cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Randomized controlled trial to evaluate the effects of topical diclofenac on the pain associated with chronic Achilles tendinopathy : a pilot study
Creators: name: Bussin, Erin Rebecca
Publisher: name: University of British Columbia
Year: 2016

description: Background: Exercise-based rehabilitation for chronic Achilles tendinopathy (CAT) has proven to be effective, but it can be a painful process. The purpose of this research is to see if a topically applied non-steroidal anti-inflammatory drug, diclofenac, will be able to relieve the pain associated with chronic tendinopathy. The effects of diclofenac on subjects’ pain and mechanical hyperalgesia will be evaluated at rest and during simple calf exercises. It is expected that diclofenac will reduce pain among subjects with Achilles tendinopathy. Methods: 19 subjects (22 Achilles) with CAT were randomly assigned to a crossover treatment order (active gel containing 10% diclofenac, or placebo). The primary outcome measure was pain level during tendon loading (hopping) and at rest. The secondary outcome measures evaluated tendon loading characteristics, and mechanical hyperalgesia over the lesion, and over the bilateral trapezius muscles. Results: Pain was significantly reduced from baseline with the use of diclofenac during tendon loading (p=0.0003) and rest (p=0.0313). At baseline the average resting pain was 3.05 (+/-1.43), with the use of diclofenac the pain was 2.32 (+/- 1.52), and with the use of placebo the pain was 2.68 (+/- 2.03). At baseline the average hopping pain was 4.82 (+/-2.1), with the use of diclofenac the average hopping pain was 3.05 (+/-1.81), and with the use of placebo the average pain was 3.77 (+/-2.76). During the hopping test, subjects were able to generate significantly more force when experiencing less pain (p<0.0001). The pressure pain threshold at the Achilles tendon was significantly increased from baseline with diclofenac treatment (p = 0.0275). There was no statistically significant difference between the diclofenac and placebo treatment in all cases. Conclusion: Diclofenac was able to improve symptoms and reduce pain during tendon loading and rest in subjects with CAT. Future studies can look at using topical diclofenac with loading exercises to build a more effective and tolerable rehabilitation program while determining the potential clinical significance of diclofenac vs placebo treatment. The pressure pain threshold at the Achilles tendon and distant regions should be further investigated to gain a better understanding of the pain mechanisms involved with this disorder.
Universal three-body physics for fermionic dipoles
Creators: name: Wang, Yujun
name: D'Incao, J. P.
name: Greene, Chris H.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: A study of the universal physics for three oriented fermionic dipoles in the hyperspherical adiabatic representation predicts a single long-lived three-dipole state, which exists in only one three-body symmetry, should form near a two-dipole resonance. Our analysis reveals the spatial configuration of the universal state, and the scaling of its binding energy and lifetime with the strength of the dipolar interaction. In addition, three-body recombination of fermionic dipoles is found to be important even at ultracold energies. An additional finding is that an effective long-range repulsion arises between a dipole and a dipolar dimer that is tunable via dipolar interactions.
description: 4 pages, 3 figures, 1 table
Topological Quantum Gate Construction by Iterative Pseudogroup Hashing
Creators: name: Burrello, Michele
name: Mussardo, Giuseppe
name: Wan, Xin
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Physics (quant-ph)
subject: Other Condensed Matter (cond-mat.other)
subject: FOS: Physical sciences

description: We describe the hashing technique to obtain a fast approximation of a target quantum gate in the unitary group SU(2) represented by a product of the elements of a universal basis. The hashing exploits the structure of the icosahedral group [or other finite subgroups of SU(2)] and its pseudogroup approximations to reduce the search within a small number of elements. One of the main advantages of the pseudogroup hashing is the possibility to iterate to obtain more accurate representations of the targets in the spirit of the renormalization group approach. We describe the iterative pseudogroup hashing algorithm using the universal basis given by the braidings of Fibonacci anyons. The analysis of the efficiency of the iterations based on the random matrix theory indicates that the runtime and the braid length scale poly-logarithmically with the final error, comparing favorably to the Solovay-Kitaev algorithm.
description: 20 pages, 5 figures
Additional file 7 of The mechanism of potato resistance to Globodera rostochiensis: comparison of root transcriptomes of resistant and susceptible Solanum phureja genotypes
Creators: name: Kochetov, Alex V.
name: Egorova, Anastasiya A.
name: Glagoleva, Anastasiya Y.
name: Strygina, Kseniya V.
name: Khlestkina, Elena K.
name: Gerasimova, Sophia V.
name: Shatskaya, Natalja V.
name: Vasilyev, Gennady V.
name: Afonnikov, Dmitry A.
name: Shmakov, Nikolay A.
name: Antonova, Olga Y.
name: Alpatyeva, Natalia V.
name: Khiutti, Alexander
name: Afanasenko, Olga S.
name: Gavrilenko, Tatjana A.
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Plant Biology

