cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Intergenerational Transmission of Chronic Pain: A Narrative Analysis of Story(telling) of Pain Journeys as Social Learning Between Parents and Youth
Creators: name: Lund, Tatiana C.
Publisher: name: Graduate Studies
Year: 2021
Subjects: subject: headache
subject: narrative
subject: social learning
subject: intergenerational transmission
subject: chronic pain
subject: Psychology
subject: FOS: Psychology
subject: Clinical

description: Background. Chronic headache is highly prevalent and persistent from childhood into adulthood and has a strong intergenerational component. The intergenerational transmission of chronic pain conceptual model posits that parental social learning factors may exert a powerful influence on children who also have chronic pain. (Story)telling occurs intergenerationally within families and between children and their parents, an avenue of social learning not previous explored. This study examined narratives of parent-child dyads where both members had pain. Method. Twenty-six youth and parents with chronic headaches recruited from a tertiary level pediatric pain clinic separately completed in-depth interviews about children’s pain journey narratives. Narrative analysis incorporated elements of socio-narratology to compare between and within dyads. Results. Five narrative types were generated: 1) Mistreated by the Medical System- neglect, harm and broken promises resulting in learned hopelessness or relying on the family system, 2) Washed Away by the Pain-unable to overcome insurmountable challenges and letting the pain take over, 3) The Invalidated-invalidation of pain permeated youth’s lives, with mothers as empathic buffers, 4) The Trauma Origin Story- parents, but not youth, positing traumatic events as the causal link to children’s pain, and 5) Taking the Power Back from Pain- children’s ability to live life and accomplish goals in spite of pain. Discussion. Findings support the clinical utility of narrative in pediatric pain, including both parents’ and children’s narrative accounts to improve clinical encounters and broader social implications of chronic pain.
Multivalent monoclonal antibodies as improved cancer therapies : proof-of-concept and mechanistic studies using rituximab-lipid nanoparticles
Creators: name: Popov, Jesse
Publisher: name: University of British Columbia
Year: 2012

description: This body of work describes a novel methodology for discovering and developing new cancer drugs based on therapeutic monoclonal antibodies. Such antibodies generally contain two sites where they bind to their target, but interesting improvements are often observed when the valence (number of target-binding sites) is increased above two. The methodology outlined in this dissertation involves using liposomes to prepare multivalent antibody-lipid nanoparticle formulations of different valence that can be utilized for preclinical drug development. As a proof-of-concept, we applied the methodology to rituximab, a therapeutic antibody used to treat lymphomas and leukemias. For the same dose of rituximab, multivalent rituximab-lipid nanoparticles with valences up to ~250 showed significantly elevated anticancer activity from enhanced complement-dependent cytotoxicity, antibody-dependent cell-mediated cytotoxicity, and direct induction of apoptosis. A valence-dependent improvement in apoptosis in lymphoma cells was observed up to levels that were 21-fold higher than those observed after treatment with bivalent rituximab. We subsequently employed the different valences of multivalent rituximab to investigate its poorly defined direct mechanism of action. We uncovered a novel mechanism consisting of upregulation and activation of CD120a which led to ensuing apoptosis. Effector cells of the immune system were capable of hypercrosslinking rituximab on lymphoma cells and reproducing this mechanism, suggesting that it contributes to the in vivo cytotoxicity of regular bivalent rituximab therapy. The methodology described in this dissertation can therefore serve to identify antibodies that are more active as multivalent rather than bivalent molecules, define the optimal valence of such antibodies, and elucidate the mechanism of action of the new multivalent drugs. Furthermore, we illustrate that this information applies to other types of constructs with similar valences, enabling use of the methodology for advancing both liposomal and non-liposomal multivalent antibody formulations to preclinical maturity. Finally, this work suggests that every therapeutic antibody may have a different valence where it shows optimal therapeutic activity. For example, antibodies directed against targets that exert therapeutic effects upon clustering may show maximum activity at valences above two. This methodology can easily be applied to other antibodies in an effort to develop superior therapies against nearly any type of cancer.
Benchmark of a modified Iterated Perturbation Theory approach on the 3d FCC lattice at strong coupling
Creators: name: Arsenault, Louis-Francois
name: Semon, Patrick
name: Tremblay, A. -M. S.
Publisher: name: arXiv
Year: 2012
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The Dynamical Mean-Field theory (DMFT) approach to the Hubbard model requires a method to solve the problem of a quantum impurity in a bath of non-interacting electrons. Iterated Perturbation Theory (IPT) has proven its effectiveness as a solver in many cases of interest. Based on general principles and on comparisons with an essentially exact Continuous-Time Quantum Monte Carlo (CTQMC) solver, here we show that the standard implementation of IPT fails away from half-filling when the interaction strength is much larger than the bandwidth. We propose a slight modification to the IPT algorithm that replaces one of the equations by the requirement that double occupancy calculated with IPT gives the correct value. We call this method IPT-$D$. We recover the Fermi liquid ground state away from half-filling. The Fermi liquid parameters, density of states, chemical potential, energy and specific heat on the FCC lattice are calculated with both IPT-$D$ and CTQMC as benchmark examples. We also calculated the resistivity and the optical conductivity within IPT-$D$. Particle-hole asymmetry persists even at coupling twice the bandwidth. Several algorithms that speed up the calculations are described in appendices.
description: 17 pages, 15 figures, minor changes to improve clarity
Additional file 1 of The relation between synovitis of individual finger joints and grip force over the first 5 years in early rheumatoid arthritis — a cohort study
Creators: name: Rydholm, Maria
name: Sharma, Ankita
name: Jacobsson, Lennart
name: Turesson, Carl
Publisher: name: figshare
Year: 2023
Subjects: subject: Neuroscience
subject: Physiology
subject: FOS: Biological sciences
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Science Policy
subject: Mental Health
subject: Computational Biology

