cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Functional metagenomics and consolidated bioprocessing for valorization of pulp and paper mill sludge
Creators: name: Sharan, Anupama Achal
Publisher: name: University of British Columbia
Year: 2018

description: Biocatalyst discovery is integral to bioeconomy development, enabling design of scalable bioprocesses that can compete with the resource-intensive petrochemical industry. Uncultivated microbial communities within natural and engineered ecosystems provide a near-infinite reservoir of genomic diversity and metabolic potential that can be harnessed for this purpose. To bridge the cultivation gap, functional metagenomic screens have been developed to recover active genes directly from environmental samples. In this thesis, a pipeline for recovery of biomass-deconstructing biocatalysts sourced from pulp and paper mill sludge (PPS) metagenome is described. This environment is targeted given its high composition of cellulose that is hypothesized to direct enrichment of enzymes capable of hydrolysing it. The resulting oligosaccharides represent platform molecules that can be fed to downstream applications using consolidated process design for converting biological waste streams into value-added products. High-molecular weight DNA was extracted from sludge and used to construct a fosmid library containing 15,000 clones using the copy control system in EPI300™-T1 R E.coli. Extracted DNA was also used in whole genome shotgun sequencing to compare the metabolic potential of the sludge community with fosmid screening outcomes as well as other waste biomass environments using MetaPathways v2.5 software pipeline, with specific emphasis on carbohydrate-active enzymes (CAZymes). Metagenomic assembling, open reading frame (ORF) prediction, binning and taxonomic assignment approaches were also used to bring out correlations between function and taxonomy. In total, 32,232 ORF’s were mapped to the CAZy database predicted to encode glycoside hydrolases, glycosyl transferases, and carbohydrate binding module families. The fosmid library was screened for glycosidase hydrolase activities using a pool of sensitive fluorogenic glycosides of 6-chloro-4-methylumbelliferone (CMU). A total of 744 clones capable of converting pooled substrates were recovered indicating an extremely high hit rate (1 hit per 43 clones). Following fosmid sequencing and annotation, two of the most promising hits with defined single GH family loci were sub-cloned and overexpressed in E.coli BL21 DE3 strain to conduct basic biochemical characterization. Activity of purified enzymes was demonstrated on model lignocellulosic substrates to evaluate the potential of implementing the proposed circular bioprocess with waste PPS as both the feedstock and source of enriched biocatalysts.
title: The GNAR Initiative: Empowering gateway communities through collaboration
Creators: name: Powell, Jake
name: Rumore, Danya
name: Smith, Jordan
Publisher: name: VIU Publications
Year: 2021
Subjects: subject: Pacific and Mountain States
subject: Tourism--Case studies

description: Gateway communities throughout the intermountain west are an important part of the tourism experience. They are often the doorstep to the national parks and public lands that draw millions of international and domestic visitors each year. Along with many benefits, tourism brings unique challenges to these communities, and they face them with limited staff, resources, and time. This chapter explains the recent development of the Gateway and Natural Amenity Region (GNAR) Initiative and its current efforts to assist gateway communities in the intermountain west region of the United States. The GNAR Initiative is a Cooperative Extension program of the Institute of Outdoor Recreation and Tourism at Utah State University. The Initiative is a hub for gateway community stakeholders to identify shared needs, and cooperatively develop, share, and access resources. The initiative utilizes the infrastructure and mission of the university land grant extension system to operationalize its own, similarly aligned three-part mission: multidisciplinary, trans-boundary research, community and student education, and community capacity building. An overview of the GNAR Initiative’s development is provided as a possible model for similar efforts in other regions. The GNAR Initiative’s internal structure and development path focused on using a collaborative, grass-roots effort to build peer-to-peer networks that link GNAR communities to GNAR communities, and GNAR communities to research and resources in an arena that continues to rapidly evolve. The Initiative’s efforts to include a diverse stakeholder group to guide its efforts resulted in the initiative being equipped to quickly respond to the evolving issues in gateway communities during the COVID-19 pandemic of 2020.
Tunneling Anisotropic Magnetoresistance and Spin-Orbit Coupling in Fe/GaAs/Au Tunnel Junctions
Creators: name: Moser, Jürgen
name: Matos-Abiague, Alex
name: Schuh, Dieter
name: Wegscheider, Werner
name: Fabian, Jaroslav
name: Weiss, Dieter
Publisher: name: Universität Regensburg
Year: 2007
Subjects: subject: 530 Physik
subject: 72.25.Dc, 75.47.−m

description: We report the observation of tunneling anisotropic magnetoresistance effect (TAMR) in the epitaxial metal-semiconductor system Fe/GaAs/Au. The observed two-fold anisotropy of the resistance can be switched by reversing the bias voltage, suggesting that the effect originates from the interference of the spin-orbit coupling at the interfaces. Corresponding model calculations reproduce the experimental findings very well.
A Systemic Receptor Network Triggered by Human cytomegalovirus Entry
Creators: name: Wang, Anyou
name: Li, Hong
Publisher: name: arXiv
Year: 2010
Subjects: subject: Molecular Networks (q-bio.MN)
subject: FOS: Biological sciences
subject: 47N70

