cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Spontaneous formation of bright solitons in self-localized impurities in Bose-Einstein condensate
Creators: name: Boudjemaa, Abdelaali
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: Pattern Formation and Solitons (nlin.PS)
subject: FOS: Physical sciences

description: We study the formation of bright solitons in the impurity component of Bose-Einstein condensate (BEC)-impurity mixture by using the time-dependent Hartree-Fock-Bogoliubov theory. While we assume the boson-boson and impurity-boson interactions to be effectively repulsive, their character can be changed spontaneously from repulsive to attractive in the presence of strong anomalous correlations. In such a regime the impurity component becomes a system of effectively attractive atoms leading automatically to the generation of bright solitons. We find that this soliton decays at higher temperatures due to the dissipation induced by the impurity-host and host-host interactions. We show that after a sudden increase of the impurity-boson strength a train of bright solitons is produced and this can be interpreted in terms of the modulational instability (MI) of the time-dependent impurity wave function.
description: 5 pages, 3 figures, minor modifications
Transcript of: Mark Solms, "Consciousness as Precision Optimization: Some Physiological and Philosophical Considerations", ActInf GuestStream #016
Creators: name: Solms, Mark
name: Douglass, David S
name: Sillett, Stephen
name: Friedman, Daniel Ari
Publisher: name: Zenodo
Year: 2022
Subjects: subject: Active Inference
subject: Consciousness
subject: Neuroanatomy
subject: Psychology
subject: FOS: Psychology
subject: Free Energy Principle

description: This document is an enhanced transcript of the live presentations and group discussions with Mark Solms in 2022 at the Active Inference Institute. The focus is the 2018 paper "How and Why Consciousness Arises: Some Considerations from Physics and Physiology" by Mark Solms and Karl Friston.
description: https://www.activeinference.org/
Researcher Insights: AI in Neuroscience
Creators: name: Lennie, Kristine
Publisher: name: figshare
Year: 2023
Subjects: Computational neuroscience (incl. mathematical neuroscience and theoretical neuroscience)
Cognitive neuroscience
Neurosciences not elsewhere classified
Social and affective neuroscience
Behavioural neuroscience
Artificial intelligence not elsewhere classified
Neurology and neuromuscular diseases
Medical biotechnology diagnostics (incl. biosensors)
Medical biotechnology not elsewhere classified

description: Artificial Intelligence in Neuroscience
 Artificial Intelligence (AI) shapes our everyday lives in ways we sometimes don’t even realise - from voice assistants, image recognition for face unlock in cellphones, and ML-based financial fraud detection. But AI is paving the way to much more than daily conveniences - it is also changing the world of neuroscience.
 After successfully launching our first report, The Neuroscience of Sleep, we are building our second one on the fascinating relationship between AI and neuroscience. Find out how AI can improve our well-being. Can algorithms perform on par with medical professionals in generating accurate diagnoses for dementia? What is neuromorphic engineering - and does it have clinical applications? Can synthetic images be the answer to selectively activating chosen regions of the brain?
 Find all the answers in our report.
title: Resistance mechanisms to gemcitabine in pancreatic cancer
Creators: name: Mann, Kulbir
Publisher: name: University of Liverpool Repository
Year: 2021

description: Treatment of pancreatic cancer involves combinations of therapeutics including use of the chemotherapy agent gemcitabine. This thesis aimed to identify gemcitabine resistance mechanisms in pancreatic cancer and so enable discovery of biomarkers to tailor chemotherapy. Clonally and adaptively resistant pancreatic cancer cell lines were developed, producing five clonally resistant cell lines (Suit-2R, Suit-2R2, Suit-2R3, Suit-2R4, Panc-R), and an adapted line (Suit-2G+). Removing the drug from Suit-2G+ restored sensitivity, giving Suit-2G- cells. Gemcitabine can cause double strand DNA (dsDNA) breaks by incorporation into DNA and as a result of replicative stress induced by deoxynucleotide (dNTP) starvation. dsDNA breaks were assessed with neutral comet assays, using gemcitabine or gamma radiation. All resistant cell lines had less damage than their parent cell line did at low doses of gemcitabine; Suit-2R2 had increased dsDNA breaks at high (250nM) levels. Suit-2G cells were less sensitive to radiation and for Suit2-R2, R3 and R4 it was greater, with the greatest increase in R4. Gemcitabine starves cells of dNTPs by inhibiting ribonucleotide reductase (RR). Suit-2R and Suit-2R4 had low levels of the RR subunit RRM1, Suit-2R2, Suit-2R3, Panc-R and Suit2G+ had higher levels. Replicative stress caused by gemcitabine incorporation, due to dNTP starvation or dsDNA breaks, can be prevented by checkpoint arrest. Expression of the checkpoint protein p21 was reduced in all resistant Suit-2 lines but increased in Panc-R. Chk1 was reduced in Suit-2R and increased in Suit-2R3, R4 and Panc-R. Suggesting that in Suit-2R there was a reduction in need/ability to activate checkpoints, while in Suit-2R3 and R4 checkpoint arrest had become predominantly Chk1 dependent (more G2/M focused). Replicative stress can also be reduced by decreasing Cyclin D1 or by relative increase in the D1b isoform (slowing S-phase entry). Panc-1 is homozygous for G870A of cyclin D1 and so has more D1b, whereas Suit-2 is heterozygous. Suit-2G+/G- had increased D1a. Suit-2R and Suit-2R2 have reduced D1 with a higher proportion of D1b. Suit-2R3 and Suit-2R4 have higher D1a. Cell cycle analysis tied together these results and suggested distinct resistance mechanisms. A: Suit-2G+ has a normal cell cycle; increased nucleotide pools overcome replicative stress. B: Suit-2R, Suit-2R2 pause at G1/S, preventing S-phase entry. Starved nucleotide pools in Suit-2R, and low Cyclin D1 and Chk1 inducing an arrest in Suit-2R2. C: Suit-2R3/R4 have many viable cells in G2, driving through S phase accepting replicative stress. D: Panc-R has a measured and controlled cell cycle through high RRM1. The different ways of achieving resistance identified in cell lines may have equivalents in patients, identification of the dominant mechanism can be exploited as a therapeutic biomarker.
