cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Feedback Regulation and its Efficiency in Biochemical Networks
Creators: name: Kobayashi, Tetsuya J.
name: Yokota, Ryo
name: Aihara, Kazuyuki
Publisher: name: arXiv
Year: 2015
Subjects: subject: Molecular Networks (q-bio.MN)
subject: Populations and Evolution (q-bio.PE)
subject: FOS: Biological sciences

description: Intracellular biochemical networks fluctuate dynamically due to various internal and external sources of fluctuation. Dissecting the fluctuation into biologically relevant components is important for understanding how a cell controls and harnesses noise and how information is transferred over apparently noisy intracellular networks. While substantial theoretical and experimental advancement on the decomposition of fluctuation was achieved for feedforward networks without any loop, we still lack a theoretical basis that can consistently extend such advancement to feedback networks. The main obstacle that hampers is the circulative propagation of fluctuation by feedback loops. In order to define the relevant quantity for the impact of feedback loops for fluctuation, disentanglement of the causally interlocked influence between the components is required. In addition, we also lack an approach that enables us to infer non-perturbatively the influence of the feedback to fluctuation as the dual reporter system does in the feedforward network. In this work, we resolve these problems by extending the work on the fluctuation decomposition and the dual reporter system. For a single-loop feedback network with two components, we define feedback loop gain as the feedback efficiency that is consistent with the fluctuation decomposition for feedforward networks. Then, we clarify the relation of the feedback efficiency with the fluctuation propagation in an open-looped FF network. Finally, by extending the dual reporter system, we propose a conjugate feedback and feedforward system for estimating the feedback efficiency only from the statistics of the system non-perturbatively.
OCCUPATIONAL EXPOSURES TO NEEDLESTICK, SHARPS INJURY AND BODY FLUID SPLASH AND DETERMINANTS AMONG HEALTH CARE WORKERS AT SELECTED HOSPITALS IN ADDIS ABABA
Creators: name: Getachew Adugna
Publisher: name: Zenodo
Year: 2019

description: Background: Needlestick injuries, sharps injuries, and blood/body fluid splash are hazards to health care professionals in their working area. Around twenty bloodborne pathogens are known to be transmitted through these occupational injuries. This problem alters the health status of health care professionals (HCPs) in different ways, including physically, mentally, and psychologically. Even though HCPs are affected at a high rate, there is a low injury report to a higher level. Objective: To assess the prevalence of occupational exposure to needlestick injuries, Sharp injuries, and body fluid splash with their determinants among health care professionals of governmental hospitals in Addis Ababa. Methods: Institution based cross-sectional study was conducted by self-administered questionnaire among health care professionals in six selected hospitals. Data was collected from March 2019 to April 2019, with the study sample size of 438. Six government hospitals selected via simple random sampling (lottery method) from twelve hospitals. Data were gathered using a self-administered questionnaire. SPSS version 25 used for data analysis. The type of analysis was bivariate and multivariate logistic regression with 95% confidence interval.
Vlasov simulation of laser-driven shock acceleration and ion turbulence
Creators: name: Grassi, Anna
name: Fedeli, Luca
name: Sgattoni, Andrea
name: Macchi, Andrea
Publisher: name: arXiv
Year: 2015
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: We present a Vlasov, i.e. a kinetic Eulerian simulation study of nonlinear collisionless ion-acoustic shocks and solitons excited by an intense laser interacting with an overdense plasma. The use of the Vlasov code avoids problems with low particle statistics and allows a validation of particle-in-cell results. A simple original correction to the splitting method for the numerical integration of the Vlasov equation has been implemented in order to ensure the charge conservation in the relativistic regime. We show that the ion distribution is affected by the development of a turbulence driven by the relativistic "fast" electron bunches generated at the laser-plasma interaction surface. This leads to the onset of ion reflection at the shock front in an initially cold plasma where only soliton solutions without ion reflection are expected to propagate. We give a simple analytic model to describe the onset of the turbulence as a nonlinear coupling of the ion density with the fast electron currents, taking the pulsed nature of the relativistic electron bunches into account.
23 February 1848: Villiers, Katharine (-1874) to Lewis, Theresa (1803-1865)
Creators: name: Orchard, Jack
Publisher: name: University of Oxford
Year: 2023
Subjects: classificationCode: 430201
subject: Archival, repository and related studies

