cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
On conformal correlators and blocks with spinors in general dimensions
Creators: name: Isono, Hiroshi
Publisher: name: arXiv
Year: 2017
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We compute conformal correlation functions with spinor, tensor, and spinor-tensor primary fields in general dimensions with Euclidean and Lorentzian metrics. The spinors are taken to be Dirac spinors, which exist for any dimensions. For this, the embedding space formalism is employed and the polarisation spinors are introduced to simplify the computations. Three-point functions are rewritten in terms of differential operators acting on scalar-scalar-tensor correlation functions. This enables us to determine conformal blocks for four-point functions with scalar and spinor fields by acting the differential operators on scalar conformal blocks, which will be useful in finding their geodesic Witten diagrams.
description: 21 pages, no figures, references added, typos corrected
Additional file 3: of Harm, benefit and costs associated with low-dose glucocorticoids added to the treatment strategies for rheumatoid arthritis in elderly patients (GLORIA trial): study protocol for a randomised controlled trial
Creators: name: Hartman, Linda
name: Rasch, Linda
name: Klausch, Thomas
name: Bijlsma, Hans
name: Christensen, Robin
name: Smulders, Yvo
name: Ralston, Stuart
name: Buttgereit, Frank
name: Cutolo, Maurizio
name: Silva, Jose Da
name: Opris, Daniela
name: RovenskĂ˝, Jozef
name: Szamosi, Szilvia
name: Middelink, Leonie
name: Lems, Willem
name: Boers, Maarten
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Medicine
subject: Physiology
subject: FOS: Biological sciences
subject: Ecology
subject: Sociology
subject: FOS: Sociology
subject: Science Policy

description: Full list of outcome measures: benefit, harm, and cost-utility. (DOCX 32Â kb)
Oscillations in the Tsallis income distribution
Creators: name: Abreu, Everton M. C.
name: Moura, Newton J.
name: Soares, Abner D.
name: Ribeiro, Marcelo B.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Physics and Society (physics.soc-ph)
subject: General Economics (econ.GN)
subject: FOS: Physical sciences
subject: FOS: Economics and business

description: Oscillations in the complementary cumulative distribution function (CCDF) of individual income data have been found in the data of various countries studied by different authors at different time periods, but the dynamical origins of this behavior are currently unknown. Although these datasets can be fitted by different functions at different income ranges, the Tsallis distribution has recently been found capable of fitting the whole distribution by means of only two parameters. This procedure showed clearly such oscillatory feature in the entire income range feature, but made it particularly visible at the tail of the distribution. Although log-periodic functions fitted to the data are capable of describing this behavior, a different approach to naturally disclose such oscillatory characteristics is to allow the Tsallis $q$-parameter to become complex. In this paper we use this idea in order to describe the behavior of the CCDF of the Brazilian personal income recently studied empirically by Soares et al.\ (2016). Typical elements of periodic motion, such as amplitude and angular frequency coupled to this income analysis, were obtained by means of this approach. A highly non-linear function for the CCDF was obtained through this methodology and a numerical test showed it capable of recovering the main oscillatory feature of the original CCDF of the personal income data of Brazil.
description: 14 pages. Final version to appear in Physica A
Edaravone inhibits the conformational transition of amyloid-β42: insights from molecular dynamics simulations
Creators: name: Liu, Fufeng
name: Ma, Zheng
name: Sang, Jingcheng
name: Lu, Fuping
Publisher: name: Taylor & Francis
Year: 2019
Subjects: Biophysics
Biochemistry
Physical Sciences not elsewhere classified
Medicine
Cell Biology
Chemical Sciences not elsewhere classified

description: Previous work has shown that edaravone inhibits fibrillogenesis of amyloid-β protein (Aβ). However, the detailed mechanism by which edaravone inhibits the conformational transition of the Aβ42 monomer is not known at the molecular level. Here, explicit-solvent molecular dynamics (MD) simulations were coupled with molecular mechanics–Poisson–Boltzmann surface area (MM–PBSA) method to address the issue. MD simulations confirmed that edaravone inhibits the conformational transition of the Aβ42 monomer in a dose-dependent manner. It was found that the direct interactions between edaravone and Aβ42 are responsible for its inhibiting effects. The analysis of binding free energy using the MM–PBSA method demonstrated that the nonpolar interactions provide favourable contributions (about −71.7 kcal/mol). Conversely, the polar interactions are unfavourable for the binding process. A total of 14 residues were identified as greatly contributing to the binding free energy between edaravone and the Aβ42 monomer. In addition, the intra-peptide hydrophobic interactions were weakened and the salt bridge D23–K28 was interrupted by edaravone. Therefore, the conformational transition was inhibited. Our studies provide molecular-level insights into how edaravone molecules inhibit the conformational transition of the Aβ42 monomer, which may be useful for designing amyloid inhibitors. Communicated by Ramaswamy H. Sarma
Additional file 4: of What do we know about managing Dupuytrenâ s disease cost-effectively?
Creators: name: Dritsaki, Melina
name: Rivero-Arias, Oliver
name: Gray, Alastair
name: Ball, Catherine
name: Jagdeep Nanchahal
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Marine Biology
subject: Science Policy