Epitope Addition and Ablation via Manipulation of a Dengue Virus Serotype 1 Infectious Clone
Creators: name: Gallichotte, Emily N.
name: Hartman, Steven
name: Yount, Boyd L.
name: Widman, Douglas G.
name: Baric, Ralph S.
name: Dinnon, Kenneth H.
name: Menachery, Vineet D.
name: de Silva, Aravinda M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: ABSTRACT Despite the clinical relevance, dengue virus (DENV) research has been hampered by the absence of robust reverse genetic systems to manipulate the viral serotypes for propagation and generation of mutant viruses. In this article, we describe application of an infectious clone system for DENV serotype 1 (DENV1). Similar to previous clones in both flaviviruses and coronaviruses, the approach constructs a panel of contiguous cDNAs that span the DENV genome and can be systematically and directionally assembled to produce viable, full-length viruses. Comparison of the virus derived from the infectious clone with the original viral isolate reveals identical sequence, comparable endpoint titers, and similar focus staining. Both focus-forming assays and percent infection by flow cytometry revealed overlapping replication levels in two different cell types. Moreover, serotype-specific monoclonal antibodies (MAbs) bound similarly to infectious clone and the natural isolate. Using the clone, we were able to insert a DENV4 type-specific epitope recognized by primate MAb 5H2 into envelope (E) protein domain I (EDI) of DENV1 and recover a viable chimeric recombinant virus. The recombinant DENV1 virus was recognized and neutralized by the DENV4 type-specific 5H2 MAb. The introduction of the 5H2 epitope ablated two epitopes on DENV1 EDI recognized by human MAbs (1F4 and 14C10) that strongly neutralize DENV1. Together, the work demonstrates the utility of the infectious clone and provides a resource to rapidly manipulate the DENV1 serotype for generation of recombinant and mutant viruses. IMPORTANCE Dengue viruses (DENVs) are significant mosquito-transmitted pathogens that cause widespread infection and can lead to severe infection and complications. Here we further characterize a novel and robust DENV serotype 1 (DENV1) infectious clone system that can be used to support basic and applied research. We demonstrate how the system can be used to probe the antigenic relationships between strains by creating viable recombinant viruses that display or lack major antibody epitopes. The DENV1 clone system and recombinant viruses can be used to analyze existing vaccine immune responses and inform second-generation bivalent vaccine designs.
Quasilocal conserved operators in isotropic Heisenberg spin 1/2 chain
Creators: name: Ilievski, Enej
name: Medenjak, Marko
name: Prosen, Tomaz
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: Mathematical Physics (math-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Composing higher auxiliary-spin transfer matrices and their derivatives, we construct a family of quasilocal conserved operators of isotropic Heisenberg spin 1/2 chain and rigorously establish their linear independence from the well-known set of local conserved charges.
description: 5 + 6 pages in RevTex; v2: slightly revised version as accepted by PRL
Observation of Rapid Change of Crystalline Structure during the Phase Transition of the Palladium-Hydrogen System
Creators: name: Kawasaki, Akio
name: Itoh, Satoshi
name: Shima, Kunihiro
name: Kato, Kenichi
name: Ohashi, Haruhiko
name: Ishikawa, Tetsuya
name: Yamazaki, Toshimitsu
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: We performed an X-ray diffraction experiment while palladium bulk absorbed and desorbed hydrogen to investigate the behavior of the crystalline lattice during the phase transition between the $α$ phase and $β$ phase. Fast growth of $β$ phase was observed around x=0.1 and x=0.45 of PdH$_x$. In addition, slight compression of the lattice at high hydrogen concentration and increase in the lattice constant and the line width of the $α$ phase after a cycle of absorption and desorption of hydrogen was observed. These behavior correlated with the change in the sample length, which may infer that the change in shape was related to the phase transition.
description: 7 pages, 7 figures
Constraining the lifetime and opening angle of quasars using fluorescent Lyman $α$ emission: the case of Q0420-388
Creators: name: Borisova, Elena
name: Lilly, Simon J.
