cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Big dams and salmon evolution: changes in thermal regimes and their potential evolutionary consequences
Creators: name: Beckman, Brian R.
name: Bartz, Krista K.
name: Crozier, Lisa G.
name: Ashley Steel, E.
name: Angilletta, Michael J.
name: Scheuerell, Mark D.
name: Kingsolver, Joel G.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: Dams designed for hydropower and other purposes alter the environments of many economically important fishes, including Chinook salmon (Oncorhynchus tshawytscha). We estimated that dams on the Rogue River, the Willamette River, the Cowlitz River, and Fall Creek decreased water temperatures during summer and increased water temperatures during fall and winter. These thermal changes undoubtedly impact the behavior, physiology, and life histories of Chinook salmon. For example, relatively high temperatures during the fall and winter should speed growth and development, leading to early emergence of fry. Evolutionary theory provides tools to predict selective pressures and genetic responses caused by this environmental warming. Here, we illustrate this point by conducting a sensitivity analysis of the fitness consequences of thermal changes caused by dams, mediated by the thermal sensitivity of embryonic development. Based on our model, we predict Chinook salmon likely suffered a decrease in mean fitness after the construction of a dam in the Rogue River. Nevertheless, these demographic impacts might have resulted in strong selection for compensatory strategies, such as delayed spawning by adults or slowed development by embryos. Because the thermal effects of dams vary throughout the year, we predict dams impacted late spawners more than early spawners. Similar analyses could shed light on the evolutionary consequences of other environmental perturbations and their interactions.
Coinfection rates in Φ6 bacteriophage are enhanced by virus-induced changes in host cells.
Creators: name: Chao, Lin
name: Burch, Christina L.
name: Joseph, Sarah B.
name: Hanley, Kathryn A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Two or more viruses infecting the same host cell can interact in ways that profoundly affect disease dynamics and control, yet the factors determining coinfection rates are incompletely understood. Previous studies have focused on the mechanisms that viruses use to suppress coinfection, but recently the phenomenon of enhanced coinfection has also been documented. In the experiments described here, we explore the hypothesis that enhanced coinfection rates in the bacteriophage Φ6 are achieved by virus-induced upregulation of the Φ6 receptor, which is the bacterial pilus. First, we confirmed that coinfection enhancement in Φ6 is virus-mediated by showing that Φ6 attaches significantly faster to infected cells than to uninfected cells. Second, we explored the hypothesis that coinfection enhancement in Φ6 depends upon changes in the expression of an inducible receptor. Consistent with this hypothesis, the closely related phage, Φ12, that uses constitutively expressed lipopolysaccharide as its receptor, attaches to infected and uninfected cells at the same rate. Our results, along with the previous finding that coinfection in Φ6 is limited to two virions, suggest that viruses may closely regulate rates of coinfection through mechanisms for both coinfection enhancement and exclusion.
G protein signaling in the parasite Entamoeba histolytica
Creators: name: Bosch, Dustin E
name: Siderovski, David P
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: The parasite Entamoeba histolytica causes amebic colitis and systemic amebiasis. Among the known amebic factors contributing to pathogenesis are signaling pathways involving heterotrimeric and Ras superfamily G proteins. Here, we review the current knowledge of the roles of heterotrimeric G protein subunits, Ras, Rho and Rab GTPase families in E. histolytica pathogenesis, as well as of their downstream signaling effectors and nucleotide cycle regulators. Heterotrimeric G protein signaling likely modulates amebic motility and attachment to and killing of host cells, in part through activation of an RGS-RhoGEF (regulator of G protein signaling–Rho guanine nucleotide exchange factor) effector. Rho family GTPases, as well as RhoGEFs and Rho effectors (formins and p21-activated kinases) regulate the dynamic actin cytoskeleton of E. histolytica and associated pathogenesis-related cellular processes, such as migration, invasion, phagocytosis and evasion of the host immune response by surface receptor capping. A remarkably large family of 91 Rab GTPases has multiple roles in a complex amebic vesicular trafficking system required for phagocytosis and pinocytosis and secretion of known virulence factors, such as amebapores and cysteine proteases. Although much remains to be discovered, recent studies of G protein signaling in E. histolytica have enhanced our understanding of parasitic pathogenesis and have also highlighted possible targets for pharmacological manipulation.
Genomic assays for Epstein–Barr virus-positive gastric adenocarcinoma
Creators: name: Gulley, Margaret L
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: A small set of gastric adenocarcinomas (9%) harbor Epstein–Barr virus (EBV) DNA within malignant cells, and the virus is not an innocent bystander but rather is intimately linked to pathogenesis and tumor maintenance. Evidence comes from unique genomic features of host DNA, mRNA, microRNA and CpG methylation profiles as revealed by recent comprehensive genomic analysis by The Cancer Genome Atlas Network. Their data show that gastric cancer is not one disease but rather comprises four major classes: EBV-positive, microsatellite instability (MSI), genomically stable and chromosome instability. The EBV-positive class has even more marked CpG methylation than does the MSI class, and viral cancers have a unique pattern of methylation linked to the downregulation of CDKN2A (p16) but not MLH1. EBV-positive cancers often have mutated PIK3CA and ARID1A and an amplified 9p24.1 locus linked to overexpression of JAK2, CD274 (PD-L1) and PDCD1LG2 (PD-L2). Multiple noncoding viral RNAs are highly expressed. Patients who fail standard therapy may qualify for enrollment in clinical trials targeting cancer-related human gene pathways or promoting destruction of infected cells through lytic induction of EBV genes. Genomic tests such as the GastroGenus Gastric Cancer Classifier are available to identify actionable variants in formalin-fixed cancer tissue of affected patients.