description: Virus entry is a multistep process that triggers a variety of cellular pathways interconnecting into a complex network, yet the molecular complexity of this network remains largely unsolved. Here, by employing systems biology approach, we reveal a systemic virus-entry network initiated by human cytomegalovirus (HCMV), a widespread opportunistic pathogen. This network contains all known interactions and functional modules (i.e. groups of proteins) coordinately responding to HCMV entry. The number of both genes and functional modules activated in this network dramatically declines shortly, within 25 min post-infection. While modules annotated as receptor system, ion transport, and immune response are continuously activated during the entire process of HCMV entry, those for cell adhesion and skeletal movement are specifically activated during viral early attachment, and those for immune response during virus entry. HCMV entry requires a complex receptor network involving different cellular components, comprising not only cell surface receptors, but also pathway components in signal transduction, skeletal development, immune response, endocytosis, ion transport, macromolecule metabolism and chromatin remodeling. Interestingly, genes that function in chromatin remodeling are the most abundant in this receptor system, suggesting that global modulation of transcriptions is one of the most important events in HCMV entry. Results of in silico knock out further reveal that this entire receptor network is primarily controlled by multiple elements, such as EGFR (Epidermal Growth Factor) and SLC10A1 (sodium/bile acid cotransporter family, member 1). Thus, our results demonstrate that a complex systemic network, in which components coordinating efficiently in time and space contributes to virus entry.
description: 26 pages
title: Dr. James A. Zimble Collection
Creators: name: Uniformed Services University of the Health Sciences
Publisher: name: University Archives, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814
Year: 2023
Subjects: classificationCode: 3
subject: FOS: Medical and health sciences
classificationCode: 6.1
subject: FOS: History and archaeology

description: USUHS Archives Finding Aid
Dr. James A. Zimble Collection
2023
Additional file 1 of Effects of HDAC inhibitors on neuroblastoma SH-SY5Y cell differentiation into mature neurons via the Wnt signaling pathway
Creators: name: Choi, Jiyun
name: Hwang, Jinsu
name: Ramalingam, Mahesh
name: Jeong, Han-Seong
name: Jang, Sujeong
Publisher: name: figshare
Year: 2023
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Neuroscience
subject: Pharmacology
subject: Biotechnology
subject: Developmental Biology
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1. Additional figures.
Additional file 1 of High-resolution structural variants catalogue in a large-scale whole genome sequenced bovine family cohort data
Creators: name: Lee, Young-Lim
name: Bosse, Mirte
name: Takeda, Haruko
name: Moreira, Gabriel Costa Monteiro
name: Karim, Latifa
name: Druet, Tom
name: Oget-Ebrad, Claire
name: Coppieters, Wouter
name: Veerkamp, Roel F.
name: Groenen, Martien A. M.
name: Georges, Michel
name: Bouwman, Aniek C.
name: Charlier, Carole
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Number of discovered SVs depending on mean sequencing depth. Figure S2. Distinctive RD distribution discerning mCNVs from biallelic duplications. Figure S3. Size distribution of overall CNVs. Figure S4. Canonical and non-canonical copy number variants. Figure S5. Number of variants before and after filtering steps. Figure S6. Mendelian error fraction obtained from the effective number of trios. Figure S7. Minor allele frequency between the discovery and validation cohort. Figure S8. Maximum LD (r2) between CNV-SNP pairs in WGS data set. Figure S9. Underlying WGS data for a 16-kb mCNV inspected in IGV. Figure S10. Underlying WGS data for two copy gain duplication events. Figure S11. Manual correction of ORM1 duplication genotypes.
The influence of cold shock proteins on transcription and translation studied in cell-free model systems
Creators: name: Hofweber, Roland
name: Horn, Gudrun
name: Langmann, Thomas
name: Balbach, Jochen
name: Kremer, Werner
name: Schmitz, Gerd
name: Kalbitzer, Hans-Robert
Publisher: name: Universität Regensburg
Year: 2005
Subjects: subject: Bc, Bacillus caldolyticus; Bs, Bacillus subtilis; CAT, chloramphenicol acetyltransferase; CSP, cold shock protein; dT7, hepta-2'-desoxy-thymidylate; IF, initiation factor; Tm, Thermotoga maritima
subject: 530 Physik