name: Cantalupo, Sebastiano
name: Prochaska, J. Xavier
name: Rakic, Olivera
name: Worseck, Gabor
Publisher: name: arXiv
Year: 2015
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: A toy model is developed to understand how the spatial distribution of fluorescent emitters in the vicinity of bright quasars could be affected by the geometry of the quasar bi-conical radiation field and by its lifetime. The model is then applied to the distribution of high equivalent width Lyman $α$ emitters (with rest-frame equivalent widths above 100 A, threshold used in e.g. Trainor & Steidel, 2013) identified in a deep narrow-band 36x36 arcmin$^2$ image centered on the luminous quasar Q0420-388. These emitters are found to the edge of the field and show some evidence of an azimuthal asymmetry on the sky of the type expected if the quasar is radiating in a bipolar cone. If these sources are being fluorescently illuminated by the quasar, the two most distant objects require a lifetime of at least 15 Myr for an opening angle of 60 degrees or more, increasing to more than 40 Myr if the opening angle is reduced to a minimum 30 degrees. However, few of the other expected signatures of boosted fluorescence are seen at the current survey limits, e.g. a fall off in Lyman $α$ brightness, or equivalent width, with distance. Furthermore, to have most of the Lyman $α$ emission of the two distant sources to be fluorescently boosted would require the quasar to have been significantly brighter in the past. This suggests that these particular sources may not be fluorescent, invalidating the above lifetime constraints. This would cast doubt on the use of this relatively low equivalent width threshold and thus on the lifetime analysis in Trainor & Steidel (2013).
description: 10 pages, 10 figures, 1 table, accepted to ApJ
Middle East Respiratory Syndrome Coronavirus Nonstructural Protein 16 Is Necessary for Interferon Resistance and Viral Pathogenesis
Creators: name: Gralinski, Lisa E.
name: Waters, Katrina M.
name: Leist, Sarah R.
name: Dinnon, Kenneth H.
name: Menachery, Vineet D.
name: McAnarney, Eileen T.
name: Debbink, Kari
name: Sims, Amy C.
name: Stratton, Kelly G.
name: Graham, Rachel L.
name: Mitchell, Hugh D.
name: Yount, Boyd L.
name: Cockrell, Adam S.
name: Baric, Ralph S.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: ABSTRACT Coronaviruses (CoVs) encode a mixture of highly conserved and novel genes, as well as genetic elements necessary for infection and pathogenesis, raising the possibility of common targets for attenuation and therapeutic design. In this study, we focused on highly conserved nonstructural protein 16 (NSP16), a viral 2′ O -methyltransferase (2′ O -MTase) that encodes critical functions in immune modulation and infection. Using reverse genetics, we disrupted a key motif in the conserved KDKE motif of Middle East respiratory syndrome CoV (MERS-CoV) NSP16 (D130A) and evaluated the effect on viral infection and pathogenesis. While the absence of 2′ O -MTase activity had only a marginal impact on propagation and replication in Vero cells, dNSP16 mutant MERS-CoV demonstrated significant attenuation relative to the control both in primary human airway cell cultures and in vivo . Further examination indicated that dNSP16 mutant MERS-CoV had a type I interferon (IFN)-based attenuation and was partially restored in the absence of molecules of IFN-induced proteins with tetratricopeptide repeats. Importantly, the robust attenuation permitted the use of dNSP16 mutant MERS-CoV as a live attenuated vaccine platform protecting from a challenge with a mouse-adapted MERS-CoV strain. These studies demonstrate the importance of the conserved 2′ O -MTase activity for CoV pathogenesis and highlight NSP16 as a conserved universal target for rapid live attenuated vaccine design in an expanding CoV outbreak setting. IMPORTANCE Coronavirus (CoV) emergence in both humans and livestock represents a significant threat to global public health, as evidenced by the sudden emergence of severe acute respiratory syndrome CoV (SARS-CoV), MERS-CoV, porcine epidemic diarrhea virus, and swine delta CoV in the 21st century. These studies describe an approach that effectively targets the highly conserved 2′ O -MTase activity of CoVs for attenuation. With clear understanding of the IFN/IFIT (IFN-induced proteins with tetratricopeptide repeats)-based mechanism, NSP16 mutants provide a suitable target for a live attenuated vaccine platform, as well as therapeutic development for both current and future emergent CoV strains. Importantly, other approaches targeting other conserved pan-CoV functions have not yet proven effective against MERS-CoV, illustrating the broad applicability of targeting viral 2′ O -MTase function across CoVs.
Zur Erinnerung an Prof. Dr. Ernst Theodor Pestalozzi, Lehrer an der Töchterschule I der Stadt Zürich, geb. am 27. Januar 1889, gest. am 22. März 1936
Creators: name: (:Unkn) Unknown
Publisher: name: Buchdruckerei Berichthaus
Year: 1936
Subjects: subject: 920 Biografien, Genealogie, Insignien
subject: Nachruf
subject: Zürich
subject: Pestalozzi-Kutter, Theodor

description: Enthält: Ansprache von Herrn Pfarrer Hermann Kutter bei der Trauerfeier in der Fraumünsterkirche; Abschiedsworte des Rektors der Töchterschule I der Stadt Zürich, Dr. Fritz Enderlin; der äussere Lebenslauf; Erinnerungen aus der Jugendzeit von Dr. H. Wolfensberger, Gymnasiallehrer in Bern; Der Geschichtslehrer von einem Freund und Kollegen, Dr. E. Sch. (Schweiz. Lehrerzeitung); Abschied vom Lehrer, M. M. (Tagesanzeiger)
Tectaria incisa Cav., Descr. Pl.