Pain and Interference of Pain With Function and Mood in Elderly Adults Involved in a Motor Vehicle Collision: A Pilot Study
Creators: name: McLean, Samuel A.
name: Swor, Robert A.
name: Clauw, Daniel J.
name: Zaleski, Erin Z.
name: Platts-Mills, Timothy F.
name: Lee, Young M.
name: Burke, Gary F.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Musculoskeletal pain after motor vehicle collision is a substantial public health problem. The number of elderly individuals experiencing motor vehicle collision is increasing. We conducted analyses of data collected as part of a prospective observational study of outcomes after motor vehicle collision to estimates rates of persistent pain, pain interference, and change in physical function in patients 65 or older.
No-go for tree-level R-symmetry breaking
Creators: name: Liu, Feihu
name: Liu, Muyang
name: Sun, Zheng
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We show that in gauge mediation models with tree-level R-symmetry breaking where supersymmetry and R-symmetries are broken by different fields, the gaugino mass either vanishes at one loop or finds a contribution from loop-level R-symmetry breaking. Thus tree-level R-symmetry breaking for phenomenology is either no-go or redundant in the simplest type of models. Including explicit messenger mass terms in the superpotential with a particular R-charge arrangement is helpful to bypass the no-go theorem, and the resulting gaugino mass is suppressed by the messenger mass scale.
description: 8 pages, 7 figures; v2: discussion on Driac gauginos and references added; v3: a section on bypassing the no-go added, R-charge notation changed; v4: typos, EPJC pre-published version
Unusual liquid phases for indented colloids with depletion interactions
Creators: name: Ashton, Douglas J.
name: Jack, Robert L.
name: Wilding, Nigel B.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We study indented spherical colloids, interacting via depletion forces. These systems exhibit liquid-vapor phase transitions whose properties are determined by a combination of strong "lock-and-key" bonds and weaker non-specific interactions. As the propensity for lock-and-key binding increases, the critical point moves to significantly lower density, and the coexisting phases change their structure. In particular, the liquid phase is "porous", exhibiting large percolating voids. The properties of this system depend strongly on the topological structure of an underlying bond network: we comment on the implications of this fact for the assembly of equilibrium states with controlled porous structures.
description: 11 pages, 9 figures
RASflow_EDC Singularity image
Creators: name: Kirsh, Olivier
name: Hennion, Magali
Publisher: name: Zenodo
Year: 2022
Subjects: Singularity
Container
RNAseq

description: Singularity image containing all softwares needed to run RASflow_EDC workflow. More information at https://parisepigenetics.github.io/bibs/edctools/workflows/rasflow_edc/#/edctools/
Quantum Gates Between Distant Qubits via Spin-Independent Scattering
Creators: name: Banchi, Leonardo
name: Compagno, Enrico
name: Korepin, Vladimir
name: Bose, Sougato
Publisher: name: arXiv
Year: 2014
Subjects: subject: Quantum Physics (quant-ph)
subject: Quantum Gases (cond-mat.quant-gas)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We show how the spin independent scattering of two initially distant qubits, say, in distinct traps or in remote sites of a lattice, can be used to implement an entangling quantum gate between them. The scattering takes place under 1D confinement for which we consider two different scenarios: a 1D wave-guide and a tight-binding lattice. We consider models with contact-like interaction between two fermionic or two bosonic particles. A qubit is encoded in two distinct spins (or other internal) states of each particle. Our scheme enables the implementation of a gate between two qubits which are initially too far to interact directly, and provides an alternative to photonic mediators for the scaling of quantum computers. Fundamentally, an interesting feature is that "identical particles" (e.g., two atoms of the same species) and the 1D confinement, are both necessary for the action of the gate. Finally, we discuss the feasibility of our scheme, the degree of control required to initialize the wave-packets momenta, and show how the quality of the gate is affected by momentum distributions and initial distance. In a lattice, the control of quasi-momenta is naturally provided by few local edge impurities in the lattice potential.
description: 10 pages, 7 figures. This article supersedes arXiv:1106.2329. Accepted in Quantum
Sequence entropy tuples and mean sensitive tuples
Creators: name: Li, Jie
name: Liu, Chunlin
name: Tu, Siming
name: Yu, Tao
Publisher: name: arXiv
Year: 2022
Subjects: subject: Dynamical Systems (math.DS)
subject: FOS: Mathematics

description: Using the idea of local entropy theory, we characterize the sequence entropy tuple via mean forms of the sensitive tuple in both topological and measure-theoretical senses. For the measure-theoretical sense, we show that for an ergodic measure-preserving system, the $μ$-sequence entropy tuple, the $μ$-mean sensitive tuple and the $μ$-sensitive in the mean tuple coincide, and give an example to show that the ergodicity condition is necessary. For the topological sense, we show that for a certain class of minimal systems, the mean sensitive tuple is the sequence entropy tuple.
