cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Cellular Therapy With Ixmyelocel-T to Treat Critical Limb Ischemia: The Randomized, Double-blind, Placebo-controlled RESTORE-CLI Trial
Creators: name: Longcore, Amy T
name: Watling, Sharon
name: Marston, William A
name: Powell, Richard J
name: Berceli, Scott A
name: Henry, Timothy D
name: Stern, Theresa P
name: Bartel, Ronnda L
name: Guzman, Raul
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Ixmyelocel-T is a patient-specific, expanded, multicellular therapy evaluated in patients with lower extremity critical limb ischemia (CLI) with no options for revascularization. This randomized, double-blind, placebo-controlled, phase 2 trial (RESTORE-CLI) compared the efficacy and safety of intramuscular injections of ixmyelocel-T with placebo. Patients received one-time injections over 20 locations in a single leg and were followed for 12 months. Safety assessments included occurrence of adverse events. Efficacy assessments included time to first occurrence of treatment failure (TTF; major amputation of injected leg; all-cause mortality; doubling of total wound surface area from baseline; de novo gangrene) and amputation-free survival (AFS; major amputation of injected leg; all-cause mortality). A total of 77 patients underwent bone marrow or sham aspiration; 72 patients received ixmyelocel-T (48 patients) or placebo (24 patients). Adverse event rates were similar. Ixmyelocel-T treatment led to a significantly prolonged TTF (P = 0.0032, logrank test). AFS had a clinically meaningful 32% reduction in event rate that was not statistically significant (P = 0.3880, logrank test). Treatment effect in post hoc analyses of patients with baseline wounds was more pronounced (TTF: P < 0.0001, AFS: P = 0.0802, logrank test). Ixmyelocel-T treatment was well tolerated and may offer a potential new treatment option.
SOFTWARE CONTRIBUTION TO THE AVAILABILITY OF MICROPROCESSOR-BASED RELAY PROTECTION
Creators: name: M.I. Uspensky
Publisher: name: Reliability: Theory & Applications
Year: 2022
Subjects: reliability
availability
software
relay protection module

description: An important characteristic of relay protection functioning is availability of microprocessor relay protection software. An approach to estimation of such parameter and correlation between it and hardware availability on the example of 110/35/10 kV distribution network microprocessor protection is considered in the paper. The behavioral nature of the availability under research, reasons and a share of various kinds of the error leading to failure of program execution, variants of program volume definition, some solution approaches to the task at hand, including methods of Jelinsky-Moranda, and also examples of assessing the ratio of these availabilities are considered. An algorithm for the software evaluation used is presented. The influence of different conditions on such evaluation is shown. Applications of different approaches to software readiness estimation for the above types of protection based on data during debugging of protection programs are given.
A new family of tight sets in $\mathcal{Q}^{+}(5,q)$
Creators: name: De Beule, Jan
name: Demeyer, Jeroen
name: Metsch, Klaus
name: Rodgers, Morgan
Publisher: name: arXiv
Year: 2014
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: 51A50, 51E20

description: In this paper, we describe a new infinite family of $\frac{q^{2}-1}{2}$-tight sets in the hyperbolic quadrics $\mathcal{Q}^{+}(5,q)$, for $q \equiv 5 \mbox{ or } 9 \bmod{12}$. Under the Klein correspondence, these correspond to Cameron--Liebler line classes of ${\rm PG}(3,q)$ having parameter $\frac{q^{2}-1}{2}$. This is the second known infinite family of nontrivial Cameron--Liebler line classes, the first family having been described by Bruen and Drudge with parameter $\frac{q^{2}+1}{2}$ in ${\rm PG}(3,q)$ for all odd $q$. The study of Cameron--Liebler line classes is closely related to the study of symmetric tactical decompositions of ${\rm PG}(3,q)$ (those having the same number of point classes as line classes). We show that our new examples occur as line classes in such a tactical decomposition when $q \equiv 9 \bmod 12$ (so $q = 3^{2e}$ for some positive integer $e$), providing an infinite family of counterexamples to a conjecture made by Cameron and Liebler in 1982; the nature of these decompositions allows us to also prove the existence of a set of type $\left(\frac{1}{2}(3^{2e}-3^{e}), \frac{1}{2}(3^{2e}+3^{e}) \right)$ in the affine plane ${\rm AG}(2,3^{2e})$ for all positive integers $e$. This proves a conjecture made by Rodgers in his PhD thesis.
description: 27 pages
First records of Testate Amoebae (Protozoa: Rhizopoda) from Mount Buffalo National Park, Victoria: preliminary notes
Creators: name: Meisterfeld, Ralf
name: Tan, Lor-wai
Publisher: name: La Trobe
Year: 2023

description: La Trobe University Faculty of Science, Technology and Engineering Murray Darling Freshwater Research Centre

MDFRC item.