Creators: name: Kessler, Michael
name: Smith, Alan R.
Publisher: name: Zenodo
Year: 2018
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Polypodiopsida
Polypodiales
Tectariaceae
Tectaria
Tectaria incisa

description: Tectaria incisa Cav., Descr. Pl. 249. 1802.
 Range: —Antilles; central Mexico to Bolivia (BE, CO, LP, PA, SC) and Brazil.
 Ecology: —Very common; terrestrial in humid forests, often among rocks and on wet, shady cliffs, in drier habitats along streams; mostly below 1200 m but reaching 2100 m.
 Notes: —The most common and most variable species of Tectaria in Bolivia; almost certainly several species are involved (H. Tuomisto, pers. comm.). However, the systematics of T. incisa and its allies (in Bolivia: T. jimenezii, T. pilosa, and T. poeppigii) are complex, involving polyploidy and hybridization, and require detailed study throughout the geographical range of the species.
 Individuals of Tectaria incisa bearing one or several proliferous buds adaxially on the blades at pinna bases have been recognized as f. vivipara (Jenm.) C.V.Morton (Tryon & Stolze 1991). This form is uncommon in Bolivia (e.g., Fay & Fay 2799, UC, from BE), usually close to and often intermixed with individuals lacking buds. Jermy & Walker (1985) described the diploid species Tectaria vivipara Jermy & T.Walker from Trinidad as distinct from tetraploid T. incisa, but it is uncertain if these ploidy levels apply throughout the range of the forms, and therefore the applicability of this name to Bolivian specimens is uncertain. A form with proliferous buds, stalked pinnae, and lacking or reduced basiscopic lobes on the proximal pinnae has been called Tectaria andina, type from Ecuador, but we retain the name T. incisa f. vivipara for now.
 Tectaria transiens (C.V.Morton) A.R.Sm. from Mexico to southern Peru may occur in Bolivia. It differs from T. incisa and T. pilosa by its serrately lobed pinnae, 2–3 basiscopic lobes on the basal pinnae, and broad (1–2.5 mm wide), ciliate rhizome scales.
description: Published as part of Kessler, Michael & Smith, Alan R., 2018, Prodromus of a fern flora for Bolivia. XXXVIII. Tectariaceae, pp. 248-254 in Phytotaxa 334 (3) on page 251, DOI: 10.11646/phytotaxa.334.3.6, http://zenodo.org/record/13720948
MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses
Creators: name: Webb-Robertson, Bobbie-Jo
name: Smith, Richard D.
name: Nakayasu, Ernesto S.
name: Schepmoes, Athena A.
name: Kim, Young-Mo
name: Metz, Thomas O.
name: Jacobs, Jon M.
name: Chu, Rosalie K.
name: Baric, Ralph S.
name: Kyle, Jennifer E.
name: Shukla, Anil K.
name: Sims, Amy C.
name: Burnum-Johnson, Kristin E.
name: Matzke, Melissa M.
name: Nicora, Carrie D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: ABSTRACT Integrative multi-omics analyses can empower more effective investigation and complete understanding of complex biological systems. Despite recent advances in a range of omics analyses, multi-omic measurements of the same sample are still challenging and current methods have not been well evaluated in terms of reproducibility and broad applicability. Here we adapted a solvent-based method, widely applied for extracting lipids and metabolites, to add proteomics to mass spectrometry-based multi-omics measurements. The m etabolite, p rotein, and l ipid ex traction (MPLEx) protocol proved to be robust and applicable to a diverse set of sample types, including cell cultures, microbial communities, and tissues. To illustrate the utility of this protocol, an integrative multi-omics analysis was performed using a lung epithelial cell line infected with Middle East respiratory syndrome coronavirus, which showed the impact of this virus on the host glycolytic pathway and also suggested a role for lipids during infection. The MPLEx method is a simple, fast, and robust protocol that can be applied for integrative multi-omic measurements from diverse sample types (e.g., environmental, in vitro , and clinical). IMPORTANCE In systems biology studies, the integration of multiple omics measurements (i.e., genomics, transcriptomics, proteomics, metabolomics, and lipidomics) has been shown to provide a more complete and informative view of biological pathways. Thus, the prospect of extracting different types of molecules (e.g., DNAs, RNAs, proteins, and metabolites) and performing multiple omics measurements on single samples is very attractive, but such studies are challenging due to the fact that the extraction conditions differ according to the molecule type. Here, we adapted an organic solvent-based extraction method that demonstrated broad applicability and robustness, which enabled comprehensive proteomics, metabolomics, and lipidomics analyses from the same sample.