description: List of 65 publications identified in the first stage after removing duplicates. (DOCX 23 kb)
Stability of the Universe Model Coupled with Phantom and Tachyon Fields
Creators: name: Sharif, M.
name: Mumtaz, Saadia
Publisher: name: arXiv
Year: 2017
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: In this paper, we study the phase space analysis of locally rotationally symmetric Bianchi type I universe model by taking interactions between dark matter and scalar field models. We define normalized dimensionless variables to develop an autonomous system of equations. We also find the corresponding critical points in order to study the dynamics of the system. The dynamical analysis indicates that all the critical points correspond to accelerated cosmic expansion for tachyon coupled field. We observe that positive values of $m$ provide more stable future attractors as compared to its negative values. We also analyze the behavior of power-law scale factor which shows different cosmological phases. It is found that the region for decelerated expansion gets larger for the phantom coupled matter by increasing $m$ while this region decreases for tachyon coupled field.
description: 30 pages, 6 figures, to appear in AHEP
Additional file 2: of Experiences with and expectations of maternity waiting homes in Luapula Province, Zambia: a mixedâ methods, cross-sectional study with women, community groups and stakeholders
Creators: name: Chibuye, Peggy
name: Bazant, Eva
name: Wallon, Michelle
name: Namratha Rao
name: Timothee Fruhauf
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Ecology
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Maternity Home Assessment Tool â document used to collect data about the structure and amenities available at each maternity home. (DOC 219Â kb)
On the role of clustering in Personalized PageRank estimation
Creators: name: Vial, Daniel
name: Subramanian, Vijay
Publisher: name: arXiv
Year: 2017
Subjects: subject: Social and Information Networks (cs.SI)
subject: FOS: Computer and information sciences

description: Personalized PageRank (PPR) is a measure of the importance of a node from the perspective of another (we call these nodes the $\textit{target}$ and the $\textit{source}$, respectively). PPR has been used in many applications, such as offering a Twitter user (the source) recommendations of who to follow (targets deemed important by PPR); additionally, PPR has been used in graph-theoretic problems such as community detection. However, computing PPR is infeasible for large networks like Twitter, so efficient estimation algorithms are necessary. In this work, we analyze the relationship between PPR estimation complexity and clustering. First, we devise algorithms to estimate PPR for many source/target pairs. In particular, we propose an enhanced version of the existing single pair estimator $\texttt{Bidirectional-PPR}$ that is more useful as a primitive for many pair estimation. We then show that the common underlying graph can be leveraged to efficiently and jointly estimate PPR for many pairs, rather than treating each pair separately using the primitive algorithm. Next, we show the complexity of our joint estimation scheme relates closely to the degree of clustering among the sources and targets at hand, indicating that estimating PPR for many pairs is easier when clustering occurs. Finally, we consider estimating PPR when several machines are available for parallel computation, devising a method that leverages our clustering findings, specifically the quantities computed $\textit{in situ}$, to assign tasks to machines in a manner that reduces computation time. This demonstrates that the relationship between complexity and clustering has important consequences in a practical distributed setting.
description: Added theoretical results for stochastic block model (Theorem 5.2)
Positional information readout in $Ca^{2+}$ signaling
Creators: name: Wasnik, Vaibhav H.
name: Lipp, Peter
name: Kruse, Karsten
Publisher: name: arXiv
Year: 2017
Subjects: subject: Subcellular Processes (q-bio.SC)
subject: FOS: Biological sciences

description: Living cells respond to spatial signals. Signal transmission to the cell interior often involves the release of second messengers like $Ca^{2+}$ . They will eventually trigger a physiological response by activating kinases that in turn activate target proteins through phosphorylation. Here, we investigate theoretically how positional information can be accurately read out by protein phosphorylation in spite of rapid second messenger diffusion. We find that accuracy is increased by binding of the kinases to the cell membrane prior to phosphorylation and by increasing the rate of $Ca^{2+}$ loss from the cell interior. These findings could explain some salient features of conventional protein kinases C.
A Prototype Knockoff Filter for Group Selection with FDR Control
Creators: name: Chen, Jiajie
name: Hou, Anthony
name: Hou, Thomas Y.
Publisher: name: arXiv
Year: 2017
Subjects: subject: Methodology (stat.ME)
subject: Statistics Theory (math.ST)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: In many applications, we need to study a linear regression model that consists of a response variable and a large number of potential explanatory variables and determine which variables are truly associated with the response. In 2015, Barber and Candes introduced a new variable selection procedure called the knockoff filter to control the false discovery rate (FDR) and proved that this method achieves exact FDR control. In this paper, we propose a prototype knockoff filter for group selection by extending the Reid-Tibshirani prototype method. Our prototype knockoff filter improves the computational efficiency and statistical power of the Reid-Tibshirani prototype method when it is applied for group selection. In some cases when the group features are spanned by one or a few hidden factors, we demonstrate that the PCA prototype knockoff filter outperforms the Dai-Barber group knockoff filter. We present several numerical experiments to compare our prototype knockoff filter with the Reid-Tibshirani prototype method and the group knockoff filter. We have also conducted some analysis of the knockoff filter. Our analysis reveals that some knockoff path method statistics, including the Lasso path statistic, may lead to loss of power for certain design matrices and a specially designed response even if their signal strengths are still relatively strong.
description: 16 pages, 5 figures
Additional file 2 of High diversity in the regulatory region of Shiga toxin encoding bacteriophages
Creators: name: Fagerlund, Annette
name: Aspholm, Marina
name: Węgrzyn, Grzegorz
name: Lindbäck, Toril
Publisher: name: figshare
Year: 2022
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Science Policy
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: 60506 Virology