description: Additional file 1: Supplementary Table 1. Relation between involvement of individual MCP and PIP joints and grip force (% of expected). Adjusted for wrist synovitis/tenderness. Supplementary Table 2. Relation between involvement of individual MCP and PIP joints and grip force (% of expected). Unadjusted. Supplementary Table 3. Relation between synovitis of individual MCP and PIP joints and grip force (% of expected), separate for the right and left hand, fully adjusted. Supplementary Table 4. Relation between tenderness of individual MCP and PIP joints and grip force (% of expected), separate for the right and left hand, fully adjusted. Supplementary Table 5. Relation between synovitis of individual MCP and PIP joints and grip force of the right hand or left hand (% of expected) in patients with early RA. Unadjusted. Supplementary Table 6. Relation between synovitis of individual MCP and PIP joints and grip force of the right hand or left hand (% of expected) in patients with early RA. Adjusted for wrist synovitis. Supplementary Table 7. Relation between joint tenderness of individual MCP and PIP joints and grip force of the right hand or left hand (% of expected) in patients with early RA. Unadjusted. Supplementary Table 8. Relation between tenderness of individual MCP and PIP joints and grip force of the right hand or left hand (% of expected) in patients with early RA. Adjusted for wrist tenderness. Supplementary Table 9. RF/anti-CCP positive patients with RA. Relation over time between involvement of individual MCP and PIP joints and grip force. Supplementary Table 10. RF- and anti-CCP negative patients with RA. Relation over time between involvement of individual MCP and PIP joints and grip force.
Increasing the Scope as You Learn: Adaptive Bayesian Optimization in Nested Subspaces
Creators: name: Papenmeier, Leonard
name: Nardi, Luigi
name: Poloczek, Matthias
Publisher: name: arXiv
Year: 2023
Subjects: subject: Machine Learning (cs.LG)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences

description: Recent advances have extended the scope of Bayesian optimization (BO) to expensive-to-evaluate black-box functions with dozens of dimensions, aspiring to unlock impactful applications, for example, in the life sciences, neural architecture search, and robotics. However, a closer examination reveals that the state-of-the-art methods for high-dimensional Bayesian optimization (HDBO) suffer from degrading performance as the number of dimensions increases or even risk failure if certain unverifiable assumptions are not met. This paper proposes BAxUS that leverages a novel family of nested random subspaces to adapt the space it optimizes over to the problem. This ensures high performance while removing the risk of failure, which we assert via theoretical guarantees. A comprehensive evaluation demonstrates that BAxUS achieves better results than the state-of-the-art methods for a broad set of applications.
description: 28 pages, 8 figures. Accepted to NeurIPS 2022. This is the revised version and includes the appendix
Investigation of the Role of Kinase-Associated Protein Phosphatase (KAPP) in Pistil-Pollen Interactions in Brassica napus (canola)
Creators: name: Ribano, Alynne Kris B.
Publisher: name: Graduate Studies
Year: 2021
Subjects: subject: Biology--Botany
subject: Biology--Cell
subject: Biology--Genetics
subject: Biology--Molecular
subject: Chemistry--Biochemistry