A secure deterministic remote state preparation via a seven-qubit entangled channel of an arbitrary two-qubit state under the impact of quantum noise
Creators: name: Singh, Deepak
name: Kumar, Sanjeev
name: Behera, Bikash K.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: As one of the most prominent subfields of quantum communication research, remote state preparation (RSP) plays a crucial role in quantum networks. Here we present a deterministic remote state preparation scheme to prepare an arbitrary two-qubit state via a seven-qubit entangled channel created from Borras \emph{et al.} state. Quantum noises are inherent to each and every protocol for quantum communication that is currently in use, putting the integrity of quantum communication systems and their dependability at risk. The initial state of the system was a pure quantum state, but as soon as there was any noise injected into the system, it transitioned into a mixed state. In this article, we discuss the six different types of noise models namely bit-flip noise, phase-flip noise, bit-phase-flip noise, amplitude damping, phase damping and depolarizing noise. The impact these noises had on the entangled channel may be seen by analysing the density matrices that have been altered as a result of the noise. For the purpose of analysing the impact of noise on the scheme, the fidelity between the original quantum state and the remotely prepared state has been assessed and graphically represented. In addition, a comprehensive security analysis is performed, demonstrating that the suggested protocol is safe against internal and external attacks.
description: 13 Pages, 3 figures
Prevalence of mixed dyslipidemia among Australian patients undergoing lipid-modifying therapy
Creators: name: The University of North Carolina at Chapel Hill University Libraries
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2013

description: Few studies have assessed the prevalence of mixed dyslipidemia (MD) and the effectiveness of lipid-modifying therapy (LMT) for the treatment of abnormal levels of low-density lipoprotein cholesterol (LDL-C), triglycerides (TG) and high-density lipoprotein cholesterol (HDL-C) in Australian clinical practice.
Continuous Mid-Infrared Star Formation Rate Indicators: Diagnostics for 0
Creators: name: Battisti, A. J.
name: Calzetti, D.
name: Johnson, B. D.
name: Elbaz, D.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present continuous, monochromatic star formation rate (SFR) indicators over the mid-infrared wavelength range of 6-70 micron. We use a sample of 58 star forming galaxies (SFGs) in the Spitzer-SDSS-GALEX Spectroscopic Survey (SSGSS) at z<0.2, for which there is a rich suite of multi-wavelength photometry and spectroscopy from the ultraviolet through to the infrared. The data from the Spitzer infrared spectrograph (IRS) of these galaxies, which spans 5-40 micron, is anchored to their photometric counterparts. The spectral region between 40-70 micron is interpolated using dust model fits to the IRS spectrum and Spitzer 70 and 160 micron photometry. Since there are no sharp spectral features in this region, we expect these interpolations to be robust. This spectral range is calibrated as a SFR diagnostic using several reference SFR indicators to mitigate potential bias. Our band-specific continuous SFR indicators are found to be consistent with monochromatic calibrations in the local universe, as derived from Spitzer, WISE, and Herschel photometry. Our local composite template and continuous SFR diagnostics are made available for public use through the NASA/IPAC Infrared Science Archive (IRSA) and have typical dispersions of 30% or less. We discuss the validity and range of applicability for our SFR indicators in the context of unveiling the formation and evolution of galaxies. Additionally, in the era of the James Webb Space Telescope this will become a flexible tool, applicable to any SFG up to z~3.
description: 23 pages, 16 figures, 4 tables; Accepted for publication in ApJ; Our composite SED template and continuous SFR indicators are publicly available at http://irsa.ipac.caltech.edu/data/SPITZER/MIR_SFR/
Additional tables and figures (TYMS gene polymorphism)
Creators: name: Mutlak, Qassim Mahdi
Publisher: name: figshare
Year: 2023
Subjects: classificationCode: 310505
subject: Gene expression (incl. microarray and other genome-wide approaches)
classificationCode: 310509
subject: Genomics
classificationCode: 310599
subject: Genetics not elsewhere classified
classificationCode: 310506
subject: Gene mapping

description: Additional files including 4 Figures and 2 tables.