description: Additional file 2. BioProjects comprising European STEC strains with Eru type
Absence of emergent supersymmetry at superconducting quantum critical points in Dirac and Weyl semimetals
Creators: name: Zhao, Peng-Lu
name: Liu, Guo-Zhu
Publisher: name: arXiv
Year: 2017
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Superconductivity (cond-mat.supr-con)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Supersymmetry plays a crucial role in superstring theory and high-energy physics, but has never been observed in experiments. Recently, an effective space-time supersymmetry was argued to emerge in the low-energy region by tuning Dirac or Weyl semimetal to approach a superconducting quantum critical point, at which the Dirac or Weyl fermion and the bosonic order parameter are both massless. Here, we study under what circumstances can space-time supersymmetry be realized at a quantum critical point. We demonstrate that the Yukawa-type coupling between the massless fermion and massless boson can dynamically generate an infinite number of non-supersymmetric terms in the effective field theory of the boson. Owing to these terms, no space-time supersymmetry emerges at the superconducting quantum critical points. The results provide important constraint on the exploration of emergent space-time supersymmetry in condensed matter systems.
description: 22+5 pages, 1 figure
Stranger Things about Forcing without AC
Creators: name: Goldstern, Martin
name: Klausner, Lukas Daniel
Publisher: name: arXiv
Year: 2017
Subjects: subject: Logic (math.LO)
subject: FOS: Mathematics
subject: 03E25 (Primary) 03E40 (Secondary)

description: Typically, set theorists reason about forcing constructions in the context of ZFC. We show that without AC, several simple properties of forcing posets fail to hold, one of which answers Miller's question from arXiv:0704.3998.
description: 5 pages
Satellite conjunction analysis and the false confidence theorem
Creators: name: Balch, Michael S.
name: Martin, Ryan
name: Ferson, Scott
Publisher: name: arXiv
Year: 2017
Subjects: subject: Statistics Theory (math.ST)
subject: FOS: Mathematics

description: Satellite conjunction analysis is the assessment of collision risk during a close encounter between a satellite and another object in orbit. A counterintuitive phenomenon has emerged in the conjunction analysis literature, namely, probability dilution, in which lower quality data paradoxically appear to reduce the risk of collision. We show that probability dilution is a symptom of a fundamental deficiency in probabilistic representations of statistical inference, in which there are propositions that will consistently be assigned a high degree of belief, regardless of whether or not they are true. We call this deficiency false confidence. In satellite conjunction analysis, it results in a severe and persistent underestimate of collision risk exposure. We introduce the Martin--Liu validity criterion as a benchmark by which to identify statistical methods that are free from false confidence. Such inferences will necessarily be non-probabilistic. In satellite conjunction analysis, we show that uncertainty ellipsoids satisfy the validity criterion. Performing collision avoidance maneuvers based on ellipsoid overlap will ensure that collision risk is capped at the user-specified level. Further, this investigation into satellite conjunction analysis provides a template for recognizing and resolving false confidence issues as they occur in other problems of statistical inference.
description: 18 pages, 3 figures
Plasmodium yoelii erythrocyte-binding-like protein modulates host cell membrane structure, immunity, and disease severity.
Creators: name: Yu-Chih Peng
name: Yanwei Qi
name: Zhang, Cui
name: Xiangyu Yao
name: Wu, Jian
name: Sittiporn Pattaradilokrat
name: Xia, Lu
name: Tumas, Keyla C
name: He, Xiao
name: Ishizaki, Takahiro
name: Chen-Feng Qi
name: Holder, Anthony A
name: Myers, Timothy G
name: Long, Carole A
name: Kaneko, Osamu
name: Li, Jian
name: Xin-Zhuan Su
Publisher: name: The Francis Crick Institute
Year: 2020
Subjects: Model organisms
Biochemistry & Proteomics
Infectious Disease
Cell Biology

description: Erythrocyte-binding-like (EBL) proteins are known to play an important role in malaria parasite invasion of red blood cells (RBCs); however, any roles of EBL proteins in regulating host immune responses remain unknown. Here, we show that Plasmodium yoelii EBL (PyEBL) can shape disease severity by modulating the surface structure of infected RBCs (iRBCs) and host immune responses. We identified an amino acid substitution (a change of C to Y at position 741 [C741Y]) in the protein trafficking domain of PyEBL between isogenic P. yoelliinigeriensis strain N67 and N67C parasites that produce different disease phenotypes in C57BL/6 mice. Exchanges of the C741Y alleles altered parasite growth and host survival accordingly. The C741Y substitution also changed protein processing and trafficking in merozoites and in the cytoplasm of iRBCs, reduced PyEBL binding to band 3, increased phosphatidylserine (PS) surface exposure, and elevated the osmotic fragility of iRBCs, but it did not affect invasion of RBCs in vitro The modified iRBC surface triggered PS-CD36-mediated phagocytosis of iRBCs, host type I interferon (IFN-I) signaling, and T cell differentiation, leading to improved host survival. This study reveals a previously unknown role of PyEBL in regulating host-pathogen interaction and innate immune responses, which may be explored for developing disease control strategies.IMPORTANCE Malaria is a deadly parasitic disease that continues to afflict hundreds of millions of people every year. Infections with malaria parasites can be asymptomatic, with mild symptoms, or fatal, depending on a delicate balance of host immune responses. Malaria parasites enter host red blood cells (RBCs) through interactions between parasite ligands and host receptors, such as erythrocyte-binding-like (EBL) proteins and host Duffy antigen receptor for chemokines (DARC). Plasmodium yoelii EBL (PyEBL) is known to play a role in parasite invasion of RBCs. Here, we show that PyEBL also affects disease severity through modulation of host immune responses, particularly type I interferon (IFN-I) signaling. This discovery assigns a new function to PyEBL and provides a mechanism for developing disease control strategies.
Optimizing Trade Profit Via Rule Based Algorithms After Stock Price Trend Analysis Through Integration of Technical Analysis and Logistic Regression
Creators: name: Baruah, Amlan
name: Changkakati, Banajit
Publisher: name: figshare
Year: 2024
Subjects: classificationCode: 350202
subject: Finance
classificationCode: 350203
subject: Financial econometrics