description: Climate change and our increasing population threatens the availability of sustainable food sources, creating greater pressure to find solutions. Increasing crop yield can mitigate these problems. Given that seeds are the most important agronomic trait, a key component of this reproductive success is pollination. The pollination pathway, both compatible and self-incompatible (SI), is comprised of complex signalling mechanisms which govern pollen-pistil communications. Even with significant contributions to our understanding of the pollination response through the identification of key players and its signalling mechanism, there remains a gap in our understanding of the SI pathway.Although kinase-associated protein phosphatase (KAPP) can interact in vitro with various receptor kinases, for decades, its specific role in SI remained unknown. In this study, biochemical approaches determined that KAPP was highly expressed in mature stigmas with poor expression in pollen. While compatible pollen did not affect KAPP levels, following SI pollination, KAPP levels were significantly increased. Through transgenic approaches, overexpressing only the phosphatase type 2C (PP2C) domain of KAPP sufficiently reduced pollen acceptance, leading to shorter pods and reduced seed production. These observations indicate that KAPP could be a positive regulator in the incompatibility response where it acts through its PP2C domain.When a PP2C domain mutated in the mitogen-activated protein kinase (MAPK) docking site (KAPP?290M) was overexpressed, a more compatible phenotype relative to PP2C overexpression was observed in the KAPP?290M transgenic lines. However, biochemical analysis revealed that this phenotype was not due to the inability of the KAPP?290M to dephosphorylate MPK4 as the mutated version KAPP?290M was able to effectively dephosphorylate MPK4 in vitro. Confocal imaging of KAPP?290M-RFP expression indicated that, lack of these key MAPK docking residues resulted in localization of KAPP?290M-RFP from the cytosol to the plasma membrane. Collectively, in this study, I have identified KAPP as a positive regulator of SI acting through its PP2C domain and provided evidence for the requirement of the MAPK docking site for precise intracellular localization. Therefore, this study bridges the knowledge gap in SI and provides another protein which can be manipulated to create novel hybrids to improve crop yield.
The Impact of Exercise on Gut Microbiota in a Survivor to Germ-free Mouse Translational Model of Breast Cancer
Creators: name: Sampsell, Kara
Publisher: name: Graduate Studies
Year: 2021
Subjects: subject: Gut Microbiota
subject: Exercise
subject: Prebiotics
subject: Nutrition
subject: Breast Cancer
subject: Biological Sciences

description: Breast cancer is the leading cause of global cancer incidence. Strategies to improve breast cancer treatment and health outcomes in survivors are needed to decrease mortality, mitigate side effects, and prevent recurrence. The gut microbiota is altered in individuals with breast cancer, can be affected by treatments such as chemotherapy, and plays a role in response to cancer treatments. It may be modified by environmental factors such as dietary components and exercise. In the present study, the Alberta Cancer Exercise (ACE) program was investigated as a strategy to favorably modify the gut microbiota of breast cancer survivors who had undergone chemotherapy. In a follow-up germ-free mouse study, the ability of exercise-responsive gut microbiota, alone or with prebiotic fiber supplementation, to alter tumor growth was interrogated using fecal microbiota transfer (FMT). In the cancer survivors, there was a significant enrichment in Dialister, Oscillospiraceae, and Paraprevotella following exercise (p < 0.01). In the germ-free mice, tumor volume trended consistently lower over time in the groups colonized with post-exercise gut microbiota compared to the group colonized with pre-exercise gut microbiota, with statistically significant differences found on day 16 and day 22. Tumor volume was further suppressed with prebiotic fiber supplementation. Gut microbial alpha and beta diversity differed across groups. Beta diversity and differential abundance analyses revealed that both the tumor cell injection and chemotherapy altered the gut microbial community in the mice. A potentially beneficial enhancement of Parasutterella and Lachnospiraceae and depletion of Anaerostipes and Ruminococcus gnavus was identified on day 22 in the group receiving prebiotic. Cytokine analysis of tumor tissue and serum indicated that the influence of the various FMTs resulted in distinct tumor microenvironments. The tumors of mice colonized with exercise-responsive microbiota exhibited lower levels of angiogenic VEGF among other markers, and greater levels of cytokines previously associated with positive Paclitaxel response. This was augmented with prebiotic supplementation. Exercise and prebiotic demonstrated potential to enhance anti-tumor immunity through advantageous gut microbiota modulation in breast cancer populations and should be further explored as adjuvants.
A Tender Revolution: An Exploration of Multiple Marginalization and Identity
Creators: name: Suehn, Megan R.
Publisher: name: Graduate Studies
Year: 2021
Subjects: subject: social justice
subject: intersectionality
subject: multiple marginalization
subject: intersectional marginalization
subject: intersectional invisibility
subject: feminist standpoint theory
subject: interpretative phenomenological analysis
subject: counselling psychology
subject: Canada
subject: reflexivity
subject: Education--Educational Psychology
subject: Health Sciences--Mental Health
subject: Psychology
subject: FOS: Psychology
subject: Social Sciences

description: Feminist standpoint theory (FST) centres the object of psychological research inquiry upon the systemic power relations that enact discrimination, violence, and inequality. By continuing to enrich Canadian counselling psychologists’ understandings of these relations of sociocultural power, researchers and clinicians alike can better appreciate and respond to the ways that they produce unique experiences of stress, especially for people who hold multiple marginalized identities. In this dissertation, multiple-marginalization (MM) refers to the interlocking nature of systemic power relations that lead to structural and person-to-person behavioral manifestations of bias against a particular group; for example, oppression. Since the 1950s, identity development has been a prominent area of research in psychology, leading to the development of numerous conceptual models in response to differing perspectives and advancements in civil rights movements. Although at times an uneasy partnership, this combination of on-the-ground and academic work has served to mutually influence wider thinking about the constructs of identity and wellness. In this dissertation, I critically explore how the field of counselling psychology approaches identity development. In relation, there is a lack of counselling psychology research that investigates the experiences of identity development under the influences of MM using an intersectional and social justice perspective. As a result, my aim was to create a body of work that might invigorate counselling psychology (and allied professions) in recognizing and working in solidarity with clients/patients, research participants, and community members against the insidious forces of MM.
Additional file 1 of An association between ATP7B expression and human cancer prognosis and immunotherapy: a pan-cancer perspective
Creators: name: Zhang, Zhanzhan
name: Zhang, Aobo
name: Shi, Yunpeng
name: Zhao, Zijun
name: Zhao, Zongmao
Publisher: name: figshare
Year: 2023
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer

