Read, J.M
name: Lessler, J
name: Smith, G.J.D
name: Jiang, C.Q
Publisher: name: Public Library of Science
Year: 2012

description: A key observation about the human immune response to repeated exposure to influenza A is that the first strain infecting an individual apparently produces the strongest adaptive immune response. Although antibody titers measure that response, the interpretation of titers to multiple strains - from the same sera - in terms of infection history is clouded by age effects, cross reactivity and immune waning. From July to September 2009, we collected serum samples from 151 residents of Guangdong Province, China, 7 to 81 years of age. Neutralization tests were performed against strains representing six antigenic clusters of H3N2 influenza circulating between 1968 and 2008, and three recent locally circulating strains. Patterns of neutralization titers were compared based on age at time of testing and age at time of the first isolation of each virus. Neutralization titers were highest for H3N2 strains that circulated in an individual's first decade of life (peaking at 7 years). Further, across strains and ages at testing, statistical models strongly supported a pattern of titers declining smoothly with age at the time a strain was first isolated. Those born 10 or more years after a strain emerged generally had undetectable neutralization titers to that strain (<1:10). Among those over 60 at time of testing, titers tended to increase with age. The observed pattern in H3N2 neutralization titers can be characterized as one of antigenic seniority: repeated exposure and the immune response combine to produce antibody titers that are higher to more 'senior' strains encountered earlier in life.
Lecture capture: Student hopes, Instructor fears
Creators: name: Williams, Benedict
name: Pfeifer, Jeffrey
name: Waller, Vivienne
Publisher: name: Swinburne
Year: 2024

description: Technology to capture and retransmit lectures has been widely available for more than two decades. However, the widespread expectation that universities will record all lectures is not matched by systematic research and theory on lecture capture use. This paper provides a brief overview of research and reports a three-phase study of lecture video use and perceptions carried out with the staff and students of an undergraduate psychology program at a large suburban university. We found that some lecturers are concerned that mandatory lecture capture creates copyright problems and reduces their ability to provide their best teaching. There is also evidence that lecture capture decreases attendance and lowers grades for some students. However, our results indicate that for students enrolled in face-to-face units, the availability of captured lecture videos offers a valuable revision tool which is integrated into 'traditional' study patterns rather than replacing them.
Novel Corrector for Variants of SLC6A8: A Therapeutic Opportunity for Creatine Transporter Deficiency
Creators: name: Pullen, Nicholas
name: Barrish, Joel C.
name: Crotty, William
name: Brandon, Nicholas
name: Brown, Dean G.
name: Deshusses, Chloe
name: Labenski, Matthew T.
name: Rosskamp, Lea
name: Muncipinto, Giovanni
name: Rusu, Victor
name: Conway, Leslie
name: van Kalken, Daniel
name: Gross, Liam
name: Blanchette, Heather S.
name: Jones, Lyn H.
name: Mathis, Robert
name: Park, Hyejin
name: Westgate, Christina
name: Rabin, Benjamin
name: Lyons, Matthew
name: Rettenmaier, T. Justin
name: Gechijian, Lara N.
name: Iantosca, Gianna
Publisher: name: American Chemical Society (ACS)
Year: 2024