description: Additional file 7. File contains the results of qRT-PCR validation of DEGs.
Transport of heat and mass in a two-phase mixture. From a continuous to a discontinuous description
Creators: name: Glavatskiy, Kirill
name: Bedeaux, Dick
Publisher: name: arXiv
Year: 2010
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: We present a theory which describes the transport properties of the interfacial region with respect to heat and mass transfer. Postulating the local Gibbs relation for a continuous description inside the interfacial region, we derive the description of the Gibbs surface in terms of excess densities and fluxes along the surface. We introduce overall interfacial resistances and conductances as the coefficients in the force-flux relations for the Gibbs surface. We derive relations between the local resistivities for the continuous description inside the interfacial region and the overall resistances of the surface for transport between the two phases for a mixture. It is shown that interfacial resistances depend among other things on the enthalpy profile across the interface. Since this variation is substantial the coupling between heat and mass flow across the surface are also substantial. In particular, the surface puts up much more resistance to the heat and mass transfer then the homogeneous phases over a distance comparable to the thickness of the surface. This is the case not only for the pure heat conduction and diffusion but also for the cross effects like thermal diffusion. For the excess fluxes along the surface and the corresponding thermodynamic forces we derive expressions for excess conductances as integrals over the local conductivities along the surface. We also show that the curvature of the surface affects only the overall resistances for transport across the surface and not the excess conductivities along the surface.
description: 25 pages, 2 figures
Benchmarking of the construct of dimensionless correlations regarding batch bubble columns with suspended solids: Performance of the Pressure Transform Approach
Creators: name: Hristov, Jordan
Publisher: name: arXiv
Year: 2010
Subjects: subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: Benchmark of dimensionless data correlations pertinent to batch bubble columns (BC) with suspended solids has been performed by the pressure transform approach (PTA). The main efforts have addressed the correct definition of dimensionless groups referring to the fact that solids dynamics and the bubble dynamics have different velocity and length scales. The correct definition of the initial set of variable in the classical dimensional analysis depends mainly on the experience of the investigator while the pressure transform approach (PTA) avoids errors at this initial stage. PTA addresses the physics of the phenomena occurring in complex systems involving many phases and allows straightforward definitions of dimensionless numbers.
description: 9 pages, 5 tables
Monitoraggio degli APC negli EPR Cosa, come e perchè
Creators: name: De Simone, Giovanni
name: Giannini, Silvia
name: Maggi, Roberta
name: Secinaro, Emanuela
Publisher: name: INFN Open Access Repository
Year: 2022
Subjects: Scienza aperta
open science
Article Processing Charges
Monitoraggio APC

description: Linee guida per il monitoraggio APC negli EPR
Effect of Crystal Growth Rate on Liquid-like Droplets Formation in the hcp Solid Helium
Creators: name: Mikhin, N. P.
name: Birchenko, A. P.
name: Neoneta, A. S.
name: Rudavskii, E. Ya.
name: Vekhov, Ye. O.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Other Condensed Matter (cond-mat.other)
subject: FOS: Physical sciences

description: The samples of hcp solid helium (1% $^3$He in $^4$He) are studied by NMR technique. The samples are grown by the blocking capillary method at different growth rates (about 8, 2, and 0.08 mK/s). The NMR technique is used for phase identification by measurements of the diffusion coefficient $D$ and the spin-spin relaxation time $T_2$ at temperatures of $1.3-2.0$ K and pressures of 34-36 bar. Along with $D$ and $T_2$ for the hcp phase, we simultaneously observe the $D$ and $T_2$ typical for a liquid at growth rates 8 and 2 mK/s. It means that liquid-like inclusions are quenched from the melting curve during fast crystallization of the samples. It is also shown that the slower growth rate corresponds to a smaller size of liquid-like droplets. It results from lower spatially restricted values of $D$ and, finally, absence of these inclusions at the longest crystallization times. The diffusion coefficient measured for liquid-like droplets is also decreasing during the NMR experiment at constant temperature which indicates the reduction of the size of these droplets. Liquid-like droplets are shown to disappear after sample annealing near the melting curve.
description: 4 pages, 3 figures, LT26 Conference
Additional file 2 of Identification of polycomb repressive complex 1 and 2 core components in hexaploid bread wheat
Creators: name: Strejčková, Beáta
name: Čegan, Radim
name: Ales Pecinka
name: Zbyněk Milec
name: Šafář, Jan
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2 : Fig. S1. This figure shows the protein alignments of plant PRC1 and PRC2 core components. The alignment contains protein sequences of Triticum aestivum, Triticum dicoccoides, Hordeum vulgare, and Arabidopsis thaliana. Conserved protein domains are highlighted in different colors. (PDF 13 Mb)
Monitoraggio degli APC negli EPR Cosa, come e perchè
Creators: name: De Simone, Giovanni
name: Giannini, Silvia
name: Maggi, Roberta
name: Secinaro, Emanuela
Publisher: name: INFN Open Access Repository
Year: 2023
Subjects: Scienza aperta
open science
Article Processing Charges
Monitoraggio APC

description: Linee guida per il monitoraggio APC negli EPR, versione aggiornata con Appendice tabella sintetica pag.3.
Additional file 5 of Identification of polycomb repressive complex 1 and 2 core components in hexaploid bread wheat
Creators: name: Strejčková, Beáta
name: Čegan, Radim
name: Ales Pecinka
name: Zbyněk Milec
name: Šafář, Jan
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 5 : Fig. S2. This figure shows protein alignment of E(z) homologs showing nine amino acid exchanges in the SET domain, allowing the division of TaE(z) paralogs into SWN-like and CLF-like groups. (PDF 661 kb)
Dynamic and Transparent Analysis of Commodity Production Systems
Creators: name: Fattori, Aristide
name: Paleari, Roberto
name: Martignoni, Lorenzo
name: Monga, Mattia
Publisher: name: arXiv
Year: 2010
Subjects: subject: Operating Systems (cs.OS)
subject: Software Engineering (cs.SE)
subject: FOS: Computer and information sciences
subject: D.2.5; D.4.9