Eighty-nine species and subspecies were identified from eight habitats surveyed in an expedition to Mount Buffalo, Victoria in the winter of 1997. Of these, six have a strict Gondwanan distribution and 34 were new records for Australia. Highest species richness occurred in the wet Sphagnum habitat of Lake Catani where 50 species and subspecies were recorded. In contrast, the lowest species numbers were in the Dry Moss (16 species) and Humus Layer (15 species) at Mount Dunn. The relatively high diversity of testate species from Mount Buffalo may be the result of both the diverse nature of the substrates sampled, and sampling of an environment that has not experienced much anthropogenic activity.
The connection between stellar mass, age and quenching timescale in massive quiescent galaxies at $z \simeq 1$
Creators: name: Hamadouche, M. L.
name: Carnall, A. C.
name: McLure, R. J.
name: Dunlop, J. S.
name: Begley, R.
name: Cullen, F.
name: McLeod, D. J.
name: Donnan, C. T.
name: Stanton, T. M.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present a spectro-photometric study of a mass-complete sample of quiescent galaxies at $1.0 < z < 1.3$ with $\mathrm{log_{10}}(M_{\star}/\mathrm{M_{\odot}}) \geq 10.3$ drawn from the VANDELS survey, exploring the relationship between stellar mass, age and star-formation history. Within our sample of 114 galaxies, we derive a stellar-mass vs stellar-age relation with a slope of $1.20^{+0.28}_{-0.27}$ Gyr per decade in stellar mass. When combined with recent literature results, we find evidence that the slope of this relation remains consistent over the redshift interval $0
description: Accepted for publication in MNRAS, 11 pages, 6 figures
The Log-Hamza distribution with statistical properties and application
Creators: name: Aijaz Ahmad
name: Ahmad, Afaq
name: I.H. Dar
name: Rajnee Tripathi
Publisher: name: Reliability: Theory & Applications
Year: 2022
Subjects: Log transfor mation
Hamza distribution
moments
maximum likelihood estimation

description: This work suggests a novel two-parameter distribution known as the log-Hamza distribution, in short (LHD). The significant property of the investigated distribution is that it belongs to the family of distributions that have support (0,1). Several statistical features of the investigated distribution were studied, including moments, moment generating functions, order statistics, and reliability measures. For different parameter values, a graphical representation of the probability density function (pdf) and the cumulative distribution function (CDF) is provided. The distribution’s parameters are determined using the well-known maximum likelihood estimation approach. Finally, an application is used to evaluate the effectiveness of the distribution.
Fact Sheet: Open Source Software
Creators: name: Gerlach, Roman
name: Rex, Jessica
name: Lang, Kevin
name: Neute, Nadine
name: Schröter, Annett
Publisher: name: Zenodo
Year: 2020
Subjects: open source
software
open format
proprietary software
freeware
source code
advantages

description: English: "Open Source" is a movement in software development which has gained more and more impact in the last decades. Software is called Open Source if (1) the source code of the application is open, readable and understandable for humans (2) the software can be copied, distributed and used without restraints and (3) the software can be modified and distributed in any form. In this fact sheet we discuss the advantages and disadvantages of open source software. We also compare them to proprietary software and freeware, discuss open formats, and present options which exist in the open source area that can be used as a free-of-charge alternative to the fee-based applications. ------------------------------------------- German: "Open Source" ist eine Bewegung in der Softwareentwicklung, welche in den letzten Jahrzehnten immer mehr Aufschwung gewonnen hat. Man bezeichnet Software als Open Source, wenn grundlegend (1) der Quellcode der Anwendung offen liegt und für Menschen lesbar und verständlich ist (2) die Software beliebig kopiert, verbreitet und genutzt werden kann und (3) die Software verändert und in veränderter Form weitergegeben werden darf. In dieser Handreichung gehen wir auf die Vor- und Nachteile von Open Source Software ein. Dabei wird auch der Vergleich zu proprietärer Software und Freeware gesetzt, auf offene Formate eingegangen und welche Optionen im Open Source Bereich existieren, die als kostenlose Alternative zu den kostenpflichtigen Anwendungen verwendet werden können.
Type 1 Topp-Leone q-Exponential Distribution and its Applications
Creators: name: Nicy Sebastian
name: Jeena Joseph
name: Princy T
Publisher: name: Reliability: Theory & Applications
Year: 2022
Subjects: Type 1 Topp-Leone generated q-exponential distribution
Quantile density function
Quantile function
Hazar d quantile function
L􀀀moments
Reliability Test Plan

description: The main purpose of this paper is to discuss a new lifetime distribution, called the type 1 Topp-Leone generated q-exponential distribution(Type 1 TLqE). Using the quantile approach various distributional properties, L-moments, order statistics, and reliability properties were established. We suggested a new reliability test plan, which is more advantageous and helps in making optimal decisions when the lifetimes follow this distribution. The new test plan is applied to illustrate its use in industrial contexts. Finally, we proved empirically the importance and the flexibility of the new model in model building by using a real data set.
Time-resolved terahertz dynamics in thin films of the topological insulator Bi$_{2}$Se$_3$
Creators: name: Aguilar, R. Valdés
name: Qi, J.
name: Brahlek, M.
name: Bansal, N.
name: Azad, A.
name: Bowlan, J.
name: Oh, S.
name: Taylor, A. J.
name: Prasankumar, R. P.
name: Yarotski, D. A.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: We use optical pump--THz probe spectroscopy at low temperatures to study the hot carrier response in thin Bi$_2$Se$_3$ films of several thicknesses, allowing us to separate the bulk from the surface transient response. We find that for thinner films the photoexcitation changes the transport scattering rate and reduces the THz conductivity, which relaxes within 10 picoseconds (ps). For thicker films, the conductivity increases upon photoexcitation and scales with increasing both the film thickness and the optical fluence, with a decay time of approximately 5 ps as well as a much higher scattering rate. These different dynamics are attributed to the surface and bulk electrons, respectively, and demonstrate that long-lived mobile surface photo-carriers can be accessed independently below certain film thicknesses for possible optoelectronic applications.
description: 4+ pages, 3 figures. Submitted
Geometry in the Transition from Primary to Post-Primary
Creators: name: Barry, Patrick D.
name: O'Farrell, Anthony G.
Publisher: name: arXiv
Year: 2014
Subjects: subject: History and Overview (math.HO)
subject: FOS: Mathematics
subject: 97B70