description: Mutations in creatine transporter SLC6A8 cause creatine transporter deficiency (CTD), which is responsible for 2% of all cases of X-linked intellectual disability. CTD has no current treatments and has a high unmet medical need. Inspired by the transformational therapeutic impact of small molecule "correctors" for the treatment of cystic fibrosis, which bind to mutated versions of the CFTR ion channel to promote its trafficking to the cell surface, we sought to identify small molecules that could stabilize SLC6A8 as a potential treatment for CTD. We leveraged a novel chemoproteomic technology for ligand discovery, reactive affinity probe interaction discovery, to identify small-molecule fragments with photoaffinity handles that bind to SLC6A8 in a cellular environment. We synthesized a library of irreversible covalent analogs of these molecules to characterize in functional assays, which revealed molecules that could promote the trafficking of mutant SLC6A8 variants to the cell surface. Further medicinal chemistry was able to identify reversible drug-like small molecules that both promoted trafficking of the transporter and also rescued creatine uptake. When profiled across the 27 most prevalent SLC6A8 missense variants, we found that 10-20% of patient mutations were amenable to correction by our molecules. These results were verified in an endogenous setting using the CRISPR knock-in of selected missense alleles. We established in vivo proof-of-mechanism for correctors in a novel CTD mouse model with the P544L patient-defined variant knocked in to the SLC6A8 locus, where treatment with our orally bioavailable and brain penetrant tool corrector increased brain creatine levels in heterozygous female mice, validating correctors as a potential therapeutic approach for CTD.
Mastrulus marshalli
Creators: name: Riedel
name: Pénigot
name: Schwarz
name: Diller
name: Johansson
name: Japoshvili, G.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Ichneumonidae
Mastrulus
Mastrulus marshalli

description: Mastrulus marshalli (BRIDGMAN & FITCH, 1882), det. Schwarz
M a t e r i a l e x a m i n e d: Trap2: 1♀ 5-20.v.
D i s t r i b u t i o n: Western Palaearctic, new record for Georgia and the Caucasus region.
description: Published as part of Riedel, Pénigot, Schwarz, Diller, Johansson & Japoshvili, G., 2023, Darwin wasps (Hymenoptera, Ichneumonidae) of the Kintrishi National Park, Sakartvelo (Georgia), with descriptions of six new species, pp. 61-153 in Linzer biologische Beiträge 55 (1) on page 123, DOI: 10.5281/zenodo.10788481
Altering TET dioxygenase levels within physiological range affects DNA methylation dynamics of HEK293 cells
Creators: name: Grosser, Christian
name: Wagner, Nicholas
name: Grothaus, Katrin
name: Horsthemke, Bernhard
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Cancer
subject: Chemistry
subject: Science Policy
subject: Biological Sciences
subject: Earth and Environmental Sciences
subject: Molecular Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Cell Biology
subject: Biochemistry

description: The TET family of dioxygenases (TET1/2/3) can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) and has been shown to be involved in active and passive DNA demethylation. Here, we demonstrate that altering TET dioxygenase levels within physiological range can affect DNA methylation dynamics of HEK293 cells. Overexpression of TET1 increased global 5hmC levels and was accompanied by mild DNA demethylation of promoters, gene bodies and CpG islands. Conversely, the simultaneous knockdown of TET1, TET2, and TET3 led to decreased global 5hmC levels and mild DNA hypermethylation of above-mentioned regions. The methylation changes observed in the overexpression and knockdown studies were mostly non-reciprocal and occurred with different preference depending on endogenous methylation and gene expression levels. Single-nucleotide 5hmC profiling performed on a genome-wide scale revealed that TET1 overexpression induced 5mC oxidation without a distribution bias among genetic elements and structures. Detailed analysis showed that this oxidation was related to endogenous 5hmC levels. In addition, our results support the notion that the effects of TET1 overexpression on gene expression are generally unrelated to its catalytic activity.
Synchrony of Sylvatic Dengue Isolations: A Multi-Host, Multi-Vector SIR Model of Dengue Virus Transmission in Senegal
Creators: name: Althouse, B.M
name: Weaver, S.C
name: Lessler, J
name: Sall, A.A
name: Watts, D.M
name: Cummings, D.A.T
name: Diallo, M
name: Hanley, K.A
Publisher: name: Public Library of Science
Year: 2012