description: We propose a framework that provides a programming interface to perform complex dynamic system-level analyses of deployed production systems. By leveraging hardware support for virtualization available nowadays on all commodity machines, our framework is completely transparent to the system under analysis and it guarantees isolation of the analysis tools running on its top. Thus, the internals of the kernel of the running system needs not to be modified and the whole platform runs unaware of the framework. Moreover, errors in the analysis tools do not affect the running system and the framework. This is accomplished by installing a minimalistic virtual machine monitor and migrating the system, as it runs, into a virtual machine. In order to demonstrate the potentials of our framework we developed an interactive kernel debugger, nicknamed HyperDbg. HyperDbg can be used to debug any critical kernel component, and even to single step the execution of exception and interrupt handlers.
description: 10 pages, To appear in the 25th IEEE/ACM International Conference on Automated Software Engineering, Antwerp, Belgium, 20-24 September 2010
Delimitation of Grain Production Functional Zones: An Empirical Analysis of Weifang District
Creators: name: LI Shouhua
name: ZHANG Yujiao
name: HOU Shuying
name: LI Shouhua
name: ZHANG Yujiao
name: HOU Shuying
Publisher: name: Unknown
Year: 2021
Subjects: subject: Agribusiness
subject: Grain production, Functional zones, Delimitation, Acceptance, Report

description: To solve some unreasonable problems in the acceptance process of the delimitation project of grain production functional zones, the acceptance results of grain production functional zones in Fangzi District, Weifang City were elaborated from the aspects of the third party organization, inspectors, expert group, acceptance criteria, acceptance method, acceptance contents, etc., and the overall performance of the project was reviewed. The problems that need to be rectified during the implementation of the project were put forward, and the irrationality of the acceptance and the places that need to be improved were pointed out, which would provide a better guiding value for the delimitation of grain production functional zone and the acceptance and performance evaluation of similar projects.
Additional file 1 of A comprehensive evaluation of long read error correction methods
Creators: name: Haowen Zhang
name: Chirag Jain
name: Aluru, Srinivas
Publisher: name: figshare
Year: 2020
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Neuroscience
subject: Evolutionary Biology
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences

description: Additional file 1 Settings of the error correction tools and correction results on subsamples of yeast PacBio and ONT sequencing data.
Monitoraggio degli APC negli EPR Cosa, come e perchè
Creators: name: De Simone, Giovanni
name: Giannini, Silvia
name: Maggi, Roberta
name: Secinaro, Emanuela
Publisher: name: INFN Open Access Repository
Year: 2022
Subjects: Scienza aperta
open science
Article Processing Charges
Monitoraggio APC

description: Linee guida per il monitoraggio APC negli EPR, versione aggiornata
Opportunistic scheduling for wireless networks with distributed architectures
Creators: name: Ge, Xin
Publisher: name: University of British Columbia
Year: 2016

description: To meet the growing demand of mobile data service with limited radio resources, wireless networks have evolved towards networks with distributed architectures. Moreover, as communication systems evolve, both service providers and users are demanding not only high data rates, but also user fairness and data security. As a result, the main objective of the dissertation is to identify key challenges in opportunistic scheduling design that meet these new needs, and propose solutions to overcome the identified issues. First, we extend the cumulative distribution function based scheduling (CS), which is well-known as an efficient opportunistic scheduling method that satisfies fair resource sharing among users, to satisfy proportional throughput fairness. Then, we investigate the joint CS and power allocation to maximize user throughput subject to the power and resource sharing constraints. Despite increasing interest in distributed antenna systems (DASs), how to guarantee resource-based fairness in multiuser DASs remains largely unexplored. In this direction, we propose a novel CS with flexible beam transmissions (CSFB) to guarantee resource-based fairness in DASs. To realize CSFB in practice, a one-bit-feedback scheme, CSFB-OB, is further proposed to reduce feedback overhead for user selection. Both CSFB and CSFB-OB can efficiently exploit multiuser diversity realized by independent fading channels, as well as spatial multiplexing by effectively utilizing the distributed remote antenna units. Subsequently, we investigate the joint user association (UA) and user scheduling (US) for load balancing in a downlink multi-tier heterogeneous network by formulating a network-wide utility maximization problem. A distributed algorithm is proposed to obtain the UA and US solutions. A remarkable feature of the proposed algorithm is that apart from load balancing, multiuser diversity is exploited in the association time to further improve system performance. Finally, opportunistic scheduling schemes are investigated for uplink wireless channels with multiple asymmetrically located legitimate users and eavesdroppers. The closed-form expressions of the secrecy outage probability and ergodic secrecy rate are derived, illustrating the interplay among system parameters. Through the secrecy outage analysis, we design a channel access ratio adjustment scheme to maximize the secrecy throughput while satisfying the required secrecy level.
Molecular Distributions in Gene Regulatory Dynamics
Creators: name: Mackey, Michael C.
name: Tyran-Kamińska, Marta
name: Yvinec, Romain
Publisher: name: arXiv
Year: 2010
Subjects: subject: Molecular Networks (q-bio.MN)
subject: Classical Analysis and ODEs (math.CA)
subject: Probability (math.PR)
subject: FOS: Biological sciences
subject: FOS: Mathematics
subject: 92B99