description: This article is intended as a kind of precursor to the document Geometry for Post-primary School Mathematics, part of the Mathematics Syllabus for Junior Certicate issued by the Irish National Council for Curriculum and Assessment in the context of Project Maths. Our purpose is to place that document in the context of an overview of plane geometry, touching on several important pedagogical and historical aspects, in the hope that this will prove useful for teachers.
description: 19 pages
Strong light-matter coupling in two-dimensional atomic crystals
Creators: name: Liu, Xiaoze
name: Galfsky, Tal
name: Sun, Zheng
name: Xia, Fengnian
name: Lin, Erh-chen
name: Lee, Yi-Hsien
name: Kéna-Cohen, Stéphane
name: Menon, Vinod M.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Optics (physics.optics)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Two dimensional (2D) atomic crystals of graphene, and transition metal dichalcogenides have emerged as a class of materials that show strong light-matter interaction. This interaction can be further controlled by embedding such materials into optical microcavities. When the interaction is engineered to be stronger than the dissipation of light and matter entities, one approaches the strong coupling regime resulting in the formation of half-light half-matter bosonic quasiparticles called microcavity polaritons. Here we report the evidence of strong light-matter coupling and formation of microcavity polaritons in a two dimensional atomic crystal of molybdenum disulphide (MoS2) embedded inside a dielectric microcavity at room temperature. A Rabi splitting of 46 meV and highly directional emission is observed from the MoS2 microcavity owing to the coupling between the 2D excitons and the cavity photons. Realizing strong coupling effects at room temperature in a disorder free potential landscape is central to the development of practical polaritonic circuits and switches.
description: 25 pages, 7 figures
Floodplain biodiversity: why are there so many species?
Creators: name: Shiel, Russell J
name: Green, John D
name: Nielsen, Daryl L
Publisher: name: La Trobe
Year: 2023

description: La Trobe University Faculty of Science, Technology and Engineering Murray Darling Freshwater Research Centre

MDFRC item.