TorchFL: A Performant Library for Bootstrapping Federated Learning Experiments
Creators: name: Khimani, Vivek
name: Jabbari, Shahin
Publisher: name: arXiv
Year: 2022
Subjects: subject: Machine Learning (cs.LG)
subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: Systems and Control (eess.SY)
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: I.2.11

description: With the increased legislation around data privacy, federated learning (FL) has emerged as a promising technique that allows the clients (end-user) to collaboratively train deep learning (DL) models without transferring and storing the data in a centralized, third-party server. We introduce TorchFL, a performant library for (i) bootstrapping the FL experiments, (ii) executing them using various hardware accelerators, (iii) profiling the performance, and (iv) logging the overall and agent-specific results on the go. Being built on a bottom-up design using PyTorch and Lightning, TorchFL provides ready-to-use abstractions for models, datasets, and FL algorithms, while allowing the developers to customize them as and when required. This paper aims to dig deeper into the architecture and design of TorchFL, elaborate on how it allows researchers to bootstrap the federated learning experience, and provide experiments and code snippets for the same. With the ready-to-use implementation of state-of-the-art DL models, datasets, and federated learning support, TorchFL aims to allow researchers with little to no engineering background to set up FL experiments with minimal coding and infrastructure overhead.
description: 21 pages, 15 figures, 4 tables. This manuscript serves as external documentation for https://github.com/vivekkhimani/torchfl
Patient experience and factors influencing willingness to utilize the emergency department among individuals living with sickle cell disease
Creators: name: Ibiloye, Elizabeth Ayooluwa
name: 0000-0002-4024-9957
Publisher: name: The University of Texas at Austin
Year: 2023
Subjects: Sickle cell disease
Patient experience
Theory of Planned Behavior

description: The purpose of this study was to describe the experiences of patients with sickle cell disease (SCD) in the emergency department (ED), and to determine the factors that influence their willingness to use the ED when in pain. This study tested the significance of the Theory of Planned Behavior (TPB) constructs (attitude, subjective norms, and perceived behavioral control) in predicting intention (willingness), and the contribution of additional constructs (prior patient experience and stigma) to the TPB model. The relationships between study constructs and covariates were also assessed. This mixed-methods study sample included SCD patients ≥ 18 years who had previously used the ED. For the qualitative portion, three focus group sessions (N=21 participants) were conducted to elicit the salient beliefs regarding patient experience when seeking care for pain in the ED. Salient beliefs were elicited by asking nine open-ended questions to assess the indirect constructs of the TPB (behavioral beliefs (BBs), normative beliefs (NBs) and control beliefs (CBs)). Eleven BBs, four NBs and ten CBs were identified as salient. The quantitative portion was conducted using a web-based survey that was developed using the TPB constructs and salient beliefs from the focus groups. A total of 114 survey responses were included in the data analyses. Data analyses were conducted using descriptive, bivariate and multivariate methods. The overall TPB model was significant and explained 61% of the variance in participants’ willingness to use the ED while in pain (adjusted R² =0.6102, p<0.0001). Of the TPB constructs, only attitude (b=0.57, p<0.0001) was significant while subjective norms and perceived behavioral control were not significant. ED use was the only significant covariate (b=0.57, p=0.0005). The additional constructs prior patient experience and stigma did not significantly contribute to the TPB model. The findings from this study support the utility of the TPB in describing the experience of SCD patients in the ED, and in predicting the factors that influence their willingness to use the ED when in pain. Interventions that focus on SCD patients’ attitude may be beneficial in increasing their willingness to use the ED when in pain.
Association between ovarian hormones and smoking behavior in women.
Creators: name: Gray, Kevin M.
name: Carpenter, Matthew J.
name: Schiller, Crystal Edler
name: Hartwell, Karen J.
name: Saladin, Michael E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Studies examining the association between menstrual cycle phases and smoking behavior in women have yielded mixed results. The purpose of this study was to elucidate the associations between ovarian hormones and smoking by directly measuring ovarian hormone levels and obtaining a laboratory assessment of smoking behaviors. Four hypotheses were tested: increased smoking will be associated with 1) low absolute levels of estradiol and progesterone; 2) decreasing (i.e., dynamic changes in) estradiol and progesterone; 3) lower ratios of progesterone to estradiol, and 4) higher ratios of estradiol to progesterone. Female smokers (≥10 cigarettes/day) with regular menstrual cycles were recruited as part of a larger, ongoing study examining the influence of ovarian hormones on smoking cessation treatment. Participants completed two study visits, including a one-hour adlib smoking topography session, which provided a detailed assessment of smoking behavior. Both the change in hormone levels over time and the relative ratios of ovarian hormones were associated with smoking behavior, but each to a limited extent. Decreases in estradiol (r=−.21, p=.048), and decreases in progesterone (r=−.23, p=.03) were associated with increased puff intensity. Lower ratios of progesterone to estradiol were associated with a greater number of puffs (r=−.26, p=.01) and weight of cigarettes smoked (r=−.29, p=.005). The best predictors of smoking behavior were the ratio of progesterone to estradiol (z=−2.7, p=.004) and the change in estradiol and progesterone over time (z=−2.1, p=.02). This pattern of results may help to explain inconsistent findings in previous studies and suggest potential mechanisms by which hormones influence nicotine addiction.