description: This study investigates the efficacy of logistic regression in conjunction with rule-based algorithms for optimizing stock price prediction by leveraging technical indicators. The methodology entails the application of logistic regression to predict price movement directions and the implementation of a rule-based algorithm to generate buying and selling signals for the ‘ITC’ share of National Stock Exchange of India. Analysis of both in-sample and out-sample data reveals a considerable accuracy of 71.4% and 71.2%, respectively, in forecasting price direction. Notably, the rule-based algorithm outperforms the conventional Buy and Hold Model, yielding a superior return. In summary, our research demonstrates a strategy return of 26.65% over a decade between 2013 and 2022 for 'ITC' shares compared to the Buy and Hold strategy. The robustness of the model is rigorously validated, indicating its congruence with observed data and underscoring the potential of predictive analytics in financial markets. This study contributes to the existing literature on predictive modeling in finance and offers practical insights for investors looking to refine their trading strategies.
Modified Hamiltonian Monte Carlo for Bayesian inference
Creators: name: Radivojević, Tijana
name: Akhmatskaya, Elena
Publisher: name: arXiv
Year: 2017
Subjects: subject: Computation (stat.CO)
subject: Methodology (stat.ME)
subject: FOS: Computer and information sciences

description: The Hamiltonian Monte Carlo (HMC) method has been recognized as a powerful sampling tool in computational statistics. We show that performance of HMC can be significantly improved by incorporating importance sampling and an irreversible part of the dynamics into a chain. This is achieved by replacing Hamiltonians in the Metropolis test with modified Hamiltonians, and a complete momentum update with a partial momentum refreshment. We call the resulting generalized HMC importance sampler---Mix & Match Hamiltonian Monte Carlo (MMHMC). The method is irreversible by construction and further benefits from (i) the efficient algorithms for computation of modified Hamiltonians; (ii) the implicit momentum update procedure and (iii) the multi-stage splitting integrators specially derived for the methods sampling with modified Hamiltonians. MMHMC has been implemented, tested on the popular statistical models and compared in sampling efficiency with HMC, Riemann Manifold Hamiltonian Monte Carlo, Generalized Hybrid Monte Carlo, Generalized Shadow Hybrid Monte Carlo, Metropolis Adjusted Langevin Algorithm and Random Walk Metropolis-Hastings. To make a fair comparison, we propose a metric that accounts for correlations among samples and weights, and can be readily used for all methods which generate such samples. The experiments reveal the superiority of MMHMC over popular sampling techniques, especially in solving high dimensional problems.
description: 30 pages, 17 figures
title: Synthesis and Biological Evaluation of Novel Capacitative Calcium Entry Blockers
Creators: name: Mala, Thadigiri Celina
Publisher: name: Old Dominion University
publisherIdentifier: https://ror.org/04zjtrb98
publisherIdentifierScheme: ROR
Year: 2003

description: Studies have shown that 2-aminoethoxydiphenyl borate (2-APB) inhibits thrombin-mediated influx of Ca2 + through store-operated calcium channels in human platelets. Based on this molecule, two sets (boron analogues and the non-boron analogues) were synthesized and characterized by IR, NMR and CHN analysis and evaluated in human platelets to block thrombin-induced [Ca2+] elevation.

The synthesis of the non-boron compounds was performed in a simple one step process. According to the literature, some of these compounds were synthesized previously by a complicated two-step process.

All the compounds synthesized were tested for biological activity and the results showed that they did not have any enhanced biological activity as calcium channel blockers compared to 2-APB.

(R)(+)-2-amino-3-phenyl propoxy diphenyl borate and (S)(-)2-amino-3- phenyl propoxy diphenyl borate (structure 12) boron containing compounds were synthesized specifically to detect for stereospecificity of 2-APB derivatives to inhibit calcium influx channel. Biological activity of these compounds demonstrated that they have potency and efficacy similar to that of 2-APB.

