cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Comparison of a Trial of Labor with an Elective Second Cesarean Section
Creators: name: Bowes Jr., Watson A.
name: Mcmahon, Michael J.
name: Olshan, Andrew F.
name: Luther, Edwin R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1996

description: BACKGROUND: In an attempt to reduce the rate of cesarean section, obstetricians now offer a trial of labor to pregnant women who have had a previous cesarean section. Although a trial of labor is usually successful and is relatively safe, few studies have directly addressed the maternal and perinatal morbidity and mortality associated with this method of delivery.

METHODS: We performed a population-based, longitudinal study of 6138 women in Nova Scotia who had previously undergone cesarean section and had delivered a singleton live infant in the period from 1986 through 1992.

RESULTS: A total of 3249 women elected a trial of labor, and 2889 women chose to undergo a second cesarean section. There were no maternal deaths. The overall rate of maternal morbidity was 8.1 percent; 1.3 percent had major complications (a need for hysterectomy, uterine rupture, or operative injury) and 6.9 percent had minor complications (puerperal fever, a need for blood transfusion, or abdominal-wound infection). Although the overall rate of maternal complications did not differ significantly between women who chose a trial of labor and the women who elected cesarean section (odds ratio for the trial-of-labor group, 0.9; 95 percent confidence interval, 0.8 to 1.1), major complications were nearly twice as likely among women undergoing a trial of labor (odds ratio, 1.8; 95 percent confidence interval, 1.1 to 3.0). Apgar scores, admission to the neonatal intensive care unit, and perinatal mortality were similar among the infants whose mothers had a trial of labor and those whose mothers underwent elective cesarean section.

CONCLUSION: Among pregnant women who have had a cesarean section, major maternal complications are almost twice as likely among those whose deliveries are managed with a trial of labor as among those who undergo an elective second cesarean section.
Decision Diagrams for Quantum Computing
Creators: name: Wille, Robert
name: Hillmich, Stefan
name: Burgholzer, Lukas
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantum computing promises to solve some important problems faster than conventional computations ever could. Currently available NISQ devices on which first practical applications are already executed demonstrate the potential -- with future fault-tolerant quantum hardware for more demanding applications on the horizon. Nonetheless, the advantages in computing power come with challenges to be addressed in the design automation and software development community. In particular, non-quantum representations of states and operations, which provide the basis, e.g., for quantum circuit simulation or verification, require an exponential amount of memory. We propose to use decision diagrams as data structure to conquer the exponential memory requirements in many cases. In this chapter, we review the fundamentals on decision diagrams and highlight their applicability in the tasks of quantum circuit simulation with and without errors as well as in verification of quantum circuits. The tools presented here are all available online as open source projects.
description: 23 pages, 8 figures. Published in Springer Book "Design Automation of Quantum Computers"
A comparison principle for the porous medium equation and its consequences
Creators: name: Avelin, Benny
name: Lukkari, Teemu
Publisher: name: arXiv
Year: 2015
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: Primary 35K55, Secondary 31C15, 35K86

description: We prove a comparison principle for the porous medium equation in more general open sets in $\mathbb{R}^{n+1}$ than space-time cylinders. We apply this result in two related contexts: we establish a connection between a potential theoretic notion of the obstacle problem and a notion based on a variational inequality. We also prove the basic properties of the PME capacity, in particular that there exists a capacitary extremal which gives the capacity for compact sets.
Data tables from Ecological pressures and the contrasting scaling of metabolism and body shape in coexisting taxa: cephalopods versus teleost fish
Creators: name: Hanrong Tan
name: Hirst, Andrew G.
name: Glazier, Douglas S.
name: Atkinson, David
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Physiology
subject: FOS: Biological sciences
subject: Ecology

description: Data tables summarising the data and data sources used in this paper.
(1264) John William Reed
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Power Line Inspection Tasks with Multi-Aerial Robot Systems via Signal Temporal Logic Specifications
Creators: name: Silano, Giuseppe
name: Baca, Tomas
name: Penicka, Robert
name: Liuzza, Davide
name: Saska, Martin
Publisher: name: arXiv
Year: 2023
Subjects: subject: Robotics (cs.RO)
subject: Multiagent Systems (cs.MA)
subject: FOS: Computer and information sciences