description: We show how one may analytically compute the stationary density of the distribution of molecular constituents in populations of cells in the presence of noise arising from either bursting transcription or translation, or noise in degradation rates arising from low numbers of molecules. We have compared our results with an analysis of the same model systems (either inducible or repressible operons) in the absence of any stochastic effects, and shown the correspondence between behaviour in the deterministic system and the stochastic analogs. We have identified key dimensionless parameters that control the appearance of one or two steady states in the deterministic case, or unimodal and bimodal densities in the stochastic systems, and detailed the analytic requirements for the occurrence of different behaviours. This approach provides, in some situations, an alternative to computationally intensive stochastic simulations. Our results indicate that, within the context of the simple models we have examined, bursting and degradation noise cannot be distinguished analytically when present alone.
description: 14 pages, 12 figures. Conferences: "2010 Annual Meeting of The Society of Mathematical Biology", Rio de Janeiro (Brazil), 24-29/07/2010. "First International workshop on Differential and Integral Equations with Applications in Biology and Medicine", Aegean University, Karlovassi, Samos island (Greece), 6-10/09/2010
Unstable Adams operations on p-local compact groups
Creators: name: Junod, Fabien
name: Libman, Assaf
name: Levi, Ran
Publisher: name: arXiv
Year: 2011
Subjects: subject: Algebraic Topology (math.AT)
subject: FOS: Mathematics

description: A p-local compact group is an algebraic object modelled on the p-local homotopy theory of classifying spaces of compact Lie groups and p-compact groups. In the study of these objects unstable Adams operations, are of fundamental importance. In this paper we define unstable Adams operations within the theory of p-local compact groups, and show that such operations exist under rather mild conditions. More precisely, we prove that for a given p-local compact group G and a sufficiently large positive integer $m$, there exists an injective group homomorphism from the group of p-adic units which are congruent to 1 modulo p^m to the group of unstable Adams operations on G
Additional file 10 of Genetic diversity of SAD and FAD genes responsible for the fatty acid composition in flax cultivars and lines
Creators: name: Dmitriev, Alexey A.
name: Kezimana, Parfait
name: Rozhmina, Tatiana A.
name: Zhuchenko, Alexander A.
name: Povkhova, Liubov V.
name: Pushkova, Elena N.
name: Novakovskiy, Roman O.
name: Pavelek, Martin
name: Vladimirov, Gleb N.
name: Nikolaev, Evgeny N.
name: Kovaleva, Oxana A.
name: Kostyukevich, Yury I.
name: Chagovets, Vitaliy V.
name: Romanova, Elena V.
name: Snezhkina, Anastasiya V.
name: Kudryavtseva, Anna V.
name: Krasnov, George S.
name: Melnikova, Nataliya V.
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 10. Clusterization of 84 flax samples based on polymorphisms in individual genes (SAD1, SAD2, FAD2A, FAD2B, FAD3A, and FAD3B) revealed by VarScan.
Additional file 12 of Genetic diversity of SAD and FAD genes responsible for the fatty acid composition in flax cultivars and lines
Creators: name: Dmitriev, Alexey A.
name: Kezimana, Parfait
name: Rozhmina, Tatiana A.
name: Zhuchenko, Alexander A.
name: Povkhova, Liubov V.
name: Pushkova, Elena N.
name: Novakovskiy, Roman O.
name: Pavelek, Martin
name: Vladimirov, Gleb N.
name: Nikolaev, Evgeny N.
name: Kovaleva, Oxana A.
name: Kostyukevich, Yury I.
name: Chagovets, Vitaliy V.
name: Romanova, Elena V.
name: Snezhkina, Anastasiya V.
name: Kudryavtseva, Anna V.
name: Krasnov, George S.
name: Melnikova, Nataliya V.
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 12. Primers for the first stage of DNA library preparation.
Cluster Evaluation of Density Based Subspace Clustering
Creators: name: Sembiring, Rahmat Widia
name: Zain, Jasni Mohamad
Publisher: name: arXiv
Year: 2010
Subjects: subject: Databases (cs.DB)
subject: FOS: Computer and information sciences

description: Clustering real world data often faced with curse of dimensionality, where real world data often consist of many dimensions. Multidimensional data clustering evaluation can be done through a density-based approach. Density approaches based on the paradigm introduced by DBSCAN clustering. In this approach, density of each object neighbours with MinPoints will be calculated. Cluster change will occur in accordance with changes in density of each object neighbours. The neighbours of each object typically determined using a distance function, for example the Euclidean distance. In this paper SUBCLU, FIRES and INSCY methods will be applied to clustering 6x1595 dimension synthetic datasets. IO Entropy, F1 Measure, coverage, accurate and time consumption used as evaluation performance parameters. Evaluation results showed SUBCLU method requires considerable time to process subspace clustering; however, its value coverage is better. Meanwhile INSCY method is better for accuracy comparing with two other methods, although consequence time calculation was longer.
description: 6 pages, 15 figures
Notch Signaling Pathway in Pancreatobiliary Tumors
Creators: name: Borlak, Francesca
name: Reutzel-Selke, Anja
name: Schirmeier, Anja
name: Gogolok, Julia
name: Von Hoerschelmann, Ellen
name: Sauer, Igor M.
name: Pratschke, Johann
name: Bahra, Marcus
name: Schmuck, Rosa B.
Publisher: name: Charité - Universitätsmedizin Berlin
Year: 2021
Subjects: subject: pancreatic cancer
subject: cholangiocarcinoma
subject: cancer stem cells
subject: notch pathway
subject: 600 Technik, Medizin, angewandte Wissenschaften::610 Medizin und Gesundheit::610 Medizin und Gesundheit

