cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Comparative Transcriptomics Reveals Clues for Differences in Pathogenicity between Hysterothylacium aduncum, Anisakis simplex sensu stricto and Anisakis pegreffii
Creators: name: Cavallero, Serena
name: Lombardo, Fabrizio
name: Salvemini, Marco
name: Pizzarelli, Antonella
name: Cantacessi, Cinzia
name: D’Amelio, Stefano
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: Hysterothylacium
Anisakis
transcriptome
pharyngeal transcripts
DEGs

description: Ascaridoid nematodes are widespread in marine fishes. Despite their major socioeconomic importance, mechanisms associated to the fish-borne zoonotic disease anisakiasis are still obscure. RNA-Seq and de-novo assembly were herein applied to RNA extracted from larvae and dissected pharynx of Hysterothylacium aduncum (HA), a non-pathogenic nematode. Assembled transcripts in HA were annotated and compared to the transcriptomes of the zoonotic species Anisakis simplex sensu stricto (AS) and Anisakis pegreffii (AP). Approximately 60,000,000 single-end reads were generated for HA, AS and AP. Transcripts in HA encoded for 30,254 putative peptides while AS and AP encoded for 20,574 and 20,840 putative peptides, respectively. Differential gene expression analyses yielded 471, 612 and 526 transcripts up regulated in the pharynx of HA, AS and AP. The transcriptomes of larvae and pharynx of HA were enriched in transcripts encoding collagen, peptidases, ribosomal proteins and in heat-shock motifs. Transcripts encoding proteolytic enzymes, anesthetics, inhibitors of primary hemostasis and virulence factors, anticoagulants and immunomodulatory peptides were up-regulated in AS and AP pharynx. This study represents the first transcriptomic characterization of a marine parasitic nematode commonly recovered in fish and probably of negligible concern for public health.
Adiabatic Approximation in the Density Matrix Approach: Non-Degenerate Systems
Creators: name: Pinto, A. C. Aguiar
name: Romero, K. M. Fonseca
name: Thomaz, M. T.
Publisher: name: arXiv
Year: 2002
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We study the adiabatic limit in the density matrix approach for a quantum system coupled to a weakly dissipative medium. The energy spectrum of the quantum model is supposed to be non-degenerate. In the absence of dissipation, the geometric phases for periodic Hamiltonians obtained previously by M.V. Berry are recovered in the present approach. We determine the necessary condition satisfied by the coefficients of the linear expansion of the non-unitary part of the Liouvillian in order to the imaginary phases acquired by the elements of the density matrix, due to dissipative effects, be geometric. The results derived are model-independent. We apply them to spin 1/2 model coupled to reservoir at thermodynamic equilibrium.
description: 24 pages (new version), accepted for publication in Physica A
Active galactic nuclei imaging programs of the RadioAstron mission
Creators: name: Bruni, Gabriele
name: Savolainen, Tuomas
name: Gómez, Jose Luis
name: Lobanov, Andrei P.
name: Kovalev, Yuri Y.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Imaging relativistic jets in active galactic nuclei (AGN) at angular resolution significantly surpassing that of the ground-based VLBI at centimetre wavelengths is one of the key science objectives of the RadioAstron space-VLBI mission. There are three RadioAstron imaging key science programs that target both nearby radio galaxies and blazars, with one of the programs specifically focusing on polarimetry of the jets. The first images from these programs reach angular resolution of a few tens of microarcseconds and reveal unprecedented details about the jet collimation profile, magnetic field configuration, and Kelvin-Helmholtz instabilities along the flow in some of the most studied AGN (3C 84, BL Lac, 3C 273, S5 0836+710). Here we give an overview of the goals and strategy of these three ongoing programs, highlight their early results, and discuss the challenges of space-VLBI imaging.
description: Accepted on the Advances in Space Research (ASR) special issue entitled "High-resolution Space-Borne Radio Astronomy"
A Novel Approach for Mixed Manual/Connected Automated Freeway Traffic Management
Creators: name: Li, Duo
name: Wagner, Peter
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: connected vehicle
freeway traffic control
type-2 fuzzy logic

description: Freeway traffic management and control often rely on input from fixed-point sensors. A sufficiently high sensor density is required to ensure data reliability and accuracy, which results in high installation and maintenance costs. Moreover, fixed-point sensors encounter difficulties to provide spatiotemporally and wide-ranging information due to the limited observable area. This research exploits the utilization of connected automated vehicles (CAVs) as an alternative data source for freeway traffic management. To handle inherent uncertainty associated with CAV data, we develop an interval type 2 fuzzy logic-based variable speed limit (VSL) system for mixed traffic. The simulation results demonstrate that when more 10% CAVs are deployed, the performance of the proposed CAV-based system can approach that of the detector-based system. It is demonstrated in addition that the introduction of CAVs may make VSL obsolete at very high CAV-equipment rates.
Temporal Density Extrapolation using a Dynamic Basis Approach
Creators: name: Krempl, Georg
name: Lang, Dominik
name: Hofer, Vera
Publisher: name: arXiv
Year: 2019
Subjects: subject: Machine Learning (cs.LG)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences

