cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Effect of tensor force on dissipation dynamics in time-dependent Hartree-Fock theory
Creators: name: Dai, Gao-Feng
name: Guo, Lu
name: Zhao, En-Guang
name: Zhou, Shan-Gui
Publisher: name: arXiv
Year: 2014
Subjects: subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: The role of tensor force on the collision dynamics of $^{16}$O+$^{16}$O is investigated in the framework of a fully three-dimensional time-dependent Hartree-Fock theory. The calculations are performed with modern Skyrme energy functional plus tensor terms. Particular attention is given on the analysis of dissipation dynamics in heavy-ion collisions. The energy dissipation is found to decrease as an initial bombarding energy increases in deep-inelastic collisions for all the Skyrme parameter sets studied here because of the competition between the collective motion and the single-particle degrees of freedom. We reveal that the tensor forces may either enhance or reduce the energy dissipation depending on the different parameter sets. The fusion cross section without tensor force overestimates the experimental value by about 25\%, while the calculation with tensor force T11 has good agreement with experimental cross section.
Mechanisms and dynamics of survival in the treatment of ovarian cancer
Creators: name: Vilas, Caroline Kate
name: 0000-0002-8080-3035
Publisher: name: The University of Texas at Austin
Year: 2022
Subjects: Ovarian cancer
HGSOC
Heterogeneity
Resistance
Chemotherapy
Carboplatin
Cisplatin
Platinum-based drugs
Tumor evolution
Intrastrand cross-link
Clonal dynamics
Lineage tracing
Functionalized lineage tracing
Single-cell RNA sequencing
scRNA-seq

description: High-grade serous ovarian cancer (HGSOC) accounts for up to 80% of deaths from ovarian cancer, and overall survival has not improved much in decades. This is largely due to vast genome instability and genetic heterogeneity in HGSOC which contribute to chemoresistance. This substantial heterogeneity has been shown to result in the presence of rare pre-existing resistant clones in the tumor and the development of acquired resistance. Alongside paclitaxel, mutagenic platinum-based drugs remain the treatment mainstay for HGSOC. While cytotoxic, platinum-based drugs also increase genome instability, heterogeneity and chemoresistance. Such extensive heterogeneity promotes unique evolutionary trajectories that warrant detailed characterizations. In a multi-scale analysis, this dissertation leverages approaches from two disciplines to better understand the mechanisms and dynamics of survival in the treatment of ovarian cancer. The cisplatin-1,2-d(GpG) (Pt-GG) intrastrand cross-link is the major lesion produced by cisplatin and carboplatin and contributes to a predominant C:A mutation signature through the misincorporation of dATP opposite Pt-GG by polymerases such as DNA polymerase β (polβ). Using X-ray crystallography, we report the first structures of polβ misincorporating dATP opposite Pt-GG and demonstrate Pt-GG behaves like an abasic site to promote the misinsertion of dATP in a non-instructional manner, elucidating a molecular mechanism contributing to platinum-induced mutagenesis. We also conduct a systems level study of the clonal dynamics and mechanisms underlying HGSOC survival to chemotherapy using a multi-functional lineage tracing approach, ClonMapper, which combines clonal tracking with single-cell RNA sequencing and clonal isolation for further characterizations. We demonstrate that pre-existing features drive survival of clones, enabling a shift to a treatment-induced cell state characterized by cell growth (mTORC1, TNF-α signaling via NF-κB, Hedgehog signaling, androgen response), stress response (EMT, hypoxia, mitotic spindle, interferon response), and metabolism (glycolysis, oxidative phosphorylation). Genetic features underlie a rapid transition to this cell state in rare clones of one cell line. We also demonstrate successful isolation of a rare pre-existing resistant clone from pre-treatment for genomic and epigenetic characterizations. By harnessing two separate approaches, we gain a more holistic understanding of the mechanisms and dynamics underlying HGSOC survival to chemotherapy and provide insights into improving drug design and therapeutic strategies.
Perspective: Markov Models for Long-Timescale Biomolecular Dynamics
Creators: name: Schwantes, Christian R.
name: McGibbon, Robert T.
name: Pande, Vijay S.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Biological Physics (physics.bio-ph)
subject: Biomolecules (q-bio.BM)
subject: FOS: Physical sciences
subject: FOS: Biological sciences