description: A framework for computing feasible and constrained trajectories for a fleet of quad-rotors leveraging on Signal Temporal Logic (STL) specifications for power line inspection tasks is proposed in this paper. The planner allows the formulation of complex missions that avoid obstacles and maintain a safe distance between drones while performing the planned mission. An optimization problem is set to generate optimal strategies that satisfy these specifications and also take vehicle constraints into account. Further, an event-triggered replanner is proposed to reply to unforeseen events and external disturbances. An energy minimization term is also considered to implicitly save quad-rotors battery life while carrying out the mission. Numerical simulations in MATLAB and experimental results show the validity and the effectiveness of the proposed approach, and demonstrate its applicability in real-world scenarios.
description: 8 pages, 12 figures, journal paper
Condannati al riuso. Mercato immobiliare e forme della riqualificazione edilizia e urbana
Creators: name: Mangialardo, Alessia
name: Micelli, Ezio
Publisher: name: Aestimum
Year: 2019

description: Urban regeneration strategies are different and depend on developers’ expectations. The study considers two in particular: the demolition and reconstruction of obsolete buildings and the reuse of existing assets. The research examines the feasibility conditions of the two strategies, highlighting the aspects that favour the processes of demolition and reconstruction over reuse with a theoretical model that holds together spatial and economic variables. The model is tested in three Italian cities of different size. The results show that demolition and reconstruction is an option that can only be pursued under favourable settlement and market conditions, forcing small and medium-sized cities to focus on strategies for retrofitting existing buildings.
description: Aestimum, Aestimum 74 (2019)
Boxy/peanut/X bulges, barlenses and the thick part of galactic bars: What are they and how did they form?
Creators: name: Athanassoula, E.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Bars have a complex three-dimensional shape. In particular their inner part is vertically much thicker than the parts further out. Viewed edge-on, the thick part of the bar is what is commonly known as a boxy-, peanut- or X- bulge and viewed face-on it is referred to as a barlens. These components are due to disc and bar instabilities and are composed of disc material. I review here their formation, evolution and dynamics, using simulations, orbital structure theory and comparisons to observations.
description: 21 pages, 7 figures, invited review to appear in "Galactic Bulges", E. Laurikainen, R. Peletier, D. Gadotti, (eds.), Springer
Figures and tables from Scaling of thermal tolerance with body mass and genome size in ectotherms: a comparison between water- and air-breathers.
Creators: name: Leiva, Félix P.
name: Calosi, Piero
name: Verberk, Wilco C. E. P.
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Physiology
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Ecology

description: Global warming appears to favour smaller-bodied organisms, but whether larger species are also more vulnerable to thermal extremes, as suggested for past mass-extinction events, is still an open question. Here, we tested whether interspecific differences in thermal tolerance (heat and cold) of ectotherm organisms are linked to differences in their body mass and genome size (as a proxy for cell size). Since the vulnerability of larger, aquatic taxa to warming has been attributed to the oxygen limitation hypothesis, we also assessed how body mass and genome size modulate thermal tolerance in species with contrasting breathing modes, habitats and life stages. A database with the upper (CTmax) and lower (CTmin) critical thermal limits and their methodological aspects was assembled comprising more than 500 species of ectotherms. Our results demonstrate that thermal tolerance in ectotherms is dependent on body mass and genome size and these relationships became especially evident in prolonged experimental trials where energy efficiency gains importance. During long-term trials, CTmax was impaired in larger-bodied water-breathers, consistent with a role for oxygen limitation. Variation in CTmin was mostly explained by the combined effects of body mass and genome size and it was enhanced in larger-celled, air-breathing species during long-term trials, consistent with a role for depolarization of cell membranes. Our results also highlight the importance of accounting for phylogeny and exposure duration. Especially when considering long-term trials, the observed effects on thermal limits are more in line with the warming-induced reduction in body mass observed during long-term rearing experiments.This article is part of the theme issue ‘Physiological diversity and global patterns of biodiversity in a time of global climate change: testing and generating key hypotheses involving temperature and oxygen’.
Optical spectroscopic observations of gamma-ray blazar candidates III. The 2013/2014 campaign in the Southern Hemisphere
Creators: name: Landoni, M.
name: Massaro, F.
name: Paggi, A.
name: D'Abrusco, R.
name: Milisavljevic, D.
name: Masetti, N.
name: Smith, Howard. A.
name: Tosti, G.
name: Chomiuk, L.
name: Strader, J.
name: Cheung, C. C.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We report the results of our exploratory program carried out with the Southern Astrophysical Research (SOAR) telescope aimed at associating counterparts and establishing the nature of the Fermi Unidentified gamma-ray Sources (UGS). We selected the optical counterparts of 6 UGSs from the Fermi catalog on the basis of our recently discovered tight connection between infrared and gamma-ray emission found for the gamma-ray blazars detected by the Wide-Field Infrared Survey Explorer (WISE) in its the all-sky survey. We perform for the first time a spectroscopic study of the low-energy counterparts of Fermi UGS, in the optical band, confirming the blazar-like nature for the whole sample. We also present new spectroscopic observations of 6 Active Galaxies of Uncertain type associated with Fermi sources (AGUs) that appear to be BL Lac objects. Finally, we report the spectra collected for 6 known gamma-ray blazars belonging to the Roma BZCAT that were obtained to establish their nature or better estimate their redshifts. Two interesting cases of high redshift and extremely luminous BL Lac objects (z>1.18 and z>1.02, based on the detection of Mg II intervening systems) are also discussed.
description: 41 pages (single column), 22 figures, 1 table, AJ accepted for publication (pre-proof version)
(1266) George Frederick Hoerle
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Impatti economici dell’interruzione del servizio irriguo consortile nell’area della Capitanata (Puglia). Stima empirica per il pomodoro da industria nel periodo 2001-2016
Creators: name: Giannoccaro, Giacomo
name: Casieri, Arturo
name: De Vito, Rossella
name: Zingaro, Donato
name: Portoghese, Ivan
Publisher: name: Aestimum
Year: 2019