description: Isolations of sylvatic dengue-2 virus from mosquitoes, humans and non-human primates in Senegal show synchronized multi-annual dynamics over the past 50 years. Host demography has been shown to directly affect the period between epidemics in other pathogen systems, therefore, one might expect unsynchronized multi-annual cycles occurring in hosts with dramatically different birth rates and life spans. However, in Senegal, we observe a single synchronized eight-year cycle across all vector species, suggesting synchronized dynamics in all vertebrate hosts. In the current study, we aim to explore two specific hypotheses: 1) primates with different demographics will experience outbreaks of dengue at different periodicities when observed as isolated systems, and that coupling of these subsystems through mosquito biting will act to synchronize incidence; and 2) the eight-year periodicity of isolations observed across multiple primate species is the result of long-term cycling in population immunity in the host populations. To test these hypotheses, we develop a multi-host, multi-vector Susceptible, Infected, Removed (SIR) model to explore the effects of coupling multiple host-vector systems of dengue virus transmission through cross-species biting rates. We find that under small amounts of coupling, incidence in the host species synchronize. Long-period multi-annual dynamics are observed only when prevalence in troughs reaches vanishingly small levels (<10-10), suggesting that these dynamics are inconsistent with sustained transmission in this setting, but are consistent with local dengue virus extinctions followed by reintroductions. Inclusion of a constant introduction of infectious individuals into the system causes the multi-annual periods to shrink, while the effects of coupling remain the same. Inclusion of a stochastic rate of introduction allows for multi-annual periods at a cost of reduced synchrony. Thus, we conclude that the eight-year period separating amplifications of dengue may be explained by cycling in immunity with stochastic introductions.
Altering TET dioxygenase levels within physiological range affects DNA methylation dynamics of HEK293 cells
Creators: name: Grosser, Christian
name: Wagner, Nicholas
name: Grothaus, Katrin
name: Horsthemke, Bernhard
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer

description: The TET family of dioxygenases (TET1/2/3) can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) and has been shown to be involved in active and passive DNA demethylation. Here, we demonstrate that altering TET dioxygenase levels within physiological range can affect DNA methylation dynamics of HEK293 cells. Overexpression of TET1 increased global 5hmC levels and was accompanied by mild DNA demethylation of promoters, gene bodies and CpG islands. Conversely, the simultaneous knockdown of TET1, TET2, and TET3 led to decreased global 5hmC levels and mild DNA hypermethylation of above-mentioned regions. The methylation changes observed in the overexpression and knockdown studies were mostly non-reciprocal and occurred with different preference depending on endogenous methylation and gene expression levels. Single-nucleotide 5hmC profiling performed on a genome-wide scale revealed that TET1 overexpression induced 5mC oxidation without a distribution bias among genetic elements and structures. Detailed analysis showed that this oxidation was related to endogenous 5hmC levels. In addition, our results support the notion that the effects of TET1 overexpression on gene expression are generally unrelated to its catalytic activity.
Obesity Medicine Provider-Directed Health Coaching in a Commercial Weight Loss Program: Proof of Concept
Creators: name: Sauls, Rachel M.
name: Alencar, Michelle
name: Fitch, Angela
name: Patel, Mayur
name: Johnson, Kelly
Publisher: name: Elsevier
Year: 2024

description: Background Obesity remains a leading serious chronic disease and cause of death in the U.S. Despite previous research in diets (i.e., caloric restriction), physical activity levels, and biochemical markers, no studies to date have investigated the combination of an obesity medicine physician with a health coach alongside a commercial program for reducing body weight. As a result, this pilot study aims to assess the relationship between a commercial diet program and health and wellness coaching (HWC) for weight reduction outcomes when delivered in conjunction with an obesity medicine physician chronic disease care model, as a proof-of-concept study. Methods This 24-week proof-of-concept study was pragmatic, being an unblinded, unrandomized, uncontrolled, longitudinal, observational study. Its purpose was to assess participant weight reduction from a commercial weight reduction program using a pre-packaged portion-controlled reduced-calorie diet while meeting with a health coach and obesity medicine physician for counseling and support. Participants in the sample underwent a commercial weight reduction program through dietary control while meeting with an HWC. A repeated measures ANOVA was conducted to determine the weight reduction trends across a 24-week program. Results This study included n=53 participants; a majority were white females (n=45; 85%), with an average (SD) age of 50.3 (12.2) years. There was a significant improvement in weight reduction (21.8±9.4 lbs. WL) seen throughout the 24-week program (F (7, 364) = 33.129, p<.001), with a large effect (η2 = 0.922). Conclusion This proof-of-concept project found that Obesity Medicine Physician-directed, portion-controlled meals and HWC can improve weight reduction across a 24-week program using portioned-controlled meals. Confirmation of these findings and their clinical significance requires a follow-up randomized, controlled clinical trial using validated assessment tools.
Amazonian conservation across archipelagos of Indigenous territories
Creators: name: Valdivia, Gabriela
name: Esbach, Michael S.
name: Lu, Flora
name: Correia, Joel E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2024