description: Background and Objectives: The Notch signaling pathway plays an important role both in the development of the ductal systems of the pancreas and the bile ducts as well as in cancer development and progression. The aim of this study was to examine the expression of central proteins of the Notch signaling pathway in pancreatobiliary tumors and its influence on patient survival. Materials and Methods: We compared the receptors (Notch1, Notch4), activating splicing factors (ADAM17), and target genes (HES1) of the Notch pathway and progenitor cell markers with relevance for the Notch signaling pathway (CD44, MSI1) between pancreatic adenocarcinomas (PDAC, n = 14), intrahepatic cholangiocarcinoma (iCC, n = 24), and extrahepatic cholangiocarcinoma (eCC, n = 22) cholangiocarcinomas via immunohistochemistry and ImageJ software-assisted analysis. An Immunohistochemistry (IHC)-score was determined by the percentage and intensity of stained (positive) cells (scale 0-7) and normal and malignant tissue was compared. In the IHC results, patients' (gender, age) and tumor (TNM Classification of Malignant Tumors, Union Internationale contre le Cancer (UICC) stages, grading, and lymphangitic carcinomatosa) characteristics were correlated to patient survival. Results: For eCC, the expression of CD44 (p = 0.043, IHC-score 3.94 vs. 3.54) and for iCC, the expression of CD44 (p = 0.026, IHC-score 4.04 vs. 3.48) and Notch1 (p < 0.001, IHC-score 2.87 vs. 1.78) was significantly higher in the tumor compared to non-malignant tissue. For PDAC, the expression of ADAM17 (p = 0.008, IHC-score 3.43 vs. 1.73), CD44 (p = 0.012, IHC-score 3.64 vs. 2.27), Notch1 (p = 0.012, IHC-score 2.21 vs. 0.64), and Notch4 (p = 0.008, IHC-score 2.86 vs. 0.91) was significantly higher in the tumor tissue. However, none of the analyzed Notch-signaling related components showed an association to patient survival. Conclusion: A significant overexpression of almost all studied components of the Notch signaling pathway can be found in the tumor tissue, however, without a significant influence on patient survival. Therefore, further studies are warranted to draw conclusions on Notch pathway's relevance for patient survival.
Toward Biofabrication of Resorbable Implants Consisting of a Calcium Phosphate Cement and Fibrin—A Characterization In Vitro and In Vivo
Creators: name: Ahlfeld, Tilman
name: Lode, Anja
name: Richter, Richard Frank
name: Pradel, Winnie
name: Franke, Adrian
name: Rauner, Martina
name: Stadlinger, Bernd
name: Lauer, Günter
name: Gelinsky, Michael
name: Korn, Paula
Publisher: name: Charité - Universitätsmedizin Berlin
Year: 2021
Subjects: subject: cleft alveolar osteoplasty
subject: 3D printing
subject: bone
subject: bone tissue engineering
subject: calcium phosphate cement
subject: fibrin
subject: mesenchymal stem cells
subject: rat model
subject: biofabrication
subject: 600 Technik, Medizin, angewandte Wissenschaften::610 Medizin und Gesundheit::610 Medizin und Gesundheit

description: Cleft alveolar bone defects can be treated potentially with tissue engineered bone grafts. Herein, we developed novel biphasic bone constructs consisting of two clinically certified materials, a calcium phosphate cement (CPC) and a fibrin gel that were biofabricated using 3D plotting. The fibrin gel was loaded with mesenchymal stromal cells (MSC) derived from bone marrow. Firstly, the degradation of fibrin as well as the behavior of cells in the biphasic system were evaluated in vitro. Fibrin degraded quickly in presence of MSC. Our results showed that the plotted CPC structure acted slightly stabilizing for the fibrin gel. However, with passing time and fibrin degradation, MSC migrated to the CPC surface. Thus, the fibrin gel could be identified as cell delivery system. A pilot study in vivo was conducted in artificial craniofacial defects in Lewis rats. Ongoing bone formation could be evidenced over 12 weeks but the biphasic constructs were not completely osseous integrated. Nevertheless, our results show that the combination of 3D plotted CPC constructs and fibrin as suitable cell delivery system enables the fabrication of novel regenerative implants for the treatment of alveolar bone defects.
Hydrodynamics of a Micro-Hunter: Chemotactic Scenario
Creators: name: Najafi, Ali
Publisher: name: arXiv
Year: 2010
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Cell Behavior (q-bio.CB)
subject: FOS: Physical sciences
subject: FOS: Biological sciences

description: Inspired by bacterial chemotaxis we propose a hydrodynamic molecular scale hunter that can swim and find its target. The system is essentially a stochastic low Reynolds swimmer with ability to move in two dimensional space and sense the local value of the chemical concentration emitted by a target. We show that by adjusting the geometrical and dynamical variables of the swimmer we can always achieve a swimmer that can navigate and search for the region with higher concentration of a chemical emitted from a source. The system discussed here can also be considered as a theoretical framework for describing the bacterial chemotaxis.
description: Submitted (2010)
Additional file 1 of Genetic diversity of SAD and FAD genes responsible for the fatty acid composition in flax cultivars and lines
Creators: name: Dmitriev, Alexey A.
name: Kezimana, Parfait
name: Rozhmina, Tatiana A.
name: Zhuchenko, Alexander A.
name: Povkhova, Liubov V.
name: Pushkova, Elena N.
name: Novakovskiy, Roman O.
name: Pavelek, Martin
name: Vladimirov, Gleb N.
name: Nikolaev, Evgeny N.
name: Kovaleva, Oxana A.
name: Kostyukevich, Yury I.
name: Chagovets, Vitaliy V.
name: Romanova, Elena V.
name: Snezhkina, Anastasiya V.
name: Kudryavtseva, Anna V.
name: Krasnov, George S.
name: Melnikova, Nataliya V.
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1. Characteristics of 84 flax cultivars and lines.
A Cartier-Gabriel-Kostant structure theorem for Hopf algebroids
Creators: name: Kalisnik, J.
name: Mrcun, J.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Algebra (math.QA)
subject: Differential Geometry (math.DG)
subject: Operator Algebras (math.OA)
subject: FOS: Mathematics
subject: 16T05, 17B35, 22A22