description: Cold shock proteins (CSPs) form a family of highly conserved bacterial proteins capable of single-stranded nucleic acid binding. They are suggested to act as RNA chaperones during cold shock inhibiting the formation of RNA secondary structures, which are unfavourable for transcription and translation. To test this commonly accepted theory, isolated CSPs from a mesophilic, thermophilic and a hyperthermophilic bacterium (Bacillus subtilis, Bacillus caldolyticus and Thermotoga maritima) were studied in an Escherichia coli based cell free expression system on their capability of enhancing protein expression by reduction of mRNA secondary structures. The E. coli based expression of chloramphenicol acetyltransferase and of H-Ras served as model systems. We observed a concentration-dependent suppression of transcription and translation by the different CSPs which makes the considered addition of CSPs for enhancing the protein expression in in vitro translation systems obsolete. Protein expression was completely inhibited at CSP concentrations present under cold shock conditions. The CSP concentrations necessary for 50% inhibition were lowest (140 µm) for the protein of the hyperthermophilic and increased when the thermophilic (215 µm) or even the mesophilic protein (451 µm) was used. Isolated in vitro transcription under the influence of CSPs showed that the transcriptory effect is independent from the rest of the cell. It could be shown in a control experiment that the inhibition of protein expression can be removed by addition of hepta-2'-desoxy-thymidylate (dT7); a heptanucleotide that competitively binds to CSP. The data are in line with a hypothesis that CSPs act on bulk protein expression not as RNA chaperones but inhibit their transcription and translation by rather unspecific nucleic acid binding.
Quantum Big Bang without fine-tuning in a toy-model
Creators: name: Znojil, Miloslav
Publisher: name: arXiv
Year: 2011
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Mathematical Physics (math-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The question of possible physics before Big Bang (or after Big Crunch) is addressed via a schematic non-covariant simulation of the loss of observability of the Universe. Our model is drastically simplified by the reduction of its degrees of freedom to the mere finite number. The Hilbert space of states is then allowed time-dependent and singular at the critical time $t=t_c$. This option circumvents several traditional theoretical difficulties in a way illustrated via solvable examples. In particular, the unitary evolution of our toy-model quantum Universe is shown interruptible, without any fine-tuning, at the instant of its bang or collapse $t= t_c$.
description: 20 pp., 1 fig., invited talk for the conference "10th Workshop on Quantization, Dualities and Integrable Systems" (April 22 - 24, 2011), http://qdis.emu.edu.tr/index.html
Non-Fermi-liquid behavior in transport across carbon nanotube quantum dots
Creators: name: Mayrhofer, Leonhard
name: Grifoni, Milena
Publisher: name: Universität Regensburg
Year: 2006
Subjects: subject: 530 Physik

description: A low energy theory for nonlinear transport in finite-size single-wall carbon nanotubes, based on a microscopic model for the interacting p_z electrons and successive bosonization, is presented. Due to the multiple degeneracy of the energy spectrum diagonal as well as off-diagonal (coherences) elements of the reduced density matrix contribute to the nonlinear transport. A four-electron periodicity with a characteristic ratio between adjacent peaks, as well as nonlinear transport features, in quantitative agreement with recent experiments, are predicted.
Early childhood lead exposure and exceptionality designations for students
Creators: name: Kim, D.
name: Miranda, Marie Lynn
name: Maxson, P.
Publisher: name: University of Notre Dame
Year: 2023

description: The achievement gap continues to be an important educational issue, with disadvantaged groups exhibiting poorer school performance. Recently, literature has shown that even very low levels of early lead exposure affect cognitive and academic performance. As individuals at the lower end of the socioeconomic spectrum are more likely to be exposed to lead, this exposure may be an important contributor to the achievement gap. In this paper, we explore whether early childhood blood lead levels are associated with membership in exceptionality designation groups. In addition, we examine the racial and socioeconomic composition of these exceptional groups. Data from the North Carolina Childhood Lead Poisoning Prevention Program surveillance registry were linked at the individual child level to educational outcomes available through the North Carolina Education Research Data Center. Designation into exceptionality groups was obtained from the end-of-grade (EOG) data. Both standard bivariate and multivariate analyses were employed. Bivariate analyses indicate that blood lead levels and reading EOG scores differ by exceptionality, as well as by race and enrollment in free/reduced lunch. Logistic regression confirmed the relationship between blood lead levels and likelihood of exceptionality. Contextual factors – enrollment in the free/reduced lunch program, race, and parental education – are also significant with regard to exceptionality. This study demonstrates that early childhood lead exposure significantly influences the likelihood of being designated exceptional. These results provide additional evidence that early childhood lead exposure is a significant explanator of the achievement gap.
Effects of non-resonant interaction in ensembles of phase oscillators
Creators: name: Komarov, Maxim
name: Pikovsky, Arkady
Publisher: name: arXiv
Year: 2011
Subjects: subject: Adaptation and Self-Organizing Systems (nlin.AO)
subject: Chaotic Dynamics (nlin.CD)
subject: FOS: Physical sciences

description: We consider general properties of groups of interacting oscillators, for which the natural frequencies are not in resonance. Such groups interact via non-oscillating collective variables like the amplitudes of the order parameters defined for each group. We treat the phase dynamics of the groups using the Ott-Antonsen ansatz and reduce it to a system of coupled equations for the order parameters. We describe different regimes of co-synchrony in the groups. For a large number of groups, heteroclinic cycles, corresponding to a sequental synchronous activity of groups, and chaotic states, where the order parameters oscillate irregularly, are possible.
description: 21 pages, 7 figs
νμ CC1π+ Events Produced in the T2K Beam at Super-Kamiokande
Creators: name: Berkman, Sophie Sattell
Publisher: name: University of British Columbia
Year: 2018

description: T2K is an experiment designed to make precision measurements of neutrino oscillation parameters. Neutrinos produced in the Japan Proton Accelerator Complex are sent 295 km across Japan to the far detector Super-Kamiokande. Charged current quasi-elastic neutrino interactions in which the neutrino produces a lepton and a nucleon are dominant at T2K beam energies, and these are the signal events used in the measurement of muon disappearance parameters θ₂₃ and ∆m²₃₂. The second most dominant neutrino interaction mode at T2K is the charged current single pion interaction (CC1π+) in which both a lepton and a charged pion are produced in addition to the nucleon. This thesis presents a method to identify charged pions and CC1π+ neutrino interactions at Super-Kamiokande. This is used to develop a selection method for muon neutrino CC1π+ interactions at Super-Kamiokande in the T2K beam. There are 93 events expected based on Monte Carlo predictions which would increase the number of muon neutrino events in the T2K analysis by 40%. Methods developed to evaluate the systematic errors associated with explicitly selecting charged pions at Super-Kamiokande for the first time are also discussed.
Key Resource Table for Sheng et al "Activity-Dependent Remodeling of Corticostriatal Axonal Boutons During Motor Learning"
Creators: name: Sheng, Mengjun
name: Lu, Di
name: Weber-Schmidt, Christine
name: Ding, Jun
Publisher: name: Zenodo
Year: 2025