description: Indigenous stewardship is essential to the conservation of biocultural diversity, yet conventional conservation models often treat Indigenous territories (ITs) as homogeneous or isolated units. We propose that archipelagos of Indigenous territories (AITs), clusters of ITs that span geographies but are connected through shared cultural or political ties maintained by Indigenous nations, are crucial for understanding and enhancing conservation strategies that recognize the complexity of Indigenous stewardship. We classified 3572 ITs in the Amazon into 4 categories-single or multiple nations with either singular IT or AIT-to assess their spatial heterogeneity, governance, and conservation potential. We then assessed species richness, carbon stocks, and pressures across these different categories. To examine how AITs can enhance biocultural conservation efforts, we conducted a case study of the Cofán Nation in Ecuador. AITs covered 45% of the Amazonian land area and had higher species richness and carbon stocks than single IT configurations. However, AITs faced greater pressures from development and extractive activities. In the case study, the Cofán AIT was shaped by colonization and land titling challenges, but their community-driven governance, cross-territorial collaboration, and adaptive responses-such as comanagement agreements and resisting extractive activities-enhanced their ecological and cultural resilience amid growing development pressures. Our findings suggest that AITs facilitate the exchange of resources, knowledge, and cultural practices, which strengthens social connectivity, reinforces governance structures, and enables adaptive management across ITs, thereby enhancing biocultural resilience across discontinuous spaces. This work advocates for a paradigm shift in conservation planning and practice that recognizes the vital role of AITs in sustaining Amazonian ecosystems and Indigenous lifeways, particularly in the face of increasing pressures.
Mastrus rufulus
Creators: name: Riedel
name: Pénigot
name: Schwarz
name: Diller
name: Johansson
name: Japoshvili, G.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Ichneumonidae
Mastrus
Mastrus rufulus

description: Mastrus rufulus (THOMSON, 1884), det. Schwarz
M a t e r i a l e x a m i n e d: Trap2: 1♀ 20.iv.-5.v., 1♀ 20.v.-1.vi., 1♀ 1-15.vi.; trap 4: 2♀♀ 20.iv.-5.v., 1♀ 5-20.v., 1♁ 15-29.vi., 1♀ 1♁ 21.ix.-5.x., 2♀♀ 21.ix.-9.x.; trap 7: 1♀ 5-20.v.; trap 12: 3♀♀ 20.iv.-5.v., 1♀ 5-20.v., 1♀ 1-15.vi., 1♀ 24.viii.-7.ix., 1♀ 7-21.ix., 2♀♀ 21.ix.-5.x., 1♀ 5- 19.x.
D i s t r i b u t i o n: Western Palaearctic, new record for Georgia and the Caucasus region.
description: Published as part of Riedel, Pénigot, Schwarz, Diller, Johansson & Japoshvili, G., 2023, Darwin wasps (Hymenoptera, Ichneumonidae) of the Kintrishi National Park, Sakartvelo (Georgia), with descriptions of six new species, pp. 61-153 in Linzer biologische Beiträge 55 (1) on page 124, DOI: 10.5281/zenodo.10788481
A continuum theory of electro-cortical activity
Creators: name: Liley, David
name: Cadusch, Peter
name: Wright, James J.
Publisher: name: Swinburne
Year: 2024

