cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Interpolation between multi-dimensional histograms using a new non-linear moment morphing method
Creators: name: Baak, Max
name: Gadatsch, Stefan
name: Harrington, Robert
name: Verkerke, Wouter
Publisher: name: arXiv
Year: 2014
Subjects: subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: A prescription is presented for the interpolation between multi-dimensional distribution templates based on one or multiple model parameters. The technique uses a linear combination of templates, each created using fixed values of the model's parameters and transformed according to a specific procedure, to model a non-linear dependency on model parameters and the dependency between them. By construction the technique scales well with the number of input templates used, which is a useful feature in modern day particle physics, where a large number of templates is often required to model the impact of systematic uncertainties.
description: 20 pages, 6 figures. Algorithm publicly available in RooFit
Wo stehen wir heute? Wissenschaftskommunikation und (nicht-)erreichte Zielgruppen
Creators: name: Humm, Christian
name: Schrögel, Philipp
name: Miriam, Welz
Publisher: name: Zenodo
Year: 2024
Subjects: subject: Science Communication
subject: Media and communications
subject: FOS: Media and communications
subject: Diversity
subject: Inclusion
subject: Exclusion
subject: Wissenschaftskommunikation
subject: Diversität
subject: Zielgruppen

description: Effektive (Wissenschafts-) Kommunikation erfordert eine zielgruppengerechte Ansprache. Jenseits des wissenschaftsinteressierten Bildungsbürgertums ist das keine einfache, aber umso wichtigere Angelegenheit im Hinblick auf den gesellschaftlichen Auftrag und die demokratische Bedeutung von Wissenschaftskommunikation.

Welche Bevölkerungsgruppen werden von Wissenschaftskommunikation bisher wenig erreicht, was charakterisiert diese? In den letzten Jahren hat das Thema zunehmend Aufmerksamkeit erfahren (Judd & McKinnon 2021), wie ist der Stand heute in Bezug auf die Identifikation von Exklusionsfaktoren und Zugangsbarrieren sowie deren Berücksichtigung in der Wissenschaftskommunikations-Praxis?

Der Kurzvortrag präsentiert den aktuellen Forschungsstand und die Entwicklungen seit Schrögel et al. (2018) auf Basis einer Expertise für die Transfer Unit. Dieser Input öffnet den Raum für eine Diskussion der Kommunikations- und Forschungspraxis.

Literatur

Judd, K., & McKinnon, M. (2021). A systematic map of inclusion, equity and diversity in science communication research: Do we practice what we preach?. Frontiers in Communication, 6.

Schrögel, P., Humm, C., Leßmöllmann, A., Kremer, B., Adler, J., & Weißkopf, M. (2018). Nicht erreichte Zielgruppen in der Wissenschaftskommunikation: Literatur-Review zu Exklusionsfaktoren und Analyse von Fallbeispielen.
title: Polizeiarbeit: „Effizienz und Herausforderungen in der heutigen Zeit"
Creators: name: Mohammed, Sayyid
name: Friedemann, Robert
Publisher: name: Westsächsische Hochschule Zwickau
publisherIdentifier: https://ror.org/04ms51788
publisherIdentifierScheme: ROR
Year: 2025
Subjects: classificationCode: 5.2
subject: FOS: Economics and business

description: Polizeibeamte stehen täglich vor den Herausforderungen und Verantwortungen, die dieser Beruf mit sich bringt. In einer Welt, die sich rasant verändert, ist es unerlässlich, einen Blick in die Zukunft zu werfen, um die Entwicklungen und Herausforderungen, die auf die Polizeiarbeit zukommen, zu verstehen und darauf vorbereitet zu sein. Diese Seminararbeit ist ein Schritt in genau diese Richtung.

Das Ziel dieser Arbeit ist es, ein umfassendes Bild der zukünftigen Landschaft der Polizeiarbeit zu zeichnen, basierend auf einer gründlichen Analyse der gegenwärtigen Situation und den Trends, die sich bereits abzeichnen.

In dieser Veröffentlichung wird ein weiterer entscheidender Aspekt beleuchtet: die Einbindung eines Expertengremiums aus verschiedenen Fachbereichen. Dieses Gremium spielt eine zentrale Rolle bei der Identifizierung und Analyse potenzieller Problemfelder in der zukünftigen Polizeiarbeit. Die Expertinnen und Experten, die sowohl aus dem polizeilichen Umfeld als auch aus anderen relevanten Themenbereichen kommen, bringen ihre umfassende Expertise und vielfältigen Perspektiven ein.

Der Fokus liegt dabei auf der Anwendung der Risikoprioritätszahl (RPZ), einem Instrument, das ermöglicht, die identifizierten Risiken nicht nur zu kategorisieren, sondern auch hinsichtlich ihrer Dringlichkeit und ihres möglichen Einflusses zu bewerten. Durch diesen methodischen Ansatz wird gewährleistet, dass die diskutierten Problemfelder nicht nur theoretisch erfasst, sondern auch in ihrer praktischen Relevanz für die Polizeiarbeit der Zukunft abgeschätzt werden.