Smoking and COVID-19: Smoking Behavior and Motivation to Quit
Creators: name: Cox, Chelsea
Publisher: name: University of Illinois at Chicago
Year: 2022
Subjects: Uncategorized

description: Understanding the factors that predict motivation to quit smoking and smoking behavior are necessary to facilitating successful quit behavior. The protection motivation theory (PMT) is one framework that has been used to explain the adoption of health-protective behavior, such as reducing or quitting smoking. This theory may also provide a framework for understanding health protective behaviors as a result of the recent outbreak of COVID-19, especially given that numerous studies have suggested that smoking may be associated with more severe outcomes of COVID-19. There is a need for understanding the relationship between perceived threat of COVID and the relationship with other smoking-related factors using a theoretical framework. We examined associations between perceived threat of COVID and smoking-related factors (motivation to quit, smoking difference) and possible moderators (health status, self-efficacy) of this relationship. We also examined associations between COVID impact and smoking-related factors. Participants were 113 adult cigarette smokers recruited using Amazon’s Mechanical Turk Website (Mturk). A “premium” qualification within Mturk was used, which directs surveys to workers with specific attributes, in this case those who identified themselves as smokers. Regression models were used to examine the influence of perceived threat on the main criterion variables and to test the individual effects of each of the moderators. Results indicated that the main effects of perceived threat, respiratory symptoms, chronic illness, and COVID impact significantly predicted motivation to quit smoking, whereas self-efficacy did not. Contrary to hypotheses, perceived threat, respiratory symptoms, chronic illness and self-efficacy did not predict smoking difference. It is possible that methodological and sampling differences, other constructs of the PMT, the intention-behavior gap, or the general lack of change in smoking difference may explain these unexpected findings.
The Sequence of Events that led to the 1963 Publications in "Nature" of 3C273, the first Quasar and the first Extragalactic Radio Jet
Creators: name: Hazard, Cyril
name: Jauncey, David
name: Goss, W. M.
name: Herald, David
Publisher: name: arXiv
Year: 2014
Subjects: subject: History and Philosophy of Physics (physics.hist-ph)
subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: We are undertaking a detailed investigation, based on the available evidence, of the sequence of events that led to the historical discovery of the first Quasar 3C273.
description: 7 pgs, 6 figs, IAU Symp 313, Ecuador, 2014; New manuscript for publication PASA; 16 pgs, 8 figs; new unpublished material from archival sources; Fig of May 1962 occultation added; Bolton's preps 1962 August occultation unnecessary; impact Bolton-Schmidt letter 1962; implications Hazard's 1966 accurate radio-optical position; new section 6, aftermath mistaken Hazard affiliation Nature 1963 article
Notch Signaling in Pericytes during Central Nervous System Vascular Development and Pathology
Creators: name: Nadeem, Taliha
Publisher: name: University of Illinois at Chicago
Year: 2022
Subjects: Uncategorized

description: Pericytes are perivascular cells of microvessels. In the central nervous system (CNS), they have critical functions in vascular development and in blood-brain and blood-retinal barrier regulation. Pericyte loss and/or dysfunction is associated with aberrant angiogenesis, impaired vessel remodeling, and breakdown of CNS barriers. Arteriovenous malformations (AVMs) and germinal matrix-intraventricular hemorrhage are some pathologies associated with pericyte loss and/or dysfunction. Our aim is to further our understanding of pericyte-endothelial communication and how it may contribute to CNS pathologies. Notch signaling is crucial for vascular development and has been proposed to regulate critical pericyte functions. We hypothesized that Notch signaling in pericytes during angiogenesis regulates pericyte homeostasis and promotes vessel stability in the CNS. We inhibited Notch signaling perinatally to study retinal angiogenesis and embryonically to study brain angiogenesis. In the retina, the deficiency of Notch signaling reduced pericyte viability and proliferation, leading to pericyte loss. This resulted in improper vascular remodeling, vessel enlargement, and AVM development. Conversely, the constitutive activation of Notch signaling promoted pericyte coverage and maturation and ameliorated vascular abnormalities in an AVM mouse model of hereditary hemorrhagic telangiectasia. Deficiency of Notch signaling in the embryonic brain revealed region-specific pericyte loss in the germinal matrix (GM). This led us to investigate whether there were differences in pericytes in the GM and the cortex in wild-type mice. We observed similar pericyte coverage, but differential marker expression between the two regions, underscoring the existence of pericyte heterogeneity in the angiogenic brain. Further, the loss of Notch signaling in the embryonic brain showed that pericyte loss was detected early in GM angiogenesis, followed by impaired vessel morphogenesis at later time-points. Our combined studies highlight the importance that Notch signaling has in regulating pericyte survival and proliferation, and how it might contribute to the pathogenesis of vascular diseases in the CNS.