description: A manuscript letter from the Bodleian Special Collections which has been transcribed, edited, and annotated by students participating in the Bodleian Student Editions workshop series, organised by Mike Webb, curator of Early Modern Manuscripts, and Miranda Lewis, Digital Editor of Early Modern Letters Online.
22 March 1848: Villiers, Katharine (-1874) to Lewis, Theresa (1803-1865)
Creators: name: Orchard, Jack
Publisher: name: University of Oxford
Year: 2023
Subjects: classificationCode: 430201
subject: Archival, repository and related studies

description: A manuscript letter from the Bodleian Special Collections which has been transcribed, edited, and annotated by students participating in the Bodleian Student Editions workshop series, organised by Mike Webb, curator of Early Modern Manuscripts, and Miranda Lewis, Digital Editor of Early Modern Letters Online.
Large deviations of Rouse polymer chain: First passage problem
Creators: name: Cao, Jing
name: Zhu, Jian
name: Wang, Zuowei
name: Likhtman, Alexei E.
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: The purpose of this paper is to investigate several analytical methods of solving first passage (FP) problem for the Rouse model, a simplest model of a polymer chain. We show that this problem has to be treated as a multi-dimensional Kramers' problem, which presents rich and unexpected behavior. We first perform direct and forward-flux sampling (FFS) simulations, and measure the mean first-passage time $τ(z)$ for the free end to reach a certain distance $z$ away from the origin. The results show that the mean FP time is getting faster if the Rouse chain is represented by more beads. Two scaling regimes of $τ(z)$ are observed, with transition between them varying as a function of chain length. We use these simulations results to test two theoretical approaches. One is a well known asymptotic theory valid in the limit of zero temperature. We show that this limit corresponds to fully extended chain when each chain segment is stretched, which is not particularly realistic. A new theory based on the well known Freidlin-Wentzell theory is proposed, where dynamics is projected onto the minimal action path. The new theory predicts both scaling regimes correctly, but fails to get the correct numerical prefactor in the first regime. Combining our theory with the FFS simulations lead us to a simple analytical expression valid for all extensions and chain lengths. One of the applications of polymer FP problem occurs in the context of branched polymer rheology. In this paper, we consider the arm-retraction mechanism in the tube model, which maps exactly on the model we have solved. The results are compared to the Milner-McLeish theory without constraint release, which is found to overestimate FP time by a factor of 10 or more.
Trajectories of group and individual-level structural brain network organization from birth to childhood and their cognitive relevance
Creators: name: Woodburn, Mackenzie Allan
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2020

description: Brain networks are theorized to become more segregated to support early cognitive specialization, and then later increase integration between networks to support more complex cognition across development. The present study examined the organization of structural brain networks derived from cortical thickness during infancy to childhood in a longitudinal sample (0-6 years). On the group level, we observed a shift towards increasing network segregation at the second year of life, and a later shift towards network integration at year six. This study also related subject-based maturational coupling across different developmental timeframes to cognitive outcomes at 7-10 years. Protracted integration of maturational coupling throughout infancy into middle childhood (0-6 years) was correlated with working memory performance in later childhood (7-10 years). These results support the model that describes early increasing segregation followed by later integration, and demonstrate that integrated structural maturation from infancy to childhood supports higher order cognition like working memory.
12 December 1847: Villiers, Katharine (-1874) to Lewis, Theresa (1803-1865)
Creators: name: Orchard, Jack
Publisher: name: University of Oxford
Year: 2023
Subjects: classificationCode: 430201
subject: Archival, repository and related studies

description: A manuscript letter from the Bodleian Special Collections which has been transcribed, edited, and annotated by students participating in the Bodleian Student Editions workshop series, organised by Mike Webb, curator of Early Modern Manuscripts, and Miranda Lewis, Digital Editor of Early Modern Letters Online.
Why Random Reshuffling Beats Stochastic Gradient Descent
Creators: name: Gürbüzbalaban, Mert
name: Ozdaglar, Asuman
name: Parrilo, Pablo
Publisher: name: arXiv
Year: 2015
Subjects: subject: Optimization and Control (math.OC)
subject: FOS: Mathematics