Addition of (R)(+)2-amino-3-phenyl-1-propanol and (S)(-)2-amino-3- phenyl-1-propanol substituents to the boroxazolidine ring of 2-APB resulted in a similar inhibitory activity. This result indicates that R and S substituents are not involved in binding to the Ca2 + channel.
Additional file 3 of High diversity in the regulatory region of Shiga toxin encoding bacteriophages
Creators: name: Fagerlund, Annette
name: Aspholm, Marina
name: Węgrzyn, Grzegorz
name: Lindbäck, Toril
Publisher: name: figshare
Year: 2022
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Science Policy
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: 60506 Virology

description: Additional file 3. Information about the 260 CI sequences used in phylogenetic analysis
MPEC 2024-F59 : 2024 FU1
Creators: name: Minor Planet Center Staff
Publisher: name: The Minor Planet Center
Year: 2024
Subjects: subject: Small Solar System bodies
valueUri: http://astrothesaurus.org/uat/1469
subject: 2024 FU1

description: The Minor Planet Electronic Circulars contain information on unusual minor planets, routine data on comets and natural satellites, and occasional editorial announcements.  They are published on behalf of Division F of the International Astronomical Union by the Minor Planet Center, Smithsonian Astrophysical Observatory, Cambridge, MA 02138, U.S.A.
Additional file 2: of Harm, benefit and costs associated with low-dose glucocorticoids added to the treatment strategies for rheumatoid arthritis in elderly patients (GLORIA trial): study protocol for a randomised controlled trial
Creators: name: Hartman, Linda
name: Rasch, Linda
name: Klausch, Thomas
name: Bijlsma, Hans
name: Christensen, Robin
name: Smulders, Yvo
name: Ralston, Stuart
name: Buttgereit, Frank
name: Cutolo, Maurizio
name: Silva, Jose Da
name: Opris, Daniela
name: RovenskĂ˝, Jozef
name: Szamosi, Szilvia
name: Middelink, Leonie
name: Lems, Willem
name: Boers, Maarten
Publisher: name: figshare
Year: 2018
Subjects: subject: Medicine
subject: Ecology
subject: FOS: Biological sciences
subject: Cancer
subject: Science Policy

description: SPIRIT Checklist. (DOC 121Â kb)
Structure of Drosophila melanogaster ARC1 reveals a repurposed molecule with characteristics of retroviral Gag.
Creators: name: Cottee, Matthew A
name: Letham, Suzanne C
name: Young, George R
name: Stoye, Jonathan P
name: Taylor, Ian A
Publisher: name: The Francis Crick Institute
Year: 2020
Subjects: Genetics & Genomics
Model organisms
Infectious Disease
Ecology,Evolution & Ethology
Structural Biology & Biophysics

description: The tetrapod neuronal protein ARC and its Drosophila melanogaster homolog, dARC1, have important but differing roles in neuronal development. Both are thought to originate through exaptation of ancient Ty3/Gypsy retrotransposon Gag, with their novel function relying on an original capacity for self-assembly and encapsidation of nucleic acids. Here, we present the crystal structure of dARC1 CA and examine the relationship between dARC1, mammalian ARC, and the CA protein of circulating retroviruses. We show that while the overall architecture is highly related to that of orthoretroviral and spumaretroviral CA, there are substantial deviations in both amino- and carboxyl-terminal domains, potentially affecting recruitment of partner proteins and particle assembly. The degree of sequence and structural divergence suggests that Ty3/Gypsy Gag has been exapted on two separate occasions and that, although mammalian ARC and dARC1 share functional similarity, the structures have undergone different adaptations after appropriation into the tetrapod and insect genomes.
Adsorption kinetics and isotherm models of heavy metals by various adsorbents: An overview
Creators: name: Wang, Jianlong
name: Guo, Xuan
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Space Science
subject: Medicine
subject: Environmental Sciences not elsewhere classified
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: FOS: Biological sciences
subject: Astronomical and Space Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified

description: Heavy metal pollution has become one of the most severe environmental issues. Adsorption is an effective method for removing heavy metals from aquatic environments. The adsorption isotherm and kinetics models can provide information on the adsorption process, maximal adsorption capacity, and mass transfer steps, which are essential to evaluate the performance of an adsorbent and to design an adsorption system. In this review, the adsorption kinetics and isotherms of heavy metals by various adsorbents were summarized and discussed in depth. First, the sources of heavy metal pollution and the adsorption technology to remove heavy metals were reviewed. The adsorption capacity of Cu, Cd, Zn, Ni, Cr, As, Fe, Hg, Co, Sr, and Cs by biosorbents (e.g. algae, agriculture waste biochar/activated carbon, and bacteria) and by abiotic adsorbents (e.g. metal–organic frameworks (MOFs), microtubes, polymers, clays, minerals, and coal) were systematically summarized. Second, the origins, basic assumptions, importance, physical meanings, and applications of the adsorption kinetics and isotherm models were discussed in depth. Third, the methods for selecting adsorption models in different conditions were explained, and the statistical parameters which can be applied to evaluate the performance of the models were illustrated. Finally, two Excel sheets are provided for solving the adsorption models, which are available in Supplementary Information. This review article will deepen the understanding of the interaction between heavy metals and adsorbents and facilitate the development of adsorptive technology for heavy metal removal from water and wastewater.
Additional file 1: of Expression of two barley proteinase inhibitors in tomato promotes endogenous defensive response and enhances resistance to Tuta absoluta
Creators: name: Hamza, Rim
name: Meritxell Pérez-Hedo
name: Urbaneja, Alberto
name: Rambla, José
name: Granell, Antonio
name: Gaddour, Kamel
name: Beltrán, José
name: Cañas, Luis
Publisher: name: figshare
Year: 2018
Subjects: subject: Pharmacology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Hematology