description: Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is insufficient, as researchers must be able to transform the data in a simulation trajectory into specific scientific insights. Although this analysis step has often been taken for granted, it deserves further attention as large-scale simulations become increasingly routine. In this perspective, we discuss the application of Markov models to the analysis of large-scale biomolecular simulations. We draw attention to recent improvements in the construction of these models as well as several important open issues. In addition, we highlight recent theoretical advances that pave the way for a new generation of models of molecular kinetics.
description: 7 pages
Novel magnetic orderings in the kagome Kondo-lattice model
Creators: name: Barros, Kipton
name: Venderbos, Jörn W. F.
name: Chern, Gia-Wei
name: Batista, C. D.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We consider the Kondo-lattice model on the kagome lattice and study its weak-coupling instabilities at band filling fractions for which the Fermi surface has singularities. These singularites include Dirac points, quadratic Fermi points in contact with a flat band, and Van Hove saddle points. By combining a controlled analytical approach with large-scale numerical simulations, we demonstrate that the weak-coupling instabilities of the Kondo-lattice model lead to exotic magnetic orderings. In particular, some of these magnetic orderings produce a spontaneous quantum anomalous Hall state.
description: 15 pages, 11 figures
Long-Range Response to Transmission Line Disturbances in DC Electricity Grids
Creators: name: Labavić, Darka
name: Suciu, Raluca
name: Meyer-Ortmanns, Hildegard
name: Kettemann, Stefan
Publisher: name: arXiv
Year: 2014
Subjects: subject: Adaptation and Self-Organizing Systems (nlin.AO)
subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We consider a DC electricity grid composed of transmission lines connecting power generators and consumers at its nodes. The DC grid is described by nonlinear equations derived from Kirchhoff's law. For an initial distribution of consumed and generated power, and given transmission line conductances, we determine the geographical distribution of voltages at the nodes. Adjusting the generated power for the Joule heating losses, we then calculate the electrical power flow through the transmission lines. Next, we study the response of the grid to an additional transmission line between two sites of the grid and calculate the resulting change in the power flow distribution. This change is found to decay slowly in space, with a power of the distance from the additional line. We find the geographical distribution of the power transmission, when a link is added. With a finite probability the maximal load in the grid becomes larger when a transmission line is added, a phenomenon that is known as Braess' paradox. We find that this phenomenon is more pronounced in a DC grid described by the nonlinear equations derived from Kirchhoff's law than in a linearised flow model studied previously in Ref. \cite{witthaut2013}. We observe furthermore that the increase in the load of the transmission lines due to an added line is of the same order of magnitude as Joule heating. Interestingly, for a fixed system size the load of the lines increases with the degree of disorder in the geographical distribution of consumers and producers.
description: 10 pages, 13 figures
Dissecting Molecular Steps in Chromatin Domain Activation during Hematopoietic Differentiation
Creators: name: Bresnick, E. H.
name: Bultman, S. J.
name: Kim, S.-I.
name: Blobel, G. A.
name: Jing, H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: GATA factors orchestrate hematopoiesis via multistep transcriptional mechanisms, but the interrelationships and importance of individual steps are poorly understood. Using complementation analysis with GATA-1-null cells and mice containing a hypomorphic allele of the chromatin remodeler BRG1, we dissected the pathway from GATA-1 binding to cofactor recruitment, chromatin loop formation, and transcriptional activation. Analysis of GATA-1-mediated activation of the β-globin locus, in which GATA-1 assembles dispersed complexes at the promoters and the distal locus control region (LCR), revealed molecular intermediates, including GATA-1-independent and GATA-1-containing LCR subcomplexes, both defective in promoting loop formation. An additional intermediate consisted of an apparently normal LCR complex and a promoter complex with reduced levels of total RNA polymerase II (Pol II) and Pol II phosphorylated at serine 5 of the carboxy-terminal domain. Reduced BRG1 activity solely compromised Pol II and serine 5-phosphorylated Pol II occupancy at the promoter, phenocopying the LCR-deleted mouse. These studies defined a hierarchical order of GATA-1-triggered events at a complex locus and establish a novel mechanism of long-range gene regulation.
From young to old: the evolutionary path of Pulsar Wind Nebulae
Creators: name: Olmi, Barbara
name: Bucciantini, Niccolò
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Pulsar wind nebulae are fascinating systems, and archetypal sources for high-energy astrophysics in general. Due to their vicinity, brightness, to the fact that they shine at multi-wavelengths, and especially to their long-living emission at gamma-rays, modelling their properties is particularly important for the correct interpretation of the visible Galaxy. A complication in this respect is the variety of properties and morphologies they show at different ages. Here we discuss the differences among the evolutionary phases of pulsar wind nebulae, how they have been modeled in the past and what progresses have been recently made. We approach the discussion from a phenomenological, theoretical (especially numerical) and observational point of view, with particular attention to the most recent results and open questions about the physics of such intriguing sources.
description: 29 pages, 12 figures, 2 tables
Geranylgeranyltransferase I Inhibitors Target RalB To Inhibit Anchorage-Dependent Growth and Induce Apoptosis and RalA To Inhibit Anchorage-Independent Growth
Creators: name: Cox, A. D.
name: Der, C. J.
name: Falsetti, S. C.
name: Peng, H.
name: Carrico, D.
name: Wang, D.-a.
name: Sebti, S. M.
name: Hamilton, A. D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: Geranylgeranyltransferase I inhibitors (GGTIs) are presently undergoing advanced preclinical studies and have been shown to disrupt oncogenic and tumor survival pathways, to inhibit anchorage-dependent and -independent growth, and to induce apoptosis. However, the geranylgeranylated proteins that are targeted by GGTIs to induce these effects are not known. Here we provide evidence that the Ras-like small GTPases RalA and RalB are exclusively geranylgeranylated and that inhibition of their geranylgeranylation mediates, at least in part, the effects of GGTIs on anchorage-dependent and -independent growth and tumor apoptosis. To this end, we have created the corresponding carboxyl-terminal mutants that are exclusively farnesylated and verified that they retain the subcellular localization and signaling activities of the wild-type geranylgeranylated proteins and that Ral GTPases do not undergo alternative prenylation in response to GGTI treatment. By expressing farnesylated, GGTI-resistant RalA and RalB in Cos7 cells and human pancreatic MiaPaCa2 cancer cells followed by GGTI-2417 treatment, we demonstrated that farnesylated RalB, but not RalA, confers resistance to the proapoptotic and anti-anchorage-dependent growth effects of GGTI-2417. Conversely, farnesylated RalA but not RalB expression renders MiaPaCa2 cells less sensitive to inhibition of anchorage-independent growth. Furthermore, farnesylated RalB, but not RalA, inhibits the ability of GGTI-2417 to suppress survivin and induce p27Kip1 protein levels. We conclude that RalA and RalB are important, functionally distinct targets for GGTI-mediated tumor apoptosis and growth inhibition.
Child nutrition updates 2016 to 2022: A Scoping review protocol.
Creators: name: Montiel, Diana
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Other Medicine and Health Sciences
subject: Human and Clinical Nutrition
subject: Nutrition
subject: Nutritional Epidemiology
subject: Life Sciences
subject: International and Community Nutrition
subject: Medicine and Health Sciences
subject: adolescent
subject: child
subject: nutrition