description: Density estimation is a versatile technique underlying many data mining tasks and techniques,ranging from exploration and presentation of static data, to probabilistic classification, or identifying changes or irregularities in streaming data. With the pervasiveness of embedded systems and digitisation, this latter type of streaming and evolving data becomes more important. Nevertheless, research in density estimation has so far focused on stationary data, leaving the task of of extrapolating and predicting density at time points outside a training window an open problem. For this task, Temporal Density Extrapolation (TDX) is proposed. This novel method models and predicts gradual monotonous changes in a distribution. It is based on the expansion of basis functions, whose weights are modelled as functions of compositional data over time by using an isometric log-ratio transformation. Extrapolated density estimates are then obtained by extrapolating the weights to the requested time point, and querying the density from the basis functions with back-transformed weights. Our approach aims for broad applicability by neither being restricted to a specific parametric distribution, nor relying on cluster structure in the data.It requires only two additional extrapolation-specific parameters, for which reasonable defaults exist. Experimental evaluation on various data streams, synthetic as well as from the real-world domains of credit scoring and environmental health, shows that the model manages to capture monotonous drift patterns accurately and better than existing methods. Thereby, it requires not more than 1.5-times the run time of a corresponding static density estimation approach.
description: Accepted for publication in Data Mining and Knowledge Discovery, Special issue of the ECML/PKDD 2019 Journal Track, Springer, 2019
Role of Employees Productivity and Organization Performance in Telecommunications Companies in Mogadishu, Somalia
Creators: name: Ibrahim, Hussein Ali
Publisher: name: Zenodo
Year: 2025
Subjects: Employees Productivity and Organization Performance in Telecommunications Companies in Mogadishu, Somalia
Organization Performance
Telecommunications Companies in Mogadishu, Somalia

description: Abstract

 Performance can be expressed through evident outcomes such as sales increase, efficiency, better productivity, return on investment, and quality improvement. However, hidden issues, such as customer satisfaction and employee knowledge and skills, may result from knowledge creation, accumulation, and spread within the organization. Performance represents a state of competitiveness achieved through effectiveness and productivity, ensuring a strong market presence. Specialists in various fields, including strategic planners, operations, finance, legal, and organizational development, are concerned with organizational performance. Performance evaluation involves assessing a company's capability to achieve constituents' aspiration levels using efficiency, effectiveness, or social referent criteria (Maria, 2016)

Organizational performance refers to the actual output or results of an organization measured against its intended outputs, goals, and objectives. It depends on how it is managedand the active involvement of employees in fulfilling strategic objectives. Fulfilling strategic goals is achieved through observing established plans and procedures, creating and accumulating new knowledge, and focusing on internal processes. Some organizations focus on customer relationships, while others focus on product development and market entry. The third group focuses on internal processes, sharing best practices, reducing costs, and improving efficiency (Doval, 2020)

Employee productivity may be hard to measure, but it has a direct effect on a company's profits. An employer fills his staff with productivity in mind and can get a handle on a worker's capabilities during the initial job interview. However, several factors on the job help maximize what an employee does on the job. Human resources are closely scrutinized for productivity in organizations, with activities such as pay, appraisal systems, training, selection, job design, and compensation directly concerned with productivity. Controlling labor costs and increasing productivity through clearer linkages between pay and performance are considered crucial components of human resource management (HRM) to achieve a competitive advantage. Performance is equivalent to the famous 3Es: economy, efficiency, and effectiveness of a certain program or activity. Organizational performance is the ability of the organization to attain its goals by using resources efficiently and effectively. Performance can be assessed based on information obtained through primary or secondary resources ( Matui, 2017)
Costly Inspections and Little Abatement: An Evaluation of I/M Efficiency
Creators: name: Giguere, Chris
name: Giguere, Chris
Publisher: name: Unknown
Year: 2016
Subjects: subject: Environmental Economics and Policy
subject: environmental regulation
subject: air quality
subject: emissions
subject: benefits
subject: costs
subject: net benefits
subject: benefit-cost analysis
subject: efficiency
subject: repairs
subject: scrappage
subject: I/M
subject: big data