Spring surveys of 112 temporary floodplain waters on River Murray tributaries demonstrated a heterogeneous habitat series, with ca. 500 species of microfauna encountered. Rotifers comprised the most diverse group (>250 taxa), however mean diversity was low (10.93 ± 7.5), in part reflecting predation by copepods and macroinvertebrates. Notably, only 10 rotifer species could be considered widespread in the study area. Ephemeral pool microfaunal communities were distinct from those of adjacent permanent billabongs; their community variability is seen as a function of, or response to, habitat heterogeneity. The significance of high species diversity in ephemeral waters is considered in the context of age of the Murray-Darling Basin, which has persisted in its present location since the breakup of Gondwana, >65 MY BP.
The LMC impact on the kinematics of the Milky Way satellites: clues from the running solar apex
Creators: name: Makarov, Dmitry
name: Khoperskov, Sergey
name: Makarov, Danila
name: Makarova, Lidia
name: Libeskind, Noam
name: Salomon, Jean-Baptiste
Publisher: name: arXiv
Year: 2023
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Dwarf galaxies provide a unique opportunity for studying the evolution of the Milky Way (MW) and the Local Group as a whole. Analysing the running solar apex based on the kinematics of the MW satellites, we discovered an unexpected behaviour of the dipole term of the radial velocity distribution as a function of the galactocentric distance. The nearby satellites (<100 kpc) have a bulk motion with an amplitude of 140-230 km/s while the more distant ones show an isotropic distribution of the radial velocities. Such strong solar apex variations can not be explained by the net rotation of the satellites, as it would require an enormously high rotation rate (~970 km/s). If we exclude the LMC and its most closely related members from our sample, this does not suppress the bulk motion of the nearby satellites strongly enough. Nevertheless, we have demonstrated that the observed peculiar kinematics of the MW satellites can be explained by a perturbation caused by the first infall of the LMC. First, we `undone' the effect of the perturbation by integrating the orbits of the MW satellites backwards (forwards) with (without) massive LMC. It appears that the present-day peculiar enhancement of the solar apex in the inner halo is diminished the most in the case of 2x10^{11} Msun LMC. Next, in self-consistent high-resolution N-body simulations of the MW-LMC interaction, we found that the solar apex shows the observed behaviour only for the halo particles with substantial angular momentum, comparable to that of the MW satellites.
description: 13 pages, 9 figures, accepted for publication in MNRAS
Enhancing Muscle Membrane Repair by Gene Delivery of MG53 Ameliorates Muscular Dystrophy and Heart Failure in δ-Sarcoglycan-deficient Hamsters
Creators: name: Xiao, Xiao
name: He, Bo
name: Cai, Chuanxi
name: Lin, Peihui
name: Li, Jianbin
name: Tang, Ru-hang
name: Zhu, Hua
name: Qiao, Chunping
name: Mayer, Christina
name: Ma, Jianjie
name: Li, Juan
name: Yuan, Zhenhua
name: Xiao, Bin
name: Weisleder, Noah
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Muscular dystrophies (MDs) are caused by genetic mutations in over 30 different genes, many of which encode for proteins essential for the integrity of muscle cell structure and membrane. Their deficiencies cause the muscle vulnerable to mechanical and biochemical damages, leading to membrane leakage, dystrophic pathology, and eventual loss of muscle cells. Recent studies report that MG53, a muscle-specific TRIM-family protein, plays an essential role in sarcolemmal membrane repair. Here, we show that systemic delivery and muscle-specific overexpression of human MG53 gene by recombinant adeno-associated virus (AAV) vectors enhanced membrane repair, ameliorated pathology, and improved muscle and heart functions in δ-sarcoglycan (δ-SG)-deficient TO-2 hamsters, an animal model of MD and congestive heart failure. In addition, MG53 overexpression increased dysferlin level and facilitated its trafficking to muscle membrane through participation of caveolin-3. MG53 also protected muscle cells by activating cell survival kinases, such as Akt, extracellular signal-regulated kinases (ERK1/2), and glycogen synthase kinase-3β (GSK-3β) and inhibiting proapoptotic protein Bax. Our results suggest that enhancing the muscle membrane repair machinery could be a novel therapeutic approach for MD and cardiomyopathy, as demonstrated here in the limb girdle MD (LGMD) 2F model.
Direct Analysis of the Broad-Line SN 2019ein: Connection with the Core-Normal SN 2011fe
Creators: name: Yarbrough, Zach
name: Baron, E.
name: DerKacy, James M.
name: Washington, I.
name: Hoeflich, Peter
name: Burrow, Anthony
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: Type Ia supernovae (SNe Ia) are important cosmological probes and contributors to galactic nucleosynthesis, particularly of the iron group elements. To improve both their reliability as cosmological probes and to understand galactic chemical evolution, it is vital to understand the binary progenitor system and explosion mechanism. The classification of SNe Ia into Branch groups has led to some understanding of the similarities and differences among the varieties of observed SNe Ia. However, partly due to small sample size, little work has been done on the broad-line or 02bo group. We perform direct spectral analysis on the pre-maximum spectra of the broad-line SN 2019ein and compare and contrast it to the core-normal SN~2011fe. Both SN 2019ein and SN 2011fe were first observed spectroscopically within two days of discovery, allowing us to follow the spectroscopic evolution of both supernovae in detail. We find that the optical depths of the primary features of both the CN and BL supernovae are very similar, except that there is a velocity shift between them. We further examine the SN 2002bo-like subclass and show that for nine objects with pre-maximum spectra in the range -6 -- -2 days with respect to B-maximum all the emission peaks of the Si II λ6355 line of BL are blueshifted pre-maximum, making this a simple classification criterion.