The lightcurve of the macronova associated with the long-short burst GRB 060614
Creators: name: Jin, Zhi-Ping
name: Li, Xiang
name: Cano, Zach
name: Covino, Stefano
name: Fan, Yi-Zhong
name: Wei, Da-Ming
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: The {\it Swift}-detected GRB 060614 was a unique burst that straddles an imaginary divide between long- and short-duration gamma-ray bursts (GRBs), and its physical origin has been heavily debated over the years. Recently, a distinct very-soft F814W-band excess at $t\sim 13.6$ days after the burst was identified in a joint-analysis of VLT and HST optical afterglow data of GRB~060614, which has been interpreted as evidence for an accompanying Li-Paczynski macronova (also called a kilonova). Under the assumption that the afterglow data in the time interval of $1.7-3.0$ days after the burst are due to external forward shock emission, when this assumption is extrapolated to later times it is found that there is an excess of flux in several multi-band photometric observations. This component emerges at $\sim$4 days after the burst, and it may represent the first time that a multi-epoch/band lightcurve of a macronova has been obtained. The macronova associated with GRB 060614 peaked at $t\lesssim 4$ days after the burst, which is significantly earlier than that observed for a supernova associated with a long-duration GRB. Due to the limited data, no strong evidence for a temperature evolution is found. We derive a conservative estimate of the macronova rate of $\sim 16.3^{+16.3}_{-8.2}~{\rm Gpc^{-3}}{\rm yr^{-1}}$, implying a promising prospect for detecting the gravitational wave radiation from compact object mergers by upcoming Advanced LIGO/VIRGO/KAGRA detectors (i.e., the rate is ${\cal R}_{\rm GW} \sim 0.5^{+0.5}_{-0.25}(D/200~{\rm Mpc})^{3}~{\rm yr^{-1}}$).
description: The version published in ApJL. Fig.1 has been updated, main conclusions are unchanged
Large-Scale Bioinformatics Analysis of Bacillus Genomes Uncovers Conserved Roles of Natural Products in Bacterial Physiology
Creators: name: Farag, Sherif
name: Shank, Elizabeth A.
name: Bleich, Rachel M.
name: Maria, Kevin C. Santa
name: Grubbs, Kirk J.
name: Bowers, Albert A.
name: Allen, Scott E.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: ABSTRACT Bacteria possess an amazing capacity to synthesize a diverse range of structurally complex, bioactive natural products known as specialized (or secondary) metabolites. Many of these specialized metabolites are used as clinical therapeutics, while others have important ecological roles in microbial communities. The biosynthetic gene clusters (BGCs) that generate these metabolites can be identified in bacterial genome sequences using their highly conserved genetic features. We analyzed an unprecedented 1,566 bacterial genomes from Bacillus species and identified nearly 20,000 BGCs. By comparing these BGCs to one another as well as a curated set of known specialized metabolite BGCs, we discovered that the majority of Bacillus natural products are comprised of a small set of highly conserved, well-distributed, known natural product compounds. Most of these metabolites have important roles influencing the physiology and development of Bacillus species. We identified, in addition to these characterized compounds, many unique, weakly conserved BGCs scattered across the genus that are predicted to encode unknown natural products. Many of these “singleton” BGCs appear to have been acquired via horizontal gene transfer. Based on this large-scale characterization of metabolite production in the Bacilli , we go on to connect the alkylpyrones, natural products that are highly conserved but previously biologically uncharacterized, to a role in Bacillus physiology: inhibiting spore development. IMPORTANCE Bacilli are capable of producing a diverse array of specialized metabolites, many of which have gained attention for their roles as signals that affect bacterial physiology and development. Up to this point, however, the Bacillus genus’s metabolic capacity has been underexplored. We undertook a deep genomic analysis of 1,566 Bacillus genomes to understand the full spectrum of metabolites that this bacterial group can make. We discovered that the majority of the specialized metabolites produced by Bacillus species are highly conserved, known compounds with important signaling roles in the physiology and development of this bacterium. Additionally, there is significant unique biosynthetic machinery distributed across the genus that might lead to new, unknown metabolites with diverse biological functions. Inspired by the findings of our genomic analysis, we speculate that the highly conserved alkylpyrones might have an important biological activity within this genus. We go on to validate this prediction by demonstrating that these natural products are developmental signals in Bacillus and act by inhibiting sporulation.
title: Data Quality Assessment in large Enterprises: A practical Evaluation
Creators: name: Doppelhammer, Christoph
Publisher: name: TU Wien
Year: 2023
Subjects: subject: data quality
subject: enterprise
subject: data quality methodology
subject: data quality tools
subject: data quality assessment

description: Arbeit an der Bibliothek noch nicht eingelangt - Daten nicht geprueft - gesperrte Arbeit (bis 2024-01-10+01:00)
description: Abweichender Titel nach Übersetzung der Verfasserin/des Verfassers
Ubaldino Peruzzi a Raffaello Busacca (26 aprile 1857)
Creators: name: Peruzzi, Ubaldino
name: Busacca, Raffaello
Publisher: name: Zenodo
Year: 2023
Subjects: Accademia dei Georgofili
Peruzzi, Ubaldino
Busacca, Raffaello
Lettera
Letter
Carteggio
Correspondence
1857

description: Lettera di Ubaldino Peruzzi a Raffaello Busacca del 26 aprile 1857. Segnatura dell’unità documentale: Archivio storico dell’Accademia dei Georgofili, Carteggio, Busta 32, 3368. Natura: manoscritto. Consistenza: cc. 2