Mit dieser Publikation wird ein Beitrag zur Diskussion über die Zukunft der Polizeiarbeit geleistet und ein Wegweiser für die Herausforderungen und Chancen aufgezeigt, die vor uns liegen.
A note on the abundance conjecture
Creators: name: Dorsch, Tobias
name: Lazić, Vladimir
Publisher: name: arXiv
Year: 2014
Subjects: subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 14E30

description: We prove that the abundance conjecture for non-uniruled klt pairs in dimension $n$ implies the abundance conjecture for uniruled klt pairs in dimension $n$, assuming the Minimal Model Program in lower dimensions.
Seafloor primary production in a changing Arctic Ocean
Creators: name: Attard, Karl
name: Singh, Rakesh Kumar
name: Gattuso, Jean-Pierre
name: Filbee-Dexter, Karen
name: Krause-Jensen, Dorte
name: Sejr, Mikael K.
name: Archambault, Philippe
name: Babin, Marcel
name: Bélanger, Simon
name: Berg, Peter
name: Glud, Ronnie N.
name: Hancke, Kasper
name: Janicke, Stefan
name: Qin, Jing
name: Rysgaard, Søren
name: Sørensen, Esben B.
name: Tachon, Foucaut
name: Wenzhöfer, Frank
name: Ardyna, Mathieu
Publisher: name: Zenodo
Year: 2024

description: Phytoplankton and sea ice algae are traditionally considered to be the main primary producers in the Arctic Ocean. In this Perspective, we explore the importance of benthic primary producers (BPPs) encompassing microalgae, macroalgae, and seagrasses, which represent a poorly quantified source of Arctic marine primary production. Despite scarce observations, models predict that BPPs are widespread, colonizing ~3 million km2 of the extensive Arctic coastal and shelf seas. Using a synthesis of published data and a novel model, we estimate that BPPs currently contribute ~77 Tg C y−1 of primary production to the Arctic, equivalent to ~20 to 35% of annual phytoplankton production. Macroalgae contribute ~43 Tg C y−1, seagrasses contribute ~23 Tg C y−1, and microalgae-dominated shelf habitats contribute ~11 to 16 Tg C y−1. Since 2003, the Arctic seafloor area exposed to sunlight has increased by ~47,000 km2 y−1, expanding the realm of BPPs in a warming Arctic. Increased macrophyte abundance and productivity is expected along Arctic coastlines with continued ocean warming and sea ice loss. However, microalgal benthic primary production has increased in only a few shelf regions despite substantial sea ice loss over the past 20 y, as higher solar irradiance in the ice-free ocean is counterbalanced by reduced water transparency. This suggests complex impacts of climate change on Arctic light availability and marine primary production. Despite significant knowledge gaps on Arctic BPPs, their widespread presence and obvious contribution to coastal and shelf ecosystem production call for further investigation and for their inclusion in Arctic ecosystem models and carbon budgets.
Variable Suites of Non-effector Genes Are Co-regulated in the Type III Secretion Virulence Regulon across the Pseudomonas syringae Phylogeny
Creators: name: Yourstone, Scott
name: Chang, Jeff H.
name: Grant, Sarah R.
name: Lind, Abigail L.
name: Biswas, Surojit
name: Nishimura, Marc T.
name: Cumbie, Jason S.
name: Jones, Corbin D.
name: Mucyn, Tatiana S.
name: Dangl, Jeffery L.
name: Baltrus, David A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2014