description: Scoping review on nutrition in healthy children and adolescents
The effect of temperature on egg development in the Australian Mayfly Genus Coloburiscoides (Ephemeroptera: Coloburiscidae) and its relationship to distribution and life history
Creators: name: Brittain, John E
name: Campbell, Ian C
Publisher: name: La Trobe
Year: 2023

description: Murray-Darling Freshwater Research Centre

MDFRC item.

The eggs of Coloburiscoides sp. (near haleuticus) were incubated in the laboratory at constant temperatures in 5-degrees-C intervals between 5-degrees-C and 30-degrees-C. There was a significant relationship between water temperature (T-degrees-C) and the length of the egg incubation period (Y days), expressed by the logarithmic equation: Y = 2217T-1.61 (r2 = 0.996, P < 0.01).Hatching success was high (> 80%) at temperatures between 10-degrees-C and 25-degrees-C. No eggs hatched either at 5-degrees-C or 30-degrees-C. The number of degree-days necessary for egg development decreased with increasing temperature. Eggs artificially fertilized in the laboratory had low (< 10%) hatching success.These results suggest that Coloburiscoides is warm adapted rather than cold adapted as previously thought, and suggest that its absence from Tasmania may be due to extinction during a recent glacial period. The low sychrony of life histories of Australian aquatic insects in lower altitude streams may be a response to higher temperatures rather than to hydrological variability.
The Webster scalar curvature flow on CR sphere. Part I
Creators: name: Ho, Pak Tung
Publisher: name: arXiv
Year: 2014
Subjects: subject: Differential Geometry (math.DG)
subject: Analysis of PDEs (math.AP)
subject: Complex Variables (math.CV)
subject: FOS: Mathematics

description: This is the first of two papers, in which we prove some properties of the Webster scalar curvature flow. More precisely, we establish the long-time existence, L^p convergence and the blow-up analysis for the solution of the flow. As a by-product, we prove the convergence of the CR Yamabe flow on the CR sphere. The results in this paper will be used to prove a result of prescribing Webster scalar curvature on the CR sphere, which is the main result of the second paper.
description: To appear in Advances in Mathematics
Interferon Regulatory Factor 7 Is Activated by a Viral Oncoprotein through RIP-Dependent Ubiquitination
Creators: name: Huye, L. E.
name: Kelliher, M.
name: Ning, S.
name: Pagano, J. S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: As a key mediator of type I interferon (IFN) (IFN-α/β) responses, IFN regulatory factor 7 (IRF7) is essential to host immune defenses. Activation of IRF7 generally requires virus-induced C-terminal phosphorylation, which leads to its nuclear accumulation and activation of target genes. Here we use the Epstein-Barr virus (EBV) oncoprotein LMP1, which activates IRF7, to identify factors involved in IRF7 activation. We demonstrate for the first time that RIP activates IRF7 and that RIP and IRF7 interact under physiological conditions in EBV-positive Burkitt's lymphoma cells. We provide evidence that both RIP and IRF7 are ubiquitinated in these cells and that IRF7 preferentially interacts with ubiquitinated RIP. RIP is required for full activation of IRF7 by LMP1, with LMP1 stimulating the ubiquitination of RIP and its interaction with IRF7. Moreover, LMP1 stimulates RIP-dependent K63-linked ubiquitination of IRF7, which regulates protein function rather than proteasomal degradation of proteins. We suggest that RIP may serve as a general activator of IRF7, responding to and transmitting the signals from various stimuli, and that ubiquitination may be a general mechanism for enhancing the activity of IRF7.
A PBPO+ Graph Rewriting Tutorial
Creators: name: Overbeek, Roy
name: Endrullis, Jörg
Publisher: name: arXiv
Year: 2023
Subjects: subject: Logic in Computer Science (cs.LO)
subject: FOS: Computer and information sciences