description: 9 pages, 9 figures, accepted for publication in MNRAS
In Vivo Gene Delivery by Nonviral Vectors: Overcoming Hurdles?
Creators: name: Huang, Leaf
name: Zhang, Yuan
name: Satterlee, Andrew
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: The promise of cancer gene therapeutics is hampered by difficulties in the in vivo delivery to the targeted tumor cells, and systemic delivery remains to be the biggest challenge to be overcome. Here, we concentrate on systemic in vivo gene delivery for cancer therapy using nonviral vectors. In this review, we summarize the existing delivery barriers together with the requirements and strategies to overcome these problems. We will also introduce the current progress in the design of nonviral vectors, and briefly discuss their safety issues.
Long-term Restoration of Cardiac Dystrophin Expression in Golden Retriever Muscular Dystrophy Following rAAV6-mediated Exon Skipping
Creators: name: Virag, Tamas
name: Sleeper, Meg M
name: Bish, Lawrence T
name: Reynolds, Caryn
name: Kornegay, Joe N
name: Wilson, James M
name: Bogan, Janet
name: Vandenborne, Krista
name: Forbes, Sean C
name: Sanmiguel, Julio
name: Morine, Kevin J
name: Sweeney, H Lee
name: Cecchini, Sylvain
name: Walter, Glenn A
name: Beley, Cyriaque
name: Vulin, Adeline
name: Wang, Bingjing
name: Kotin, Robert M
name: Garcia, Luis
name: Trafny, Dennis
name: Singletary, Gretchen E
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Although restoration of dystrophin expression via exon skipping in both cardiac and skeletal muscle has been successfully demonstrated in the mdx mouse, restoration of cardiac dystrophin expression in large animal models of Duchenne muscular dystrophy (DMD) has proven to be a challenge. In large animals, investigators have focused on using intravenous injection of antisense oligonucleotides (AO) to mediate exon skipping. In this study, we sought to optimize restoration of cardiac dystrophin expression in the golden retriever muscular dystrophy (GRMD) model using percutaneous transendocardial delivery of recombinant AAV6 (rAAV6) to deliver a modified U7 small nuclear RNA (snRNA) carrying antisense sequence to target the exon splicing enhancers of exons 6 and 8 and correct the disrupted reading frame. We demonstrate restoration of cardiac dystrophin expression at 13 months confirmed by reverse transcription-PCR (RT-PCR) and immunoblot as well as membrane localization by immunohistochemistry. This was accompanied by improved cardiac function as assessed by cardiac magnetic resonance imaging (MRI). Percutaneous transendocardial delivery of rAAV6 expressing a modified U7 exon skipping construct is a safe, effective method for restoration of dystrophin expression and improvement of cardiac function in the GRMD canine and may be easily translatable to human DMD patients.
Static Neutron Stars Perspective of Quadratic and Induced Inflationary Attractor Scalar-tensor Theories
Creators: name: Oikonomou, V. K.
Publisher: name: arXiv
Year: 2023
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: This study focuses on the static neutron star perspective for two types of cosmological inflationary attractor theories, namely the induced inflationary attractors and the quadratic inflationary attractors. The two cosmological models can be discriminated cosmologically, since one of the two does not provide a viable inflationary phenomenology, thus in this paper we investigate the predictions of these theories for static neutron stars, mainly focusing on the mass and radii of neutron stars. We aim to demonstrate that although the models have different inflationary phenomenology, the neutron star phenomenology predictions of the two models are quite similar. We solve numerically the Tolman-Oppenheimer-Volkoff equations in the Einstein frame using a powerful double shooting numerical technique, and after deriving the mass-radius graphs for three types of polytropic equations of state, we derive the Jordan frame mass and radii. With regard the equations of state we use polytropic equation of state with the small density part being either the WFF1, the APR or the intermediate stiffness equation of state SLy. The results of our models will be confronted with quite stringent recently developed constraints on the radius of neutron stars with specific mass. As we show, the only equation of state which provides results compatible with the constraints is the SLy, for both the quadratic and induced inflation attractors. Thus nowadays, scalar-tensor descriptions of neutron stars are quite scrutinized due to the growing number of constraining observations, which eventually may also constrain theories of inflation.
description: CQG Accepted
Proceedings Third Workshop on Behavioural Types
Creators: name: Carbone, Marco
Publisher: name: arXiv
Year: 2014
Subjects: subject: Programming Languages (cs.PL)
subject: Logic in Computer Science (cs.LO)
subject: FOS: Computer and information sciences