description: Pseudomonas syringae is a phylogenetically diverse species of Gram-negative bacterial plant pathogens responsible for crop diseases around the world. The HrpL sigma factor drives expression of the major P. syringae virulence regulon. HrpL controls expression of the genes encoding the structural and functional components of the type III secretion system (T3SS) and the type three secreted effector proteins (T3E) that are collectively essential for virulence. HrpL also regulates expression of an under-explored suite of non-type III effector genes (non-T3E), including toxin production systems and operons not previously associated with virulence. We implemented and refined genome-wide transcriptional analysis methods using cDNA-derived high-throughput sequencing (RNA-seq) data to characterize the HrpL regulon from six isolates of P. syringae spanning the diversity of the species. Our transcriptomes, mapped onto both complete and draft genomes, significantly extend earlier studies. We confirmed HrpL-regulation for a majority of previously defined T3E genes in these six strains. We identified two new T3E families from P. syringae pv. oryzae 1_6, a strain within the relatively underexplored phylogenetic Multi-Locus Sequence Typing (MLST) group IV. The HrpL regulons varied among strains in gene number and content across both their T3E and non-T3E gene suites. Strains within MLST group II consistently express the lowest number of HrpL-regulated genes. We identified events leading to recruitment into, and loss from, the HrpL regulon. These included gene gain and loss, and loss of HrpL regulation caused by group-specific cis element mutations in otherwise conserved genes. Novel non-T3E HrpL-regulated genes include an operon that we show is required for full virulence of P. syringae pv. phaseolicola 1448A on French bean. We highlight the power of integrating genomic, transcriptomic, and phylogenetic information to drive concise functional experimentation and to derive better insight into the evolution of virulence across an evolutionarily diverse pathogen species.
The metallicity of galactic winds
Creators: name: Creasey, Peter
name: Theuns, Tom
name: Bower, Richard G.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The abundance evolution of galaxies depends critically on the balance between the mixing of metals in their interstellar medium, the inflow of new gas and the outflow of enriched gas. We study these processes in gas columns perpendicular to a galactic disk using sub-parsec resolution simulations that track stellar ejecta with the Flash code. We model a simplified interstellar medium stirred and enriched by supernovae and their progenitors. We vary the density distribution of the gas column and integrate our results over an exponential disk to predict wind and ISM enrichment properties for disk galaxies. We find that winds from more massive galaxies are hotter and more highly enriched, in stark contrast to that which is often assumed in galaxy formation models. We use these findings in a simple model of galactic enrichment evolution, in which the metallicity of forming galaxies is the result of accretion of nearly pristine gas and outflow of enriched gas along an equilibrium sequence. We compare these predictions to the observed mass-metallicity relation, and demonstrate how the galaxy's gas fraction is a key controlling parameter. This explains the observed flattening of the mass-metallicity relation at higher stellar masses.
description: 19 pages, 15 figures, accepted to MNRAS
A Pyranose-2-Phosphate Motif Is Responsible for Both Antibiotic Import and Quorum-Sensing Regulation in Agrobacterium tumefaciens
Creators: name: Vigouroux, Armelle
name: Li, Si-Zhe
name: Queneau, Yves
name: Soulère, Laurent
name: Reader, John
name: Guimaraes, Beatriz G.
name: Ahmar, Mohammed
name: El Sahili, Abbas
name: Lang, Julien
name: Faure, Denis
name: Aumont-Nicaise, Magali
name: Virus, Cornelia
name: Planamente, Sara
name: Moréra, Solange
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Periplasmic binding proteins (PBPs) in association with ABC transporters select and import a wide variety of ligands into bacterial cytoplasm. They can also take up toxic molecules, as observed in the case of the phytopathogen Agrobacterium tumefaciens strain C58. This organism contains a PBP called AccA that mediates the import of the antibiotic agrocin 84, as well as the opine agrocinopine A that acts as both a nutrient and a signalling molecule for the dissemination of virulence genes through quorum-sensing. Here, we characterized the binding mode of AccA using purified agrocin 84 and synthetic agrocinopine A by X-ray crystallography at very high resolution and performed affinity measurements. Structural and affinity analyses revealed that AccA recognizes an uncommon and specific motif, a pyranose-2-phosphate moiety which is present in both imported molecules via the L-arabinopyranose moiety in agrocinopine A and the D-glucopyranose moiety in agrocin 84. We hypothesized that AccA is a gateway allowing the import of any compound possessing a pyranose-2-phosphate motif at one end. This was structurally and functionally confirmed by experiments using four synthetic compounds: agrocinopine 3’-O-benzoate, L-arabinose-2-isopropylphosphate, L-arabinose-2-phosphate and D-glucose-2-phosphate. By combining affinity measurements and in vivo assays, we demonstrated that both L-arabinose-2-phosphate and D-glucose-2-phosphate, which are the AccF mediated degradation products of agrocinopine A and agrocin 84 respectively, interact with the master transcriptional regulator AccR and activate the quorum-sensing signal synthesis and Ti plasmid transfer in A. tumefaciens C58. Our findings shed light on the role of agrocinopine and antibiotic agrocin 84 on quorum-sensing regulation in A. tumefaciens and reveal how the PBP AccA acts as vehicle for the importation of both molecules by means of a key-recognition motif. It also opens future possibilities for the rational design of antibiotic and anti-virulence compounds against A. tumefaciens or other pathogens possessing similar PBPs.
Additional file 1 of Potential use of EGFR-targeted molecular therapies for tumor suppressor CYLD-negative and poor prognosis oral squamous cell carcinoma with chemoresistance
Creators: name: Kanemaru, Ayumi
name: Shinriki, Satoru
name: Kai, Mimi
name: Tsurekawa, Kanae
name: Ozeki, Kazuya
name: Uchino, Shota
name: Suenaga, Naoki
name: Yonemaru, Kou
name: Miyake, Shunsuke
name: Masuda, Takeshi
name: Kariya, Ryusho
name: Okada, Seiji
name: Takeshita, Hisashi
name: Seki, Yuki
name: Yano, Hiromu
name: Komohara, Yoshihiro
name: Yoshida, Ryoji
name: Nakayama, Hideki
name: Li, Jian-Dong
name: Saito, Hideyuki
name: Jono, Hirofumi
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Cancer