description: In this paper we give an extension of the Cartier-Gabriel-Kostant structure theorem to Hopf algebroids.
description: 14 pages
Spatio-Temporal Bone Remodeling after Hematopoietic Stem Cell Transplantation
Creators: name: Schwarz, Constanze S.
name: Bucher, Christian H.
name: Schlundt, Claudia
name: Mertlitz, Sarah
name: Riesner, Katarina
name: Kalupa, Martina
name: Verlaat, Lydia
name: Schmidt-Bleek, Oskar
name: Sass, Radost A.
name: Schmidt-Bleek, Katharina
name: Duda, Georg N.
name: Penack, Olaf
name: Na, Il-Kang
Publisher: name: Charité - Universitätsmedizin Berlin
Year: 2020
Subjects: subject: hematopoietic stem cell transplantation
subject: T lymphocytes
subject: bone remodeling
subject: 600 Technik, Medizin, angewandte Wissenschaften::610 Medizin und Gesundheit::610 Medizin und Gesundheit

description: The interaction of hematopoietic cells and the bone microenvironment to maintain bone homeostasis is increasingly appreciated. We hypothesized that the transfer of allogeneic T lymphocytes has extensive effects on bone biology and investigated trabecular and cortical bone structures, the osteoblast reconstitution, and the bone vasculature in experimental hematopoietic stem cell transplantations (HSCT). Allogeneic or syngeneic hematopoietic stem cells (HSC) and allogeneic T lymphocytes were isolated and transferred in a murine model. After 20, 40, and 60 days, bone structures were visualized using microCT and histology. Immune cells were monitored using flow cytometry and bone vessels, bone cells and immune cells were fluorescently stained and visualized. Remodeling of the bone substance, the bone vasculature and bone cell subsets were found to occur as early as day +20 after allogeneic HSCT (including allogeneic T lymphocytes) but not after syngeneic HSCT. We discovered that allogeneic HSCT (including allogeneic T lymphocytes) results in a transient increase of trabecular bone number and bone vessel density. This was paralleled by a cortical thinning as well as disruptive osteoblast lining and loss of B lymphocytes. In summary, our data demonstrate that the adoptive transfer of allogeneic HSCs and allogeneic T lymphocytes can induce profound structural and spatial changes of bone tissue homeostasis as well as bone marrow cell composition, underlining the importance of the adaptive immune system for maintaining a balanced bone biology.
Ambiente kapazitive EKG-Messung - Elektroden, Systeme und Konzepte
Creators: name: Heuer, Stephan
Publisher: name: Karlsruhe
Year: 2011
Subjects: Kapazitive Elektroden
Kontaktloses EKG
Capacitive ECG
Smart Textiles
Textile Sensorik

description: Kapazitive Elektroden sind ein vielversprechender Ansatz für alltagstaugliche EKG-Systeme, da sie Biosignale auch ohne direkten Hautkontakt erfassen können. Im Rahmen der Arbeit werden textile kapazitive Elektroden entwickelt, die für ambiente Szenarien geeignet sind und an 2 Beispielsystemen demonstriert: einem textilintegrierten System zum mobilen EKG-Monitoring, und einem ambienten System zur EKG-Ableitung im Automobil. Daneben werden Konzepte zum Umgang mit Bewegungsartefakten vorgestellt
Additional file 9 of Genetic diversity of SAD and FAD genes responsible for the fatty acid composition in flax cultivars and lines
Creators: name: Dmitriev, Alexey A.
name: Kezimana, Parfait
name: Rozhmina, Tatiana A.
name: Zhuchenko, Alexander A.
name: Povkhova, Liubov V.
name: Pushkova, Elena N.
name: Novakovskiy, Roman O.
name: Pavelek, Martin
name: Vladimirov, Gleb N.
name: Nikolaev, Evgeny N.
name: Kovaleva, Oxana A.
name: Kostyukevich, Yury I.
name: Chagovets, Vitaliy V.
name: Romanova, Elena V.
name: Snezhkina, Anastasiya V.
name: Kudryavtseva, Anna V.
name: Krasnov, George S.
name: Melnikova, Nataliya V.
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 9. Clusterization of 84 flax cultivars and lines based on polymorphisms in SAD1, SAD2, FAD2A, FAD2B, FAD3A, and FAD3B genes revealed by freeBayes.
The ecology of microbial metabolic pathways
Creators: name: Louca, Stilianos
Publisher: name: University of British Columbia
Year: 2017