description: Automobile emissions inspection and maintenance (I/M) programs are used by 31 states and Washington D.C. as well as a number of foreign counties to maintain or improve ambient air quality. Past literature provides evidence that the current design of most programs in the United States is ineffective. The efficiency of these programs, however, has yet to be analyzed. I fill a considerable gap in the literature by developing a comprehensive estimation framework to evaluate the efficiency of I/M. I use data from the North Carolina I/M program between 1999 and 2013 to estimate seven e m p i r i c a l m o d e l s r e q u i r e d b y t h e f r a m e w o r k . T h e c o s t s a n d b e n e f i t s f r o m b o t h I / M i n d u c e d r e p a i r s a n d s c r a p p a g e a r e t h e n c a l c u l a t e d f o r v a r i o u s r e g i m e s u s i n g d i f f e r e n t i n s p e c t i o n f r e q u e n c i e s a n d automobile exemptions. My results indicate that the North Carolina I/M program, as it existed between 1999 and 2013 was inefficient. The estimated mean benefits, costs, and net benefits were $28.5, $73.0, and ­$44.5 per year respectively, in millions of June 2015 U.S. dollars. The recent increase in automobile exemptions (s elective automobile targeting) in North Carolina’s program is estimated to decrease benefits and costs by 11 and 49 percent. Thus net benefits will increase by 63 percent to ­$16.3 million per year. Further reductions to the scope of automobiles inspected are estimated to generate positive net benefits. For example, a regime that inspects only automobiles older than 5 years and are driven more than 20 thousand miles per year is estimated to generate net benefits of $2.13 million per year. These efficiency gains are possible because automobiles are selected for inspections based on where they sit on their emissions trajectory. Programs that fail to account for this “location” are estimated to inspect too many automobiles and yield negative net benefits.
QCD sum rule analysis of V and A current correlators from tau-decay data
Creators: name: Zyablyuk, K. N.
Publisher: name: arXiv
Year: 2001
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: 2-point correlators of vector and axial currents, obtained from tau-decay data, are studied within the framework of perturbative QCD and Operator Product Expansion. Various sum rules, obtained from Borel transformation of the correlators in complex plane, are used to separate the contributions of different operators from each other. The analysis confirms the Q^2-dependence of the correlators in the space-like region, predicted by QCD+OPE. However the operator values are found to be in certain disagreement with the estimations, obtained from other data.
description: Invited talk at Workshop on e+e- physics at intermediate energies, SLAC, May 2001, (T18), 6 pages, 5 figures, latex
Is MyPlate really Affordable? An analysis of SNAP Benefits and the actual cost of eating according to the dietary guidelines
Creators: name: Mulik, Kranti
name: Haynes Maslow, Lindsey
name: Mulik, Kranti
name: Haynes Maslow, Lindsey
Publisher: name: Unknown
Year: 2016
Subjects: subject: Agricultural and Food Policy
subject: Consumer/Household Economics
subject: Food Consumption/Nutrition/Food Safety
subject: Health Economics and Policy
subject: SNAP
subject: MyPlate
subject: Budgetary shortfall

description: The Supplemental Nutrition Assistance Program (SNAP) is a vital federal food assistance program under The Farm Bill that offers benefits usable as cash for the purchase of food by lower-income individuals. For lower-income families, SNAP benefits help provide assistance to consume heathy foods. However, current benefits from SNAP are insufficient to support a healthy diet recommended by federal nutrition guidelines (MyPlate). We estimate the funds required to support a MyPlate diet and the current budgetary shortfall in the SNAP program needed for recipients to adhere to a nutritionally sound diet.
Matrix Elements and Parton Showers in Hadronic Interactions
Creators: name: Krauss, F.
Publisher: name: arXiv
Year: 2002
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: A method is suggested to combine tree level QCD matrix for the production of multi jet final states and the parton shower in hadronic interactions. The method follows closely an algorithm developed recently for the case of $e^+e^-$ annihilations.
description: 14 pages, 8 figures
Common Functions of Disordered Proteins across Evolutionary Distant Organisms
Creators: name: Wallmann, Arndt
name: Kesten, Christopher
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: intrinsically disordered proteins
protein function
plants
functional comparison

description: Intrinsically disordered proteins and regions typically lack a well-defined structure and thus fall outside the scope of the classic sequence−structure−function relationship. Hence, classic sequence- or structure-based bioinformatic approaches are often not well suited to identify homology or predict the function of unknown intrinsically disordered proteins. Here, we give selected examples of intrinsic disorder in plant proteins and present how protein function is shared, altered or distinct in evolutionary distant organisms. Furthermore, we explore how examining the specific role of disorder across different phyla can provide a better understanding of the common features that protein disorder contributes to the respective biological mechanism.
Algorithmic scalability in globally constrained conservative parallel discrete event simulations of asynchronous systems
Creators: name: Kolakowska, A.
name: Novotny, M. A.
name: Korniss, G.
Publisher: name: arXiv
Year: 2002
Subjects: subject: Distributed, Parallel, and Cluster Computing (cs.DC)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Data Structures and Algorithms (cs.DS)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences
subject: D.1.3; F.1.1; F.2.0; G.3