description: Additional file 1: Figure S1. CYLD-knockdown by CYLD-specific siRNA at mRNA level. Figure S2. The proteins involved in Akt and ERK signaling pathway in CYLD-negative OSCC cells. Figure S3. Cell survival rate in CYLD-knockdown OSCC cells by different siCYLD #2 and in other OSCC cells. Figure S4. Gefitinib treatment increased the expression of E-cadherin, an EMT biomarker. Figure S5. NF-κB signaling pathway does not participate in cell survival in CYLD-negative OSCC cells. Figure S6. TGF-β signaling pathway does not participate in cell survival in CYLD-negative OSCC cells. Figure S7. Cetuximab treatment suppressed anchorage-independent growth of CYLD-negative OSCC cells. Figure S8. Immunohistochemical analysis for OSCC marker expression in tumor tissues from PDX models (PDX st.1 & PDX st.2).
A new non-convex model of the binary asteroid 90 Antiope obtained with the SAGE modelling technique
Creators: name: Bartczak, P.
name: Michałowski, T.
name: Santana-Ros, T.
name: Dudziński, G.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: Computational Physics (physics.comp-ph)
subject: FOS: Physical sciences

description: We present a new non-convex model of the 90 Antiope binary asteroid, derived with a modified version of the SAGE (Shaping Asteroids with Genetic Evolution) method using disk-integrated photometry only. A new variant of the SAGE algorithm capable of deriving models of binary systems is described. The model of 90 Antiope confirms the system's pole solution ($λ=199^{\circ}$, $β=38^{\circ}$, $σ=\pm5^{\circ}$) and the orbital period ($16.505046 \pm 0.000005$ h). A comparison between the stellar occultation chords obtained during the 2011 occultation and the projected shape solution has been used to scale the model. The resulting scaled model allowed us to obtain the equivalent radii ($R_{1}=40.4\pm0.9$ km and $R_{2}=40.2\pm0.9$ km) and the distance between the two system components ($176\pm4$ km), leading to a total system mass of ($9.14\pm0.62$)$\cdot10^{17}$ kg. The non-convex shape description of the components permitted a refined calculation of the components' volumes, leading to a density estimation of $1.67\pm0.23$ g cm$^{-3}$. The intermediate-scale features of the model may also offer new clues on the components' origin and evolution.
An siRNA Screen Identifies the U2 snRNP Spliceosome as a Host Restriction Factor for Recombinant Adeno-associated Viruses
Creators: name: Bressin, Robert K.
name: Koide, Kazunori
name: Hickey, Raymond D.
name: Asokan, Aravind
name: Izumiya, Yoshihiro
name: Schreiber, Claire A.
name: Ikeda, Yasuhiro
name: Sakuma, Toshie
name: Basu, Upamanyu
name: Holditch, Sara J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Adeno-associated viruses (AAV) have evolved to exploit the dynamic reorganization of host cell machinery during co-infection by adenoviruses and other helper viruses. In the absence of helper viruses, host factors such as the proteasome and DNA damage response machinery have been shown to effectively inhibit AAV transduction by restricting processes ranging from nuclear entry to second-strand DNA synthesis. To identify host factors that might affect other key steps in AAV infection, we screened an siRNA library that revealed several candidate genes including the PHD finger-like domain protein 5A (PHF5A), a U2 snRNP-associated protein. Disruption of PHF5A expression selectively enhanced transgene expression from AAV by increasing transcript levels and appears to influence a step after second-strand synthesis in a serotype and cell type-independent manner. Genetic disruption of U2 snRNP and associated proteins, such as SF3B1 and U2AF1, also increased expression from AAV vector, suggesting the critical role of U2 snRNP spliceosome complex in this host-mediated restriction. Notably, adenoviral co-infection and U2 snRNP inhibition appeared to target a common pathway in increasing expression from AAV vectors. Moreover, pharmacological inhibition of U2 snRNP by meayamycin B, a potent SF3B1 inhibitor, substantially enhanced AAV vector transduction of clinically relevant cell types. Further analysis suggested that U2 snRNP proteins suppress AAV vector transgene expression through direct recognition of intact AAV capsids. In summary, we identify U2 snRNP and associated splicing factors, which are known to be affected during adenoviral infection, as novel host restriction factors that effectively limit AAV transgene expression. Concurrently, we postulate that pharmacological/genetic manipulation of components of the spliceosomal machinery might enable more effective gene transfer modalities with recombinant AAV vectors.
A transient event in AD 775 reported by al-Tabari: A bolide - not a nova, supernova, or kilonova
Creators: name: Neuhaeuser, Ralph
name: Kunitzsch, Paul
Publisher: name: arXiv
Year: 2014
Subjects: subject: History and Philosophy of Physics (physics.hist-ph)
subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: Given that the cause for the strong increase in 14C in AD 774/5 in Japanese and German trees is still a matter of debate (e.g. short Gamma-Ray Burst or solar super-flare), we have searched in Arabic chronicles for reports about unusual transient celestial events. In the History of al-Tabari we found two (almost identical) reports about such an event. The group around caliph al-Mansur observed a transient event while on the way from Baghdad to Mecca on AD 775 Aug 29 - Sep 1 (Julian calendar). A celestial object (kawkab) was seen to fall or set (inqadda), and its trace (atharuhu) was seen for at least tens of minutes (up to 70-90 min) during morning twilight. The reports use the Arabic words kawkab and athar(uhu), which were also used in the known Arabic reports about supernovae SN 1006 and 1054, so that one might consider an interpretation as a nova-like event. The kawkab (celestial object) was observed only during the morning twilight at a brightness of probably between about -3 and 0 mag. Such a brightness and time-scale would be expected for optical kilonovae (at 3 to 9 kpc) in the context of short Gamma-Ray Bursts. There are no similar reports from eastern Asia for this time. However, the short reports are fully consistent with a bolide: The word kawkab can be used for meteor, the verb inqadda normally means "falling down", the word atharuhu can mean "its trace". We therefore prefer the interpretation as bolide. We discuss in detail how to convert the Muslim calendar date to a date in the Julian calendar using first the calculated Islamic calendar and then considering the time when the crescent new moon could be visible at the given location.
description: 12 pages with three figures, paper in press (Astronomical Notes 2014) - small corrections applied
ETD & Open Science: Maximizing the Discoverability and Impact through Persistent Identifiers (PIDs)
Creators: name: Mejias, Gabriela
name: Mostafa, Mohamad
Publisher: name: Zenodo
Year: 2023
Subjects: ETDs
DOIs
OpenScience
Electronic Theses and Dissertations
PIDs
DataCite
Impact