description: Additional file 1: Table 1. Results of MSI and TMB. Table 2. Screening out small molecule drugs on CMap website. Supplementary Figure 1. Analyses of ATP7B expression levels across cancer types. Supplementary Figure 2. Correlation analysis between ATP7B expression and immune infiltration in 8 types of cancer. Supplementary Figure 3. Expression of ATP7B in HA cell lines and glioma cell lines and in normal and glioma tissues.
An Exploration of Canadian Multicultural and Social Justice Training: Centring the Voices of Minoritized Students
Creators: name: Cohen, Julie A.
Publisher: name: Graduate Studies
Year: 2020
Subjects: subject: Social Justic
subject: Multiculturalism
subject: Training
subject: Non-Dominant Cultural Identities
subject: Feminist Standpoint Theory
subject: Interpretative Phenomenological Analysis
subject: Canada
subject: Reflexivity
subject: Psychology
subject: FOS: Psychology
subject: Education--Educational Psychology
subject: Education--Higher

description: The Canadian discipline of counselling psychology has taken leadership in inciting change in the broader field of professional psychology—striving to adopt innovative multicultural (MC) and social justice (SJ) orientations and training. At the same time, most Canadian research that examines MC and SJ training relies on the experiences of participants who hold multiple dominant identities and social locations. While more recent MC and SJ scholarship has included an exploration of culture, there is still limited focus on non-dominant cultural influences outside of race and ethnicity. Hence, there is a lack of research that investigates MC and SJ training using a culturally inclusive perspective—one that recognizes the intersectionality and multiplicity of identities. This dissertation explores the perspectives of MC and SJ training from the standpoints of culturally non-dominant students, using an inclusive lens (e.g., those identities that are minoritized by dominant discourses and structures). This body of work offers a path to refocus Canadian counselling psychology towards culturally responsive and socially just training and research practices. Consisting of three linked manuscripts, which employ a feminist lens as a guiding framework, this research makes several contributions to research and practice. First, in Manuscript I, I explore current ways in which MC and SJ training are understood and taken up by counselling psychology graduate students. Second, in Manuscript II, I examine how a pluralistic approach that adopts a feminist standpoint theory epistemology to guide an interpretative phenomenological analysis method can provide a meaningful framework to conduct research with minoritized communities, offering suggestions for working through philosophical and methodological considerations that arise from this integration. Lastly, in Manuscript III, I explore the standpoints of eight culturally non-dominant counselling psychology doctoral students with respect to MC and SJ training in Canada to examine the following research question: How do counselling psychology doctoral students who self-identify with culturally non-dominant identities perceive their experiences of MC and SJ training? This body of work highlights unique aspects of culturally non-dominant students’ experiences, provides meaningful recommendations to advance MC and SJ training, and informs future pedagogical and methodological approaches in the Canadian field of counselling psychology.
Measuring BAO and non-Gaussianity via QSO clustering
Creators: name: Sawangwit, U.
name: Shanks, T.
name: Croom, S. M.
name: Drinkwater, M. J.
name: Fine, S.
name: Parkinson, D.
name: Ross, Nicholas P.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: Our goals are (i) to search for BAO and large-scale structure in current QSO survey data and (ii) to use these and simulation/forecast results to assess the science case for a new, >10x larger, QSO survey. We first combine the SDSS, 2QZ and 2SLAQ surveys to form a survey of ~60000 QSOs. We find a hint of a peak in the QSO 2-point correlation function, xi(s), at the same scale (~105h^-1 Mpc) as detected by Eisenstein et al (2005) in their sample of DR5 LRGs but only at low statistical significance. We then compare these data with QSO mock catalogues from the Hubble Volume simulation used by Hoyle et al (2002) and find that both routes give statistical error estimates that are consistent at ~100h^-1 Mpc scales. Mock catalogues are then used to estimate the nominal survey size needed for a 3-4 sigma detection of the BAO peak. We find that a redshift survey of ~250000 z<2.2 QSOs is required over ~3000 deg^2. This is further confirmed by static log-normal simulations where the BAO are clearly detectable in the QSO power spectrum and correlation function. The nominal survey would on its own produce the first detection of, for example, discontinuous dark energy evolution in the so far uncharted 1
description: 11 pages, 9 figures, typo corrected, references added, accepted by MNRAS
Improved Churn Causal Analysis Through Restrained High-Dimensional Feature Space Effects in Financial Institutions
Creators: name: Rudd, David Hason
name: Huo, Huan
name: Xu, Guandong
Publisher: name: arXiv
Year: 2023
Subjects: subject: Machine Learning (cs.LG)
subject: Human-Computer Interaction (cs.HC)
subject: FOS: Computer and information sciences