description: We consider parallel simulations for asynchronous systems employing L processing elements that are arranged on a ring. Processors communicate only among the nearest neighbors and advance their local simulated time only if it is guaranteed that this does not violate causality. In simulations with no constraints, in the infinite L-limit the utilization scales (Korniss et al, PRL 84, 2000); but, the width of the virtual time horizon diverges (i.e., the measurement phase of the algorithm does not scale). In this work, we introduce a moving window global constraint, which modifies the algorithm so that the measurement phase scales as well. We present results of systematic studies in which the system size (i.e., L and the volume load per processor) as well as the constraint are varied. The constraint eliminates the extreme fluctuations in the virtual time horizon, provides a bound on its width, and controls the average progress rate. The width of the window constraint can serve as a tuning parameter that, for a given volume load per processor, could be adjusted to optimize the utilization so as to maximize the efficiency. This result may find numerous applications in modeling the evolution of general spatially extended short-range interacting systems with asynchronous dynamics, including dynamic Monte Carlo studies.
description: 14 pages, 11 figures
Metric-tensor flexible-cell algorithm for isothermal-isobaric molecular dynamics simulations
Creators: name: Hernandez, E.
Publisher: name: arXiv
Year: 2001
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: An extended Hamiltonian approach to conduct isothermal-isobaric molecular dynamics simulations with full cell flexibility is presented. The components of the metric tensor are used as the fictitious degrees of freedom for the cell, thus avoiding the problem of spurious cell rotations and artificial symmetry breaking effects present in the original Parrinello-Rahman scheme. This is complemented by the Nose-Poincare approach for isothermal sampling. The combination of these two approaches leads to equations of motion that are Hamiltonian in structure, and which can therefore be solved numerically using recently developed powerful symplectic integrators. One such integrator, the generalised leap-frog, is employed to provide a numerical algorithm for integrating the isothermal-isobaric equations of motion obtained.
description: REVTeX 4.0, 10 pages, 7 figures, to appear in Journal of Chemical Physics
Factorial Structure and Validity of Depression (PHQ-9) and Anxiety (GAD-7) Scales after Traumatic Brain Injury
Creators: name: Teymoori, Ali
name: Gorbunova, Anastasia
name: Haghish, Fardzadeh E.
name: Real, Ruben
name: Zeldovich, Marina
name: Wu, Yi-Jhen
name: Polinder, Suzanne
name: Asendorf, Thomas
name: Menon, David
name: Investigators, CENTER-TBI
name: V. Steinbüchel, Nicole
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: depression
anxiety
bifactorial model
validity
comorbidity

description: Background: The dimensionality of depression and anxiety instruments have recently been a source of controversy. Objectives and Design: In a European-wide sample of patients after Traumatic Brain Injury (TBI), we aim to examine the factorial structure, validity, and association of the Patient Health Questionnaire for depression (PHQ-9) and the Generalized Anxiety Disorder (GAD-7) instruments. This study is based on longitudinal observational data. We conducted analyses of factorial structure and discriminant validity of outcomes six-months after TBI. We also examined the prevalence, co-occurrence, and changes of scores on the PHQ-9 and GAD-7 at 3-, 6-, and 12-month post-TBI assessments. Participants: At six-months post-TBI assessment, 2137 (738 (34.5%) women) participants completed the PHQ-9 and GAD-7 questionnaires. For the longitudinal analysis, we had 1922 participants (672 (35.0%) women). Results: The results of exploratory factor analysis suggested a general latent construct underlying both PHQ-9 and GAD-7 measures. Confirmatory factor analyses showed a slight improvement in the fit indices for the bifactorial model. The Omega hierarchical test clearly differentiated two subfactors of PHQ-9 and GAD-7 items over and above the underlying general factor; however, most of the variance (85.0%) was explained by the general factor and the explained variance of the subfactors was small. The PHQ-9 and GAD-7 performed similarly in detecting post-traumatic stress disorder (PTSD). As defined by conventional cut-offs, depression and anxiety have different prevalence rates in the sample. The scales also differed in their relationships with the short form of health survey (SF-36v2) subscales. The longitudinal analysis showed high stability of depression and anxiety symptoms: 49−67% of the post-TBI patients with comorbid depression and anxiety reported the persistence of the symptoms over time. Discussion: The factorial structure analysis favors a general latent construct underlying both depression and anxiety scales among patients after TBI. We discuss the implications our findings and future research directions.
Additional file 1 of Long-read-based human genomic structural variation detection with cuteSV
Creators: name: Jiang, Tao
name: Liu, Yongzhuang
name: Jiang, Yue
name: Li, Junyi
name: Gao, Yan
name: Cui, Zhe
name: Liu, Yadong
name: Liu, Bo
name: Wang, Yadong
Publisher: name: figshare
Year: 2020
Subjects: subject: Biophysics
subject: Biochemistry
subject: Space Science
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Cancer
subject: Virology

description: Additional file 1: Figs. S1-S11. Supplemental Figures. Tables S1-S20. Supplemental Tables. Supplementary Notes. Command lines for evaluation.
Heteroporus Cameron 1939
Creators: name: Hlaváč, Peter
name: Newton, Alfred F.
name: Maruyama, Munetoshi
Publisher: name: Zenodo
Year: 2011
Subjects: Biodiversity
Taxonomy
Fungi
Basidiomycota
Agaricomycetes
Polyporales
Meruliaceae
Heteroporus

description: Heteroporus Cameron
 Heteroporus Cameron, 1939d: 25. Type species: Heteroporus ferrugineus Cameron, by monotypy ferrugineus Cameron, 1939d: 25 (Heteroporus, TL: G. Tangkoeban Prahoe, 4000-5000 feet) Distribution: Indonesia (Java)
description: Published as part of Hlaváč, Peter, Newton, Alfred F. & Maruyama, Munetoshi, 2011, World catalogue of the species of the tribe Lomechusini (Staphylinidae: Aleocharinae) 3075, pp. 1-151 in Zootaxa 3075 on page 45
Translational readthrough of GLA nonsense mutations suggests dominant-negative effects exerted by the interaction of wild-type and missense variants
Creators: name: Lombardi, Silvia
name: Ferrarese, Mattia
name: Marchi, Saverio
name: Pinton, Paolo
name: Pinotti, Mirko
name: Bernardi, Francesco
name: Branchini, Alessio
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Plant Biology