description: This volume contains the proceedings of BEAT 2014, the third Workshop on Behavioural Types. The workshop took place in Rome, Italy, on September 1st 2014, as a satellite even of CONCUR 2014, the 25th International Conference on Concurrency Theory. The aim of this workshop is to bring together researchers in all aspects of behavioural type theory and its applications, in order to share results, consolidate the community, and discover opportunities for new collaborations and future directions.
Additional file 1 of Intensive care unit caseload and workload and their association with outcomes in critically unwell patients: a large registry-based cohort analysis
Creators: name: Zajic, Paul
name: Engelbrecht, Teresa
name: Graf, Alexandra
name: Metnitz, Barbara
name: Moreno, Rui
name: Posch, Martin
name: Rhodes, Andrew
name: Metnitz, Philipp
Publisher: name: figshare
Year: 2024
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology

description: Additional file1.
Electronic Supplementary Materials from Reduced strength and increased variability of extinction selectivity during mass extinctions
Creators: name: Monarrez, Pedro M.
name: Heim, Noel A.
name: Payne, Jonathan L.
Publisher: name: The Royal Society
Year: 2023
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Palaeontology (incl. Palynology)

description: Contains supplementary information that supports the main text, including results of supplementary analyses.
A reconnection driven magnetic flux cancellation and a quiet Sun Ellerman bomb
Creators: name: Kaithakkal, Anjali. J.
name: Borrero, J. M.
name: Yabar, A. Pastor
name: Rodríguez, J. de la Cruz
Publisher: name: arXiv
Year: 2023
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: The focus of this investigation is to quantify the conversion of magnetic to thermal energy initiated by a quiet Sun cancellation event and to explore the resulting dynamics from the interaction of the opposite polarity magnetic features. We used imaging spectroscopy in the H$α$ line, along with spectropolarimetry in the \ion{Fe}{I} 6173~Å and \ion{Ca}{II} 8542~Å lines from the Swedish Solar Telescope (SST) to study a reconnection-related cancellation and the appearance of a quiet Sun Ellerman bomb (QSEB). We observed, for the first time, QSEB signature in both the wings and core of the \ion{Fe}{I} 6173~Å line. We also found that, at times, the \ion{Fe}{I} line-core intensity reaches higher values than the quiet Sun continuum intensity. From FIRTEZ-dz inversions of the Stokes profiles in \ion{Fe}{I} and \ion{Ca}{II} lines, we found enhanced temperature, with respect to the quiet Sun values, at the photospheric ($\logτ_c$ = -1.5; $\sim$1000 K) and lower chromospheric heights ($\logτ_c$ = -4.5; $\sim$360 K). From the calculation of total magnetic energy and thermal energy within these two layers it was confirmed that the magnetic energy released during the flux cancellation can support heating in the aforesaid height range. Further, the temperature stratification maps enabled us to identify cumulative effects of successive reconnection on temperature pattern, including recurring temperature enhancements. Similarly, Doppler velocity stratification maps revealed impacts on plasma flow pattern, such as a sudden change in the flow direction.
description: 16 pages, 12 figures, accepted for publication in MNRAS
Phase 1 Gene Therapy for Duchenne Muscular Dystrophy Using a Translational Optimized AAV Vector
Creators: name: Samulski, R Jude
name: Govindasamy, Lakshmanan
name: Li, Juan
name: Li, Chengwen
name: Bowles, Dawn E
name: Xiao, Xiao
name: Agbandje-McKenna, Mavis
name: Monahan, Paul E
name: Wang, Bing
name: Camp, Angelique S
name: Samulski, Jade J
name: Grieger, Joshua C
name: Rabinowitz, Joseph E
name: Gray, Steven J
name: McPhee, Scott WJ
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Efficient and widespread gene transfer is required for successful treatment of Duchenne muscular dystrophy (DMD). Here, we performed the first clinical trial using a chimeric adeno-associated virus (AAV) capsid variant (designated AAV2.5) derived from a rational design strategy. AAV2.5 was generated from the AAV2 capsid with five mutations from AAV1. The novel chimeric vector combines the improved muscle transduction capacity of AAV1 with reduced antigenic crossreactivity against both parental serotypes, while keeping the AAV2 receptor binding. In a randomized double-blind placebo-controlled phase I clinical study in DMD boys, AAV2.5 vector was injected into the bicep muscle in one arm, with saline control in the contralateral arm. A subset of patients received AAV empty capsid instead of saline in an effort to distinguish an immune response to vector versus minidystrophin transgene. Recombinant AAV genomes were detected in all patients with up to 2.56 vector copies per diploid genome. There was no cellular immune response to AAV2.5 capsid. This trial established that rationally designed AAV2.5 vector was safe and well tolerated, lays the foundation of customizing AAV vectors that best suit the clinical objective (e.g., limb infusion gene delivery) and should usher in the next generation of viral delivery systems for human gene transfer.
Quantitative 3D Tracing of Gene-delivery Viral Vectors in Human Cells and Animal Tissues
Creators: name: Neumann, Aaron
name: Li, Chengwen
name: Xiao, Ping-Jie
name: Samulski, R Jude