description: Using persistent identifiers (PIDs) can maximize Electronic Theses and Dissertations (ETDs) discoverability and support in making the affiliated research data FAIR. PIDs are unique and permanent identifiers that can be used to identify and cite various research outputs over time. Digital Object Identifiers (DOIs) ensure the persistent and unique identification of ETDs, facilitating their proper citation, tracking, and linkage to related research overtime. This is important for Open Science because it allows researchers to share their work with others and to track its impact.This presentation has been delivered during the 26th International Symposium on Electronic Theses and Dissertations ETD 2023, hosted by Information and Library Network Centre (INFLIBNET) in Gujarat, India.
Additional file 1 of How much does effective health facility inspection cost? An analysis of the economic costs of Kenya’s Joint Health Inspection innovations
Creators: name: Chege, Timothy
name: Wafula, Francis
name: Tama, Eric
name: Khayoni, Irene
name: Ogira, Dosila
name: Gitau, Njeri
name: Goodman, Catherine
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 1. Methods for calculating cost of each resource used in JHI pilot.
WFIRST Ultra-Precise Astrometry II: Asteroseismology
Creators: name: Gould, A.
name: Huber, D.
name: Penny, M.
name: Stello, D.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: WFIRST microlensing observations will return high-precision parallaxes, sigma(pi) < 0.3 microarcsec, for the roughly 1 million stars with H<14 in its 2.8 deg^2 field toward the Galactic bulge. Combined with its 40,000 epochs of high precision photometry (~0.7 mmag at H_vega=14 and ~0.1 mmag at H=8), this will yield a wealth of asteroseismic data of giant stars, primarily in the Galactic bulge but including a substantial fraction of disk stars at all Galactocentric radii interior to the Sun. For brighter stars, the astrometric data will yield an external check on the radii derived from the two asteroseismic parameters, and nu_max, while for the fainter ones, it will enable a mass measurement from the single measurable asteroseismic parameter nu_max. Simulations based on Kepler data indicate that WFIRST will be capable of detecting oscillations in stars from slightly less luminous than the red clump to the tip of the red giant branch, yielding roughly 1 million detections.
description: 13 pages, 6 figures, submitted to JKAS
CARD9-Dependent Neutrophil Recruitment Protects against Fungal Invasion of the Central Nervous System
Creators: name: Lionakis, Michail S.
name: Datta, Sandip K.
name: Chittiboina, Prashant
name: Karauzum, Hatice
name: Fink, Danielle L.
name: Rosenzweig, Sergio D.
name: Drummond, Rebecca A.
name: Weimer, Eric T.
name: Kuhns, Douglas B.
name: Lim, Jean K.
name: Mendez, Laura M.
name: Belhorn, Thomas H.
name: Yockey, Lynne
name: Ferre, Elise M. N.
name: Mikelis, Constantinos M.
name: Lemberg, Kimberly
name: Hernandez, Michelle L.
name: Hsu, Amy P.
name: Collar, Amanda L.
name: Rose, Stacey R.
name: Lin, Xin
name: Rodriguez, Carlos A.
name: Hohl, Tobias M.
name: Zhai, Bing
name: Kuehn, Hye Sun
name: Swamydas, Muthulekha