description: In this research an empirical evaluation of the economic impacts on tomato production due to the reduced water availability for irrigation is proposed. A 16-years’ time series is considered (2001-2016) with regard to the Tavoliere delle Puglie agricultural district. Drought events occurred in the period of interest have caused economic impacts in terms of gross product and irrigation costs, with losses reaching 30% compared to years with regular water availability. These preliminary results calls for a wider drought management plan in which also economic instruments are included with the aim of minimizing economic impacts of irrigation water shortage.
description: Aestimum, Aestimum 74 (2019)
Unitarity, Crossing Symmetry and Duality in the scattering of ${\cal N}=1$ Susy Matter Chern-Simons theories
Creators: name: Inbasekar, Karthik
name: Jain, Sachin
name: Mazumdar, Subhajit
name: Minwalla, Shiraz
name: Umesh, V.
name: Yokoyama, Shuichi
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We study the most general renormalizable ${\cal N}=1$ $U(N)$ Chern-Simons gauge theory coupled to a single (generically massive) fundamental matter multiplet. At leading order in the 't Hooft large $N$ limit we present computations and conjectures for the $2 \times 2$ $S$ matrix in these theories; our results apply at all orders in the 't Hooft coupling and the matter self interaction. Our $S$ matrices are in perfect agreement with the recently conjectured strong weak coupling self duality of this class of theories. The consistency of our results with unitarity requires a modification of the usual rules of crossing symmetry in precisely the manner anticipated in arXiv:1404.6373, lending substantial support to the conjectures of that paper. In a certain range of coupling constants our $S$ matrices have a pole whose mass vanishes on a self dual codimension one surface in the space of couplings.
description: 63 pages + 26 pages appendices, 6 figures, V2: Corrected typos, added references, V3: Corrected typos, added clarifications
Supplementary results from Evolution and plasticity of thermal performance: an analysis of variation in thermal tolerance and fitness in 22 Drosophila species
Creators: name: MacLean, Heidi J.
name: Sørensen, Jesper G.
name: Kristensen, Torsten N.
name: Loeschcke, Volker
name: Beedholm, Kristian
name: Kellermann, Vanessa
name: Overgaard, Johannes
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Physiology
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Ecology

description: Additional analysis of the data.
References for Raw data from Scaling of thermal tolerance with body mass and genome size in ectotherms: a comparison between water- and air-breathers.
Creators: name: Leiva, Félix P.
name: Calosi, Piero
name: Verberk, Wilco C. E. P.
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Physiology
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Ecology