description: Customer churn describes terminating a relationship with a business or reducing customer engagement over a specific period. Customer acquisition cost can be five to six times that of customer retention, hence investing in customers with churn risk is wise. Causal analysis of the churn model can predict whether a customer will churn in the foreseeable future and identify effects and possible causes for churn. In general, this study presents a conceptual framework to discover the confounding features that correlate with independent variables and are causally related to those dependent variables that impact churn. We combine different algorithms including the SMOTE, ensemble ANN, and Bayesian networks to address churn prediction problems on a massive and high-dimensional finance data that is usually generated in financial institutions due to employing interval-based features used in Customer Relationship Management systems. The effects of the curse and blessing of dimensionality assessed by utilising the Recursive Feature Elimination method to overcome the high dimension feature space problem. Moreover, a causal discovery performed to find possible interpretation methods to describe cause probabilities that lead to customer churn. Evaluation metrics on validation data confirm the random forest and our ensemble ANN model, with %86 accuracy, outperformed other approaches. Causal analysis results confirm that some independent causal variables representing the level of super guarantee contribution, account growth, and account balance amount were identified as confounding variables that cause customer churn with a high degree of belief. This article provides a real-world customer churn analysis from current status inference to future directions in local superannuation funds.
description: Human-Centric Intelligent Systems 2022. arXiv admin note: substantial text overlap with arXiv:2304.10604
Structural and functional investigation of the role of Gcn5-related N-acetyltransferase (GNAT) activity in the host manipulation strategies of pathogenic bacteria of order Legionellales
Creators: name: Syriste, Lukas
Publisher: name: Graduate Studies
Year: 2021
Subjects: subject: pathogen-host interaction
subject: acetylation
subject: Legionella
subject: GNAT
subject: Gcn5-related N-acetyltransferase
subject: Type IV secretion system
subject: effectors
subject: structural biology
subject: eIF3
subject: eukaryotic translation initiation factor 3
subject: Biology--Cell
subject: Biology--Molecular
subject: Chemistry--Biochemistry
subject: Biology--Microbiology

description: The pathogenic strategy of intracellular parasite Legionella pneumophila relies on the translocation of over 330 proteins, called effectors, into the eukaryotic host cell during infection. The collective action of these effectors modulates host biochemistry to facilitate survival and proliferation of the pathogen. Among the ~18,000 effectors of genus Legionella, a subset of 8 effectors is conserved in all members sequenced to date. This universal group of effectors include a putative Gcn5-related N-acetyltransferase (GNAT) termed VipF. GNAT enzymes catalyze the acetylation of a broad range of small molecule and protein substrates, however to our knowledge this is the first instance of a secreted effector with homology to GNAT acetyltransferases. Here, using structural, biochemical, and in vivo strategy, we show VipF is a GNAT acetyltransferase with homology to bacterial Rim-family acetyltransferases showing preference for N-terminal acetylation of peptide substrates in vitro. We identify host interactors of VipF using affinity purification coupled to mass spectrometry and confirm by binary interaction in yeast 2-hybrid the physical interaction of VipF with the K subunit of human translation initiation factor 3 (eIF3) complex. We further characterize the interaction interface between these proteins and demonstrate residues critical for VipF interactions with eIF3K. Despite significant diversification in sequence in representatives of VipF in Legionella, we demonstrate that several selected members of this effector family interact with eIF3K.
Population genetics of conifer seed orchards
Creators: name: Funda, Tomas
Publisher: name: University of British Columbia
Year: 2012

description: Seed orchards represent the link between breeding and silvicultural activities. They were expected to act as closed, panmictic populations in Hardy-Weinberg equilibrium, meaning that desired genes drafted during previous selection stage would be effectively transmitted from parental to offspring populations; however, extensive research has indicated that this expectation is not met. Scrutinizing seed orchards’ efficiency is of vital importance as it determines the genetic quality of future forest stands. Population genetics of four tree species’ seed orchards (western larch, Douglas-fir, lodgepole pine, and western redcedar) was studied using microsatellite DNA markers. Partial (family array) and full (bulk seed) pedigree reconstruction of offspring population (seed crops) were conducted using the likelihood-based parentage inference program CERVUS to estimate parental reproductive success, selfing rate, pollen contamination, effective number of parents (Ne), and seedlot genetic worth. Several simplified methods for predicting seed crops’ genetic quality and quantity were evaluated by comparing parental reproductive success with parental fecundities. In all species, the top 20% of males contributed approximately one half of successful within-orchard pollen, substantially reducing male Ne (45 to 62% of the orchards’ census numbers). Even larger distortion was observed among females (the top 20% of females produced 77% of seed crop in Douglas-fir), reducing female Ne to as little as 13% of the census. Selfing and pollen contamination rates were in the range of previously reported studies, with the exception of high (15.2%) and low (7.3%) selfing rates in Douglas-fir and western redcedar, respectively. Pollen bud production and seed-cone volume were found to be the most reliable proxies to parental reproductive success, genetic worth, and Ne estimates. An optimization protocol was developed for creating custom seedlots with maximized genetic gain at any Ne while collectively considering parental male and female fecundities, co-ancestry among parents, inbreeding, and variation in seed germination capacity. This protocol can be utilized in any generation’s seed orchard e.g. when seed supply exceeds demand, for mixing surpluses from multiple years, or if a given seed lot fails to meet minimum Ne requirements.
Analytical Approximations for the Collapse of an Empty Spherical Bubble
Creators: name: Obreschkow, Danail
name: Bruderer, Martin
name: Farhat, Mohamed
Publisher: name: arXiv
Year: 2012
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: The Rayleigh equation 3/2 R'+RR"+p/rho=0 with initial conditions R(0)=Rmax, R'(0)=0 models the collapse of an empty spherical bubble of radius R(T) in an ideal, infinite liquid with far-field pressure p and density rho. The solution for r=R/Rmax as a function of time t=T/Tcollapse, where R(Tcollapse)=0, is independent of Rmax, p, and rho. While no closed-form expression for r(t) is known we find that s(t)=(1-t^2)^(2/5) approximates r(t) with an error below 1%. A systematic development in orders of t^2 further yields the 0.001%-approximation r*(t)=s(t)[1-a Li(2.21,t^2)], where a=-0.01832099 is a constant and Li is the polylogarithm. The usefulness of these approximations is demonstrated by comparison to high-precision cavitation data obtained in microgravity.
description: 5 pages, 2 figures
Assessing the Adoption of Improved Bean Varieties in Rwanda and the Role of Varietal Attributes in Adoption Decisions
Creators: name: Larochelle, Catherine
name: Asare-Marfo, Dorene
name: Birol, Ekin
name: Alwang, Jeffrey
Publisher: name: Gates Open Research
Year: 2019