description: We provide a tutorial introduction to the algebraic graph rewriting formalism PBPO+. We show how PBPO+ can be obtained by composing a few simple building blocks, and model the reduction rules for binary decision diagrams as an example. Along the way, we comment on how alternative design decisions lead to related formalisms in the literature, such as DPO. We close with a detailed comparison with Bauderon's double pullback approach.
description: In Proceedings TERMGRAPH 2022, arXiv:2303.14219
Noncanonical Function of MEKK2 and MEK5 PB1 Domains for Coordinated Extracellular Signal-Regulated Kinase 5 and c-Jun N-Terminal Kinase Signaling
Creators: name: Johnson, G. L.
name: Nakamura, K.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: MEKK2 and MEK5 encode Phox/Bem1p (PB1) domains that heterodimerize with one another. MEKK2, MEK5, and extracellular signal-related kinase 5 (ERK5) form a ternary complex through interactions involving the MEKK2 and MEK5 PB1 domains and a 34-amino-acid C-terminal extension of the MEK5 PB1 domain. This C-terminal extension encodes an ERK5 docking site required for MEK5 activation of ERK5. The PB1 domains bind in a front-to-back arrangement, with a cluster of basic amino acids in the front of the MEKK2 PB1 domain binding to the back-end acidic clusters of the MEK5 PB1 domain. The C-terminal moiety, including the acidic cluster of the MEKK2 PB1 domain, is not required for MEK5 binding and binds MKK7. Quiescent MEKK2 preferentially binds MEK5, and MEKK2 activation results in ERK5 activation. Activated MEKK2 binds and activates MKK7, leading to JNK activation. The findings define how the MEKK2 and MEK5 PB1 domains are uniquely used for differential binding of two mitogen-activated protein kinase kinases, MEK5 and MKK7, for the coordinated control of ERK5 and c-Jun N-terminal kinase activation.
(:unas) unassigned
Creators: name: (:Unkn) Unknown
Publisher: name: Universita' degli Studi di Salerno
Year: 2024

description: La «pandemia abitativa» da cui i firmatari del Manifesto Breve del Realismo Terminale mettono profeticamente in guardia è quella di uno scenario apocalittico e post-umano il cui virus produce una perdita d’identità che è ormai insita alla condizione antropica dell’uomo contemporaneo, inglobato/assimilato nell’organismo immateriale che ha preso il sopravvento sulla natura. Joseph Tusiani, il poeta dei due mondi e delle quattro lingue, si mostra costantemente alla ricerca di un sofferto punto di equilibrio nella coscienza – lacerata e mai pacifica – fra le sue radici pugliesi e l’americanizzazione. Anziano e debilitato da un ictus, il poeta fonde queste due anime negli ultimi versi newyorkesi, composti in italiano e in inglese fra il 2014 e il 2019 e pubblicati postumi nella raccolta Poesie per un anno. Fortemente disposto a riappropriarsi dell’esistenza, appigliato alla vita in modo perfino esasperato, Tusiani finisce per essere «oggetto fra gli oggetti» (Pegorari, 2020) imprigionato nel circuito della sua camera, in un grattacielo di Manhattan, parla col suo girello e vagheggia dalla finestra il ricordo del suo Gargano.
description: The «housing pandemic» against which the signatories of the Short Manifest of Terminal Realism prophetically warn is that of an apocalyptic and post-human scenario whose virus produces a loss of identity which is now inherent to the anthropic condition of contemporary man, incorporated/assimilated into the immaterial organism that has taken over nature. Joseph Tusiani, the poet of two worlds and four languages, appears to be constantly searching for a painful point of balance in his conscience – torn and never peaceful – between his Apulian roots and Americanisation. Elderly and debilitated by a stroke, the poet merges these two souls in his last New York verses, composed in Italian and English between 2014 and 2019 and published posthumously in the collection Poesie per un anno. Strongly willing to regain possession of existence, clinging to life in an even exasperated way, Tusiani ends up being «an object among objects» (Pegorari, 2020) imprisoned in the circuit of his room, in a Manhattan skyscraper, he talks with his walker and longs for from the window the memory of his Gargano.
Comparative Study of MAC Layer Protocols in Wireless Sensor Networks: A Survey
Creators: name: Lanjewar, Rahul R
name: Adane, D S
Publisher: name: arXiv
Year: 2014
Subjects: subject: Networking and Internet Architecture (cs.NI)
subject: FOS: Computer and information sciences