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Trafficking through a variety of cellular structures and organelles is essential for the interaction between gene-delivery vectors (i.e., adeno-associated virus (AAV) and liposomes) and host cells/tissues. Here, we present a method of computer-assisted quantitative 3D biodistribution microscopy that samples the whole population of fluorescently-labeled vectors and document their trafficking routes. Using AAV as a working model, we first experimentally defined numerical parameters for the singularity of Cy5-labeled particles by combining confocal microscopy and atomic force microscopy (AFM). We then developed a robust approach that integrates single-particle fluorescence imaging with 3D deconvolution and isosurface rendering to quantitate viral distribution and trafficking in human cells as well as animal tissues at the single-particle level. Using this quantitative method, we uncovered an as yet uncharacterized rate-limiting step during viral cell entry, while delineating nuclear accumulation of virions during the first 8 hours postinfection. Further, our studies revealed for the first time that following intramuscular injection, AAV spread progressively across muscle tissues through endomysium between myofibers instead of traversing through target cells. Such 3D resolution and quantitative dissection of vector–host interactions at the subcellular level should significantly improve our ability to resolve trafficking mechanisms of gene-delivery particles and facilitate the development of enhanced viral vectors.
Experimental realization of a Coulomb blockade refrigerator
Creators: name: Feshchenko, A. V.
name: Koski, J. V.
name: Pekola, J. P.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We present an experimental realization of a Coulomb blockade refrigerator (CBR) based on a single - electron transistor (SET). In the present structure, the SET island is interrupted by a superconducting inclusion to permit charge transport while preventing heat flow. At certain values of the bias and gate voltages, the current through the SET cools one of the junctions. The measurements follow theoretical model down to about 80 mK, which was the base temperature of the current measurements. The observed cooling increases rapidly with decreasing temperature in agreement with the theory, reaching about 15 mK drop at the base temperature. CBR appears as a promising electronic cooler at temperatures well below 100 mK.
description: 5 pages, 5 figures
Safety and Feasibility of High-pressure Transvenous Limb Perfusion With 0.9% Saline in Human Muscular Dystrophy
Creators: name: Howard, James F
name: Kocis, Keith
name: Fan, Zheng
name: Lin, Weili
name: An, Hongyu
name: Muenzer, Joseph
name: Chopra, Manisha
name: Valley, Robert
name: Powers, William
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: We evaluated safety and feasibility of the transvenous limb perfusion gene delivery method in muscular dystrophy. A dose escalation study of single limb perfusion with 0.9% saline starting with 5% of limb volume was carried out in adults with muscular dystrophies under intravenous analgesia/anesthesia. Cardiac, vascular, renal, muscle, and nerve functions were monitored. A tourniquet was placed above the knee with inflated pressure of 310 mm Hg. Infusion was carried out with a clinically approved infuser via an intravenous catheter inserted in the saphenous vein with a goal infusion rate of 80 ml/minute. Infusion volume was escalated stepwise to 20% limb volume in seven subjects. No subject complained of any post procedure pain other than due to needle punctures. Safety warning boundaries were exceeded only for transient depression of limb tissue oximetry and transient elevation of muscle compartment pressures; these were not associated with nerve, muscle, or vascular damage. Muscle magnetic resonant imaging (MRI) demonstrated fluid accumulation in muscles of the perfused lower extremity. High-pressure retrograde transvenous limb perfusion with saline up to 20% of limb volume at above infusion parameters is safe and feasible in adult human muscular dystrophy. This study will serve as a basis for future gene transfer clinical trials.
Hot Ammonia in the Center of the Seyfert 2 galaxy NGC 3079
Creators: name: Miyamoto, Yusuke
name: Nakai, Naomasa
name: Seta, Masumichi
name: Salak, Dragan
name: Hagiwara, Kenzaburo
name: Nagai, Makoto
name: Ishii, Shun
name: Yamauchi, Aya
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present the results of ammonia observations toward the center of NGC 3079. The NH3(J, K) = (1, 1) and (2, 2) inversion lines were detected in absorption with the Tsukuba 32-m telescope, and the NH3(1,1) through (6,6) lines with the VLA, although the profile of NH3(3,3) was in emission in contrast to the other transitions. The background continuum source, whose flux density was ~50 mJy, could not be resolved with the VLA beam of ~< 0."09 x 0."08. All ammonia absorption lines have two distinct velocity components: one is at the systemic velocity and the other is blueshifted, and both components are aligned along the nuclear jets. For the systemic components, the relatively low temperature gas is extended more than the high temperature gas. The blueshifted NH3(3,3) emission can be regarded as ammonia masers associated with shocks by strong winds probably from newly formed massive stars or supernova explosions in dense clouds in the nuclear megamaser disk. Using para-NH3(1,1), (2,2), (4,4) and (5,5) lines with VLA, we derived the rotational temperature Trot = 120 +- 12 K and 157 +- 19 K for the systemic and blueshifted components, respectively. The total column densities of NH3(0,0)-(6,6), assuming Tex ~Trot, were (8.85+-0.70) x 10^16 cm^-2 and (4.47+-0.78) x 10^16 cm-2 for the systemic and blueshifted components, respectively. The fractional abundance of NH3 relative to molecular hydrogen H2 for the systemic and blueshifted was [NH3]/[H2]=1.3x10^-7 and 6.5 x 10^-8, respectively. We also found the F = 4-4 and F = 5-5 doublet lines of OH 2{Pi}3/2 J = 9/2 in absorption, which could be fitted by two velocity components, systemic and redshifted components. The rotational temperature of OH was estimated to be Trot,OH >~ 175 K, tracing hot gas associated with the interaction of the fast nuclear outflow with dense molecular material around the nucleus.
description: 25 pages, 9 figures, Accepted for publication in PASJ
Freshwater macroinvertebrates of Mount Buffalo
Creators: name: Hawking, John H
Publisher: name: La Trobe
Year: 2023