description: Global warming appears to favour smaller-bodied organisms, but whether larger species are also more vulnerable to thermal extremes, as suggested for past mass-extinction events, is still an open question. Here, we tested whether interspecific differences in thermal tolerance (heat and cold) of ectotherm organisms are linked to differences in their body mass and genome size (as a proxy for cell size). Since the vulnerability of larger, aquatic taxa to warming has been attributed to the oxygen limitation hypothesis, we also assessed how body mass and genome size modulate thermal tolerance in species with contrasting breathing modes, habitats and life stages. A database with the upper (CTmax) and lower (CTmin) critical thermal limits and their methodological aspects was assembled comprising more than 500 species of ectotherms. Our results demonstrate that thermal tolerance in ectotherms is dependent on body mass and genome size and these relationships became especially evident in prolonged experimental trials where energy efficiency gains importance. During long-term trials, CTmax was impaired in larger-bodied water-breathers, consistent with a role for oxygen limitation. Variation in CTmin was mostly explained by the combined effects of body mass and genome size and it was enhanced in larger-celled, air-breathing species during long-term trials, consistent with a role for depolarization of cell membranes. Our results also highlight the importance of accounting for phylogeny and exposure duration. Especially when considering long-term trials, the observed effects on thermal limits are more in line with the warming-induced reduction in body mass observed during long-term rearing experiments.This article is part of the theme issue ‘Physiological diversity and global patterns of biodiversity in a time of global climate change: testing and generating key hypotheses involving temperature and oxygen’.
On the Defect Group of a 6D SCFT
Creators: name: Del Zotto, Michele
name: Heckman, Jonathan J.
name: Park, Daniel S.
name: Rudelius, Tom
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We use the F-theory realization of 6D superconformal field theories (SCFTs) to study the corresponding spectrum of stringlike, i.e. surface defects. On the tensor branch, all of the stringlike excitations pick up a finite tension, and there is a corresponding lattice of string charges, as well as a dual lattice of charges for the surface defects. The defect group is data intrinsic to the SCFT and measures the surface defect charges which are not screened by dynamical strings. When non-trivial, it indicates that the associated theory has a partition vector rather than a partition function. We compute the defect group for all known 6D SCFTs, and find that it is just the abelianization of the discrete subgroup of U(2) which appears in the classification of 6D SCFTs realized in F-theory. We also explain how the defect group specifies defining data in the compactification of a (1,0) SCFT.
description: 24 pages
Atovaquone Compared with Dapsone for the Prevention of Pneumocystis carinii Pneumonia in Patients with HIV Infection Who Cannot Tolerate Trimethoprim, Sulfonamides, or Both
Creators: name: Murphy, Robert L.
name: Kerkering, Thomas M.
name: Balfour, Henry H.
name: Luskin-Hawk, Roberta
name: Van Der Horst, Charles D.
name: El-Sadr, Wafaa M.
name: Hafner, Richard
name: Yurik, Teresa Mc Cabe
name: Schutz, Malte
name: Eng, Robert
name: Cheung, Tony W.
name: Hooton, Thomas M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1998

description: BACKGROUND: Although trimethoprim-sulfamethoxazole is the drug of choice for the prevention of Pneumocystis carinii pneumonia, many patients cannot tolerate it and must switch to an alternative agent.

METHODS: We conducted a multicenter, open-label, randomized trial comparing daily atovaquone (1500-mg suspension) with daily dapsone (100 mg) for the prevention of P. carinii pneumonia among patients infected with the human immunodeficiency virus who could not tolerate trimethoprim-sulfamethoxazole. The median follow-up period was 27 months.

RESULTS: Of 1057 patients enrolled, 298 had a history of P. carinii pneumonia. P. carinii pneumonia developed in 122 of 536 patients assigned to atovaquone (15.7 cases per 100 person-years), as compared with 135 of 521 in the dapsone group (18.4 cases per 100 person-years; relative risk for atovaquone vs. dapsone, 0.85; 95 percent confidence interval, 0.67 to 1.09; P=0.20). The relative risk of death was 1.07 (95 percent confidence interval, 0.89 to 1.30; P=0.45), and the relative risk of discontinuation of the assigned medication because of adverse events was 0.94 (95 percent confidence interval, 0.74 to 1.19; P=0.59). Among the 546 patients who were receiving dapsone at base line, the relative risk of discontinuation because of adverse events was 3.78 for atovaquone as compared with dapsone (95 percent confidence interval, 2.37 to 6.01; P<0.001); among those not receiving dapsone at base line, it was 0.42 (95 percent confidence interval, 0.30 to 0.58; P<0.001).

CONCLUSIONS: Among patients who cannot tolerate trimethoprim-sulfamethoxazole, atovaquone and dapsone are similarly effective for the prevention of P. carinii pneumonia. Our results support the continuation of dapsone prophylaxis among patients who are already receiving it. However, among those not receiving dapsone, atovaquone is better tolerated and may be the preferred choice for prophylaxis against P. carinii pneumonia.
Exploring drivers of farmland value and growth in Italy and Germany at regional level
Creators: name: De Noni, Ivan
name: Ghidoni, Alessandro
name: Menzel, Friederike
name: Bahrs, Enno
name: Corsi, Stefano
Publisher: name: Aestimum
Year: 2019

description: The recent renewed growing attractiveness of investments in farmland for agricultural and non-agricultural reasons have raised new attention by European Union on factors able to influence the farmland value and on the enhancement of agricultural policies for supporting the development of European regions. Despite its importance, there is a very limited number of studies focusing on European context and a little concordance between the drivers affecting the farmland value and growth. Attempting to reduce the gap, this study investigates the determinants of farmland prices from 2000 to 2010 by exploring and comparing Italy and Germany that are interesting because of their similarity with respect to the outlined dichotomy between urbanized and farming counties/provinces. The comparison across models allows to discuss the cross-cutting and country-specific drivers affecting farmland value and the implication of these findings on agricultural policies recommendations.
description: Aestimum, Aestimum 74 (2019)
Confronto fra modelli di gestione forestale tradizionale e carbon oriented in ambito alpino
Creators: name: Blanc, Simone
name: Accastello, Cristian
name: Mosso, Angela
name: Bianchi, Ettore
name: Lingua, Federico
name: Brun, Filippo
Publisher: name: Aestimum
Year: 2019