description: Wireless Sensor Networks (WSN) is the collection of many small size low cost, battery operated sensor nodes distributed over the targeted region to collect the information of interest. We can say these networks can be a fruitful solution for many applications such as target tracking, intrusion detection etc. Whenever we are talking about MAC layer protocols we need to give stress on energy efficiency factor.
description: 7 pages, 7 figures, "Published with International Journal of Engineering Trends and Technology (IJETT)"
p18Ink4c, but Not p27Kip1, Collaborates with Men1 To Suppress Neuroendocrine Organ Tumors
Creators: name: Nishikawa, T.
name: Bai, F.
name: Xiong, Y.
name: Smith, M. D.
name: Pei, X.-H.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: Mutant mice lacking both cyclin-dependent kinase (CDK) inhibitors p18Ink4c and p27Kip1 develop a tumor spectrum reminiscent of human multiple endocrine neoplasia (MEN) syndromes. To determine how p18 and p27 genetically interact with Men1, the tumor suppressor gene mutated in familial MEN1, we characterized p18-Men1 and p27-Men1 double mutant mice. Compared with their corresponding single mutant littermates, the p18−/−; Men1+/− mice develop tumors at an accelerated rate and with an increased incidence in the pituitary, thyroid, parathyroid, and pancreas. In the pituitary and pancreatic islets, phosphorylation of the retinoblastoma (Rb) protein at both CDK2 and CDK4/6 sites was increased in p18−/− and Men1+/− cells and was further increased in p18−/−; Men1+/− cells. The remaining wild-type Men1 allele was lost in most tumors from Men1+/− mice but was retained in most tumors from p18−/−; Men1+/− mice. Combined mutations of p27−/− and Men1+/−, in contrast, did not exhibit noticeable synergistic stimulation of Rb kinase activity, cell proliferation, and tumor growth. These results demonstrate that functional collaboration exists between p18 and Men1 and suggest that menin may regulate additional factor(s) that interact with p18 and p27 differently.
Regulation of Neuron Survival through an Intersectin-Phosphoinositide 3'-Kinase C2 -AKT Pathway
Creators: name: Martin, N. P.
name: Scappini, E.
name: Domin, J.
name: Chen, Y.-J.
name: Dunn, S.
name: O'Bryan, J. P.
name: Miller, S. L. H.
name: Das, M.
name: Wong, K. A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: While endocytosis attenuates signals from plasma membrane receptors, recent studies suggest that endocytosis also serves as a platform for the compartmentalized activation of cellular signaling pathways. Intersectin (ITSN) is a multidomain scaffolding protein that regulates endocytosis and has the potential to regulate various biochemical pathways through its multiple, modular domains. To address the biological importance of ITSN in regulating cellular signaling pathways versus in endocytosis, we have stably silenced ITSN expression in neuronal cells by using short hairpin RNAs. Decreasing ITSN expression dramatically increased apoptosis in both neuroblastoma cells and primary cortical neurons. Surprisingly, the loss of ITSN did not lead to major defects in the endocytic pathway. Yeast two-hybrid analysis identified class II phosphoinositide 3′-kinase C2β (PI3K-C2β) as an ITSN binding protein, suggesting that ITSN may regulate a PI3K-C2β-AKT survival pathway. ITSN associated with PI3K-C2β on a subset of endomembrane vesicles and enhanced both basal and growth factor-stimulated PI3K-C2β activity, resulting in AKT activation. The use of pharmacological inhibitors, dominant negatives, and rescue experiments revealed that PI3K-C2β and AKT were epistatic to ITSN. This study represents the first demonstration that ITSN, independent of its role in endocytosis, regulates a critical cellular signaling pathway necessary for cell survival.
The Webster scalar curvature flow on CR sphere. Part II
Creators: name: Ho, Pak Tung
Publisher: name: arXiv
Year: 2014
Subjects: subject: Differential Geometry (math.DG)
subject: Analysis of PDEs (math.AP)
subject: Complex Variables (math.CV)
subject: FOS: Mathematics

description: This is the second of two papers, in which we study the problem of prescribing Webster scalar curvature on the CR sphere as a given function f. Using the Webster scalar curvature flow, we prove an existence result under suitable assumptions on the Morse indices of f.
description: To appear in Advances in Mathematics
Co-requisite support for STEM-bound students at a Texas community college
Creators: name: Flores, Kristina Joanne Penfold
name: 0000-0003-4086-9897
Publisher: name: The University of Texas at Austin
Year: 2022
Subjects: Co-requisite support
Community colleges
Developmental mathematics
Developmental education
STEM

description: This dissertation examines the co-requisite support structure for entry-level mathematics as applied to STEM-bound students, those students who have declared a STEM major but have been deemed underprepared for entry-level mathematics by Texas Success Initiative standards. Using data from a very large community college in Texas, the first study found STEM-bound students differed from STEM students (students who passed Calculus with a C or better) with prior developmental mathematics (DM) by race/ethnicity, sex, and socioeconomic status, suggesting systems and mechanisms in place to reach Calculus served to reduce the diversity present among STEM-bound students. The study also found that STEM students with prior DM navigated 13 different course sequences within four main sequences before successfully completing Calculus. DM grade point averages were significantly different between the main sequences. The second study utilized propensity score matching to compare: (1) a control group of STEM-bound students enrolled in Elementary Algebra to a treatment group of STEM-bound students enrolled in co-requisite College Algebra (CA) and (2) a control group of students enrolled in Intermediate Algebra to a treatment group of STEM-bound students enrolled in co-requisite CA. After matching, enrolling in co-requisite CA was associated with higher odds of completing DM, earning CA credit, and persisting along the path to Calculus compared to enrolling in Elementary Algebra. There was no statistically significant difference in outcomes for students enrolled in co-requisite CA compared to Intermediate Algebra. The last study utilized generalized hierarchical linear modeling to examine the impact of co-requisite CA course design on student outcomes. The model examined two different course designs: (1) a redesigned CA course with just-in-time (JIT) remediation and (2) a traditional CA course with an emporium lab. The study found that the JIT model increased the likelihood that STEM-bound students completed DM requirements, earned CA credit, and persisted along the path to Calculus, compared to the emporium model, controlling for Level-1 and Level-2 covariates. These findings have practical implications for practice as colleges across Texas are scaling up the use of co-requisite support for STEM-bound students. The studies also create a framework for additional research into this emerging DM intervention.
Novel approaches to conservation biogeography across public and private lands
Creators: name: LeVine, Daniel Stephen
name: 0000-0001-5161-473X
Publisher: name: The University of Texas at Austin
Year: 2022
Subjects: Conservation biogeography
Landscape ecology