description: We analyze the convergence rate of the random reshuffling (RR) method, which is a randomized first-order incremental algorithm for minimizing a finite sum of convex component functions. RR proceeds in cycles, picking a uniformly random order (permutation) and processing the component functions one at a time according to this order, i.e., at each cycle, each component function is sampled without replacement from the collection. Though RR has been numerically observed to outperform its with-replacement counterpart stochastic gradient descent (SGD), characterization of its convergence rate has been a long standing open question. In this paper, we answer this question by showing that when the component functions are quadratics or smooth and the sum function is strongly convex, RR with iterate averaging and a diminishing stepsize $α_k=Θ(1/k^s)$ for $s\in (1/2,1)$ converges at rate $Θ(1/k^{2s})$ with probability one in the suboptimality of the objective value, thus improving upon the $Ω(1/k)$ rate of SGD. Our analysis draws on the theory of Polyak-Ruppert averaging and relies on decoupling the dependent cycle gradient error into an independent term over cycles and another term dominated by $α_k^2$. This allows us to apply law of large numbers to an appropriately weighted version of the cycle gradient errors, where the weights depend on the stepsize. We also provide high probability convergence rate estimates that shows decay rate of different terms and allows us to propose a modification of RR with convergence rate ${\cal O}(\frac{1}{k^2})$.
title: Understanding antimicrobial activity in live cells
Creators: name: Serrano Sanchez, Angela
Publisher: name: University of Kent
Year: 2022

description: The critical rise of antimicrobial resistance (AMR) requires the discovery of new antibiotics, particularly against Gram-negative bacteria. The permeability barrier of bacteria is a vital property to consider within the drug development process. In this work, we describe a new NMR method to assess membrane permeability and membrane interaction affinity of a new family of antimicrobial compounds exploiting the enhanced paramagnetic relaxation enhancement (PRE) effect induced by solvent paramagnetic agents in non-permeable drugs mixed with lipid vesicles. The results exhibited differences in the permeability rate and membrane interaction affinity of drugs among membranes with different lipid composition, confirming that our method is applicable to any type of cell/bacterial membrane. In addition, we have expanded this assay to live cells making use of a NMR-coupled bioreactor. With this setup, we have been able to measure NMR metabolomics to simultaneously monitor membrane permeation, membrane affinity and changes in the bacterial metabolism as a result of the addition of antimicrobial agents, providing evidence on their mechanism of action at the metabolite level. In general, our study introduces a new method for assessing drug permeability in lipid vesicles or live cells that will allow the design of more efficacious drugs and antimicrobial agents in a standard chemistry lab environment.
Waiting for rare entropic fluctuations
Creators: name: Saito, Keiji
name: Dhar, Abhishek
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: Non-equilibrium fluctuations of various stochastic variables, such as work and entropy production, have been widely discussed recently in the context of large deviations, cumulants and fluctuation relations. Typically, one looks at the distribution of these observables, at large fixed time. To characterize the precise stochastic nature of the process, we here address the distribution in the time domain. In particular, we focus on the first passage time distribution (FPTD) of entropy production, in several realistic models. We find that the fluctuation relation symmetry plays a crucial role in getting the typical asymptotic behavior. Similarities and differences to the simple random walk picture are discussed. For a driven particle in the ring geometry, the mean residence time is connected to the particle current and the steady state distribution, and it leads to a fluctuation relation-like symmetry in terms of the FPTD.
description: 5+7 pages, 3 figures
Prevalence of Autoimmune Hemolytic Anemia in HIV Infected Anemic Adults, a Cross Sectional study at Tikur Anbessa Specialized Teaching Hospital from June 5, 2015 to September 10, 2015, Addis Ababa,
Creators: name: Mignot Taye
Publisher: name: Zenodo
Year: 2024