description: Key Resource table for the publication: "Activity-Dependent Remodeling of Corticostriatal Axonal Boutons During Motor Learning", Sheng et al 2024.
Bosonic color-flavor transformation for the special unitary group
Creators: name: Wei, Yi
name: Wettig, Tilo
Publisher: name: Universität Regensburg
Year: 2005
Subjects: subject: 530 Physik

description: We extend Zirnbauer's color-flavor transformation in the bosonic sector to the color group SU({\it N}$_{{\it c}}$). Because the flavor group U({\it N}$_{{\it b}}$,{\it N}$_{{\it b}}$) is noncompact,$^{ }$the algebraic method by which the original color-flavor transformation was$^{ }$derived leads to a useful result only for 2{\it N}$_{{\it b}}$$\lt${\it N}$_{{\it c}}$. This result can$^{ }$also be used for the color group U({\it N}$_{{\it c}}$). The integrals$^{ }$to which the transformation can be applied are of relevance$^{ }$for the recently proposed boson-induced lattice gauge theory.
Large peak-to-valley ratio of negative-differential-conductance in graphene p-n junctions
Creators: name: Nguyen, V. Hung
name: Bournel, A.
name: Dollfus, P.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We investigate the transport characteristics of monolayer graphene p-n junctions by means of the non-equilibrium Green's function technique. It is shown that thanks to the high interband tunneling of chiral fermions and to a finite bandgap opening when the inversion symmetry of graphene plane is broken, a strong negative-differential-conductance behavior with peak-to-valley ratio as large as a few tens can be achieved even at room temperature. The dependence of this behavior on the device parameters such as the Fermi energy, the barrier height, and the transition length is then discussed.
description: 5 pages, 5 figures
Spin Precession and Alternating Spin Polarization in Spin-3/2 Hole Systems
Creators: name: Culcer, Dimitrie
name: Lechner, Christian
name: Winkler, R.
Publisher: name: Universität Regensburg
Year: 2006
Subjects: subject: 530 Physik

description: The spin density matrix for spin-3/2 hole systems can be decomposed into a sequence of multipoles which has important higher-order contributions beyond the ones known for electron systems [R. Winkler, Phys. Rev. B 70, 125301 (2004)]. We show here that the hole spin polarization and the higher-order multipoles can precess due to the spin-orbit coupling in the valence band, yet in the absence of external or effective magnetic fields. Hole spin precession is important in the context of spin relaxation and offers the possibility of new device applications. We discuss this precession in the context of recent experiments and suggest a related experimental setup in which hole spin precession gives rise to an alternating spin polarization.
Low-crosstalk bifurcation detectors for coupled flux qubits
Creators: name: de Groot, P. C.
name: van Loo, A. F.
name: Lisenfeld, J.
name: Schouten, R. N.
name: Lupascu, A.
name: Harmans, C. J. P. M.
name: Mooij, J. E.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Superconductivity (cond-mat.supr-con)
subject: FOS: Physical sciences

description: We present experimental results on the crosstalk between two AC-operated dispersive bifurcation detectors, implemented in a circuit for high-fidelity readout of two strongly coupled flux qubits. Both phase-dependent and phase-independent contributions to the crosstalk are analyzed. For proper tuning of the phase the measured crosstalk is 0.1 % and the correlation between the measurement outcomes is less than 0.05 %. These results show that bifurcative readout provides a reliable and generic approach for multi-partite correlation experiments.
description: Copyright 2010 American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. The following article appeared in Applied Physics Letters and may be found at http://link.aip.org/link/?apl/96/123508
Generation of correlated photon pairs in a chalcogenide As2S3 waveguide
Creators: name: Xiong, C.
name: Marshall, G. D.
name: Peruzzo, A.
name: Lobino, M.
name: Clark, A. S.
name: Choi, D. -Y.
name: Madden, S. J.
name: Natarajan, C. M.
name: Tanner, M. G.
name: Hadfield, R. H.
name: Dorenbos, S. N.
name: Zijlstra, T.
name: Zwiller, V.
name: Thompson, M. G.
name: Rarity, J. G.
name: Steel, M. J.
name: Luther-Davies, B.
name: Eggleton, B. J.
name: O'Brien, J. L.
Publisher: name: arXiv
Year: 2010
Subjects: subject: Quantum Physics (quant-ph)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: We demonstrate the first 1550 nm correlated photon-pair source in an integrated glass platform-a chalcogenide As2S3 waveguide. A measured pair coincidence rate of 80 per second was achieved using 57 mW of continuous-wave pump. The coincidence to accidental ratio was shown to be limited by spontaneous Raman scattering effects that are expected to be mitigated by using a pulsed pump source.
description: 3 pages, 4 figures
title: Screening and prevention for inherited cancer: exploring the experiences of BRCA mutation carriers in Newfoundland Labrador
Creators: name: Hynes, Jaclyn
Publisher: name: Memorial University of Newfoundland
Year: 2020