description: This paper compares the traditional vs carbon-oriented forest management of two coniferous stands in the Alpine environment, quantifying the carbon sink, the carbon credit generated and the economic results. The results show the economic feasibility of the transition from current forest management strategies to a carbon-oriented method in the considered context. Carbon-oriented management provides relevant environmental benefits, combatting climate change, even though some elements of uncertainty still persist, particularly in relation to achieving a profitable management, specifically due to the volatile voluntary carbon credit market.
description: Aestimum, Aestimum 74 (2019)
LUXE: A new experiment to study non-perturbative QED in electron-laser and photon-laser collisions
Creators: name: Yap, Yee Chinn
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Physics - Experiment (hep-ex)
subject: Accelerator Physics (physics.acc-ph)
subject: FOS: Physical sciences

description: The LUXE experiment (Laser Und XFEL Experiment) is an experiment in planning at DESY Hamburg using the electron beam of the European XFEL. LUXE is intended to study collisions between a high-intensity optical laser pulse and 16.5 GeV electrons, as well as collisions between the laser pulse and high-energy secondary photons. This will elucidate quantum electrodynamics (QED) at the strong-field frontier, where the electromagnetic field of the laser is above the Schwinger limit. In this regime, QED is non-perturbative. This manifests itself in the creation of physical electron-positron pairs from the QED vacuum, similar to Hawking radiation from black holes. LUXE intends to measure the positron production rate in an unprecedented laser intensity regime. An overview of the LUXE experimental setup and its challenges and progress is given in this article, along with a discussion of the expected physics reach in the context of testing QED in the non-perturbative regime.
description: 6 pages
Failure of Cytarabine in Progressive Multifocal Leukoencephalopathy Associated with Human Immunodeficiency Virus Infection
Creators: name: Mcarthur, Justin
name: Simpson, David
name: Millar, Linda
name: Clifford, David
name: Yainnoutsos, Constantin
name: Hollander, Harry
name: Wetherill, Patricia E.
name: Hall, Colin D.
name: Major, Eugene
name: Timpone, Joseph
name: Cohen, Bruce
name: Dafni, Urania
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 1998

description: Background Progressive multifocal leukoencephalopathy affects about 4 percent of patients with the acquired immunodeficiency syndrome (AIDS), and survival after the diagnosis of leukoencephalopathy averages only about three months. There have been anecdotal reports of improvement but no controlled trials of therapy with antiretroviral treatment plus intravenous or intrathecal cytarabine. Methods In this multicenter trial, 57 patients with human immunodeficiency virus (HIV) infection and biopsy-confirmed progressive multifocal leukoencephalopathy were randomly assigned to receive one of three treatments: antiretroviral therapy alone, antiretroviral therapy plus intravenous cytarabine, or antiretroviral therapy plus intrathecal cytarabine. After a lead-in period of 1 to 2 weeks, active treatment was given for 24 weeks. For most patients, antiretroviral therapy consisted of zidovudine plus either didanosine or stavudine. Results At the time of the last analysis, 14 patients in each treatment group had died, and there were no significant differences in survival among the three groups (P=0.85 by the log-rank test). The median survival times (11, 8, and 15 weeks) were similar to those in previous studies. Only seven patients completed the 24 weeks of treatment. Anemia and thrombocytopenia were more frequent in patients who received antiretroviral therapy in combination with intravenous cytarabine than in the other groups. Conclusions Cytarabine administered either intravenously or intrathecally does not improve the prognosis of HIV-infected patients with progressive multifocal leukoencephalopathy who are treated with the antiretroviral agents we used, nor does high-dose antiretroviral therapy alone appear to improve survival over that reported in untreated patients.
Galaxy Genome Annotation: Galaxy as a platform for the annotation of genomes
Creators: name: Bretaudeau, Anthony
name: Rasche, Helena
Publisher: name: F1000 Research Limited
Year: 2023