description: Background:- Hematologic manifestations in HIV/AIDS positive patients are many. A high prevalence of anemia and significantly reduced white blood cell and neutrophil counts were observed in HIV-infected individuals. Presence of auto antibody also contributes for the development of anemia in HIV positive individuals. Few studies are conducted to show the prevalence of anemia in HIV positive individuals, but there is no documented data that rule out the prevalence of AIHA in HIV positive individuals in Ethiopia. Objective:- To determine the prevalence of autoimmune haemolytic anemia in HIV-infected adult patients at Tikur Anbessa Specialized teaching Hospital, Addis Ababa, Ethiopia. Methods:- Hospital based cross sectional study was conducted on 384 HIV positive individuals using convenient sampling method at Tikur Anbessa Hospital from June 5, 2015 to September 10, 2015. Participants’ soco-demographic data, CD4 result and some important information was extracted from participants’ records; from patient card and request paper using Microsoft excel. And 5 ml of venous blood was collected for determination of HGB, RBC count, RBC indices, reticulocyte count and other CBC results. After all, DAT was performed and blood film examination was done to confirm hemolysis. Finally data was imported and analyzed using SPSS version 16 statistical soft ware package, and Descriptive statistic and Chi-square tests were used.
The structure of post-starburst galaxies at $0.5 < z < 2$: evidence for two distinct quenching routes at different epochs
Creators: name: Maltby, David T.
name: Almaini, Omar
name: Wild, Vivienne
name: Hatch, Nina A.
name: Hartley, William G.
name: Simpson, Chris
name: Rowlands, Kate
name: Socolovsky, Miguel
Publisher: name: arXiv
Year: 2018
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present an analysis of the structure of post-starburst (PSB) galaxies in the redshift range $0.5 < z < 2$, using a photometrically-selected sample identified in the Ultra Deep Survey (UDS) field. We examine the structure of $\sim80$ of these transient galaxies using radial light $μ(r)$ profiles obtained from CANDELS $\textit{Hubble Space Telescope}$ near-infrared/optical imaging, and compare to a large sample of $\sim2000$ passive and star-forming galaxies. For each population, we determine their typical structural properties (effective radius $r_{\rm e}$, Sérsic index $n$) and find significant differences in PSB structure at different epochs. At high redshift ($z > 1$), PSBs are typically massive ($M_* > 10^{10}\rm\,M_{\odot}$), very compact and exhibit high Sérsic indices, with structures that differ significantly from their star-forming progenitors but are similar to massive passive galaxies. In contrast, at lower redshift ($0.5 < z < 1$), PSBs are generally of low mass ($M_* < 10^{10}\rm\,M_{\odot}$) and exhibit compact but less concentrated profiles (i.e. lower Sérsic indices), with structures similar to low-mass passive discs. Furthermore, for both epochs we find remarkably consistent PSB structure across the optical/near-infrared wavebands (which largely trace different stellar populations), suggesting that any preceding starburst and/or quenching in PSBs was not strongly centralized. Taken together, these results imply that PSBs at $z > 1$ have been recently quenched during a major disruptive event (e.g. merger or protogalactic collapse) which formed a compact remnant, while at $z < 1$ an alternative less disruptive process is primarily responsible. Our results suggest that high-$z$ PSBs are an intrinsically different population to those at lower redshifts, and indicate different quenching routes are active at different epochs.
description: 21 pages, 12 figures, accepted for publication in MNRAS
07 August 1847: Villiers, Katharine (-1874) to Lewis, Theresa (1803-1865)
Creators: name: Orchard, Jack
Publisher: name: University of Oxford
Year: 2023
Subjects: classificationCode: 430201
subject: Archival, repository and related studies

description: A manuscript letter from the Bodleian Special Collections which has been transcribed, edited, and annotated by students participating in the Bodleian Student Editions workshop series, organised by Mike Webb, curator of Early Modern Manuscripts, and Miranda Lewis, Digital Editor of Early Modern Letters Online.
18 June 1847: Villiers, Katharine (-1874) to Lewis, Theresa (1803-1865)
Creators: name: Orchard, Jack
Publisher: name: University of Oxford
Year: 2023
Subjects: classificationCode: 430201
subject: Archival, repository and related studies

description: A manuscript letter from the Bodleian Special Collections which has been transcribed, edited, and annotated by students participating in the Bodleian Student Editions workshop series, organised by Mike Webb, curator of Early Modern Manuscripts, and Miranda Lewis, Digital Editor of Early Modern Letters Online.