description: Background Females with BRCA 1/2 gene mutations have increased lifetime risk of breast and ovarian cancers. BRCA mutation carriers in NL are not engaging in cancer prevention and screening behaviors according to recommended guidelines. Methods Qualitative interviews were combined with a provincial survey to conduct a comprehensive assessment of BRCA mutation carriers’ opinions towards risk management services. Results Female BRCA mutation carriers’ risk management is influenced by numerous and varied factors including clinical and social influences, family and personal history of cancer, life stage, health system access, and family physicians’ BRCA knowledge and expertise. Individuals were overwhelmingly in support of a centralized and coordinated inherited cancer program. Conclusion The current system of patient self-navigation and reliance on family doctors to coordinate screening and prevention services results in some patients struggling to access the ongoing management they require. An inherited cancer risk service must recognize the complexities that influences individuals’ behaviors towards risk reducing services.
Rashba and Dresselhaus Spin-Splittings in Semiconductor Quantum Wells measured by Spin Photocurrents
Creators: name: Giglberger, Stephan
name: Golub, Leonid
name: Belkov, Vassilij
name: Danilov, Sergey
name: Schuh, Dieter
name: Gerl, Christian
name: Rohlfing, Franziska
name: Stahl, Joachim
name: Wegscheider, Werner
name: Weiss, Dieter
name: Prettl, Wilhelm
name: Ganichev, Sergey
Publisher: name: Universität Regensburg
Year: 2007
Subjects: subject: 530 Physik

description: The spin-galvanic effect and the circular photogalvanic effect induced by terahertz radiation are applied to determine the relative strengths of Rashba and Dresselhaus band spin-splitting in (001)- grown GaAs and InAs based two dimensional electron systems. We observed that shifting the $\\delta$-doping plane from one side of the quantum well to the other results in a change of sign of the photocurrent caused by Rashba spin-splitting while the sign of the Dresselhaus term induced photocurrent remains. The measurements give the necessary feedback for technologists looking for structures with equal Rashba and Dresselhaus spin-splittings or perfectly symmetric structures with zero Rashba constant.
Micromegas for imaging hadronic calorimetry
Creators: name: Adloff, C.
name: Blaha, J.
name: Cap, S.
name: Chefdeville, M.
name: Dalmaz, A.
name: Drancourt, C.
name: Espargiliere, A.
name: Gaglione, R.
name: Gallet, R.
name: Geffroy, N.
name: Jacquemier, J.
name: Karyotakis, Y.
name: Peltier, F.
name: Prast, J.
name: Vouters, G.
Publisher: name: arXiv
Year: 2011
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: The recent progress in R&D of the Micromegas detectors for hadronic calorimetry including new engineering-technical solutions, electronics development, and accompanying simulation studies with emphasis on the comparison of the physics performance of the analog and digital readout is described. The developed prototypes are with 2 bit digital readout to exploit the Micromegas proportional mode and thus improve the calorimeter linearity. In addition, measurements of detection efficiency, hit multiplicity, and energy shower profiles obtained during the exposure of small size prototypes to radioactive source quanta, cosmic particles and accelerator beams are reported. Eventually, the status of a large scale chamber (1{\times}1 m2) are also presented with prospective towards the construction of a 1 m3 digital calorimeter consisting of 40 such chambers.
description: 6 pages, 9 figures, CALOR2010 conference
Absorption and Emission Spectroscopic Characterization of 10-Phenyl-Isoalloxazine Derivatives
Creators: name: Shirdel, Javid
name: Penzkofer, Alfons
name: Procházka, R.
name: Daub, Joerg
name: Hochmuth, Eduard
name: Deutzmann, Rainer
Publisher: name: Universität Regensburg
Year: 2006
Subjects: subject: Isoalloxazine dyes; Flavoquinone dyes; Absorption spectroscopy; Fluorescence spectroscopy; Photo-degradation; Mass-spectroscopic analysis
subject: 530 Physik

description: The flavoquinone dyes 10-phenyl-isoalloxazine-3-acetic acid ethyl ester (1) and 10-(4-bromo-phenyl)-3-methyl-isoalloxazine (2) in dichloromethane, acetonitrile, and methanol are characterized by absorption and emission spectroscopy. Absorption cross-section spectra, stimulated emission cross-section spectra, fluorescence quantum distributions, quantum yields, lifetimes, and degrees of fluorescence polarization are determined. The blue-light photo-degradation of the dyes is studied. Mass spectroscopic measurements reveal the formation of phenyl-benzo-pteridine (isoalloxazine) derivatives, tetraaza-benzo-aceanthrylene derivatives, dihydro-quinooxaline derivatives, and pyrazino-carbazole derivatives. An enhancement of photo-degradation is observed by the formed photo-fragments.
Lysophosphatidic Acid Modulates Ovarian Cancer Multi-Cellular Aggregate Dynamics.
Creators: name: Bos, Brandi
name: Loughran, Elizabeth
name: Yang, Jing
name: Campbell, Leigh
name: Stack, Sharon
name: Kim, Oleg
name: Liu, Yueying
name: Klymenko, Yuliya
Publisher: name: University of Notre Dame
Year: 2023