description: Galaxy Genome Annotation (GGA) is a project focusing on developments and resources to turn Galaxy into a complete and efficient platform for the structural and functional annotation of genome sequences. In this talk, we will present an update on the material produced by the GGA community in the last years on this topic.
 First, GGA has developed Galaxy tool wrappers for widely used, state-of-the-art annotation tools (e.g. Prokka, Maker, Braker, Funannotate, BUSCO, InterProScan, repeat masking tools) and Galaxy annotation workflows making use of these tools for real-life data analysis. This talk will give an overview of these developments, and discuss a few challenging issues that were encountered (e.g. complex dependencies, licensing, specific computing requirements).
 Another aspect of the GGA work is the integration of powerful genomics data visualizations directly within Galaxy, such as Circos, JBrowse (1 and 2) or GeneNoteBook. An important effort has also been carried out on the integration of more complex web applications, using specialized Docker images and Python libraries, such as Tripal or Apollo, a real-time, multi-user, collaborative manual curation of genome annotation, deployed on https://usegalaxy.eu/apollo.
 Based on all these results, training material was produced in the frame of the Gallantries project (Erasmus+), integrated into the Galaxy Training Network, and adopted by hundreds of students who attended the three GTN Smörgåsbord editions, and several other local training events.
 Put together, the various outcomes of the GGA project now enable scientists to perform complete genome annotation projects using Galaxy. Just as large scale sequencing projects (VGP, ERGA, Atlasea) are using Galaxy for genome assembly of thousands of genomes, GGA allows to go one step further by providing high quality, state-of-the-art Galaxy components for the annotation of these newly sequenced and assembled genomes.
Figures and tables from Scaling of thermal tolerance with body mass and genome size in ectotherms: a comparison between water- and air-breathers
Creators: name: Leiva, Félix P.
name: Calosi, Piero
name: Verberk, Wilco C. E. P.
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Physiology
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Ecology

description: Global warming appears to favour smaller-bodied organisms, but whether larger species are also more vulnerable to thermal extremes, as suggested for past mass-extinction events, is still an open question. Here, we tested whether interspecific differences in thermal tolerance (heat and cold) of ectotherm organisms are linked to differences in their body mass and genome size (as a proxy for cell size). Since the vulnerability of larger, aquatic taxa to warming has been attributed to the oxygen limitation hypothesis, we also assessed how body mass and genome size modulate thermal tolerance in species with contrasting breathing modes, habitats and life stages. A database with the upper (CTmax) and lower (CTmin) critical thermal limits and their methodological aspects was assembled comprising more than 500 species of ectotherms. Our results demonstrate that thermal tolerance in ectotherms is dependent on body mass and genome size and these relationships became especially evident in prolonged experimental trials where energy efficiency gains importance. During long-term trials, CTmax was impaired in larger-bodied water-breathers, consistent with a role for oxygen limitation. Variation in CTmin was mostly explained by the combined effects of body mass and genome size and it was enhanced in larger-celled, air-breathing species during long-term trials, consistent with a role for depolarization of cell membranes. Our results highlight the importance of accounting for phylogeny and exposure duration. Especially when considering long-term trials, the observed effects on thermal limits are more in line with the warming-induced reduction in body mass observed during long-term rearing experiments.This article is part of the theme issue ‘Physiological diversity and global patterns of biodiversity in a time of global climate change: testing and generating key hypotheses involving temperature and oxygen’.
Time-dependent massless Dirac fermions in graphene
Creators: name: Khantoul, Boubakeur
name: Fring, Andreas
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Using the Lewis-Riesenfeld method of invariants we construct explicit analytical solutions for the massless Dirac equation in 2+1 dimensions describing quasi-particles in graphene. The Hamiltonian of the system considered contains some explicit time-dependence in addition to one resulting from being minimally coupled to a time-dependent magnetic field. The eigenvalue equations for the two spinor components of the Lewis-Riesenfeld invariant are found to decouple into a pair of supersymmetric invariants in a similar fashion as the known decoupling for the time-independent Dirac Hamiltonians.
description: 5 pages
De novo functional transcriptomics with RNA-seq and Ribo-seq
Creators: name: Albanese, Roberto
name: Campbell, Amy E.
name: Dossena, Francesco
name: Mancino, Marilena
name: Sujatha Jagannathan
name: Calviello, Lorenzo
Publisher: name: F1000 Research Limited
Year: 2023

description: Our genome sequencing and assembly capabilities have hugely increased. However, annotating our genome is still challenging. Genes can produce multiple isoforms, which may have different expression levels and roles. Transcript functions can be elucidated by profiling ribosome positions with the protocol Ribo-seq. By using ribosome profiling data, it is possible to study the fates of cytoplasmic transcripts and to quantify translational levels. Moreover, data coming from proteomics technologies can support the functional characterization of coding transcript isoforms.

 The main goal of this project is the detection and characterization of sample-specific and condition-specific transcripts, ORFs, and proteins. We implemented a computational pipeline for de novo transcriptome assembly and de novo detection of Open Reading Frames (ORFs). We use a proteogenomic approach for the identification and quantification of peptides and proteins, and we perform differential expression analyses at the peptide and protein levels.