description: A set of non-linear continuum field equations are presented which describe the macroscopic dynamics of neural activity in cortex. Numerical solutions of the coupled non-linear system of partial differential equations show properties analogous to cortical evoked potentials, oscillations at the frequency of the mammalian alpha rhythm and non-stationary epileptic spikes.
Mastrus silbernageli
Creators: name: Riedel
name: Pénigot
name: Schwarz
name: Diller
name: Johansson
name: Japoshvili, G.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Ichneumonidae
Mastrus
Mastrus silbernageli

description: Mastrus silbernageli (KISS, 1929), det. Schwarz
M a t e r i a l e x a m i n e d: Trap 4: 1♀ 20.v.-1.vi.; trap 12: 1♀ 13-27.vii., 1♀ 7-21.ix.
D i s t r i b u t i o n: Western Palaearctic, new record for Georgia and the Caucasus region.
description: Published as part of Riedel, Pénigot, Schwarz, Diller, Johansson & Japoshvili, G., 2023, Darwin wasps (Hymenoptera, Ichneumonidae) of the Kintrishi National Park, Sakartvelo (Georgia), with descriptions of six new species, pp. 61-153 in Linzer biologische Beiträge 55 (1) on page 124, DOI: 10.5281/zenodo.10788481
SYK regulates macrophage MHC-II expression via activation of autophagy in response to oxidized LDL
Creators: name: Soo-Ho Choi
name: Jungsu Kim
name: Almazan, Felicidad
name: Gonen, Ayelet
name: Diehl, Cody J
name: Witztum, Joseph L
name: Miller, Yury I
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Computational Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Marine Biology
subject: Biological Sciences
subject: Immunology
subject: FOS: Clinical medicine
subject: Meta Science
subject: Genetics
subject: FOS: Biological sciences
subject: Cell Biology
subject: Microbiology
subject: Biochemistry

description: Adaptive immunity, which plays an important role in the development of atherosclerosis, is mediated by major histocompatibility complex (MHC)-dependent antigen presentation. In atherosclerotic lesions, macrophages constitute an important class of antigen-presenting cells that activate adaptive immune responses to oxidized low-density lipoprotein (OxLDL). It has been reported that autophagy regulates adaptive immune responses by enhancing antigen presentation to MHC class II (MHC-II). In a previous study, we have demonstrated that SYK (spleen tyrosine kinase) regulates generation of reactive oxygen species (ROS) and activation of MAPK8/JNK1 in macrophages. Because ROS and MAPK8 are known to regulate autophagy, in this study we investigated the role of SYK in autophagy, MHC-II expression and adaptive immune response to OxLDL. We demonstrate that OxLDL induces autophagosome formation, MHC-II expression, and phosphorylation of SYK in macrophages. Gene knockout and pharmacological inhibitors of NOX2 and MAPK8 reduced OxLDL-induced autophagy. Using bone marrow-derived macrophages isolated from wild-type and myeloid-specific SYK knockout mice, we demonstrate that SYK regulates OxLDL-induced ROS generation, MAPK8 activation, BECN1-BCL2 dissociation, autophagosome formation and presentation of OxLDL-derived antigens to CD4+ T cells. ldlr−/−syk−/− mice fed a high-fat diet produced lower levels of IgG to malondialdehyde (MDA)-LDL, malondialdehyde-acetaldehyde (MAA)-LDL, and OxLDL compared to ldlr−/− mice. These results provide new insights into the mechanisms by which SYK regulates MHC-II expression via autophagy in macrophages and may contribute to regulation of adaptive immune responses in atherosclerosis.
title: Equilibria in Finite Games
Creators: name: Gupta, A
Publisher: name: University of Liverpool Repository
Year: 2016