description: Extensive land use change and global climate change present major threats to native ecosystems due to shifts in species ranges and the alteration of species assemblages through non-native species introductions. The conservation of these landscapes and associated biodiversity is pertinent and requires comprehensive biogeographic and ecological analyses that identify past, present, and future patterns of species distributions and ecosystem function. With an ever-increasing amount of spatial data related to species occurrences available through online citizen science platforms, the number and types of questions that can be answered related to conservation biogeography are rapidly expanding. However, spatial and taxonomic biases are known to exist in these datasets and the implementation of such data requires proper consideration. The application of these opportunistic datasets to conservation planning is further complicated by issues of access in settings with public/private land divides. The conceptual approach taken for this dissertation pulls from multiple subfields of environmental geography in order to adequately encapsulate the challenges inherent to local and regional scale conservation research and implementation. The assessment of a public/private landscape in the Texas Hill Country via satellite imagery and in situ vegetation surveys provides an example of spatially- and temporally- dynamic landscape assessment in a heterogeneous land tenure setting. The included spatial analyses of citizen science data investigate socioeconomic and demographic patterns in opportunistic species datasets and inform approaches to accounting for inherent spatial and taxonomic gaps in these data using the monarch butterfly (Danaus plexxipus) as a baseline species of analysis. Lastly, these studies are bridged together by an investigation of novel landscapes in Texas’ Blackland Prairies and the influence of exotic game ranching across Texas with discussion of the impacts of novel species assemblages and habitat fragmentation. The collected discussions and conclusions in this dissertation support recommendations for land managers and landowners and provide insight for conservation biogeographers working across spatially- and temporally- heterogeneous land tenure settings.
Self-assembled Zeeman slower based on spherical permanent magnets
Creators: name: Lebedev, V.
name: Weld, D. M.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: We present a novel type of longitudinal Zeeman slower. The magnetic field profile is generated by a 3D array of permanent spherical magnets, which are self-assembled into a stable structure. The simplicity and stability of the design make it quick to assemble and inexpensive. In addition, as with other permanent magnet slowers, no electrical current or water cooling is required. We describe the theory, assembly, and testing of this new design.
The Hubble/STIS Near-ultraviolet Transmission Spectrum of HD 189733b
Creators: name: Cubillos, Patricio E.
name: Fossati, Luca
name: Koskinen, Tommi
name: Huang, Chenliang
name: Sreejith, A. G.
name: France, Kevin
name: Cauley, P. Wilson
name: Haswell, Carole A.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: The benchmark hot Jupiter HD 189733b has been a key target to lay out the foundations of comparative planetology for giant exoplanets. As such, HD 189733b has been extensively studied across the electromagnetic spectrum. Here, we report the observation and analysis of three transit light curves of HD 189733b obtained with {\Hubble}/STIS in the near ultraviolet, the last remaining unexplored spectral window to be probed with present-day instrumentation for this planet. The NUV is a unique window for atmospheric mass-loss studies owing to the strong resonance lines and large photospheric flux. Overall, from a low-resolution analysis ($R=50$) we found that the planet's near-ultraviolet spectrum is well characterized by a relatively flat baseline, consistent with the optical-infrared transmission, plus two regions at $\sim$2350 and $\sim$2600 Å that exhibit a broad and significant excess absorption above the continuum. From an analysis at a higher resolution ($R=4700$), we found that the transit depths at the core of the magnesium resonance lines are consistent with the surrounding continuum. We discarded the presence of \ion{Mg}{ii} absorption in the upper atmosphere at a $\sim$2--4$σ$ confidence level, whereas we could place no significant constraint for \ion{Mg}{i} absorption. These broad absorption features coincide with the expected location of \ion{Fe}{ii} bands; however, solar-abundance hydrodynamic models of the upper atmosphere are not able to reproduce the amplitude of these features with iron absorption. Such scenario would require a combination of little to no iron condensation in the lower-atmosphere, super-solar metallicities, and a mechanism to enhance the absorption features (such as zonal wind broadening). The true nature of this feature remains to be confirmed.
description: Accepted for publication at Astronomy and Astrophysics
Transient pressure gradients in the lacunar system of the submerged macrophyte Egeria densa Planch
Creators: name: Sorrell, B. K
Publisher: name: La Trobe
Year: 2023

description: Murray-Darling Freshwater Research Centre

MDFRC item.