description: Table. Primers used in this work (DOCX 11 kb)
Additional file 4 of High diversity in the regulatory region of Shiga toxin encoding bacteriophages
Creators: name: Fagerlund, Annette
name: Aspholm, Marina
name: Węgrzyn, Grzegorz
name: Lindbäck, Toril
Publisher: name: figshare
Year: 2022
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Cell Biology
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Ecology
subject: Science Policy
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer
subject: 60506 Virology

description: Additional file 4. Percent Identity Matrix (Clustal2.1) between clades of CI repressor sequences
On the heat content for the poisson kernels over the unit ball in the euclidean space
Creators: name: Valverde, Luis Acuna
Publisher: name: arXiv
Year: 2017
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics

description: This paper studies, by employing analytical tools, the small time behavior of the heat content for the Poisson kernel over the unit ball in $\Rd$, $d\geq 2$ by working with its related set covariance function. As a result, we obtain a representation for the third term in the expansion of the heat content over the unit ball and provide the explicit form of the this term in the particular cases $d=2$ and $d=3$.
Additional file 10: Table S3. of The pivotal role of aristaless in development and evolution of diverse antennal morphologies in moths and butterflies
Creators: name: Ando, Toshiya
name: Fujiwara, Haruhiko
name: Kojima, Tetsuya
Publisher: name: figshare
Year: 2018
Subjects: subject: Biochemistry
subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Plant Biology

description: Sequences of Morpholino oligomers used to knock down al1. (PDF 29Â kb)
title: Development of a Solid Phase Enzyme Immunoassay for Total Serum Testosterone
Creators: name: Li, Li
Publisher: name: Old Dominion University
publisherIdentifier: https://ror.org/04zjtrb98
publisherIdentifierScheme: ROR
Year: 1990

description: An enzyme-labeled immunoassay of sufficient range and sensitivity was developed for serum testosterone determination. In this method, the testosterone in the serum sample and testosterone-HRPO conjugate compete with each other for the limited antibody binding sites on the anti-testosterone gamma globulin coated microwell. The assay can be performed in only 2.5 hours.

The gamma globulin fraction was isolated from the anti-testosterone whole serum by DEAE-cellulose column chromatography. Testosterone-peroxidase conjugate was prepared by a carbodiimide coupling method. The interference which arises from the binding of testosterone to steroid hormone binding protein was eliminated by the addition of 17 beta-estradiol. All assay conditions including incubation temperature, incubation time, incubation solution, and washing solution were analyzed and optimized.

The detection limit of the competitive enzyme immunoassay was determined to be 0.119 ng/mL. The coefficients of variation (CV) for intra-assay were found to be 8.48%, 11.6% and 13.4% at testosterone concentrations of 9.30 ng/mL, 3.00 ng/mL, and 0.460 ng/mL. The CVs for inter-assay were determined to be 9.16%, 12.1% and 14.6% at testosterone concentrations of 9.27 ng/mL, 2.88 ng/mL, and 0.493 ng/mL. The cross reactivities with 5 alpha-dihydrotestosterone, 17 beta-estradiol, 4- androstene-3,17-dione, and 5-androstene-3 beta,17 beta-diol were found to be 72%, 0.028%, 0.76%, and 0.30% respectively. Excellent agreement was obtained in the comparison study of serum samples with both EIA and RIA.
Additional file 1: of Experiences with and expectations of maternity waiting homes in Luapula Province, Zambia: a mixedâ methods, cross-sectional study with women, community groups and stakeholders
Creators: name: Chibuye, Peggy
name: Bazant, Eva
name: Wallon, Michelle
name: Namratha Rao
name: Timothee Fruhauf
Publisher: name: figshare
Year: 2018
Subjects: subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Field Guide: Focus Group Discussions and Key Informant Interviews â documents used by interviewers to guide the different focus group discussions and key informant interviews. (DOCX 64Â kb)
Covariantly functorial wrapped Floer theory on Liouville sectors
Creators: name: Ganatra, Sheel
name: Pardon, John
name: Shende, Vivek
Publisher: name: arXiv
Year: 2017
Subjects: subject: Symplectic Geometry (math.SG)
subject: FOS: Mathematics

description: We introduce a class of Liouville manifolds with boundary which we call Liouville sectors. We define the wrapped Fukaya category, symplectic cohomology, and the open-closed map for Liouville sectors, and we show that these invariants are covariantly functorial with respect to inclusions of Liouville sectors. From this foundational setup, a local-to-global principle for Abouzaid's generation criterion follows.
description: Final version to appear in Publ Math IHES, 115 pages, 15 figures
Synthesis of the final Regional Scalability Plans
Creators: name: Ojanen, Maria
name: Penning, Ellis
name: Buijse, Tom
Publisher: name: Zenodo
Year: 2024

description: 1. The 17 MERLIN Regional Scalability Plans (RSPs) offer visions for upscaling restoration at wider landscape levels with a time horizon up to 2050 created through collaborative efforts to upscale freshwater restoration initiatives. The RSPs address 'why', 'where', 'what, 'how', and 'who' questions to upscale freshwater restoration.

2. The RSPs mainstream Nature-based Solutions (NbS) thinking and interaction with stakeholders towards common goals.

3. The starting point for developing an ambitious and feasible regional scale-up plan requires insight into current approaches to restoring freshwater ecosystems. The MERLIN case studies differed greatly in this regard which determined the scope and content of their RSPs.