description: Microbial metabolic activity drives biogeochemical cycling in virtually every ecosystem. Yet, microbial ecology and its role in ecosystem biochemistry remain poorly understood, partly because the enormous diversity found in microbial communities hinders their modeling. Despite this diversity, the bulk of global biogeochemical fluxes is driven by a few metabolic pathways encoded by a small set of genes, which through time have spread across microbial clades that can replace each other within metabolic niches. Hence, the question arises whether the dynamics of these pathways can be modeled regardless of the hosting organisms, for example based on environmental conditions. Such a pathway-centric paradigm would greatly simplify the modeling of microbial processes at ecosystem scales. Here I investigate the applicability of a pathway-centric paradigm for microbial ecology. By examining microbial communities in replicate "miniature" aquatic environments, I show that similar ecosystems can exhibit similar metabolic functional community structure, despite highly variable taxonomic composition within individual functional groups. Further, using data from a recent ocean survey I show that environmental conditions strongly explain the distribution of microbial metabolic functional groups across the world's oceans, but only poorly explain the taxonomic composition within individual functional groups. Using statistical tools and mathematical models I conclude that biotic interactions, such as competition and predation, likely underlie much of the taxonomic variation within functional groups observed in the aforementioned studies. The above findings strongly support a pathway-centric paradigm, in which the distribution and activity of microbial metabolic pathways is strongly determined by energetic and stoichiometric constraints, whereas additional mechanisms shape the taxonomic composition within metabolic guilds. These findings motivated me to explore concrete pathway-centric mathematical models for specific ecosystems. Notably, I constructed a biogeochemical model for Saanich Inlet, a seasonally anoxic fjord with biogeochemistry analogous to oxygen minimum zones. The model describes the dynamics of individual microbial metabolic pathways involved in carbon, nitrogen and sulfur cycling, and largely explains geochemical depth profiles as well as DNA, mRNA and protein sequence data. This work yields insight into ocean biogeochemistry and demonstrates the potential of pathway-centric models for microbial ecology.
Analyse des regionalen atmosphärischen Wasserhaushalts unter Verwendung von COSMO-Simulationen und GPS-Beobachtungen
Creators: name: Sasse, Romi
Publisher: name: Karlsruhe
Year: 2011
Subjects: Atmosphärischer Wasserhaushalt
Einfluss von Wetterlagen und Topographie
Regionale Klimamodellierung
COSMO
GPS

description: This thesis addresses the question how mesoscale atmospheric conditions and land surface characteristics affect the regional atmospheric water budget. For its detailed and reliable quantification, the model system COSMO is extended and the high-resolution simulation results are combined with water vapour observations using an innovative method. Furthermore, the impact of synoptic conditions and topography on the water budget is analysed to derive conclusions relevant for climate change issues.
Simulation study of miscible gas injection for gas enriched above the minimum miscibility enrichment
Creators: name: Parakh, Harshad Champaklal
Publisher: name: The University of Texas at Austin
Year: 2004
Subjects: Miscible gas injection
WAG parameters
Water-alternating-gas injection
Minimum miscibility enrichment

description: Miscible gas injection mobilizes residual oil to improve the displacement efficiency of oil recovery processes. Large density contrasts and an unfavorable mobility ratio between the displacing (injected gas) and displaced fluid (reservoir oil) leads to poor volumetric sweep efficiency of gas floods. Water-alternating-gas injection (WAG) is commonly used to improve volumetric sweep efficiency in heterogeneous reservoirs. WAG reduces density and mobility contrasts, and increases mixing of injected and reservoir fluids. Little has been reported in the literature, however, on the effectiveness of WAG processes where the gas is enriched above the minimum miscibility enrichment (MME). The amount of induced mixing is also relatively unknown, partially because the true dispersion level remains unknown. This research examines optimization of WAG processes for enriched gas floods above the MME, particularly as a primary recovery method. Compositional simulations of x-z cross-sections are used to quantify the effects of WAG parameters, heterogeneity, and level of enrichment on local displacement efficiency and sweep efficiency. Stochastic permeability fields with different vertical to horizontal permeability ratios are used to represent the impact of heterogeneity on recovery from miscible WAG floods. The results of this study show that over-enrichment decreases the optimum number of WAG cycles and the amount of gas required to be injected per cycle to maximize recovery. A moderate level of heterogeneity increases WAG recovery. Reservoirs with high permeability layers at the bottom benefit most from enriched WAG. This research also explores the use of compositional core data in the form of stripping ratios to estimate the level of dispersion at field scale. Results from 1-D simulation of continuous slug injection along with analytical gas injection theory are used to determine an appropriate definition of stripping ratio for certain gas injection processes. The stripping ratio calculated with an intermediate component as the lightest component in the oil not present in the injected gas, best estimates the displacement mechanism. Horizontal and vertical sections from 2-D simulations are used to analyze the effect of viscous and gravity crossflow on interpretation of stripping ratio. Resaturation of gas swept regions is significant even for low vertical permeability and a high level of heterogeneity, and complicates the interpretation of stripping ratio. Nevertheless, the magnitude of stripping ratios in resaturated regions can be used to qualitatively estimate the level of dispersion at the field scale
Additional file 11 of Genetic diversity of SAD and FAD genes responsible for the fatty acid composition in flax cultivars and lines
Creators: name: Dmitriev, Alexey A.
name: Kezimana, Parfait
name: Rozhmina, Tatiana A.
name: Zhuchenko, Alexander A.
name: Povkhova, Liubov V.
name: Pushkova, Elena N.
name: Novakovskiy, Roman O.
name: Pavelek, Martin
name: Vladimirov, Gleb N.
name: Nikolaev, Evgeny N.
name: Kovaleva, Oxana A.
name: Kostyukevich, Yury I.
name: Chagovets, Vitaliy V.
name: Romanova, Elena V.
name: Snezhkina, Anastasiya V.
name: Kudryavtseva, Anna V.
name: Krasnov, George S.
name: Melnikova, Nataliya V.
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 11. Clusterization of 84 flax samples based on polymorphisms in individual genes (SAD1, SAD2, FAD2A, FAD2B, FAD3A, and FAD3B) revealed by freeBayes.
Combining biology and mathematics in educational comics to explain evolution
Creators: name: Abrori, Fadhlan Muchlas
name: Tejera, Mathias
name: Lavicza, Zsolt
Publisher: name: Taylor & Francis
Year: 2024
Subjects: subject: Biochemistry
subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Environmental Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Mathematical Sciences not elsewhere classified
subject: Cancer
subject: Science Policy
subject: Plant Biology