description: MDFRC item.

The macroinvertebrate fauna of Mount Buffalo is reported from surveys and the scientific literature. Five non-insect groups and 10 insect orders were found to occur on Mount Buffalo. Where possible the distribution, biology and ecology of the common and/or ecologically interesting species is documented.
SHAPE-directed Discovery of Potent shRNA Inhibitors of HIV-1
Creators: name: Weeks, Kevin M
name: Knoepfel, Stefanie A
name: Low, Justin T
name: ter Brake, Olivier
name: Berkhout, Ben
name: Watts, Joseph M
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: The RNA interference (RNAi) pathway can be exploited using short hairpin RNAs (shRNAs) to durably inactivate pathogenic genes. Prediction of optimal target sites is notoriously inaccurate and current approaches applied to HIV-1 show weak correlations with virus inhibition. In contrast, using a high-content model for disrupting pre-existing intramolecular structure in the HIV-1 RNA, as achievable using high-resolution SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) chemical probing information, we discovered strong correlations between inhibition of HIV-1 production in a quantitative cell-based assay and very simple thermodynamic features in the target RNA. Strongest inhibition occurs at RNA target sites that both have an accessible “seed region” and, unexpectedly, are structurally accessible in a newly identified downstream flanking sequence. We then used these simple rules to create a new set of shRNAs and achieved inhibition of HIV-1 production of 90% or greater for up to 82% of designed shRNAs. These shRNAs inhibit HIV-1 replication in therapy-relevant T cells and show no or low cytotoxicity. The remarkable success of this straightforward SHAPE-based approach emphasizes that RNAi is governed, in significant part, by very simple, predictable rules reflecting the underlying RNA structure and illustrates principles likely to prove broadly useful in understanding transcriptome-scale biological recognition and therapeutics involving RNA.
Gamma-Ray Bursts, Quasars, Baryonic Acoustic Oscillations, and Supernovae Ia: new statistical insights and cosmological constraints
Creators: name: Bargiacchi, G.
name: Dainotti, M. G.
name: Nagataki, S.
name: Capozziello, S.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: The recent $\sim 4 \, σ$ Hubble constant, $H_{0}$, tension is observed between the value of $H_{0}$ from the Cosmic Microwave Background (CMB) and Type Ia Supernovae (SNe Ia). It is a decade since this tension is excruciating the modern astrophysical community. To shed light on this problem is key to consider probes at intermediate redshifts between SNe Ia and CMB and reduce the uncertainty on $H_0$. Toward these goals, we fill the redshift gap by employing Gamma-Ray Bursts (GRBs) and Quasars (QSOs), reaching $z=9.4$ and $z=7.6$, respectively, combined with Baryonic Acoustic Oscillations (BAO) and SNe Ia. To this end, we employ the ``Dainotti GRB 3D relation" among the rest-frame end time of the X-ray plateau emission, its corresponding luminosity, and the peak prompt luminosity, and the ``Risaliti-Lusso" QSO relation between ultraviolet and X-ray luminosities. We inquire the commonly adopted Gaussianity assumption on GRBs, QSOs, and BAO. With the joint sample, we fit the flat $Λ$ Cold Dark Matter model with both the Gaussian and the newly discovered likelihoods. We also investigate the impact of the calibration assumed for \textit{Pantheon} and \textit{Pantheon +} SNe Ia on this analysis. Remarkably, we show that only GRBs fulfill the Gaussianity assumption. We achieve small uncertainties on the matter density parameter $Ω_M$ and $H_0$. We find $H_0$ values compatible within 2 $σ$ with the one from the Tip of the Red Giant Branch. Finally, we show that the cosmological results are heavily biased against the arbitrary calibration choice for SNe Ia.
description: 17 pages, 6 figures, 1 table, accepted in MNRAS
Importance of realistic phase space representations of initial quantum fluctuations using the stochastic mean-field approach for fermions
Creators: name: Yilmaz, Bulent
name: Lacroix, Denis
name: Curebal, Resul
Publisher: name: arXiv
Year: 2014
Subjects: subject: Nuclear Theory (nucl-th)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: In the stochastic mean-field (SMF) approach, an ensemble of initial values for a selected set of one-body observables is formed by stochastic sampling from a phase-space distribution that reproduces the initial quantum fluctuations. Independent mean-field evolutions are performed with each set of initial values followed by averaging over the resulting ensemble. This approach has been recently shown to be rather versatile and accurate in describing the correlated dynamics beyond the independent particle picture. In the original formulation of SMF, it was proposed to use a Gaussian assumption for the phase-space distribution. This assumption turns out to be rather effective when the dynamics of an initially uncorrelated state is considered, which was the case in all applications of this approach up to now. Using the Lipkin-Meshkov-Glick (LMG) model, we show that such an assumption might not be adequate if the quantum system under interest is initially correlated and presents configuration mixing between several Slater determinants. In this case, a more realistic description of the initial phase-space is necessary. We show that the SMF approach can be advantageously combined with standard methods to describe phase-space in quantum mechanics. As an illustration, the Husimi distribution function is used here to obtain a realistic representation of the phase-space of a quantum many-body system. This method greatly improves the description of initially correlated fermionic many-body states. In the LMG model, while the Gaussian approximation failed to describe these systems in all interaction strength range, the novel approach gives a perfect agreement with the exact evolution in the weak coupling regime and significantly improves the description of correlated systems in the strong coupling regime.
description: 12 pages, 10 figures
Systemic Delivery of siRNA via LCP Nanoparticle Efficiently Inhibits Lung Metastasis
Creators: name: Liu, Feng
name: Huang, Leaf
name: Li, Jun
name: Yang, Yang
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: Targeted delivery remains the major challenge for the application of small interfering RNA (siRNA). We have developed a lipid/calcium/phosphate (LCP) nanoparticle (NP) to improve siRNA delivery efficiency. The LCP NP was prepared by using microemulsion technology to form calcium/phosphate (CaP) core and further coated with cationic lipids. The final NP was grafted with polyethylene glycol (PEG) and anisamide (AA) ligand on the surface to target sigma receptor-expressing B16F10 melanoma cells. The LCP NP exhibited a 40 nm particle size, a +25 mV zeta-potential, and 91% siRNA encapsulation efficiency. After a single intravenous (i.v.) injection of antiluciferase siRNA (0.12 mg siRNA/kg) formulated in targeted LCP NP, luciferase activity in metastatic B16F10 tumor-loaded lungs decreased by 78% in C57BL/6 mice. In a therapeutic experiment, siRNA against MDM2, c-myc, and VEGF coformulated in the targeted LCP NP resulted in simultaneous silencing of the respective oncogenes in metastatic nodules. Treatment with siRNA in the targeted NP significantly reduced lung metastases (~70–80%) at a relatively low dose (0.36 mg/kg), whereas control group showed little therapeutic effect. Moreover, this targeted LCP NP significantly prolonged the mean survival time of the animals by 27.8% compared to control group without showing any toxicity at the therapeutic dose.
The AAV Vector Toolkit: Poised at the Clinical Crossroads
Creators: name: Schaffer, David V
name: Jude Samulski, R
name: Asokan, Aravind
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2012

description: The discovery of naturally occurring adeno-associated virus (AAV) isolates in different animal species and the generation of engineered AAV strains using molecular genetics tools have yielded a versatile AAV vector toolkit. Promising results in preclinical animal models of human disease spurred the much awaited transition toward clinical application, and early successes in phase I/II clinical trials for a broad spectrum of genetic diseases have recently been reported. As the gene therapy community forges ahead with cautious optimism, both preclinical and clinical studies using first generation AAV vectors have highlighted potential challenges. These include cross-species variation in vector tissue tropism and gene transfer efficiency, pre-existing humoral immunity to AAV capsids and vector dose-dependent toxicity in patients. A battery of second generation AAV vectors, engineered through rational and combinatorial approaches to address the aforementioned concerns, are now available. This review will provide an overview of preclinical studies with the ever-expanding AAV vector portfolio in large animal models and an update on new lead AAV vector candidates poised for clinical translation.