Increased oxidative stress is associated with balanced increases in hepatocyte apoptosis and proliferation in glycerol-3-phosphate acyltransferase-1 deficient mice
Creators: name: Albright, Craig D.
name: Lemasters, John J.
name: Coleman, Rosalind A.
name: Hammond, Linda E.
name: He, Lihua
name: Doughman, Scott D.
name: Watkins, Steven M.
name: Rusyn, Ivan
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: The absence of mouse mitochondrial glycerol-3-phosphate acyltransferase-1 (Gpat1-/-) increases the amount of arachidonate in liver phospholipids and increases β-hydroxybutyrate and acyl-carnitines, suggesting an elevated rate of liver fatty acid oxidation. We asked whether these alterations might increase reactive oxygen species (ROS), apoptosis, or hepatocyte proliferation. Compared to wildtype controls, liver mitochondria from Gpat1-/- mice showed a 20% increase in the rate of ROS production and a markedly increased sensitivity to the induction of the mitochondrial permeability transition. Mitochondrial phosphatidylethanolamine and phosphatidylcholine from Gpat1-/- liver contained 21% and 67% more arachidonate, respectively, than wildtype controls, and higher amounts of 4-hydroxynonenal, a product of arachidonate peroxidation. Oxidative stress was associated with an increase in apoptosis, and with 3-fold and 15-fold higher TUNEL positive cells in liver from young and old Gpat1-/- mice, respectively, compared to age-matched controls. Compared to controls, bromodeoxyuridine labeling was 50% and 7-fold higher in livers from young and old Gpat1-/- mice, respectively, but fewer glutathione-S-transferase positive cells were present. Thus, Gpat1-/- liver exhibits increased oxidative stress and sensitivity of the mitochondrial permeability transition pore, and a balanced increase in apoptosis and proliferation.
Teleportation-Based Quantum Computation, Extended Temperley-Lieb Diagrammatical Approach and Yang--Baxter Equation
Creators: name: Zhang, Yong
name: Zhang, Kun
name: Pang, Jinglong
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: This paper focuses on the study of topological features in teleportation-based quantum computation as well as aims at presenting a detailed review on teleportaiton-based quantum computation (Gottesman and Chuang, Nature 402, 390, 1999). In the extended Temperley-Lieb diagrammatical approach, we clearly show that such topological features bring about the fault-tolerant construction of both universal quantum gates and four-partite entangled states more intuitive and simpler. Furthermore, we describe the Yang--Baxter gate by its extended Temperley-Lieb configuration, and then study teleportation-based quantum circuit models using the Yang--Baxter gate. Moreover, we discuss the relationship between the extended Temperley-Lieb diagrammatical approach and the Yang-Baxter gate approach. With these research results, we propose a worthwhile subject, the extended Temperley-Lieb diagrammatical approach, for physicists in quantum information and quantum computation.
description: Latex, 47 pages, many figures
Mapping of an origin of DNA replication in the promoter of fragile X gene FMR1
Creators: name: Brylawski, Bruna P.
name: Cordeiro-Stone, Marila
name: Chastain, Paul D.
name: Cohen, Stephanie M.
name: Kaufman, David G.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: An origin of bidirectional DNA replication was mapped to the promoter of the FMR1 gene in human chromosome Xq27.3, which has been linked to the fragile X syndrome. This origin is adjacent to a CpG island and overlaps the site of expansion of the triplet repeat (CGG) at the fragile X instability site, FRAXA. The promoter region of FMR2 in the FRAXE site (approximately 600 kb away, in chromosome band Xq28) also includes an origin of replication, as previously described. FMR1 transcripts were detected in foreskin and male fetal lung fibroblasts, while FMR2 transcripts were not. However, both FMR1 and FMR2 were found to replicate late in S phase (approximately six hours into the S phase of normal human fibroblasts). The position of the origin of replication relative to the CGG repeat, and perhaps the late replication of these genes, might be important factors in the susceptibility to triplet repeat amplification at the FRAXA and FRAXE sites.
Essential Elements Required for a Successful AI Application in the Healthcare Industry
Creators: name: Muhammad A. B
name: Isa A.I.
Publisher: name: gjrpublication
Year: 2024

description: In a broad sense, artificial intelligence (AI) is any behavior shown by a computer or other system that is comparable to human behavior. Thanks to a type of artificial intelligence called "machine learning," computers can learn from data without explicit human programming. One of the most significant contemporary developments in international healthcare is the use of artificial intelligence (AI) technologies in medicine. Because artificial intelligence-based technologies enable a dramatic reconstruction of the medical diagnostics system and a commensurate reduction in healthcare costs. A sickness must be classified into the appropriate class of illnesses before therapy can start. The disease type can be categorized based on the feature space of the illness. Machine learning algorithms can help address this challenge. This article covers the essential elements required for a successful AI application in the healthcare industry.