description: Nonsense mutations are relatively frequent in the rare X-linked lysosomal α-galactosidase A (α-Gal) deficiency (Fabry disease; FD), but have been poorly investigated. Here, we evaluated the responsiveness of a wide panel (n = 14) of GLA premature termination codons (PTCs) to the RNA-based approach of drug-induced readthrough through expression of recombinant α-Gal (rGal) nonsense and missense variants. We identified four high-responders to the readthrough-inducing aminoglycoside G418 in terms of full-length protein (C56X/W209X, ≥10% of wild-type rGal) and/or activity (Q119X/W209X/Q321X, ~5-7%), resulting in normal (Q119X/Q321X) or reduced (C56X, 0.27 ± 0.11; W209X, 0.35 ± 0.1) specific activity. To provide mechanistic insights we investigated the predicted amino acid substitutions mediated by readthrough (W209C/R, C56W/R), which resulted in correct lysosomal localization and appreciable protein/activity levels for the W209C/R variants. Differently, the C56W/R variants, albeit appreciably produced and localized into lysosomes, were inactive, thus indicating detrimental effects of substitutions at this position. Noticeably, when co-expressed with the functional W209C or W209R variants, the wild-type rGal displayed a reduced specific activity (0.5 ± 0.2 and 0.6 ± 0.2, respectively) that, considering the dimeric features of the α-Gal enzyme, suggested dominant-negative effects of missense variants through their interaction with the wild-type. Overall, we provide a novel mechanism through which amino acids inserted during readthrough might impact on the functional protein output. Our findings may also have implications for the interpretation of pathological phenotypes in heterozygous FD females, and for other human disorders involving dimeric or oligomeric proteins.
Store Choice and Consumer Behavior in Food Deserts: An Empirical Application of the Distance Metric Method
Creators: name: Chenarides, Lauren
name: Jaenicke, Edward C.
name: Chenarides, Lauren
name: Jaenicke, Edward C.
Publisher: name: Unknown
Year: 2016
Subjects: subject: Agricultural and Food Policy
subject: Consumer/Household Economics
subject: Demand and Price Analysis
subject: Food Consumption/Nutrition/Food Safety
subject: Food Security and Poverty
subject: store choice
subject: scanner data
subject: food access
subject: food deserts
subject: distance metric method

description: Shopping and store-choice decisions are intertwined with firms’ decisions to enter or exit a market, as well as with heterogeneous consumer demographics. The importance of food access becomes apparent in determining where households choose to purchase food, as consumers residing in underserved areas are faced with shopping at non-traditional stores that may result in negative welfare outcomes. Research regarding consumer purchasing behavior has traditionally looked at store choice as a nested discrete choice decision; however, we propose an alternative approach that models consumer store choice preferences for store attribute bundles, including product assortment, store services, and price via the Distance Metric (DM) method of Pinkse, Slade, and Brett (2002). Methodologically, the use of the DM method offers a straightforward way to measure substitution patterns between stores with similar attributes. In addition, the importance of product assortment, store services, and price can be described to create a more flexible model of store selection within different markets across the U.S.
Chromosomal Signatures Corroborate the Phylogenetic Relationships within Akodontini (Rodentia, Sigmodontinae)
Creators: name: Oliveira Da Silva, Willam
name: Malcher, Stella Miranda
name: Pereira, Adenilson Leão
name: Pieczarka, Julio Cesar
name: Ferguson-Smith, Malcolm Andrew
name: O’Brien, Patricia Caroline Mary
name: Mendes-Oliveira, Ana Cristina
name: Geise, Lena
name: Nagamachi, Cleusa Yoshiko
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: conserved syntenic block
chromosome painting
rodents
FISH