description: Assessing the Adoption of Improved Bean Varieties in Rwanda and the Role of Varietal Attributes in Adoption Decisions
CO2 Injectivity Under Varying Thermal Conditions in Deep Saline Geologic CO2 Storage Reservoir Systems
Creators: name: Tawiah, Paul
Publisher: name: Graduate Studies
Year: 2021
Subjects: subject: CO2 Storage
subject: Carbon Capture and Storage
subject: CCS
subject: CO2 Injectivity
subject: Non-isothermal injectivity
subject: thermal effects
subject: CO2 phase mobility
subject: thermal stimulation
subject: Geology
subject: FOS: Earth and related environmental sciences

description: CO2 injectivity is critical to achieving the rapidly-scaled and significant rates of CO2 injection into subsurface geologic reservoirs for Carbon Capture & Storage (CCS) as an important greenhouse gas (GHG) emissions reduction technology. In this research, the influence of injected CO2 bottomhole temperature (BHT) variability on CO2 injectivity has been investigated at the field-scale using field performance observations and data analysis of a large-scale (>1Mtpa injected CO2) commercial CCS operation, the Quest CCS site, and lab-scale experimental CO2 corefloods at varying equilibrium temperatures. The results of this study indicate that CO2 injectivity exhibits an inverse relationship with CO2 BHT. A 10oC decrease in CO2 BHT causes CO2 injectivity to increase by 10% for a constant continuous mass rate of CO2 injection into a deep saline aquifer, where the temperature difference (?T) between the CO2 BHT and the reservoir fluctuates between 27oC (summer) and 40oC (winter). Neither CO2 kinematic viscosity changes alone with temperature or CO2 physico-chemical reactions with in-situ reservoir fluids under non-isothermal conditions can explain the inverse relationship between seasonally cyclical CO2 BHT and injectivity. Non-isothermal cyclic CO2/brine drainage-imbibition can change CO2/brine two-phase flow characteristics. CO2 drainage endpoint phase mobility increases as temperature increases, but the mobility increases cannot explain the inverse relationship between CO2 BHT and injectivity. CO2 endpoint relative permeability contributes marginally to the CO2 phase mobility changes with temperature. Thermo-geomechanical mechanisms linked to continuous injection of “colder” CO2 at BHTs lower than the average deep saline aquifer reservoir temperatures, can induce thermal stimulation of existing natural fractures around the vicinity of the CO2 injector well through thermoelastic effects. Thermoelasticity enhances CO2 injectivity as the CO2 BHT decreases, even when bottomhole injection pressures (BHIPs) are considerably (tens of MPa) below the fracture pressure of the reservoir rocks. CO2 phase mobility changes with BHT and thermally induced stimulation mechanisms act contemporaneously and in opposite directions to influence injectivity. Thermal stimulation effects on CO2 injectivity can be more dominant than CO2 phase mobility effects, implying a need to distinguish thermoelasticity from poroelastic effects in CO2 injection regulatory requirements for improved injection efficiency in geologic CO2 storage while maintaining permanent storage security.
Detecting Socially Abnormal Highway Driving Behaviors via Recurrent Graph Attention Networks
Creators: name: Hu, Yue
name: Zhang, Yuhang
name: Wang, Yanbing
name: Work, Daniel
Publisher: name: arXiv
Year: 2023
Subjects: subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: With the rapid development of Internet of Things technologies, the next generation traffic monitoring infrastructures are connected via the web, to aid traffic data collection and intelligent traffic management. One of the most important tasks in traffic is anomaly detection, since abnormal drivers can reduce traffic efficiency and cause safety issues. This work focuses on detecting abnormal driving behaviors from trajectories produced by highway video surveillance systems. Most of the current abnormal driving behavior detection methods focus on a limited category of abnormal behaviors that deal with a single vehicle without considering vehicular interactions. In this work, we consider the problem of detecting a variety of socially abnormal driving behaviors, i.e., behaviors that do not conform to the behavior of other nearby drivers. This task is complicated by the variety of vehicular interactions and the spatial-temporal varying nature of highway traffic. To solve this problem, we propose an autoencoder with a Recurrent Graph Attention Network that can capture the highway driving behaviors contextualized on the surrounding cars, and detect anomalies that deviate from learned patterns. Our model is scalable to large freeways with thousands of cars. Experiments on data generated from traffic simulation software show that our model is the only one that can spot the exact vehicle conducting socially abnormal behaviors, among the state-of-the-art anomaly detection models. We further show the performance on real world HighD traffic dataset, where our model detects vehicles that violate the local driving norms.
Additional file 1 of Micro-genetic environmental sensitivity across macro-environments of chickens reared in Burkina Faso and France
Creators: name: Madsen, Mette Dam
name: Duijvesteijn, Naomi
name: van der Werf, Julius
name: Clark, Sam
Publisher: name: figshare
Year: 2023
Subjects: subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Ecology
subject: Plant Biology