Pressure gradients in the lacunar system of Egeria densa Planch. were measured by attaching constant-volume manometers to cut surfaces of the shoot system. Upon illumination, the total pressure of the lacunar gas increased up to 30 kPa above the initial pressure, due to the increase in the internal oxygen pressure in the lacunae. The rate of pressurisation was not constant throughout the lacunar system because the more active regions of the shoots pressurised more rapidly than older shoot portions with lower chlorophyll contents. It can be proven mathematically that the resulting pressure gradients (approximately 2 kPa) within shoots during the pressurisation phase could not generate a flow-through ventilation of the type found in some emergent macrophytes, but that a small gas displacement down the stem would occur. The total pressure reached its maximum within 1 h of illumination; at this time, the pressure had equilibrated throughout the shoot lacunae and mass flow was completed. Such pressure gradients are, therefore, of little importance to steady-state aeration, but may relate to the need to rapidly establish a constant partial pressure gradient within a plant with long non-photosynthetic stems.
Interaction of solar jets with filaments: Triggering of large-amplitude filament oscillations
Creators: name: Joshi, Reetika
name: Luna, Manuel
name: Schmieder, Brigitte
name: Moreno-Insertis, Fernando
name: Chandra, Ramesh
Publisher: name: arXiv
Year: 2023
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Large-amplitude oscillations (LAOs) are often detected in filaments. Using multiwavelength observations, their origin can be traced back to the interaction with eruptions and jets. We present two different case studies as observational evidence in support of 2.5D MHD numerical experiments that show that the LAOs in the filament channels can be initiated by solar jets. In the two studied events, we can identify a quadrupolar configuration with an X-point at the top of the parasitic region suggestive of a classical null-point. A reconnection flow emanates from this structure leading to a jet that propagates along the filament channel. In both cases we can identify the quiescent and eruptive phases of the jet. The triggered LAOs have periods of around 70-80 minutes and are damped after a few oscillations. The minimum magnetic field intensity inferred with seismology for the filament turns out to be around 30 Gauss. We conclude that the two case studies are consistent with the recent numerical model of Luna and Moreno-Insertis (2021), in which the LAOs are initiated by jets. The relationship between the onset of the jet and filament oscillations is straight-forward for the first case and less for the second case. In the second event, although there is some evidence, we cannot rule out other possibilities such as activity unrelated to the null-point or changes in the magnetic structure of the filament. Both jets are associated with very weak flares which did not launch any EUV wave. Therefore the role of EUV waves for triggering the filament oscillations can be eliminated for these two case.
description: 12 pages, 13 figures, Accepted for publication in Astronomy & Astrophysics
Weed community composition and rice husbandry practices in New South Wales, Australia
Creators: name: McIntyre, S
name: Finlayson, C. M
name: Ladiges, P. Y
name: Mitchell, D. S
Publisher: name: La Trobe
Year: 2023

description: Murray-Darling Freshwater Research Centre

MDFRC item.

The composition of weed communities in rice fields is described in relation to crop husbandry and soil factors in New South Wales. Four species characterized the weed community: Cyperus difformis, Elatine gratioloides, Damasonium minus and Echinochloa crus-galli all occurred at over 70% of sites. Variation in floristic composition was mainly associated with less common species that were present in addition to these four. Intensity of rice cropping appeared to be a major environmental factor influencing community composition. The four character species, together with Diplachne fusca and Chara were positively correlated with intensive rice production. Two groups of plants were found to be associated with less intensive production. A group of semi-aquatic and terrestrial pasture species commonly occurred after sod sowing (direct drilling) of rice and/or pasture rotation. The second group comprised native wetland species which were mainly associated with sites in which rice cropping was more recent and less intensive. The data suggest that the weed communities are not in equilibrium with the comparatively recent practice of rice farming in the region. Continuation or intensification of rice cropping in the study area may reduce the incidence of wetland species and favour the character and pasture species. The range of husbandry practices available to rice growers and their flexible application could also contribute to the maintenance of disequilibrium between the weed populations and their environment, thus preventing the build-up of some species.
Towards versatile, high-performing and interactive humanoids
Creators: name: Ahn, Junhyeok
name: 0000-0002-7934-6543
Publisher: name: The University of Texas at Austin
Year: 2022
Subjects: Humanoid
Control
Planning
Machine learning
Optimization