description: Comparative chromosome-painting analysis among highly rearranged karyotypes of Sigmodontinae rodents (Rodentia, Cricetidae) detects conserved syntenic blocks, which are proposed as chromosomal signatures and can be used as phylogenetic markers. In the Akodontini tribe, the molecular topology (Cytb and/or IRBP) shows five low-supported clades (divisions: “Akodon”, “Bibimys”, “Blarinomys”, “Oxymycterus”, and “Scapteromys”) within two high-supported major clades (clade A: “Akodon”, “Bibimys”, and “Oxymycterus”; clade B: “Blarinomys” and “Scapteromys”). Here, we examine the chromosomal signatures of the Akodontini tribe by using Hylaeamys megacephalus (HME) probes to study the karyotypes of Oxymycterus amazonicus (2n = 54, FN = 64) and Blarinomys breviceps (2n = 28, FN = 50), and compare these data with those from other taxa investigated using the same set of probes. We strategically employ the chromosomal signatures to elucidate phylogenetic relationships among the Akodontini. When we follow the evolution of chromosomal signature states, we find that the cytogenetic data corroborate the current molecular relationships in clade A nodes. We discuss the distinct events that caused karyotypic variability in the Oxymycterus and Blarinomys genera. In addition, we propose that Blarinomys may constitute a species complex, and that the taxonomy should be revised to better delimit the geographical boundaries and their taxonomic status.
Equivalence of the Siegert-pseudostate and Lagrange-mesh R-matrix methods
Creators: name: Baye, D.
name: Goldbeter, J.
name: Sparenberg, J. -M.
Publisher: name: arXiv
Year: 2002
Subjects: subject: Quantum Physics (quant-ph)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: Siegert pseudostates are purely outgoing states at some fixed point expanded over a finite basis. With discretized variables, they provide an accurate description of scattering in the s wave for short-range potentials with few basis states. The R-matrix method combined with a Lagrange basis, i.e. functions which vanish at all points of a mesh but one, leads to simple mesh-like equations which also allow an accurate description of scattering. These methods are shown to be exactly equivalent for any basis size, with or without discretization. The comparison of their assumptions shows how to accurately derive poles of the scattering matrix in the R-matrix formalism and suggests how to extend the Siegert-pseudostate method to higher partial waves. The different concepts are illustrated with the Bargmann potential and with the centrifugal potential. A simplification of the R-matrix treatment can usefully be extended to the Siegert-pseudostate method.
description: 19 pages, 1 figure
p-brane production in Fat brane or Universal extra dimension scenario
Creators: name: Cheung, Kingman
name: Chou, Chung-Hsien
Publisher: name: arXiv
Year: 2002
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: In models of large extra dimensions, the fundamental Planck scale can be as low as TeV. Thus, in hadronic collisions interesting objects like black holes, string balls, or $p$-branes can be produced. In scenarios of fat brane or universal extra dimensions, the SM particles are allowed to propagate in the extra spatial dimensions, which leads to the enhancement of production cross sections of black holes and $p$-branes. Especially, the ratio of $p$-brane cross section to the black hole cross section increases substantially, in comparison with the original confined scenario. The ratio can be as large as 105 (for the case $n=7,m=5=p=r=k$).
description: 12 pages
Kenyanella Levasseur
Creators: name: Hlaváč, Peter
name: Newton, Alfred F.
name: Maruyama, Munetoshi
Publisher: name: Zenodo
Year: 2011
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Staphylinidae
Kenyanella

description: Kenyanella Levasseur
 Kenyanella Levasseur, 1966a: 170 [= Levasseur, 1965b: 569, NOMEN NUDUM]. Type species: Kenyanella aberdarensis Levasseur, by original designation aberdarensis Levasseur, 1966a: 172 (Kenyanella, TL: Kenya, Maison forestière de Kinangop, Mts. Aberdare, versant Ouest, 2600 m) Distribution: Kenya
description: Published as part of Hlaváč, Peter, Newton, Alfred F. & Maruyama, Munetoshi, 2011, World catalogue of the species of the tribe Lomechusini (Staphylinidae: Aleocharinae) 3075, pp. 1-151 in Zootaxa 3075 on page 47
Probing new physics using Rydberg states of atomic hydrogen
Creators: name: Jones, Matthew P. A.
name: Potvliege, Robert M.
name: Spannowsky, Michael
Publisher: name: arXiv
Year: 2019
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: We consider the role of high-lying Rydberg states of simple atomic systems such as $^1$H in setting constraints on physics beyond the Standard Model. We obtain highly accurate bound states energies for a hydrogen atom in the presence of an additional force carrier (the energy levels of the Hellmann potential). These results show that varying the size and shape of the Rydberg state by varying the quantum numbers provides a way to probe the range of new forces. By combining these results with the current state-of-the-art QED corrections, we determine a robust global constraint on new physics that includes all current spectroscopic data in hydrogen. Lastly we show that improved measurements that fully exploit modern cooling and trapping methods as well as higher-lying states could lead to a strong, statistically robust global constraint on new physics based on laboratory measurements only.
description: Accepted for publication in Physical Review Research
Complex Structure of Lasiopodomys mandarinus vinogradovi Sex Chromosomes, Sex Determination, and Intraspecific Autosomal Polymorphism
Creators: name: Romanenko, Svetlana A.
name: Smorkatcheva, Antonina V.
name: Kovalskaya, Yulia M.
name: Prokopov, Dmitry Yu.
name: Lemskaya, Natalya A.
name: Gladkikh, Olga L.
name: Polikarpov, Ivan A.
name: Serdyukova, Natalia A.
name: Trifonov, Vladimir A.
name: Molodtseva, Anna S.
name: O’Brien, Patricia C. M.
name: Golenishchev, Feodor N.
name: Ferguson-Smith, Malcolm A.
name: Graphodatsky, Alexander S.
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: aberrant sex determination
chromosome painting
comparative cytogenetics
genome architecture
mandarin vole
microdissection
high-throughput sequencing
rearrangements
rodents
sex chromosomes