description: Biologists use mathematical models as part of their research regularly. However, in schools, biology lessons rarely use mathematics, even if using it benefits understanding the biological content. Aiming for this integration, we designed an interdisciplinary educational comic with biological and mathematical content, where the chosen theme from biology was natural selection. This paper outlines the educational comic content and the principles used for the development based on the story, visual and content aspects. In addition, it focuses on how the content of natural selection is combined with the mathematical content in a way that we call a symbiotic approach.
Additional file 5 of Genetic diversity of SAD and FAD genes responsible for the fatty acid composition in flax cultivars and lines
Creators: name: Dmitriev, Alexey A.
name: Kezimana, Parfait
name: Rozhmina, Tatiana A.
name: Zhuchenko, Alexander A.
name: Povkhova, Liubov V.
name: Pushkova, Elena N.
name: Novakovskiy, Roman O.
name: Pavelek, Martin
name: Vladimirov, Gleb N.
name: Nikolaev, Evgeny N.
name: Kovaleva, Oxana A.
name: Kostyukevich, Yury I.
name: Chagovets, Vitaliy V.
name: Romanova, Elena V.
name: Snezhkina, Anastasiya V.
name: Kudryavtseva, Anna V.
name: Krasnov, George S.
name: Melnikova, Nataliya V.
Publisher: name: figshare
Year: 2020
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 5. Heatmap reflecting polymorphisms of SAD1, SAD2, FAD2A, FAD2B, FAD3A, and FAD3B genes identified in 84 flax cultivars and lines using freeBayes. Flax cultivars and lines are arranged along the horizontal axis and polymorphisms in SAD1, SAD2, FAD2A, FAD2B, FAD3A, and FAD3B genes are arranged along the vertical axis. The content of PAL (palmitic), STE (stearic), OLE (oleic), LIO (linoleic), and LIN (linolenic) and the alternative allele ratio (Alt. ratio) for each identified polymorphism are reflected in color scales for all studied cultivars and lines.
New bases for a general definition for the moving preferred basis
Creators: name: Castagnino, Mario
name: Fortin, Sebastian
Publisher: name: arXiv
Year: 2011
Subjects: subject: Quantum Physics (quant-ph)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: One of the challenges of the Environment-Induced Decoherence (EID) approach is to provide a simple general definition of the moving pointer basis or moving preferred basis. In this letter we prove that the study of the poles that produce the decaying modes in non-unitary evolution, could yield a general definition of the relaxation, the decoherence times, and the moving preferred basis. These probably are the most important concepts in the theory of decoherence, one of the most relevant chapters of theoretical (and also practical) quantum mechanics. As an example we solved the Omnes (or Lee-Friedrich) model using our theory.
description: 6 pages
The Interplay of Nonlinearity and Architecture in Equilibrium Cytoskeletal Mechanics
Creators: name: Wang, Shenshen
name: Shen, Tongye
name: Wolynes, Peter G.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Soft Condensed Matter (cond-mat.soft)
subject: Cell Behavior (q-bio.CB)
subject: FOS: Physical sciences
subject: FOS: Biological sciences

description: The interplay between cytoskeletal architecture and the nonlinearity of the interactions due to bucklable filaments plays a key role in modulating the cell's mechanical stability and affecting its structural rearrangements. We study a model of cytoskeletal structure treating it as an amorphous network of hard centers rigidly cross-linked by nonlinear elastic strings, neglecting the effects of motorization. Using simulations along with a self-consistent phonon method, we show that this minimal model exhibits diverse thermodynamically stable mechanical phases that depend on excluded volume, crosslink concentration, filament length and stiffness. Within the framework set by the free energy functional formulation and making use of the random first order transition theory of structural glasses, we further estimate the characteristic densities for a kinetic glass transition to occur in this model system. Network connectivity strongly modulates the transition boundaries between various equilibrium phases, as well as the kinetic glass transition density.
description: 17 pages, 18 figures
Atom Optics Quantum Pendulum
Creators: name: Ayub, Muhammad
name: Naseer, Khalid
name: Ali, Manzoor
name: Saif, Farhan
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We explain the dynamics of cold atoms, initially trapped and cooled in a magneto-optic trap, in a monochromatic stationary standing electromagnetic wave field. In the large detuning limit the system is modeled as a nonlinear quantum pendulum. We show that wave packet evolution of the quantum particle probes parametric regimes in the quantum pendulum which support classical period, quantum mechanical revival and super revival phenomena. Interestingly, complete reconstruction in particular parametric regime at quantum revival times is independent of potential height.
description: 14 pages, 7 figures