description: This thesis studies various equilibrium concepts in the context of finite games of infinite duration and in the context of bi-matrix games. We considered the game settings where a special player - the leader - assigns the strategy profile to herself and to every other player in the game alike. The leader is given the leeway to benefit from deviation in a strategy profile whereas no other player is allowed to do so. These leader strategy profiles are asymmetric but stable as the stability of strategy profiles is considered w.r.t. all other players. The leader can further incentivise the strategy choices of other players by transferring a share of her own payoff to them that results in incentive strategy profiles. Among these class of strategy profiles, an 'optimal' leader resp. incentive strategy profile would give maximal reward to the leader and is a leader resp. incentive equilibrium. We note that computing leader and incentive equilibrium is no more expensive than computing Nash equilibrium. For multi-player non-terminating games, their complexity is NP complete in general and equals the complexity of computing two-player games when the number of players is kept fixed. We establish the use of memory and study the effect of increasing the memory size in leader strategy profiles in the context of discounted sum games. We discuss various follower behavioural models in bi-matrix games assuming both friendly follower and an adversarial follower. This leads to friendly incentive equilibrium and secure incentive equilibrium for the resp. follower behaviour. While the construction of friendly incentive equilibrium is tractable and straight forward the secure incentive equilibrium needs a constructive approach to establish their existence and tractability. Our overall observation is that the leader return in an incentive equilibrium is always higher (or equal to) her return in a leader equilibrium that in turn would provide higher or equal leader return than from a Nash equilibrium. Optimal strategy profiles assigned this way therefore prove beneficial for the leader.
Urban Cholera Transmission Hotspots and Their Implications for Reactive Vaccination: Evidence from Bissau City, Guinea Bissau
Creators: name: Azman, A.S
name: Luquero, F.J
name: Grenfell, B.T
name: Banga, C.N
name: Palma, P.P
name: Grais, R.F
name: Rodrigues, A
name: Lessler, J
Publisher: name: Public Library of Science
Year: 2012

description: Background: Use of cholera vaccines in response to epidemics (reactive vaccination) may provide an effective supplement to traditional control measures. In Haiti, reactive vaccination was considered but, until recently, rejected in part due to limited global supply of vaccine. Using Bissau City, Guinea-Bissau as a case study, we explore neighborhood-level transmission dynamics to understand if, with limited vaccine and likely delays, reactive vaccination can significantly change the course of a cholera epidemic. Methods and Findings: We fit a spatially explicit meta-population model of cholera transmission within Bissau City to data from 7,551 suspected cholera cases from a 2008 epidemic. We estimated the effect reactive vaccination campaigns would have had on the epidemic under different levels of vaccine coverage and campaign start dates. We compared highly focused and diffuse strategies for distributing vaccine throughout the city. We found wide variation in the efficiency of cholera transmission both within and between areas of the city. "Hotspots", where transmission was most efficient, appear to drive the epidemic. In particular one area, Bandim, was a necessary driver of the 2008 epidemic in Bissau City. If vaccine supply were limited but could have been distributed within the first 80 days of the epidemic, targeting vaccination at Bandim would have averted the most cases both within this area and throughout the city. Regardless of the distribution strategy used, timely distribution of vaccine in response to an ongoing cholera epidemic can prevent cases and save lives. Conclusions: Reactive vaccination can be a useful tool for controlling cholera epidemics, especially in urban areas like Bissau City. Particular neighborhoods may be responsible for driving a city's cholera epidemic; timely and targeted reactive vaccination at such neighborhoods may be the most effective way to prevent cholera cases both within that neighborhood and throughout the city.
A global model of malaria climate sensitivity: Comparing malaria response to historic climate data based on simulation and officially reported malaria incidence
Creators: name: Kaufman, J.H
name: Davis, M
name: Douglas, J.V
name: Waraporn, N
name: Lessler, J
name: Kershenbaum, A
name: Edlund, S
Publisher: name: BioMed Central Ltd.
Year: 2012