description: The mandarin vole, Lasiopodomys mandarinus, is one of the most intriguing species among mammals with non-XX/XY sex chromosome system. It combines polymorphism in diploid chromosome numbers, variation in the morphology of autosomes, heteromorphism of X chromosomes, and several sex chromosome systems the origin of which remains unexplained. Here we elucidate the sex determination system in Lasiopodomys mandarinus vinogradovi using extensive karyotyping, crossbreeding experiments, molecular cytogenetic methods, and single chromosome DNA sequencing. Among 205 karyotyped voles, one male and three female combinations of sex chromosomes were revealed. The chromosome segregation pattern and karyomorph-related reproductive performances suggested an aberrant sex determination with almost half of the females carrying neo-X/neo-Y combination. The comparative chromosome painting strongly supported this proposition and revealed the mandarin vole sex chromosome systems originated due to at least two de novo autosomal translocations onto the ancestral X chromosome. The polymorphism in autosome 2 was not related to sex chromosome variability and was proved to result from pericentric inversions. Sequencing of microdissection derived of sex chromosomes allowed the determination of the coordinates for syntenic regions but did not reveal any Y-specific sequences. Several possible sex determination mechanisms as well as interpopulation karyological differences are discussed.
Anterior cruciate ligament reconstruction-related patient injuries: a nationwide registry study in Finland
Creators: name: Kirsi-Maaria Nyrhinen
name: Bister, Ville
name: Helkamaa, Teemu
name: Schlenzka, Arne
name: Sandelin, Henrik
name: Sandelin, Jerker
name: Harilainen, Arsi
Publisher: name: Taylor & Francis
Year: 2019
Subjects: subject: Medicine
subject: Cell Biology
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Background and purpose — Treatment outcomes of anterior cruciate ligament (ACL) injuries are generally good, but complications after ACL reconstruction (ACLR) can result in long-lasting problems. Patient injury claims usually fall on the more severe end of the complication spectrum. They are important to investigate because they may reveal the root causes of adverse events, which are often similar regardless of the complication’s severity. Therefore, we analyzed ACL-related patient injuries in Finland, the reasons for these claims, causes of complications, and grounds for compensation. Patients and methods — We analyzed all claims filed at the Patient Insurance Centre (PIC) between 2005 and 2013 in which the suspected patient injury occurred between 2005 and 2010. This study also reviewed all original patient records and available imaging studies. General background data were obtained from the National Care Register for Social Welfare and Health Care (HILMO). Results — There were 248 patient injury claims, and 100 of these were compensated. Compensated claims were divided into 4 main categories: skill-based errors (n = 46), infections (n = 34), knowledge-based errors (n = 6), and others (n = 14). Of the compensated skill-based errors, 34 involved graft malposition, 26 of them involved the femoral-side tunnel. All compensated infections were deep surgical site infections (DSSI). Interpretation — This is the first nationwide study of patient injuries concerning ACLRs in Finland. The most common reasons for compensation were DSSI and malposition of the drill tunnel. Therefore, it would be possible to decrease the number of serious complications by concentrating on infection prevention and optimal surgical technique.
Quadrupolar Order in Isotropic Heisenberg Models with Biquadratic Interaction
Creators: name: Harada, Kenji
name: Kawashima, Naoki
Publisher: name: arXiv
Year: 2001
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: Through Quantum Monte Carlo simulation, we study the biquadratic-interaction model with the SU(2) symmetry in two and three dimensions. The zero-temperature phase diagrams for the two cases are identical and exhibit an intermediate phase characterized by finite quadrupole moment, in agreement with mean-field type arguments and the semi-classical theory. In three dimensions, we demonstrate that the model in the quadrupolar regime has a phase transition at a finite temperature. In contrast to predictions by mean-field theories, the phase transition to the quadrupolar phase turns out to be of the second order. We also examine the critical behavior in the two marginal cases with the SU(3) symmetry.
description: 4 pages 5 figures
2-Aminopyridine Analogs Inhibit Both Enzymes of the Glyoxylate Shunt in Pseudomonas aeruginosa
Creators: name: McVey, Alyssa C.
name: Bartlett, Sean
name: Kajbaf, Mahmud
name: Pellacani, Annalisa
name: Gatta, Viviana
name: Tammela, Päivi
name: Spring, David R.
name: Welch, Martin
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: Pseudomonas aeruginosa
glyoxylate shunt
isocitrate lyase
malate synthase G
conditionally essential target
enzyme inhibitor
isothermal titration calorimetry