Methylation-dependent silencing of CST6 in primary human breast tumors and metastatic lesions
Creators: name: Coleman, William B.
name: Keppler, Daniel
name: Livasy, Chad A.
name: Boyd, Courtney E.
name: Rivenbark, Ashley G.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: CST6 is a breast tumor suppressor gene that is expressed in normal breast epithelium, but is epigenetically silenced as a consequence of promoter hypermethylation in metastatic breast cancer cell lines. In the current study, we investigated the expression and methylation status of CST6 in primary breast tumors and lymph node metastases. 25/45 (56%) primary tumors and 17/20 (85%) lymph node metastases expressed significantly lower levels of cystatin M compared to normal breast tissue. Bisulfite sequencing demonstrated CST6 promoter hypermethylation in 11/23 (48%) neoplastic lesions analyzed, including 3/11 (27%) primary tumors and 8/12 (67%) lymph node metastases. In most cases (12/23, 52%), the expression of cystatin M directly reflected CST6 promoter methylation status. In remaining lesions (8/23, 35%) loss of cystatin M was not associated with CST6 promoter hypermethylation, indicating that other mechanisms can account for loss of CST6 expression. These results show that methylation-dependent silencing of CST6 occurs in a subset of primary breast cancers, but more frequently in metastatic lesions, possibly reflecting progression-related genomic events. To examine this possibility, primary breast tumors and matched lymph node metastases were analyzed. In 2/3 (67%) patients, primary tumors were positive for cystatin M and negative for CST6 promoter methylation, and matched metastatic lesions lacked cystatin M expression and CST6 was hypermethylated. This observation suggests that progression-related epigenetic alterations in CST6 gene expression can accompany metastatic spread from a primary tumor site. Overall, the results of the current investigation suggest that methylation-dependent epigenetic silencing of CST6 represents an important mechanism for loss of CST6 during breast tumorigenesis and/or progression to metastasis.
$^{178}$Hg and asymmetric fission of neutron-deficient pre-actinides
Creators: name: Jhingan, A.
name: Schmitt, C.
name: Lemasson, A.
name: Biswas, S.
name: Kim, Y. H.
name: Ramos, D.
name: Andreyev, A. N.
name: Curien, D.
name: Ciemala, M.
name: Clément, E.
name: Dorvaux, O.
name: De Canditiis, B.
name: Didierjean, F.
name: Duchêne, G.
name: Dudouet, J.
name: Frankland, J.
name: Frémont, G.
name: Goupil, J.
name: Jacquot, B.
name: Raison, C.
name: Ralet, D.
name: Retailleau, B. -M.
name: Stuttgé, L.
name: Tsekhanovich, I.
name: Andreev, A. V.
name: Goriely, S.
name: Hilaire, S.
name: Lemaître, J-F.
name: Möller, P.
name: Schmidt, K. -H.
Publisher: name: arXiv
Year: 2022
Subjects: subject: Nuclear Experiment (nucl-ex)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: Fission at low excitation energy is an ideal playground to probe the impact of nuclear structure on nuclear dynamics. While the importance of structural effects in the nascent fragments is well-established in the (trans-)actinide region, the observation of asymmetric fission in several neutron-deficient pre-actinides can be explained by various mechanisms. To deepen our insight into that puzzle, an innovative approach based on inverse kinematics and an enhanced version of the VAMOS++ heavy-ion spectrometer was implemented at the GANIL facility, Caen. Fission of $^{178}$Hg was induced by fusion of $^{124}$Xe and $^{54}$Fe. The two fragments were detected in coincidence using VAMOS++ supplemented with a new SEcond Detection arm. For the first time in the pre-actinide region, access to the pre-neutron mass and total kinetic energy distributions, and the simultaneous isotopic identification of one the fission fragment, was achieved. The present work describes the experimental approach, and discusses the pre-neutron observables in the context of an extended asymmetric-fission island located south-west of $^{208}Pb. A comparison with different models is performed, demonstrating the importance of this "new" asymmetric-fission island for elaborating on driving effects in fission.
Mass Additivity and A Priori Entailment
Creators: name: McQueen, Kelvin J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: History and Philosophy of Physics (physics.hist-ph)
subject: Classical Physics (physics.class-ph)
subject: FOS: Physical sciences

description: The principle of mass additivity states that the mass of a composite object is the sum of the masses of its elementary components. Mass additivity is true in Newtonian mechanics but false in special relativity. Physicists have explained why mass additivity is true in Newtonian mechanics by reducing it to Newton's microphysical laws. This reductive explanation does not fit well with deducibility theories of reductive explanation such as the modern Nagelian theory of reduction, and the a priori entailment theory of reduction that is prominent in the philosophy of mind. Nonetheless, I argue that a reconstruction of the explanation that incorporates distinctively philosophical concepts in fact fits both theories. I discuss the implications of this result for both theories and for the reductive explanation of consciousness.
Reframing scientometrics: How ontological understanding of science influences what we count and how we interpret it
Creators: name: Emanuel, Kulczycki
Publisher: name: Zenodo
Year: 2023
Subjects: Science of Science
Scientometrics
Poland
Research Evaluation
Science Policy

description: Keynote given at ETH Zürich, 11 October 2023
The second lecture of the Swiss Year of Scientometrics: reframing scientometrics
The event tookplace on 11 October 2023 in collaboration with the CHESS. Prof. Emanuel Kulczycki explored how ontological understanding of science influences what we count and how we interpret it.