description: Epithelial ovarian cancer (EOC) metastasis occurs by exfoliation of cells and multicellular aggregates (MCAs) from the tumor into the peritoneal cavity,adhesion to and retraction of peritoneal mesothelial cells and subsequent anchoring. Elevated levels of lysophosphatidic acid (LPA) have been linked to aberrant cell proliferation,oncogenesis,and metastasis. LPA disrupts junctional integrity and epithelial cohesion in vitro however,the fate of free-floating cells/MCAs and the response of host peritoneal tissues to LPA remain unclear. EOC MCAs displayed significant LPA-induced changes in surface ultrastructure with the loss of cell surface protrusions and poor aggregation,resulting in increased dissemination of small clusters compared to untreated control MCAs. LPA also diminished the adhesive capacity of EOC single cells and MCAs to murine peritoneal explants and impaired MCA survival and mesothelial clearance competence. Peritoneal tissues from healthy mice injected with LPA exhibited enhanced mesothelial surface microvilli. Ultrastructural alterations were associated with restricted peritoneal susceptibility to metastatic colonization by single cells as well as epithelial-type MCAs. The functional consequence is an LPA-induced dissemination of small mesenchymal-type clusters,promoting a miliary mode of peritoneal seeding that complicates surgical removal and is associated with worse prognosis.
Solution structure of the Ran-binding domain 2 of RanBP2 and its interaction with the C terminus of Ran
Creators: name: Geyer, J. Peter
name: Döker, Rolf
name: Kremer, Werner
name: Zhao, Xiaodong
name: Kuhlmann, Jürgen
name: Kalbitzer, Hans-Robert
Publisher: name: Universität Regensburg
Year: 2005
Subjects: subject: Ran; Ran-binding domain; RanBP2; nucleocytoplasmic transport; NMR structure
subject: 530 Physik

description: The termination of export processes from the nucleus to the cytoplasm in higher eukaryotes is mediated by binding of the small GTPase Ran as part of the export complexes to the Ran-binding domains (RanBD) of Ran-binding protein 2 (RanBP2) of the nuclear pore complex. So far, the structures of the first RanBD of RanBP2 and of RanBP1 in complexes with Ran have been known from X-ray crystallographic studies. Here we report the NMR solution structure of the uncomplexed second RanBD of RanBP2. The structure shows a pleckstrin homology (PH) fold featuring two almost orthogonal β-sheets consisting of three and four strands and an α-helix sitting on top. This is in contrast to the RanBD in the crystal structure complexes in which one β-strand is missing. That is probably due to the binding of the C-terminal α-helix of Ran to the RanBD in these complexes. To analyze the interaction between RanBD2 and the C terminus of Ran, NMR-titration studies with peptides comprising the six or 28 C-terminal residues of Ran were performed. While the six-residue peptide alone does not bind to RanBD2 in a specific manner, the 28-residue peptide, including the entire C-terminal helix of Ran, binds to RanBD2 in a manner analogous to the crystal structures. By solving the solution structure of the 28mer peptide alone, we confirmed that it adopts a stable α-helical structure like in native Ran and therefore serves as a valid model of the Ran C terminus. These results support current models that assume recognition of the transport complexes by the RanBDs through the Ran C terminus that is exposed in these complexes.
Additional file 1 of The genetic landscape of inherited retinal dystrophies in Arabs
Creators: name: Jaffal, Lama
name: Joumaa, Hawraa
name: Noureldine, Jinane
name: Banjak, Malak
name: Ibrahim, Mariam
name: Mrad, Zamzam
name: Salami, Ali
name: Shamieh, Said El
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy

description: Supplementary Material 1
Large-scale seismic data compression : application to full waveform inversion and extended image volume
Creators: name: Zhang, Yiming
Publisher: name: University of British Columbia
Year: 2018

description: Conventional oil and gas fields are increasingly difficult to explore and image, resulting in a call for more complex wave-equation based inversion algorithms that require dense long-offset samplings. Consequently, there is an exponential growth in the size of data volumes and prohibitive demands on computational resources. In this work, we propose a method to compress and process seismic data directly in a low-rank tensor format, which drastically reduces the amount of storage required to represent the data. We first outline how seismic data exhibits low-rank structure in a particular transform-domain, which can be exploited to compress the dense data in one extremely storage-efficient tensor format when the data is fully sampled. In the more realistic case of missing data, we can use interpolation techniques based on the same tensor format to recover fully sampled data volume in compressed form. In either case, once we have our data represented in its compressed tensor form, we design an algorithm to extract source or receiver gathers directly from the compressed parameters. This extraction process can be done on-the-fly directly on the compressed data, in the full waveform inversion context, and does not require scanning through the entire dataset in order to form shot gathers. To the best of our knowledge, this work is one of the first major contributions to working with seismic data applications directly in the compressed domain without reconstructing the entire data volume. We use a stochastic inversion approach, which works with small subsets of source experiments at each iteration, further to reduce the computational and memory costs of full waveform inversion. We also demonstrate how this data compression and extraction technique can be applied to forming full subsurface image gathers through probing techniques.
Additional file 1 of Prevalence of G6PD deficiency and diagnostic accuracy of a G6PD point-of-care test among a population at risk of malaria in Myanmar
Creators: name: Aung, Than Htike
name: Suansomjit, Chayanut
name: Tun, Zaw Min
name: Hlaing, Tin Maung
name: Kaewkungwal, Jaranit
name: Cui, Liwang
name: Sattabongkot, Jetsumon
name: Roobsoong, Wanlapa
Publisher: name: figshare
Year: 2023
Subjects: subject: Medicine
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Science Policy
subject: Immunology
subject: FOS: Clinical medicine
subject: Computational Biology