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Candida is the most common human fungal pathogen and causes systemic infections that require neutrophils for effective host defense. Humans deficient in the C-type lectin pathway adaptor protein CARD9 develop spontaneous fungal disease that targets the central nervous system (CNS). However, how CARD9 promotes protective antifungal immunity in the CNS remains unclear. Here, we show that a patient with CARD9 deficiency had impaired neutrophil accumulation and induction of neutrophil-recruiting CXC chemokines in the cerebrospinal fluid despite uncontrolled CNS Candida infection. We phenocopied the human susceptibility in Card9-/- mice, which develop uncontrolled brain candidiasis with diminished neutrophil accumulation. The induction of neutrophil-recruiting CXC chemokines is significantly impaired in infected Card9-/- brains, from both myeloid and resident glial cellular sources, whereas cell-intrinsic neutrophil chemotaxis is Card9-independent. Taken together, our data highlight the critical role of CARD9-dependent neutrophil trafficking into the CNS and provide novel insight into the CNS fungal susceptibility of CARD9-deficient humans.
Chitin Recognition via Chitotriosidase Promotes Pathologic Type-2 Helper T Cell Responses to Cryptococcal Infection
Creators: name: Lee, Chun G.
name: Levitz, Stuart M.
name: Bohjanen, Paul R.
name: Jenkins, Marc K.
name: Nielsen, Kirsten
name: Specht, Charles A.
name: Elias, Jack A.
name: Smith, Kyle D.
name: Lee, S. Thera
name: Mukaremera, Liliane
name: Nielsen, Judith N.
name: Lee, Chrono K.
name: Boulware, David R.
name: Wiesner, Darin L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Pulmonary mycoses are often associated with type-2 helper T (Th2) cell responses. However, mechanisms of Th2 cell accumulation are multifactorial and incompletely known. To investigate Th2 cell responses to pulmonary fungal infection, we developed a peptide-MHCII tetramer to track antigen-specific CD4+ T cells produced in response to infection with the fungal pathogen Cryptococcus neoformans. We noted massive accruement of pathologic cryptococcal antigen-specific Th2 cells in the lungs following infection that was coordinated by lung-resident CD11b+ IRF4-dependent conventional dendritic cells. Other researchers have demonstrated that this dendritic cell subset is also capable of priming protective Th17 cell responses to another pulmonary fungal infection, Aspergillus fumigatus. Thus, higher order detection of specific features of fungal infection by these dendritic cells must direct Th2 cell lineage commitment. Since chitin-containing parasites commonly elicit Th2 responses, we hypothesized that recognition of fungal chitin is an important determinant of Th2 cell-mediated mycosis. Using C. neoformans mutants or purified chitin, we found that chitin abundance impacted Th2 cell accumulation and disease. Importantly, we determined Th2 cell induction depended on cleavage of chitin via the mammalian chitinase, chitotriosidase, an enzyme that was also prevalent in humans experiencing overt cryptococcosis. The data presented herein offers a new perspective on fungal disease susceptibility, whereby chitin recognition via chitotriosidase leads to the initiation of harmful Th2 cell differentiation by CD11b+ conventional dendritic cells in response to pulmonary fungal infection.
Multi Circle Detection on Images Using Artificial Bee Colony (ABC) Optimization
Creators: name: Cuevas, Erik
name: Sencion-Echauri, Felipe
name: Zaldivar, Daniel
name: Cisneros, Marco Perez
Publisher: name: arXiv
Year: 2014
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Neural and Evolutionary Computing (cs.NE)
subject: FOS: Computer and information sciences