description: Additional file 1. Simulation study of the impacts of mixed full- and half-sib data in sire models. Methods used to conduct the simulation study examining the impact of having mixed full- and half-sib data in sire models and the results of this simulation study in Tables S1 and S2. Table S1. Estimated additive genetic variance from the analysis of simulated datasets with varying mating ratio (standard error of the mean across 100 replicates) on the level of the model and converted to the animal level assuming the additive genetic sire variance is 0.25 of the additive genetic variance or using the average relationship of sire progeny groups. Table S2. Estimated additive genetic variance of micro-GES from the analysis of simulated datasets with varying mating ratio (standard error of the mean across 100 replicates) on the level of the model and converted to the animal level assuming the additive genetic sire variance is 0.25 of the additive genetic variance or using the actual relationship of sire progeny groups.
Additional file 7: of Downregulation of miR-133a-3p promotes prostate cancer bone metastasis via activating PI3K/AKT signaling
Creators: name: Tang, Yubo
name: Pan, Jincheng
name: Huang, Shuai
name: Peng, Xinsheng
name: Zou, Xuenong
name: Luo, Yongxiang
name: Ren, Dong
name: Zhang, Xin
name: Li, Ronggang
name: He, Peiheng
name: Wa, Qingde
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Plant Biology

description: Table S6. The relationship between miR-133a-3p expression level and clinical pathological characteristics in 245 patients with prostate adenocarcinoma. (PDF 61Â kb)
Local deformations and incommensurability of high quality epitaxial graphene on a weakly interacting transition metal
Creators: name: Blanc, Nils
name: Coraux, Johann
name: Vo-Van, Chi
name: N'Diaye, Alpha T.
name: Geaymond, Olivier
name: Renaud, Gilles
Publisher: name: arXiv
Year: 2012
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We investigate the fine structure of graphene on iridium, which is a model for graphene weakly interacting with a transition metal substrate. Even the highest quality epitaxial graphene displays tiny imperfections, i.e. small biaxial strains, ca. 0.3%, rotations, ca. 0.5^{\circ}, and shears over distances of ca. 100 nm, and is found incommensurate, as revealed by X-ray diffraction and scanning tunneling microscopy. These structural variations are mostly induced by the increase of the lattice parameter mismatch when cooling down the sample from the graphene preparation temperature to the measurement temperature. Although graphene weakly interacts with iridium, its thermal expansion is found positive, contrary to free-standing graphene. The structure of graphene and its variations are very sensitive to the preparation conditions. All these effects are consistent with initial growth and subsequent pining of graphene at steps.
Formation of surface nanobubbles and universality of their contact angles: A molecular dynamics approach
Creators: name: Weijs, J. H.
name: Snoeijer, J. H.
name: Lohse, D.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We study surface nanobubbles using molecular dynamics simulation of ternary (gas, liquid, solid) systems of Lennard-Jones fluids. They form for sufficiently low gas solubility in the liquid, i.e., for large relative gas concentration. For strong enough gas-solid attraction, the surface nanobubble is sitting on a gas layer, which forms in between the liquid and the solid. This gas layer is the reason for the universality of the contact angle, which we calculate from the microscopic parameters. Under the present equilibrium conditions the nanobubbles dissolve within less of a microsecond, consistent with the view that the experimentally found nanobubbles are stabilized by a nonequilibrium mechanism.
description: 5p,4f
The strange and light quark contributions to the nucleon mass from Lattice QCD
Creators: name: Bali, Gunnar S.
name: Collins, Sara
name: Gockeler, Meinulf
name: Horsley, Roger
name: Nakamura, Yoshifumi
name: Nobile, Andrea
name: Pleiter, Dirk
name: Rakow, P. E. L.
name: Schafer, Andreas
name: Schierholz, Gerrit
name: Sternbeck, Andre
name: Zanotti, James M.
Publisher: name: arXiv
Year: 2011
Subjects: subject: High Energy Physics - Lattice (hep-lat)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: We determine the strangeness and light quark fractions of the nucleon mass by computing the quark line connected and disconnected contributions to the matrix elements m_q in lattice QCD, using the non-perturbatively improved Sheikholeslami-Wohlert Wilson Fermionic action. We simulate n_F=2 mass degenerate sea quarks with a pion mass of about 285 MeV and a lattice spacing a approx 0.073 fm. The renormalization of the matrix elements involves mixing between contributions from different quark flavours. The pion-nucleon sigma-term is extrapolated to physical quark masses exploiting the sea quark mass dependence of the nucleon mass. We obtain the renormalized values σ_{πN} = 38(12) MeV at the physical point and f_{T_s}=σ_s/m_N= 0.012(14)^{+10}_{-3} for the strangeness contribution at our larger than physical sea quark mass.
description: 11 pages, 7 figures, v2: 1 reference added, some corrections
Arabidopsis thaliana D group MPKs interactions with RLPH2 and PP1
Creators: name: Toth, Ryan B.
Publisher: name: Graduate Studies
Year: 2021
Subjects: subject: Phosphorylation
subject: Phosphatase
subject: Tyrosine
subject: Arabidopsis
subject: Biology--Botany
subject: Biology--Molecular
subject: Biology--Plant Physiology