description: Digitalizzato come parte della Mostra virtuale: Ubaldino Peruzzi : un percorso in rete : in occasione del bicentenario della nascita https://www.georgofili.it/contenuti/ubaldino-peruzzi-un-percorso-in-rete/17485
Acceptabilité d'un dispositif de mutuelles de santé innovant au centre du Mali : une recherche en méthodes mixtes
Creators: name: Boivin, Pauline
name: Ravalihasy, Andrainolo
name: Diarra, Dansiné
name: Sissoko, Fodé
name: Diabaté, Seydou
name: Diarra, Yacouba
name: Touré, Laurence
name: Ridde, Valéry
Publisher: name: Zenodo
Year: 2023
Subjects: mutuelles de santé, innovation, acceptabilité, Mali, Régime d'assurance maladie universelle

description: Alors que le Régime d’Assurance Maladie Universelle (RAMU) se met progressivement en place au Mali, les mutuelles de santé, considérées comme l’un des piliers de ce régime, doivent innover pour faire face à ce défi de la couverture sanitaire universelle. Dans le cadre d’un programme expérimental, un dispositif mutualiste a été testé entre 2017 et 2021 dans le centre du Mali. Ce dispositif novateur professionnalise et structure les mutuelles à une plus large échelle qu’auparavant, passant des communes aux cercles. Une étude par méthodes mixtes a été menée dans la région de Mopti pour évaluer l’acceptabilité de ce dispositif auprès des élus des bureaux mutualistes. Ainsi, 118 questionnaires ont été administrés auprès d’élus en avril 2021. Des entretiens qualitatifs ont ensuite été réalisés en octobre 2021 auprès de 43 élus de ce même échantillon. L’approche de Sekhon et ses collègues, qui propose sept dimensions de l’acceptabilité (attitude, fardeau, valeurs, cohérence, coûts d’opportunité, efficacité perçue, efficacité personnelle), a servi de modèle conceptuel pour analyser les données. Le score global obtenu par l’analyse factorielle montre que plus de la moitié des individus (58%) rapportent une acceptabilité supérieure à la moyenne. Les élus se sentent accompagnés efficacement dans leurs activités par l’Union Technique de la Mutualité malienne (UTM), faîtière des mutuelles. Ils montrent une certaine assurance quant à leur capacité à assumer pleinement leurs fonctions, malgré un engagement très variable et souvent en deçà des attentes et des besoins, qu’ils justifient par leur statut bénévole. Les élus constatent une très bonne efficacité du dispositif malgré des conditions non optimales liées à l’insécurité prégnante dans la région. La nouvelle offre mutualiste est jugée très avantageuse pour les populations, au plan du contenu et de l’accès financier et géographique. La professionnalisation apparaît comme une condition incontournable de la performance du dispositif, tout comme le nouveau montage communautaire. Cependant, les élus s’inquiètent de la pérennité de ce dispositif et misent sur une prise de responsabilité de l’État et de ses partenaires. L’UTM aura un rôle important à jouer en poursuivant son accompagnement et en remplissant ses fonctions d’organisme de gestion déléguée dans le cadre du RAMU. https://www.ceped.org/wp57
title: ESSAYS IN HEALTH ECONOMICS: The Design of Primary Care Incentives
Creators: name: Wu, Yunchou
Publisher: name: University of Liverpool Repository
Year: 2020

description: The continuous upward trend in health spending and the perpetual rise in the demand for healthcare underlines the importance of designing efficient resource allocation mechanisms. In the healthcare sector, physicians play a crucial role in directing resources. This thesis analyses the design of primary care incentive contracts in presence of two complicating issues. From society’s perspective, the physician may provide an inefficient amount of treatment (“moral hazard”) or be offered a sub-optimal contract (“adverse selection”), as neither the physician’s knowledge about patients’ health nor his personal characteristics be perfectly observed. This thesis is structured into three essays. The first essay discusses theory and evidence related to physician altruism. It also comprehensively surveys optimal incentive contracting when physicians have private information about their characteristics (e.g. costs, abilities), their patients’ health, or their actions (efforts, service qualities). The impact of using different types of restrictions for controlling the cost of physician services are also reviewed. Finally, research gaps in the literature are identified and the context of subsequent analysis is established. The second essay studies the optimal design of publicly funded health insurance schemes when physicians have private knowledge about their preferences and patients’ health as well as being paid on a price per service basis (“fee-for-service”). This is formalised in a math model, where the regulator chooses a policy vector of price, insurance premium and cost-control policies, while physicians subsequently choose medical service quantities. In this setup, it is shown that the welfare-maximizing price system fails to align different providers’ objectives and major trends such as population ageing further exacerbates this distortion. Widely applied physician cost-control restrictions, such as maximal amount of service, fixed budgets or a payment per patient (“capitation”), can be imposed on the price system to improve efficiency. In particular, capitation performs better than other restrictions. The last essay extends the analysis by letting primary care physicians select their practice sizes. The optimal payment must ensure that the entire population has access to healthcare. It is shown that the welfare-maximizing price system induces medical service overproduction and distorts physicians’ incentives. Nevertheless, physician cost-control restrictions are still efficiency enhancing while the highest welfare level is generated by using a capitation. Overall, the thesis provides a framework which not only captures key features of the health market but also can be used to analyse the impact of using different physician cost-control policies.