description: Hough transform (HT) has been the most common method for circle detection, exhibiting robustness, but adversely demanding considerable computational effort and large memory requirements. Alternative approaches include heuristic methods that employ iterative optimization procedures for detecting multiple circles. Since only one circle can be marked at each optimization cycle, multiple executions must be enforced in order to achieve multi detection. This paper presents an algorithm for automatic detection of multiple circular shapes that considers the overall process as a multi-modal optimization problem. The approach is based on the artificial bee colony (ABC) algorithm, a swarm optimization algorithm inspired by the intelligent foraging behavior of honey bees. Unlike the original ABC algorithm, the proposed approach presents the addition of a memory for discarded solutions. Such memory allows holding important information regarding other local optima which might have emerged during the optimization process. The detector uses a combination of three non-collinear edge points as parameters to determine circle candidates. A matching function (nectar- amount) determines if such circle candidates (bee-food-sources) are actually present in the image. Guided by the values of such matching functions, the set of encoded candidate circles are evolved through the ABC algorithm so that the best candidate (global optimum) can be fitted into an actual circle within the edge only image. Then, an analysis of the incorporated memory is executed in order to identify potential local optima, i.e., other circles.
description: 19 Pages
Compartmentalized Replication of R5 T Cell-Tropic HIV-1 in the Central Nervous System Early in the Course of Infection
Creators: name: Joseph, Sarah B.
name: Schnell, Gretja
name: Sturdevant, Christa Buckheit
name: Price, Richard W.
name: Swanstrom, Ronald
name: Spudich, Serena
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Compartmentalized HIV-1 replication within the central nervous system (CNS) likely provides a foundation for neurocognitive impairment and a potentially important tissue reservoir. The timing of emergence and character of this local CNS replication has not been defined in a population of subjects. We examined the frequency of elevated cerebrospinal fluid (CSF) HIV-1 RNA concentration, the nature of CSF viral populations compared to the blood, and the presence of a cellular inflammatory response (with the potential to bring infected cells into the CNS) using paired CSF and blood samples obtained over the first two years of infection from 72 ART-naïve subjects. Using single genome amplification (SGA) and phylodynamics analysis of full-length env sequences, we compared CSF and blood viral populations in 33 of the 72 subjects. Independent HIV-1 replication in the CNS (compartmentalization) was detected in 20% of sample pairs analyzed by SGA, or 7% of all sample pairs, and was exclusively observed after four months of infection. In subjects with longitudinal sampling, 30% showed evidence of CNS viral replication or pleocytosis/inflammation in at least one time point, and in approximately 16% of subjects we observed evolving CSF/CNS compartmentalized viral replication and/or a marked CSF inflammatory response at multiple time points suggesting an ongoing or recurrent impact of the infection in the CNS. Two subjects had one of two transmitted lineages (or their recombinant) largely sequestered within the CNS shortly after transmission, indicating an additional mechanism for establishing early CNS replication. Transmitted variants were R5 T cell-tropic. Overall, examination of the relationships between CSF viral populations, blood and CSF HIV-1 RNA concentrations, and inflammatory responses suggested four distinct states of viral population dynamics, with associated mechanisms of local viral replication and the early influx of virus into the CNS. This study considerably enhances the generalizability of our results and greatly expands our knowledge of the early interactions of HIV-1 in the CNS.
Correction: Molecular and Functional Analyses of a Maize Autoactive NB-LRR Protein Identify Precise Structural Requirements for Activity
Creators: name: Dangl, Jeffery L.
name: EI-Kasmi, Farid
name: Balint-Kurti, Peter J.
name: Johal, Guri
name: Ji, Jiabing
name: Wang, Guan-Feng
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Plant disease resistance is often mediated by nucleotide binding-leucine rich repeat (NLR) proteins which remain auto-inhibited until recognition of specific pathogen-derived molecules causes their activation, triggering a rapid, localized cell death called a hypersensitive response (HR). Three domains are recognized in one of the major classes of NLR proteins: a coiled-coil (CC), a nucleotide binding (NB-ARC) and a leucine rich repeat (LRR) domains. The maize NLR gene Rp1-D21 derives from an intergenic recombination event between two NLR genes, Rp1-D and Rp1-dp2 and confers an autoactive HR. We report systematic structural and functional analyses of Rp1 proteins in maize and N. benthamiana to characterize the molecular mechanism of NLR activation/auto-inhibition. We derive a model comprising the following three main features: Rp1 proteins appear to self-associate to become competent for activity. The CC domain is signaling-competent and is sufficient to induce HR. This can be suppressed by the NB-ARC domain through direct interaction. In autoactive proteins, the interaction of the LRR domain with the NB-ARC domain causes de-repression and thus disrupts the inhibition of HR. Further, we identify specific amino acids and combinations thereof that are important for the auto-inhibition/activity of Rp1 proteins. We also provide evidence for the function of MHD2, a previously uncharacterized, though widely conserved NLR motif. This work reports several novel insights into the precise structural requirement for NLR function and informs efforts towards utilizing these proteins for engineering disease resistance.
MULLA MUHAMMAD SODIQXOJA VA UNING ADABIY MЕROSI
Creators: name: Qodirova, Nasima
Publisher: name: Zenodo
Year: 2024