description: While studies on humanoid robots have matured in recent years, deploying a practical and versatile humanoid in real life remains a challenge. This challenge comes from the multidisciplinary nature of the field; indeed, elaborate actuation technologies, robust whole-body planning and control frameworks, and intelligent high-level decision-making policies are all necessary for a versatile and high-performing humanoid. To this end, this dissertation presents my research to bring these technologies to the next level and achieve intelligent and practical humanoids. First, I studied an actuation technology that is designed for energy efficiency, torque density, impact resistance, joint position, and force controllability. I implemented a disturbance observer-based force controller to achieve a wide range of impedance behaviors. I performed experiments on mechanical robustness by studying the response of the actuator to external impacts. I further evaluated the performance of the actuation technology by testing a variety of robotics platforms such as a single-leg testbed and a DRACO biped. Second, I investigated versatile planning and control solutions to various problem setups for humanoids. For long-horizon locomotion planning problems such as maze navigation, I proposed a sampling-based kinodynamic planning framework by combining an inverted pendulum model and rapidly-exploring random tree. For the problems that require a more descriptive yet still computationally efficient model and decisions on how to interact with the environment in addition to motion trajectories, I formulated a trajectory optimization framework based on a phase-based parameterization and a learned centroidal model. For a reactive footstep planning problem, I incorporated hierarchical reinforcement learning into a model-based footstep planner to improve robustness. Lastly, I studied the machine learning of system dynamics and safety that can be utilized for humanoid planning and control. In particular, I studied a neural network structure that can represent and learn hybrid systems efficiently using a mixture of experts. I demonstrated that this network structure can optimize the bias-variance problem in dynamical system representation and enable data-efficient learning of dynamics. For safety learning, I proposed a probabilistic verification framework that verifies the safety of planned trajectories by learning an assessment function from trajectories collected from a closed-loop system.
The NuSTAR view of the changing look AGN ESO 323-G77
Creators: name: Serafinelli, Roberto
name: Braito, Valentina
name: Reeves, James N.
name: Severgnini, Paola
name: De Rosa, Alessandra
name: Della Ceca, Roberto
name: Turner, Tracey Jane
Publisher: name: arXiv
Year: 2023
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: The presence of an obscuring torus at pc-scale distances from the central black hole is the main ingredient for the Unified Model of Active Galactic Nuclei (AGN), as obscured sources are thought to be seen through this structure. However, the Unified Model fails to describe a class of sources that undergo dramatic spectral changes, transitioning from obscured to unobscured and vice-versa through time. The variability in such sources, so-called Changing Look AGN (CLAGN), is thought to be produced by a clumpy medium at much smaller distances than the conventional obscuring torus. ESO 323-G77 is a CLAGN that was observed in various states through the years with Chandra, Suzaku, Swift-XRT and XMM-Newton, from unobscured ($N_{\rm H}<3\times10^{22}$ cm$^{-2}$) to Compton-thin ($N_{\rm H}\sim1-6\times10^{23}$ cm$^{-2}$) and even Compton-thick ($N_{\rm H}>1\times10^{24}$ cm$^{-2}$), with timescales as short as one month. We present the analysis of the first NuSTAR monitoring of ESO 323-G77, consisting of 5 observations taken at different timescales (1, 2, 4 and 8 weeks from the first one) in 2016-2017, in which the AGN was caught in a persistent Compton-thin obscured state ($N_{\rm H}\sim2-4\times10^{23}$ cm$^{-2}$). We find that a Compton-thick reflector is present ($N_{\rm H,refl}=5\times10^{24}$ cm$^{-2}$), most likely associated with the presence of the putative torus. Two ionized absorbers are unequivocally present, located within maximum radii of $r_{\rm max,1}=1.5$ pc and $r_{\rm max,2}=0.01$ pc. In one of the observations, the inner ionized absorber is blueshifted, indicating the presence of a possible faster ($v_{\rm out}=0.2c$) ionized absorber, marginally detected at $3σ$. Finally, we are able to constrain the coronal temperature and the optical depth of ESO 323-G77, obtaining $kT_e=38$ keV or $kT_e=36$ keV, and $τ=1.4$ or $τ=2.8$, depending on the coronal geometry assumed.
description: 10 pages, 7 figures, 3 tables. Accepted for publication in Astronomy & Astrophysics
The Human Tim/Tipin Complex Coordinates an Intra-S Checkpoint Response to UV That Slows Replication Fork Displacement
Creators: name: Chastain, P. D.
name: Unsal-Kacmaz, K.
name: Minoo, P.
name: Kaufmann, W. K.
name: Sancar, A.
name: Qu, P.-P.
name: Cordeiro-Stone, M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: UV-induced DNA damage stalls DNA replication forks and activates the intra-S checkpoint to inhibit replicon initiation. In response to stalled replication forks, ATR phosphorylates and activates the transducer kinase Chk1 through interactions with the mediator proteins TopBP1, Claspin, and Timeless (Tim). Murine Tim recently was shown to form a complex with Tim-interacting protein (Tipin), and a similar complex was shown to exist in human cells. Knockdown of Tipin using small interfering RNA reduced the expression of Tim and reversed the intra-S checkpoint response to UVC. Tipin interacted with replication protein A (RPA) and RPA-coated DNA, and RPA promoted the loading of Tipin onto RPA-free DNA. Immunofluorescence analysis of spread DNA fibers showed that treating HeLa cells with 2.5 J/m2 UVC not only inhibited the initiation of new replicons but also reduced the rate of chain elongation at active replication forks. The depletion of Tim and Tipin reversed the UV-induced inhibition of replicon initiation but affected the rate of DNA synthesis at replication forks in different ways. In undamaged cells depleted of Tim, the apparent rate of replication fork progression was 52% of the control. In contrast, Tipin depletion had little or no effect on fork progression in unirradiated cells but significantly attenuated the UV-induced inhibition of DNA chain elongation. Together, these findings indicate that the Tim-Tipin complex mediates the UV-induced intra-S checkpoint, Tim is needed to maintain DNA replication fork movement in the absence of damage, Tipin interacts with RPA on DNA and, in UV-damaged cells, Tipin slows DNA chain elongation in active replicons.