description: Mitogen activated protein kinases (MPK) are key members of the MPK cascade, a pathway that results in an immediate response from (external) stimuli such as infection, cold, or drought. The activation of an MPK relies its activation loop being phosphorylated on a threonine and tyrosine residue. A unique bacteria-like phosphatase Rhizobiales-like phosphatase 2 (RLPH2), which we bioinformatically characterized as a serine/threonine phosphatase, has been discovered to act as a tyrosine phosphatase. In this thesis, data monitoring RLPH2s dephosphorylation of different peptides derived from MPK activation loops would reveal a preference for the dephosphorylation of D group MPKs over non-D group MPKs, and indicate that the central residue in the TXY motif plays a key role in RLPH2 substrate determination. Additionally, RLPH2 would show a preference for the in vitro dephosphorylation of MPK9 (a D group MPK) over MPK3 (a non-D group MPK). An engaging observation is that right next to the TxY motif in D group MPKs is a putative Protein Phosphatase 1 (PP1) regulatory protein binding RVxF motif. This motif is not present in any other characterized MPK, suggesting an interaction between PP1 and D group MPKs. In this thesis, PP1 protein binding assays with MPK9 WT and an MPK9 RASA mutant would show binding occurs between MPK9 and PP1 through the RVXF motif in vitro. Peptide and protein substrate dephosphorylation assays with PP1 would show threonine dephosphorylation on MPK9 and the effect the RVXF motif plays on this interaction. In summary, the specificity of RLPH2 as a D group MPK regulator was examined along with the interaction between PP1 and the D group MPKs via the RVXF motif, with mention of a potential relationship between these three interactions.
Additional file 1 of The health perceptions, dengue knowledge and control willingness among Dai ethnic minority in Yunnan Province, China
Creators: name: Liu, Hui
name: Fang, Cheng-Jiang
name: Xu, Jian-Wei
Publisher: name: figshare
Year: 2021
Subjects: subject: Medicine
subject: Neuroscience
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Science Policy

description: Additional file 1.
Hierarchical Weight Averaging for Deep Neural Networks
Creators: name: Gu, Xiaozhe
name: Zhang, Zixun
name: Jiang, Yuncheng
name: Luo, Tao
name: Zhang, Ruimao
name: Cui, Shuguang
name: Li, Zhen
Publisher: name: arXiv
Year: 2023
Subjects: subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Despite the simplicity, stochastic gradient descent (SGD)-like algorithms are successful in training deep neural networks (DNNs). Among various attempts to improve SGD, weight averaging (WA), which averages the weights of multiple models, has recently received much attention in the literature. Broadly, WA falls into two categories: 1) online WA, which averages the weights of multiple models trained in parallel, is designed for reducing the gradient communication overhead of parallel mini-batch SGD, and 2) offline WA, which averages the weights of one model at different checkpoints, is typically used to improve the generalization ability of DNNs. Though online and offline WA are similar in form, they are seldom associated with each other. Besides, these methods typically perform either offline parameter averaging or online parameter averaging, but not both. In this work, we firstly attempt to incorporate online and offline WA into a general training framework termed Hierarchical Weight Averaging (HWA). By leveraging both the online and offline averaging manners, HWA is able to achieve both faster convergence speed and superior generalization performance without any fancy learning rate adjustment. Besides, we also analyze the issues faced by existing WA methods, and how our HWA address them, empirically. Finally, extensive experiments verify that HWA outperforms the state-of-the-art methods significantly.
description: Accept by TNNLS