description: Additional file 1: Table S1. Primers and PCR-RFLP conditions for genotyping of G6PD variants.
High-frequency 94 GHz ENDOR characterization of the metal binding site in wild type Ras. GDP and its oncogenic mutant G12V in frozen solution
Creators: name: Bennati, M.
name: Hertel, M.
name: Fritscher, J.
name: Prisner, T.
name: Weiden, N.
name: Hofweber, R.
name: Spörner, M.
name: Horn, G.
name: Kalbitzer, Hans-Robert
Publisher: name: Universität Regensburg
Year: 2006
Subjects: subject: 530 Physik

description: The guanine nucleotide binding protein Ras plays a central role as molecular switch in cellular signal transduction. Ras cycles between a GDP-bound "off" state and a GTP-bound "on" state. Specific oncogenic mutations in the Ras protein are found in up to 30% of all human tumors. Previous 31P NMR studies had demonstrated that in liquid solution different conformational states in the GDP-bound as well as in the GTP-bound form coexist. High-field EPR spectroscopy of the GDP complexes in solution displayed differences in the ligand sphere of the wild-type complex as compared to its oncogenic mutant Ras(G12V). Only three water ligands were found in the former with respect to four in the G12V mutant [Rohrer, M. et al. (2001) Biochemistry 40, 1884-1889]. These differences were not detected in previous X-ray structures in the crystalline state. In this paper, we employ high-frequency electron nuclear double resonance (ENDOR) spectroscopy to probe the ligand sphere of the metal ion in the GDP-bound state. This technique in combination with selective isotope labeling has enabled us to detect the resonances of nuclei in the first ligand sphere of the ion with high spectral resolution. We have observed the 17O ENDOR spectra of the water ligands, and we have accurately determined the 17O hyperfine coupling with aiso = -0.276 mT, supporting the results of previous line shape analysis in solution. Further, the distinct resonances of the -, -, and -phosphorus of the bound nucleotides are illustrated in the 31P ENDOR spectra, and their hyperfine tensors lead to distances in agreement with the X-ray structures. Finally, 13C ENDOR spectra of uniformly 13C-labeled Ras(wt)·GDP and Ras(G12V)·GDP complexes as well as of the Ras(wt)·GppNHp and the selectively 1,4-13C-Asp labeled Ras(wt)·GDP complexes have revealed that in frozen solution only one amino acid is ligated to the ion in the GDP state, whereas two are bound in the GppNHp complex. Our results suggest that a second conformational state of the protein, if correlated with a different ligand sphere of the Mn2+ ion, is not populated in the GDP form of Ras at low temperatures in frozen solution.
title: Reactivity of Isocyanate-Functionalized Lignins: A Key Factor for the Preparation of Lignin-Based Polyurethanes
Creators: name: Zieglowski, Mareike
name: Trosien, Simon
name: Rohrer, Jochen
name: Mehlhase, Sabrina
name: Weber, Simone
name: Bartels, Kerstin
name: Siegert, Gregor
name: Trellenkamp, Taina
name: Albe, Karsten
name: Biesalski, Markus
Publisher: name: Frontiers Media S.A.
Year: 2023

description: Using isocyanate-functionalized Kraft lignin as a reactive macromonomer for the preparation of polyurethane foams by a prepolymer technique is a well-known strategy to incorporate the biomacromolecule into a higher value polymer material. However, as of today the mechanical properties of the resulting materials are still insufficient for a number of possible applications. One reason for this limitation is that the reaction pathway and the morphological arrangement of such foams is of uttermost complexity and depends on a large number of influencing material-intrinsic factors. One important parameter is the reactivity of the functionalized lignin, which has a great impact on the interphase reaction kinetics and thus, on the geometry and mechanical properties of the resulting polyurethane foams. The reactivity is implied, amongst others, by the electron affinity of the isocyanate moiety. Herein, we investigate the reactivity of Kraft lignin modified with different commercially used isocyanates in the reaction with conventional polyols. Therefore, differently reactive prepolymers were synthesized, characterized and polyurethane foams were prepared thereof by using these compounds and the foam formation kinetics, morphological as well as mechanical properties were investigated. Finally, the results were supported by quantum mechanical calculations of the electron affinities of representative model compounds for the lignin-based prepolymers. This work gives rise to a better understanding of the effect of the reactivity and isocyanate structure linked to Kraft lignin on the polyurethane formation and enables rational choice of the isocyanate for pre-functionalization of lignin to prepare materials with better mechanical performance.
Duality relations in the auxiliary field method
Creators: name: Silvestre-Brac, Bernard
name: Semay, Claude
Publisher: name: arXiv
Year: 2011
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The eigenenergies $ε^{(N)}(m;\{n_i,l_i\})$ of a system of $N$ identical particles with a mass $m$ are functions of the various radial quantum numbers $n_i$ and orbital quantum numbers $l_i$. Approximations $E^{(N)}(m;Q)$ of these eigenenergies, depending on a principal quantum number $Q(\{n_i,l_i\})$, can be obtained in the framework of the auxiliary field method. We demonstrate the existence of numerous exact duality relations linking quantities $E^{(N)}(m;Q)$ and $E^{(p)}(m';Q')$ for various forms of the potentials (independent of $m$ and $N$) and for both nonrelativistic and semirelativistic kinematics. As the approximations computed with the auxiliary field method can be very close to the exact results, we show with several examples that these duality relations still hold, with sometimes a good accuracy, for the exact eigenenergies $ε^{(N)}(m;\{n_i,l_i\})$.
QCD Dirac operator at nonzero chemical potential: lattice data and matrix model
Creators: name: Akemann, Gernot
name: Wettig, Tilo
Publisher: name: Universität Regensburg
Year: 2004
Subjects: subject: 530 Physik