description: Background: The role of the Anopheles vector in malaria transmission and the effect of climate on Anopheles populations are well established. Models of the impact of climate change on the global malaria burden now have access to high-resolution climate data, but malaria surveillance data tends to be less precise, making model calibration problematic. Measurement of malaria response to fluctuations in climate variables offers a way to address these difficulties. Given the demonstrated sensitivity of malaria transmission to vector capacity, this work tests response functions to fluctuations in land surface temperature and precipitation. Methods. This study of regional sensitivity of malaria incidence to year-to-year climate variations used an extended Macdonald Ross compartmental disease model (to compute malaria incidence) built on top of a global Anopheles vector capacity model (based on 10years of satellite climate data). The predicted incidence was compared with estimates from the World Health Organization and the Malaria Atlas. The models and denominator data used are freely available through the Eclipse Foundations Spatiotemporal Epidemiological Modeller (STEM). Results: Although the absolute scale factor relating reported malaria to absolute incidence is uncertain, there is a positive correlation between predicted and reported year-to-year variation in malaria burden with an averaged root mean square (RMS) error of 25% comparing normalized incidence across 86 countries. Based on this, the proposed measure of sensitivity of malaria to variations in climate variables indicates locations where malaria is most likely to increase or decrease in response to specific climate factors. Bootstrapping measures the increased uncertainty in predicting malaria sensitivity when reporting is restricted to national level and an annual basis. Results indicate a potential 20x improvement in accuracy if data were available at the level ISO 3166-2 national subdivisions and with monthly time sampling. Conclusions: The high spatial resolution possible with state-of-the-art numerical models can identify regions most likely to require intervention due to climate changes. Higher-resolution surveillance data can provide a better understanding of how climate fluctuations affect malaria incidence and improve predictions. An open-source modelling framework, such as STEM, can be a valuable tool for the scientific community and provide a collaborative platform for developing such models.
Implications of the non-traditional student becoming the traditional
Creators: name: Fleckhammer, Lorraine
name: Richardson, Helene
Publisher: name: Swinburne
Year: 2024

description: The challenge that the new digital technologies brings to education today is in the shift to online education. Online education, as delivered through Open Universities Australia, is open access, and affords entry into Higher Education for many non-traditional students who are much more diverse in terms of academic skills than traditional-entry students. The aim of this study was to improve academic writing skills, specifically in the correct use of APA formatting for psychology research reports. A „low-stakes‟ assessment task worth 5% replaced optional referencing, formatting and report writing exercises. The results found no improvement in student reports (i.e., no increase in assignment grades) in the intervention year compared to three other years where the tasks were optional.
Uvrag targeting by Mir125a and Mir351 modulates autophagy associated with Ewsr1 deficiency
Creators: name: Rhyu, Im Joo
name: Her, Song
name: Kim, Sun
name: Lee, Sean Bong
name: Junghee Lee
name: Yunha Kim
name: Kang, Young-Sook
name: Lee, Na-Young
name: Kim, Ki Yoon
name: Hwang, Yu Jin
name: Hyun-Wook Kim
name: Jung, Min-Kyung
name: Chai-Jin Lee
name: Seyoon Ko
name: Kowall, Neil W
name: Ryu, Hoon
Publisher: name: Taylor & Francis
Year: 2015
Subjects: subject: Hematology
subject: Developmental Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Genetics
subject: Cell Biology
subject: Physics
subject: Biochemistry
subject: Biophysics

description: The EWSR1 (EWS RNA-binding protein 1/Ewing Sarcoma Break Point Region 1) gene encodes a RNA/DNA binding protein that is ubiquitously expressed and involved in various cellular processes. EWSR1 deficiency leads to impairment of development and accelerated senescence but the mechanism is not known. Herein, we found that EWSR1 modulates the Uvrag (UV radiation resistance associated) gene at the post-transcription level. Interestingly, EWSR1 deficiency led to the activation of the DROSHA-mediated microprocessor complex and increased the level of Mir125a and Mir351, which directly target Uvrag. Moreover, the Mir125a- and Mir351-mediated reduction of Uvrag was associated with the inhibition of autophagy that was confirmed in ewsr1 knockout (KO) MEFs and ewsr1 KO mice. Taken together, our data indicate that EWSR1 is involved in the post-transcriptional regulation of Uvrag via a miRNA-dependent pathway, resulting in the deregulation of autophagy inhibition. The mechanism of Uvrag and autophagy regulation by EWSR1 provides new insights into the role of EWSR1 deficiency-related cellular dysfunction.