Abstract: Scientometrics faces challenges in addressing criticism of university rankings and publication metrics. Merely developing new indicators is not enough; understanding what is being quantified and the reasons behind it is crucial. This lecture explores how an ontological understanding of science influences what we count and how we interpret it. It argues that scientometrics should focus on information flows and view scientists as part of a self-organizing system, rather than competing entities.The lecture highlights how contemporary scientometrics and the effects of research evaluation regimes, including publication pressure and the misuse of metrics, stems from an atomistic and individualistic ontology pioneered by Derek J. de Solla Price. By examining Price's approach, we gain insights into the shaping of our current understanding of science measurement. While Price's paradigm remains unchallenged in Western scientometrics, this lecture explores alternative perspectives that emerged in Central-Eastern European countries over a century ago. By shedding light on neglected historical reflections, this lecture reveals that many attempted solutions were unsuccessful due to underlying ontological assumptions. In conclusion, the lecture outlines lessons from this historical analysis to inform current scientometric practices at both local and global levels.
Heparin cofactor II in atherosclerotic lesions from the Pathobiological Determinants of Atherosclerosis in Youth (PDAY) study
Creators: name: Church, Frank C.
name: Thomas, David B.
name: Rau, Jill C.
name: Deans, Carolyn
name: Koch, Gary G.
name: Malcom, Gray T.
name: Hoffman, Maureane R.
name: Zieske, Arthur W.
name: Strong, Jack P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: Heparin cofactor II (HCII) is a serine protease inhibitor (serpin) that has been shown to be a predictor of decreased atherosclerosis in the elderly and protective against atherosclerosis in mice. HCII inhibits thrombin in vitro and HCII-thrombin complexes have been detected in human plasma. Moreover, the mechanism of protection against atherosclerosis in mice was determined to be the inhibition of thrombin. Despite this evidence, the presence of HCII in human atherosclerotic tissue has not been reported. In this study, using samples of coronary arteries obtained from the Pathobiological Determinants of Atherosclerosis in Youth (PDAY) study, we explore the local relationship between HCII and (pro)thrombin in atherosclerosis. We found that HCII and (pro)thrombin are co-localized in the lipid-rich necrotic core of atheromas. A significant positive correlation between each protein and the severity of the atherosclerotic lesion was present. These results suggest that HCII is in a position to inhibit thrombin in atherosclerotic lesions where thrombin can exert a proatherogenic inflammatory response. However, these results should be tempered by the additional findings from this, and other studies, that indicate the presence of other plasma proteins (antithrombin, albumin, and α1-protease inhibitor) in the same localized region of the atheroma.
Exploration of the Sequence of Antimicrobial Peptide Api-137, a Translation Termination Inhibitor
Creators: name: Skowron, Kornelia Joanna
Publisher: name: University of Illinois at Chicago
Year: 2022
Subjects: Uncategorized

description: Proline-rich antimicrobial peptides (PrAMPs) are endogenously expressed by multicellular organisms as a part of their innate immune response. These PrAMPs have been identified as a source of novel antibiotics. Previous studies indicate that Apidaecin, a PrAMP produced by European honeybees, passively permeates the outer membrane of Gram-negative bacteria and reaches the cytoplasm via the SbmA transporter located in the inner membrane. In the cytoplasm, Apidaecin inhibits translation termination by binding in the nascent peptide exit tunnel after peptidyl-tRNA hydrolysis and trapping release factors on the ribosome. Structural analysis shows that the Apidaecin C-terminus interacts with the P-site t-RNA and the A-site bound release factor, while the N-terminus stretches down the length of the exit tunnel. This orientation mimics that of the nascent peptide, therefore, multiple Apidaecin residues interact with rRNA nucleotides and ribosomal proteins of the exit tunnel; however, it is unclear which of these interactions are necessary for binding and inhibitory action. Informed by structural and biochemical data, synthetic Apidaecin variants were designed, synthesized, and tested to determine necessary binding interactions and to improve its antimicrobial activity and proteolytic stability. Unnatural amino acids and constraints were incorporated into the Apidaecin sequence. This work provides compelling new research avenues for a novel antibiotic mechanism.
Nonrelativistic Approximations of Closed Bosonic String Theory
Creators: name: Hartong, Jelle
name: Have, Emil
Publisher: name: arXiv
Year: 2022
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We further develop the string $1/c^2$ expansion of closed bosonic string theory, where $c$ is the speed of light. The expansion will be performed up to and including the next-to-next-to-leading order (NNLO). We show that the next-to-leading order (NLO) theory is equal to the Gomis--Ooguri string, generalised to a curved target space, provided the target space geometry admits a certain class of co-dimension-2 foliations. We compute the energy of the string up to NNLO for a flat target space with a circle that must be wound by the string, and we show that it agrees with the $1/c^2$ expansion of the relativistic energy. We also compute the algebra of Noether charges for a flat target space and show that this matches order-by-order with an appropriate expansion of the Poincaré algebra, which at NLO gives the string Bargmann algebra. Finally, we expand the phase space action, which allows us to perform the Dirac procedure and pass to the quantum theory. It turns out that the Poisson brackets change at each order, and we show that the normal ordering constant of the relativistic theory, which does not depend on $c$, can be reproduced by the NLO and NNLO theories.
description: 64 pages incl. 3 appendices, 2 figures; v2: updated to published version