description: Recently, a non-Hermitian chiral random matrix model was proposed to describe the eigenvalues of the QCD Dirac operator at nonzero chemical potential. This matrix model can be constructed from QCD by mapping it to an equivalent matrix model which has the same symmetries as QCD with chemical potential. Its microscopic spectral correlations are conjectured to be identical to those of the QCD Dirac operator. We investigate this conjecture by comparing large ensembles of Dirac eigenvalues in quenched SU(3) lattice QCD at a nonzero chemical potential to the analytical predictions of the matrix model. Excellent agreement is found in the two regimes of weak and strong non-Hermiticity, for several different lattice volumes.
Rapid assignment of solution ^{31}P NMR spectra of large proteins by solid-state spectroscopy
Creators: name: Iuga, Adriana
name: Spörner, Michael
name: Ader, Christian
name: Brunner, Eike
name: Kalbitzer, Hans-Robert
Publisher: name: Universität Regensburg
Year: 2006
Subjects: subject: 31P NMR; Phosphate-binding proteins; Solid-state NMR; Liquid-state NMR; Two-dimensional techniques
subject: 530 Physik

description: The application of the 31P NMR spectroscopy to large proteins or protein complexes in solution is hampered by a relatively low intrinsic sensitivity coupled with large line widths. Therefore, the assignment of the phosphorus signals by two-dimensional NMR methods in solution is often extremely time consuming. In contrast, the quality of solid-state NMR spectra is not dependent on the molecular mass and the solubility of the protein. For the complex of Ras with the GTP-analogue GppCH2p we show solid-state 31P NMR methods to be more sensitive by almost one order of magnitude than liquid-state NMR. Thus, solid-state NMR seems to be the method of choice for obtaining the resonance assignment of the phosphorus signals of protein complexes in solution. Experiments on Ras·GDP complexes show that the microcrystalline sample can be substituted by a precipitate of the sample and that unexpectedly the two structural states observed earlier in solution are present in crystals as well.
Advanced Radio Resource Management for Multi Antenna Packet Radio Systems
Creators: name: Nonchev, Stanislav
name: Valkama, Mikko
Publisher: name: arXiv
Year: 2010
Subjects: subject: Networking and Internet Architecture (cs.NI)
subject: FOS: Computer and information sciences

description: In this paper, we propose fairness-oriented packet scheduling (PS) schemes with power-efficient control mechanism for future packet radio systems. In general, the radio resource management functionality plays an important role in new OFDMA based networks. The control of the network resource division among the users is performed by packet scheduling functionality based on maximizing cell coverage and capacity satisfying, and certain quality of service requirements. Moreover, multiantenna transmit-receive schemes provide additional flexibility to packet scheduler functionality. In order to mitigate inter-cell and co-channel interference problems in OFDMA cellular networks soft frequency reuse with different power masks patterns is used. Stemming from the earlier enhanced proportional fair scheduler studies for single-input multiple-output (SIMO) and multiple-input multipleoutput (MIMO) systems, we extend the development of efficient packet scheduling algorithms by adding transmit power considerations in the overall priority metrics calculations and scheduling decisions. Furthermore, we evaluate the proposed scheduling schemes by simulating practical orthogonal frequency division multiple access (OFDMA) based packet radio system in terms of throughput, coverage and fairness distribution among users. As a concrete example, under reduced overall transmit power constraint and unequal power distribution for different sub-bands, we demonstrate that by using the proposed power-aware multi-user scheduling schemes, significant coverage and fairness improvements in the order of 70% and 20%, respectively, can be obtained, at the expense of average throughput loss of only 15%.
description: 14 Pages, IJWMN
Zeeman ratchets for ballistic spin currents
Creators: name: Scheid, Matthias
name: Wimmer, Michael
name: Bercioux, Dario
name: Richter, Klaus
Publisher: name: Universität Regensburg
Year: 2007
Subjects: subject: 530 Physik
subject: 71.70.Ej, 72.25.Dc, 73.40.Ei

description: We investigate the possiblity of creating directed spin-polarized currents in a two-dimensional electron gas (2DEG) subject to an asymmetric magnetic field and an external adiabatic driving. We thereby generalize concepts of quantum charge ratchets to the case with spin. Due to the Zeeman term in the Hamiltonian, spin-up and -down electrons experience different effective potentials, which can be tailored to achieve net spin currents without corresponding charge currents. We consider ballistic, coherent transport in waveguides defined in a 2DEG, where the magnetic field modulation is induced by ferromagnetic stripes on top of the 2DEG.
Lorentz Violation and Extended Supersymmetry
Creators: name: Colladay, Don
name: McDonald, Patrick
Publisher: name: arXiv
Year: 2010
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We construct a collection of Lorentz violating Yang-Mills theories exhibiting supersymmetry.
description: Presented at the Fifth Meeting on CPT and Lorentz Symmetry, Bloomington, Indiana, June 28-July 2, 2010