4. Upscaling freshwater ecosystem restoration entails mainstreaming Nature-based Solutions (NbS) into policies and practices and interaction with stakeholders towards common goals. In MERLIN, this has been done through the EU Green Deal ambitions.

5. Biodiversity net gain, climate change mitigation and inclusivity are the main EU Green Deal goals of the RSPs.

6. The RSPs highlight that transformative change requires actions in three areas: practical work in the field, changes in policies, and efforts to involve the public. To successfully restore freshwater on a large scale, all these actions need to work together.

7. It is essential that upscaling entails replication and expansion of current good practices as well as the development of inclusive multiple benefit projects for nature, climate, water as well as society and economy.

8. Mainstreaming restoration requires collaboration and collective action with diverse set of actors. The RSPs highlight the need to build new coalitions and cross-sectoral collaboration as well as strengthen existing networks.

9. Forming multidisciplinary teams that address the biophysical, socioeconomic, legal and financial aspects is critical to the overarching success of RSPs.

10. Adapting plans and measures due to changing conditions (e.g. climate change, land use) is key to ensuring long-term success.

11. A well embedded monitoring strategy and monitoring systemic impacts of freshwater restoration is needed to better understand the impact of restoration on nature, society and the economy. This in turn can lead to better appreciation and support.
Novel broad-spectrum activity-based probes to profile malarial cysteine proteases.
Creators: name: Tan, Michele SY
name: Davison, Dara
name: Sanchez, Mateo I
name: Anderson, Bethany M
name: Howell, Stephen
name: Snijders, Ambrosius
name: Edgington-Mitchell, Laura E
name: Deu, Edgar
Publisher: name: The Francis Crick Institute
Year: 2020
Subjects: Model organisms
Biochemistry & Proteomics
Cell Biology
Chemical Biology & High Throughput
Infectious Disease
Computational & Systems Biology

description: Clan CA cysteine proteases, also known as papain-like proteases, play important roles throughout the malaria parasite life cycle and are therefore potential drug targets to treat this disease and prevent its transmission. In order to study the biological function of these proteases and to chemically validate some of them as viable drug targets, highly specific inhibitors need to be developed. This is especially challenging given the large number of clan CA proteases present in Plasmodium species (ten in Plasmodium falciparum), and the difficulty of designing selective inhibitors that do not cross-react with other members of the same family. Additionally, any efforts to develop antimalarial drugs targeting these proteases will also have to take into account potential off-target effects against the 11 human cysteine cathepsins. Activity-based protein profiling has been a very useful tool to determine the specificity of inhibitors against all members of an enzyme family. However, current clan CA proteases broad-spectrum activity-based probes either target endopeptidases or dipeptidyl aminopeptidases, but not both subfamilies efficiently. In this study, we present a new series of dipeptydic vinyl sulfone probes containing a free N-terminal tryptophan and a fluorophore at the P1 position that are able to label both subfamilies efficiently, both in Plasmodium falciparum and in mammalian cells, thus making them better broad-spectrum activity-based probes. We also show that some of these probes are cell permeable and can therefore be used to determine the specificity of inhibitors in living cells. Interestingly, we show that the choice of fluorophore greatly influences the specificity of the probes as well as their cell permeability.
Additional file 1 of Diagnostic performance and comparison of ultrasensitive and conventional rapid diagnostic test, thick blood smear and quantitative PCR for detection of low-density Plasmodium falciparum infections during a controlled human malaria infection study in Equatorial Guinea
Creators: name: Mpina, Maxmillian
name: Stabler, Thomas C.
name: Schindler, Tobias
name: Raso, Jose
name: Deal, Anna
name: Acuche Pupu, Ludmila
name: Nyakarungu, Elizabeth
name: del Carmen Ovono Davis, Maria
name: Urbano, Vicente
name: Mtoro, Ali
name: Hamad, Ali
name: Lopez, Maria Silvia A.
name: Pasialo, Beltran
name: Eyang, Marta Alene Owono
name: Rivas, Matilde Riloha
name: Falla, Carlos Cortes
name: García, Guillermo A.
name: Momo, Juan Carlos
name: Chuquiyauri, Raul
name: Saverino, Elizabeth
name: Preston Church, L. W.
name: Kim lee Sim, B.
name: Manguire, Bonifacio
name: Tanner, Marcel
name: Maas, Carl
name: Abdulla, Salim
name: Billingsley, Peter F.
name: Hoffman, Stephen L.
name: Jongo, Said
name: Richie, Thomas L.
name: Daubenberger, Claudia A.
Publisher: name: figshare
Year: 2022
Subjects: subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Biotechnology
subject: Cancer
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Additional file 1: Figure S1. Trend ofparasite density over time between individuals in selected and unselected groups.Trend of parasite density over time between selected and unselectedparticipants. Parasite density was determined by quantitative polymerase chainreaction assays (qPCR). Figure S2. Overall distribution of parasite densityamong groups of selected and unselected participants. Scatter plots of parasitedensity measured by quantitative polymerase reaction assays (qPCR) betweenselected and unselected data points. Figure S3. Distribution of parasitedensity by individuals participants in selected and unselected groups. Barplotsof parasite density as measured by quantitative polymerase reaction assays(qPCR) between selected vs. unselected individual volunteers.
The AHR pathway represses TGFβ-SMAD3 signalling and has a potent tumour suppressive role in SHH medulloblastoma.
Creators: name: Sarić, Nemanja
name: Selby, Matthew
name: Ramaswamy, Vijay
name: Kool, Marcel
name: Stockinger, Brigitta
name: Hogstrand, Christer
name: Williamson, Daniel
name: Marino, Silvia
name: Taylor, Michael D
name: Clifford, Steven C
name: M Albert Basson
Publisher: name: The Francis Crick Institute
Year: 2020
Subjects: subject: Immunology
subject: FOS: Clinical medicine