description: Pseudomonas aeruginosa is an opportunistic pathogen responsible for many hospital-acquired infections. P. aeruginosa can thrive in diverse infection scenarios by rewiring its central metabolism. An example of this is the production of biomass from C2 nutrient sources such as acetate via the glyoxylate shunt when glucose is not available. The glyoxylate shunt is comprised of two enzymes, isocitrate lyase (ICL) and malate synthase G (MS), and flux through the shunt is essential for the survival of the organism in mammalian systems. In this study, we characterized the mode of action and cytotoxicity of structural analogs of 2-aminopyridines, which have been identified by earlier work as being inhibitory to both shunt enzymes. Two of these analogs were able to inhibit ICL and MS in vitro and prevented growth of P. aeruginosa on acetate (indicating cell permeability). Moreover, the compounds exerted negligible cytotoxicity against three human cell lines and showed promising in vitro drug metabolism and safety profiles. Isothermal titration calorimetry was used to confirm binding of one of the analogs to ICL and MS, and the mode of enzyme inhibition was determined. Our data suggest that these 2-aminopyridine analogs have potential as anti-pseudomonal agents.
Finite-size scaling of the density of states inside band gaps of ideal and disordered photonic crystals
Creators: name: Skipetrov, Sergey E.
Publisher: name: arXiv
Year: 2019
Subjects: subject: Disordered Systems and Neural Networks (cond-mat.dis-nn)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We study the density of states (DOS) in band gaps of ideal and disordered three-dimensional photonic crystals of finite size. The ideal crystal is a diamond lattice of resonant point scatterers (atoms) whereas the disordered one is obtained from it by displacing the scatterers by random distances in random directions. We find that DOS inside a band gap of the ideal crystal decreases as the inverse of the crystal size. Disorder narrows the band gap and DOS exhibits enhanced fluctuations near the new band edges. However, the average DOS still exhibits the same scaling with the crystal size within the remaining band gap. A phenomenological explanation of this scaling suggests that it should hold for one- and two-dimensional photonic crystals as well.
description: Revised text, 6 pages, 4 figures
Arf6 Can Trigger Wave Regulatory Complex-Dependent Actin Assembly Independent of Arno
Creators: name: Singh, Vikash
name: Davidson, Anthony C.
name: Hume, Peter J.
name: Koronakis, Vassilis
Publisher: name: Apollo - University of Cambridge Repository
Year: 2020
Subjects: Arf GTPases
actin cytoskeleton
wave regulatory complex
phagocytosis
macrophages
host–pathogen interplay

description: The small GTPase ADP-ribosylation factor 6 (Arf6) anchors at the plasma membrane to orchestrate key functions, such as membrane trafficking and regulating cortical actin cytoskeleton rearrangement. A number of studies have identified key players that interact with Arf6 to regulate actin dynamics in diverse cell processes, yet it is still unknown whether Arf6 can directly signal to the wave regulatory complex to mediate actin assembly. By reconstituting actin dynamics on supported lipid bilayers, we found that Arf6 in co-ordination with Rac1(Ras-related C3 botulinum toxin substrate 1) can directly trigger actin polymerization by recruiting wave regulatory complex components. Interestingly, we demonstrated that Arf6 triggers actin assembly at the membrane directly without recruiting the Arf guanine nucleotide exchange factor (GEF) ARNO (ARF nucleotide-binding site opener), which is able to activate Arf1 to enable WRC-dependent actin assembly. Furthermore, using labelled E. coli, we demonstrated that actin assembly by Arf6 also contributes towards efficient phagocytosis in THP-1 macrophages. Taken together, this study reveals a mechanism for Arf6-driven actin polymerization.
Manikaella Levasseur 1967
Creators: name: Hlaváč, Peter
name: Newton, Alfred F.
name: Maruyama, Munetoshi
Publisher: name: Zenodo
Year: 2011
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Coleoptera
Staphylinidae
Manikaella

description: Manikaella Levasseur
 Manikaella Levasseur, 1967: 970. Type species: Manikaella bicolor Levasseur, by original designation bicolor Levasseur, 1967: 971 (Manikaella, TL: région de Kolwézi, Katanga, plateau de Manika) Distribution: Dem. Rep. Congo
description: Published as part of Hlaváč, Peter, Newton, Alfred F. & Maruyama, Munetoshi, 2011, World catalogue of the species of the tribe Lomechusini (Staphylinidae: Aleocharinae) 3075, pp. 1-151 in Zootaxa 3075 on page 51
Approximate quantum data storage and teleportation
Creators: name: Laustsen, Thomas
name: Molmer, Klaus
Publisher: name: arXiv
Year: 2002
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: In this paper we present an optimal protocol by which an unknown state on a Hilbert space of dimension $N$ can be approximately stored in an $M$-dimensional quantum system or be approximately teleported via an $M$-dimensional quantum channel. The fidelity of our procedure is determined for pure states as well as for mixed states and states which are entangled with auxiliary quantum systems of varying Hilbert space dimension, and it is compared with theoretical results for the maximally achievable fidelity.
description: More detailed discussion of teleportation of entangled and mixed states. Added reference to work by Banaszek. 8 pages, 1 figure
Generalized Einstein relation for disordered semiconductors - implications for device performance
Creators: name: Roichman, Yohai
name: Tessler, Nir
Publisher: name: arXiv
Year: 2001
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: The ratio between mobility and diffusion parameters is derived for a Gaussian-like density of states. This steady-state analysis is expected to be applicable to a wide range of organic materials (polymers or small molecules) as it relies on the existence of quasi-equilibrium only. Our analysis shows that there is an inherent dependence of the transport in trap-free disordered organic-materials on the charge density. The implications for the contact phenomena and exciton generation rate in light emitting diodes as well as channel-width in field-effect transistors is discussed.