The innate immune properties of airway mucosal surfaces are regulated by dynamic interactions between mucins and interacting proteins: the mucin interactome
Creators: name: Kesimer,
name: Ford,
name: Wang,
name: Li,
name: Radicioni,
name: Cao,
name: Carpenter,
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2016

description: Chronic lung diseases such as cystic fibrosis, chronic bronchitis and asthma, are characterized by hypersecretion and poor clearance of mucus, which are associated with poor prognosis and mortality. Little is known about the relationship between the biophysical properties of mucus and its molecular composition. The mucins MUC5B and MUC5AC are traditionally believed to generate the characteristic biophysical properties of airway mucus. However, the contribution of hundreds of globular proteins to the biophysical properties of mucus is not clear. Approximately one-third of the total mucus proteome comprises distinct, multi-protein complexes centered around airway mucins. These complexes constitute a discrete entity we call the “mucin interactome”. The data suggest that while the majority of these proteins interact with mucins via electrostatic and weak interactions, some interact through very strong hydrophobic and/or covalent interactions. Using reagents that interfere with protein-protein interactions, the complexes can be disassembled, and mucus rheology can be dramatically altered. Using MUC5B-glutathione S-transferase (GST) and MUC5B-galectin-3 as a representative of these interactions, we provide evidence that individual mucin protein interactions can alter the biophysical properties of mucus and modulate the biological function of the protein. We propose that the key mechano- and bio-active functions of mucus depend on the dynamic interactions between mucins and globular proteins. These observations challenge the paradigm that mucins are the only molecules that confer biophysical properties of mucus. These observations may ultimately lead to a greater understanding of the system and guide the development of strategies for more effective interventions using better therapeutic agents.
The VIMOS Public Extragalactic Redshift Survey (VIPERS): On the correct recovery of the count-in-cell probability distribution function
Creators: name: Bel, J.
name: Branchini, E.
name: Di Porto, C.
name: Cucciati, O.
name: Granett, B. R.
name: Iovino, A.
name: de la Torre, S.
name: Marinoni, C.
name: Guzzo, L.
name: Moscardini, L.
name: Cappi, A.
name: Abbas, U.
name: Adami, C.
name: Arnouts, S.
name: Bolzonella, M.
name: Bottini, D.
name: Coupon, J.
name: Davidzon, I.
name: De Lucia, G.
name: Fritz, A.
name: Franzetti, P.
name: Fumana, M.
name: Garilli, B.
name: Ilbert, O.
name: Krywult, J.
name: Brun, V. Le
name: Fèvre, O. Le
name: Maccagni, D.
name: Małek, K.
name: Marulli, F.
name: McCracken, H. J.
name: Paioro, L.
name: Polletta, M.
name: Pollo, A.
name: Schlagenhaufer, H.
name: Scodeggio, M.
name: Tasca, L. A. M.
name: Tojeiro, R.
name: Vergani, D.
name: Zanichelli, A.
name: Burden, A.
name: Marchetti, A.
name: Mellier, Y.
name: Nichol, R. C.
name: Peacock, J. A.
name: Percival, W. J.
name: Phleps, S.
name: Wolk, M.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We compare three methods to measure the count-in-cell probability density function of galaxies in a spectroscopic redshift survey. From this comparison we found that when the sampling is low (the average number of object per cell is around unity) it is necessary to use a parametric method to model the galaxy distribution. We used a set of mock catalogues of VIPERS, in order to verify if we were able to reconstruct the cell-count probability distribution once the observational strategy is applied. We find that in the simulated catalogues, the probability distribution of galaxies is better represented by a Gamma expansion than a Skewed Log-Normal. Finally, we correct the cell-count probability distribution function from the angular selection effect of the VIMOS instrument and study the redshift and absolute magnitude dependency of the underlying galaxy density function in VIPERS from redshift $0.5$ to $1.1$. We found very weak evolution of the probability density distribution function and that it is well approximated, independently from the chosen tracers, by a Gamma distribution.
description: 14 pages, 11 figures, 2 tables
Prethermalization and Thermalization of a Quenched Interacting Luttinger Liquid
Creators: name: Buchhold, Michael
name: Heyl, Markus
name: Diehl, Sebastian
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We study the relaxation dynamics of interacting, one-dimensional fermions with band curvature after a weak quench in the interaction parameter. After the quench, the system is described by a non-equilibrium initial state, which relaxes towards thermal equilibrium, featuring prethermal behavior on intermediate time and length scales. The model corresponds to the class of interacting Luttinger Liquids, which extends the quadratic Luttinger theory by a weak integrability breaking phonon scattering term. In order to solve for the non-equilibrium time evolution, we use kinetic equations for the phonon densities, exploiting the resonant but subleading character of the phonon interaction term. The interplay between phonon scattering and the quadratic Luttinger theory leads to the emergence of three distinct spatio-temporal regimes for the fermionic real-space correlation function. It features the crossover from a prequench to a prethermal state, finally evolving towards a thermal state on increasing length and time scales. The characteristic algebraically decaying real-space correlations in the prethermalized regime become modulated by an amplitude, which, as an effect of the interactions, is decaying in time according to a stretched-exponential, while in the thermal regime exponentially decaying real-space correlations emerge. The asymptotic thermalization dynamics is governed by energy transport over large distances from the thermalized to the non-thermalized regions, which is carried out by macroscopic, dynamical slow modes. This is revealed in an algebraic decay of the system's effective temperature. The numerical value of the associated exponent agrees with the dynamical critical exponent of the Kardar-Parisi-Zhang universality class, which shares with the present interacting Luttinger Liquid the conservation of total energy and momentum.