description: Sonic Hedgehog (SHH) medulloblastomas are brain tumours that arise in the posterior fossa. Cancer-propagating cells (CPCs) provide a reservoir of cells capable of tumour regeneration and relapse post-treatment. Understanding and targeting the mechanisms by which CPCs are maintained and expanded in SHH medulloblastoma could present novel therapeutic opportunities. We identified the aryl hydrocarbon receptor (AHR) pathway as a potent tumour suppressor in a SHH medulloblastoma mouse model. Ahr-deficient tumours and CPCs grown in vitro, showed elevated activation of the TGFβ mediator, SMAD3. Pharmacological inhibition of the TGFβ/SMAD3 signalling axis was sufficient to inhibit the proliferation and promote the differentiation of Ahr-deficient CPCs. Human SHH medulloblastomas with high expression of the AHR repressor (AHRR) exhibited a significantly worse prognosis compared to AHRRlow tumours in two independent patient cohorts. Together, these findings suggest that reduced AHR pathway activity promotes SHH medulloblastoma progression, consistent with a tumour suppressive role for AHR. We propose that TGFβ/SMAD3 inhibition may represent an actionable therapeutic approach for a subset of aggressive SHH medulloblastomas characterised by reduced AHR pathway activity.
Typologia zanurzenia w Mojżesza (Chrystusa) (1 Kor 10, 1-2) jako źródło nauczania św. Pawła o Eucharystii
Creators: name: Kosek, Wojciech
Publisher: name: Zenodo
Year: 2022
Subjects: Biblical studies
Eucharist
New Testament Exegesis
Jesus Christ
Book of Exodus
Liturgy
Holy Mass
The First Letter to the Corinthians
egzegeza biblijna

description: It is the original Polish text of the article, the English version of which was previously published at https://www.academia.edu/56388841/The_typology_of_immersion_into_Moses_immersion_into_Christ_1Cor_10_1_2_as_a_source_for_St_Pauls_teaching_on_the_Eucharist.

As in the English abstract, the same can be described in Polish, namely:

Niniejsze opracowanie jest tłumaczeniem artykułu: W. Kosek, Typologia zanurzenia w Mojżesza (Chrystusa) (1 Kor 10, 1-2) jako źródło nauczania św. Pawła o Eucharystii, [w:] T. M. Dąbek OSB, S. Witkowski MS, B. Zbroja (red.), Któż potrafi opowiedzieć dzieło miłosierdzia Bożego? Księga pamiątkowa ku czci ks. prof. dra hab. Stanisława Hałasa SCJ w siedemdziesiątą rocznicę urodzin, s. 139-157. ISBN: 9788363241520.

Typologia wymaga, aby egzegeta najpierw zrozumiał teksty biblijne na poziomie dosłownym i dopiero na tej podstawie ukazał typologiczne powiązania między nimi. W związku z tym zostanie przedstawiona komputerowa analiza gramatyczna Pierwszego Listu św. Pawła do Koryntian 10,1-2 w celu ukazania dokładnego znaczenia tego tekstu. W artykule zostaną również wykorzystane wyniki komputerowych analiz Księgi Wyjścia 1-18, na podstawie których przejście z miejsca spożywania Paschy nad Morze Czerwone i przez jego wody, przecięte na pół, okazuje się być aktem zawarcia przymierza między Bogiem a Izraelem, analogicznym do aktu zawarcia przymierza między Bogiem a Abramem (por. Rdz 15) poprzez przejście pomiędzy połówkami zwierząt. Zostanie przestudiowane nauczanie Nowego Testamentu, dotyczące teologii zanurzenia w Chrystusa, w Jego śmierć. Zostaną przedstawione wyniki komputerowych analiz Ewangelii św. Jana, które dowiodły, że przejście Jezusa z Wieczernika na Golgotę, a z niej do Otchłani i przez nią było Jego aktem zawarcia przymierza. Przedstawione zostaną również wyniki komputerowych badań 1Kor 11,26 i 1Kor 12,3, które wykazały, że każdorazowe zgromadzenie eucharystyczne jest wspólnotą głoszącą śmierć Jezusa jako Ofiary-Anathemy do momentu Jego przyjścia do nich jako Pana-Kyriosa, który właśnie powstał spośród umarłych. Na tej podstawie zostanie ukazane nauczanie św. Pawła odnośnie uczestnictwa w Eucharystii i modlitwach następujących bezpośrednio po niej, co Apostoł przedstawił poprzez typologię zanurzenia w Mojżesza / zanurzenia w Chrystusa.
description: Niniejszy artykuł wnosi wkład do literatury poprzez precyzyjne analizy komputerowe tekstu biblijnego i głębokie typologiczne zrozumienie relacji między Wyjściem Izraela a życiem Chrystusa jako środkiem zawierania przymierza.
description: This paper contributes to the literature through precise computer analyses of the biblical text and a profound typological understanding of the relation between Israel's Exodus and Christ's life as the means of covenant-making.