 We demonstrate that our computational workflow can be used to study the effects on gene expression of DUX4 activation in human skeletal muscle cells. DUX4 misexpression in skeletal muscle is known to cause facioscapulohumeral muscular dystrophy (FSHD). It also inhibits Nonsense-Mediated Decay (NMD), thus leading to the accumulation of incomplete transcripts and truncated proteins. While we use RNA-seq data to assemble known and novel transcripts, we exploit Ribo-seq data to identify unannotated translated transcript regions. Finally, by using a custom protein database as well as a proteomic dataset matching the time-points of the transcriptomic dataset, we identify differentially expressed novel proteins otherwise invisible to classical analysis methods.

 In conclusion, this work shows that integration of data about different steps of the regulatory cascade helps the identification, quantification and functional characterization of human transcripts and proteins.
How quantum are classical spin ices?
Creators: name: Rau, Jeffrey G.
name: Gingras, Michel J. P.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: FOS: Physical sciences

description: The pyrochlore spin ice compounds Dy2Ti2O7 and Ho2Ti2O7 are well described by classical Ising models down to very low temperatures. Given the empirical success of this description, the question of the importance of quantum effects in these materials has been mostly ignored. We show that the common wisdom that the strictly Ising moments of Dy3+ and Ho3+ imply strictly Ising interactions is too naive; a more complex argument is needed to explain the close agreement between theory and experiment. From a microscopic picture of the interactions in rare-earth oxides, we show that the high-rank multipolar interactions needed to induce quantum effects are generated only very weakly by super-exchange. Using this framework, we formulate an estimate of the scale of quantum effects in Ho2Ti2O7 and Dy2Ti2O7, finding it to be well below experimentally relevant temperatures. We discuss the implications of these results for realizing quantum spin ice in other materials.
description: 5 pages + 12 pages
(1260) Charles Everard Upton
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Rural environment and landscape quality: an evaluation model integrating social media analysis and geostatistics techniques
Creators: name: Alampi Sottini, Veronica
name: Barbierato, Elena
name: Bernetti, Iacopo
name: Capecchi, Irene
name: Fabbrizzi, Sara
name: Menghini, Silvio
Publisher: name: Aestimum
Year: 2019

description: The use of geo-tagged photographs seems to be a promising alternative for assessing the scenic beauty of the agricultural landscape compared to the traditional investigation based on expert and perceptual approaches. The aim of this study is integrating the cumulative viewshed calculated from geotagged photo metadata publicly shared on Flickr with raster data on geomorphology, historical sites, and the natural environment, using landscape ecology metrics and Geographically Weighted Regression modelling. Crowdsourced data provided empirical assessments of the covariates associated with visitor distribution, highlighting how changes in infrastructure, crops and environmental factors can affect visitor’s use. This information can help researchers, managers, and public planners to develop projects, plans and guidelines to increase the visual quality of the agricultural landscape.
description: Aestimum, Aestimum 74 (2019)
(1261) Fanny Eleanor Upton
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Giovanni Galloni e l’esperienza dell’insegnamento del diritto agro-ambientale
Creators: name: Masini, Stefano
Publisher: name: Aestimum
Year: 2019

description: The appeal to production needs, in a system linked to the enjoyment of property, matures in the teaching of Giovanni Galloni towards a development open to the territory through the redefinition of relations with social life, following a renewed attention to the environment. The support to the claim of a changed order is found in the rationality of the mode of production, together with the establishment of equitable relations, which an evolutionary interpretation of the Constitution promotes in the dimension of the person, to which a modern sustainable and competitive agriculture meets with the satisfaction of health and safety rights.
description: Aestimum, Aestimum 74 (2019)
An Application of Stereo Thermal Vision for Preliminary Inspection of Electrical Power Lines by MAVs
Creators: name: Demkiv, Lyubomyr
name: Ruffo, Massimiliano
name: Silano, Giuseppe
name: Bednar, Jan
name: Saska, Martin
Publisher: name: arXiv
Year: 2023
Subjects: subject: Robotics (cs.RO)
subject: FOS: Computer and information sciences