description: 6 figures, published version
Contribution of mucus concentration and secreted mucins Muc5ac and Muc5b to the pathogenesis of muco-obstructive lung disease
Creators: name: O'Neal,
name: Evans,
name: Livraghi-Butrico,
name: Burns,
name: Grubb,
name: Volmer,
name: Boucher,
name: Wilkinson,
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: Airway diseases, including cigarette smoke-induced chronic bronchitis, cystic fibrosis, and primary ciliary dyskinesia are associated with decreased mucociliary clearance (MCC). However, it is not known whether a simple reduction in MCC or concentration-dependent mucus adhesion to airway surfaces dominates disease pathogenesis or whether decreasing the concentration of secreted mucins may be therapeutic. To address these questions, Scnn1b-Tg mice, which exhibit airway mucus dehydration/adhesion, were compared to and crossed with Muc5b- and Muc5ac-deficient mice. Absence of Muc5b caused a 90% reduction in MCC, whereas Scnn1b-Tg mice exhibited an ~50% reduction. However, the degree of MCC reduction did not correlate with bronchitic airways pathology, which was observed only in Scnn1b-Tg mice. Ablation of Muc5b significantly reduced the extent of mucus plugging in Scnn1b-Tg mice. However, complete absence of Muc5b in Scnn1b-Tg mice was associated with increased airway inflammation, suggesting that Muc5b is required to maintain immune homeostasis. Loss of Muc5ac had few phenotypic consequences in Scnn1b-Tg mice. These data suggest that: (1) mucus hyperconcentration dominates over MCC reduction alone to produce bronchitic airways pathology; (2) Muc5b is the dominant contributor to the Scnn1b-Tg phenotype; and (3) therapies that limit mucin secretion may reduce plugging, but complete Muc5b removal from airway surfaces may be detrimental.
Toward a realistic description of multilayer black phosphorus: from $GW$ approximation to large-scale tight-binding simulations
Creators: name: Rudenko, A. N.
name: Yuan, Shengjun
name: Katsnelson, M. I.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: We provide a tight-binding model parametrization for black phosphorus (BP) with an arbitrary number of layers. The model is derived from partially self-consistent $GW_0$ approach, where the screened Coulomb interaction $W_0$ is calculated within the random phase approximation on the basis of density functional theory. We thoroughly validate the model by performing a series of benchmark calculations, and determine the limits of its applicability. The application of the model to the calculations of electronic and optical properties of multilayer BP demonstrates good quantitative agreement with \emph{ab initio} results in a wide energy range. We also show that the proposed model can be easily extended for the case of external fields, yielding the results consistent with those obtained from first principles. The model is expected to be suitable for a variety of realistic problems related to the electronic properties of multilayer BP including different kinds of disorder, external fields, and many-body effects.
description: 10 pages, 9 figures, 2 tables (final version, minor changes)
Experimental vaccine induces Th1-driven immune responses and resistance to Neisseria gonorrhoeae infection in a murine model
Creators: name: Egilmez,
name: Russell,
name: Sikora,
name: Zielke,
name: Liu,
name: Liu,
name: Hobbs,
name: Hammer,
name: Jerse,
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2017

description: Female mice were immunized intravaginally with gonococcal outer membrane vesicles (OMV) plus microencapsulated IL-12, and challenged using an established model of genital infection with Neisseria gonorrhoeae. Whereas sham-immunized and control animals cleared the infection in 10–13 days, those immunized with OMV plus IL-12 cleared infection with homologous gonococcal strains in 6–9 days. Significant protection was also seen after challenge with antigenically distinct strains of N. gonorrhoeae, and protective anamnestic immunity persisted for at least 6 months after immunization. Serum and vaginal IgG and IgA antibodies were generated against antigens expressed by homologous and heterologous strains. Iliac lymph node CD4+ T cells secreted IFNγ, but not IL-4, in response to immunization, and produced IL-17 in response to challenge regardless of immunization. Antigens recognized by immunized mouse serum included several shared between gonococcal strains, including two identified by immunoproteomics approaches as EF-Tu and PotF3. Experiments with immunodeficient mice showed that protective immunity depended upon IFNγ and B cells, presumably to generate antibodies. The results demonstrated that immunity to gonococcal infection can be induced by immunization with a non-living gonococcal antigen, and suggest that efforts to develop a human vaccine should focus on strategies to generate Th1-driven immune responses in the genital tract.
Weak upper topologies and duality for cones
Creators: name: Keimel, Klaus
Publisher: name: arXiv
Year: 2015
Subjects: subject: Logic in Computer Science (cs.LO)
subject: FOS: Computer and information sciences

description: In functional analysis it is well known that every linear functional defined on the dual of a locally convex vector space which is continuous for the weak topology is the evaluation at a uniquely determined point of the given vector space. M. Schroeder and A. Simpson have obtained a similar result for lower semicontinuous linear functionals on the cone of all Scott-continuous valuations on a topological space endowed with the weak upper topology, an asymmetric version of the weak topology. This result has given rise to several proofs, originally by the Schroeder and Simpson themselves and, more recently, by the author of these Notes and by J. Goubault-Larrecq. The proofs developed from very technical arguments to more and more conceptual ones. The present Note continues on this line, presenting a conceptual approach inspired by classical functional analysis which may prove useful in other situations.