description: An application of stereo thermal vision to perform preliminary inspection operations of electrical power lines by a particular class of small Unmanned Aerial Vehicles (UAVs), aka Micro Unmanned Aerial Vehicles (MAVs), is presented in this paper. The proposed hardware and software setup allows the detection of overheated power equipment, one of the major causes of power outages. The stereo vision complements the GPS information by finely detecting the potential source of damage while also providing a measure of the harm extension. The reduced sizes and the light weight of the vehicle enable to survey areas otherwise difficult to access with standard UAVs. Gazebo simulations and real flight experiments demonstrate the feasibility and effectiveness of the proposed setup.
description: 8 pages, 15 figures, conference
From Floquet to Dicke: quantum spin-Hall insulator interacting with quantum light
Creators: name: Gulácsi, Balázs
name: Dóra, Balázs
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: Time-periodic perturbations due to classical electromagnetic fields are useful to engineer the topological properties of matter using the Floquet theory. Here we investigate the effect of quantized electromagnetic fields by focusing on the quantized light-matter interaction on the edge state of a quantum spin-Hall insulator. A Dicke-type superradiant phase transition occurs at arbitrary weak coupling, the electronic spectrum acquires a finite gap and the resulting ground state manifold is topological with Chern number $\pm 1$. When the total number of excitations is conserved, a photocurrent is generated along the edge, being pseudo-quantized as $ω\ln(1/ω)$ in the low frequency limit, and decaying as $1/ω$ for high frequencies with $ω$ the photon frequency. The photon spectral function exhibits a clean Goldstone mode, a Higgs like collective mode at the optical gap and the polariton continuum.
description: 5 pages, 3 figures, revised version
The assessment of compensation for the electric transmission line easement through a study of land market in Apulia
Creators: name: Sardaro, Ruggiero
name: Bozzo, Francesco
name: Fucilli, Vincenzo
Publisher: name: Aestimum
Year: 2019

description: High-voltage overhead transmission lines on farmland imply a permanent easement. System operators should compensate for expropriation of land and depreciation of the remaining farm area, but recognize only the former. Therefore, landowners often appeal to the law courts for fairer refunds. This study highlights that the area occupied by plinths and cabins, the height of pylons and the type of intersection are the main sources of depreciation. Moreover, electric transmission lines depreciate the residual farm area, but involving only two narrow strips of land on either side of infrastructures. Finally, the depreciation tends to decrease rapidly as the distance from the transmission line increases.
description: Aestimum, Aestimum 73 (2018)
A sustainability indicator for building projects in presence of risk/uncertainty over time: a research experience
Creators: name: Fregonara, Elena
name: Pattono, Sara
Publisher: name: Aestimum
Year: 2019

description: Aim of the paper is to present the results of a research experience focused on the setting of a sustainability indicator in presence of risk/uncertainty over time. Firstly, a literature review of the most widespread methodologies for the evaluation of project economic sustainability in a life cycle perspective is presented, extrapolating the most relevant research lines; secondly, a four steps research experience is illustrated. The methodology for calculating a stochastic economic-environmental indicator is proposed, by adopting a stochastic Global Cost approach to solve Life Cycle Cost Analysis (LCCA). The input for the analysis are modeled through Probability Distribution Functions, while the durability of components is modeled through the stochastic approach to the Factor Method.
description: Aestimum, Aestimum 73 (2018)
References for Raw data from Scaling of thermal tolerance with body mass and genome size in ectotherms: a comparison between water- and air-breathers
Creators: name: Leiva, Félix P.
name: Calosi, Piero
name: Verberk, Wilco C. E. P.
Publisher: name: The Royal Society
Year: 2019
Subjects: subject: Physiology
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Ecology

description: Global warming appears to favour smaller-bodied organisms, but whether larger species are also more vulnerable to thermal extremes, as suggested for past mass-extinction events, is still an open question. Here, we tested whether interspecific differences in thermal tolerance (heat and cold) of ectotherm organisms are linked to differences in their body mass and genome size (as a proxy for cell size). Since the vulnerability of larger, aquatic taxa to warming has been attributed to the oxygen limitation hypothesis, we also assessed how body mass and genome size modulate thermal tolerance in species with contrasting breathing modes, habitats and life stages. A database with the upper (CTmax) and lower (CTmin) critical thermal limits and their methodological aspects was assembled comprising more than 500 species of ectotherms. Our results demonstrate that thermal tolerance in ectotherms is dependent on body mass and genome size and these relationships became especially evident in prolonged experimental trials where energy efficiency gains importance. During long-term trials, CTmax was impaired in larger-bodied water-breathers, consistent with a role for oxygen limitation. Variation in CTmin was mostly explained by the combined effects of body mass and genome size and it was enhanced in larger-celled, air-breathing species during long-term trials, consistent with a role for depolarization of cell membranes. Our results highlight the importance of accounting for phylogeny and exposure duration. Especially when considering long-term trials, the observed effects on thermal limits are more in line with the warming-induced reduction in body mass observed during long-term rearing experiments.This article is part of the theme issue ‘Physiological diversity and global patterns of biodiversity in a time of global climate change: testing and generating key hypotheses involving temperature and oxygen’.