description: maqola Buxoro adabiy muhitida ijod qilgan shoir, tarixchi, geograf Mulla Muhammad Sodiqxoja Gulshaniy hayoti va ijodiga bag’ishlangan. Ijodkorning yashab ijod etgan davri, muhiti, davrdosh ijodkorlarining unga munosabati borasida mulohazalar yoritilgan. Gulshaniyning “Tarixi Humoyun” asariga doir ma’lumotlar berilgan, shuningdek, badiiy ijodiga ham to‘xtanilgan.
Kompaneets Model Fitting of the Orion-Eridanus Superbubble
Creators: name: Pon, Andy
name: Johnstone, Doug
name: Bally, John
name: Heiles, Carl
Publisher: name: arXiv
Year: 2014
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Winds and supernovae from OB associations create large cavities in the interstellar medium referred to as superbubbles. The Orion molecular clouds are the nearest high mass star-forming region and have created a highly elongated, 20 degree x 45 degree, superbubble. We fit Kompaneets models to the Orion-Eridanus superbubble and find that a model where the Eridanus side of the superbubble is oriented away from the Sun provides a marginal fit. Because this model requires an unusually small scaleheight of 40 pc and has the superbubble inclined 35 degrees from the normal to the Galactic plane, we propose that this model should be treated as a general framework for modelling the Orion-Eridanus superbubble, with a secondary physical mechanism not included in the Kompaneets model required to fully account for the orientation and elongation of the superbubble.
description: 15 pages, 5 figures, 2 tables, accepted by MNRAS, minor grammatical changes
Correction: Nanoformulations of Rilpivirine for Topical Pericoital and Systemic Coitus-Independent Administration Efficiently Prevent HIV Transmission
Creators: name: Council, Olivia D.
name: Nochii, Tomonori
name: Williams, Peter
name: Garcia, J. Victor
name: Belshan, Michael
name: Kovarova, Martina
name: Baker, Caroline E.
name: Date, Abhijit A.
name: Vincent, Heather
name: Long, Julie M.
name: Thayer, William O.
name: Destache, Christopher J.
name: Shibata, Annemarie
name: Kraus, Guenter
name: Lachaud-Durand, Sophie
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: Vaginal HIV transmission accounts for the majority of new infections worldwide. Currently, multiple efforts to prevent HIV transmission are based on pre-exposure prophylaxis with various antiretroviral drugs. Here, we describe two novel nanoformulations of the reverse transcriptase inhibitor rilpivirine for pericoital and coitus-independent HIV prevention. Topically applied rilpivirine, encapsulated in PLGA nanoparticles, was delivered in a thermosensitive gel, which becomes solid at body temperature. PLGA nanoparticles with encapsulated rilpivirine coated the reproductive tract and offered significant protection to BLT humanized mice from a vaginal high-dose HIV-1 challenge. A different nanosuspension of crystalline rilpivirine (RPV LA), administered intramuscularly, protected BLT mice from a single vaginal high-dose HIV-1 challenge one week after drug administration. Using transmitted/founder viruses, which were previously shown to establish de novo infection in humans, we demonstrated that RPV LA offers significant protection from two consecutive high-dose HIV-1 challenges one and four weeks after drug administration. In this experiment, we also showed that, in certain cases, even in the presence of drug, HIV infection could occur without overt or detectable systemic replication until levels of drug were reduced. We also showed that infection in the presence of drug can result in acquisition of multiple viruses after subsequent exposures. These observations have important implications for the implementation of long-acting antiretroviral formulations for HIV prevention. They provide first evidence that occult infections can occur, despite the presence of sustained levels of antiretroviral drugs. Together, our results demonstrate that topically- or systemically administered rilpivirine offers significant coitus-dependent or coitus-independent protection from HIV infection.
Additional file 2 of How much does effective health facility inspection cost? An analysis of the economic costs of Kenya’s Joint Health Inspection innovations
Creators: name: Chege, Timothy
name: Wafula, Francis
name: Tama, Eric
name: Khayoni, Irene
name: Ogira, Dosila
name: Gitau, Njeri
name: Goodman, Catherine
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 2. Methods for scaling up JHI pilot costs to the national level.
Additional file 1 of A comparative evaluation of the effects of seed invigoration treatments with precursor zinc salt and nano-sized zinc oxide (ZnO) particles on vegetative growth, grain yield, and quality characteristics of Zea mays
Creators: name: Tondey, Manisha
name: Kalia, Anu
name: Singh, Alla
name: Abd-Elsalam, Kamel
name: Hassan, Montaser M.
name: Dheri, Gurmeet Singh
Publisher: name: figshare
Year: 2022
Subjects: subject: Plant Biology
subject: FOS: Biological sciences

description: Additional file 1. Supplementary Table 1. Details of the treatments evaluated in the field study. Supplementary Table 2. Mean effect of DAS, seed treatments and concentration of Zn-source on soil (a) enzyme and (b) rhizosphere soil microbial viable cell counts characteristics in maize crop (variety PMH-1) grown under field conditions. Supplementary figure 1. Effect of seed priming and coating with bulk salt and ZnONPs in maize variety PMH-1 cultivated under field conditions. Supplementary figure 2. Effect of ZnONPs and salt precursor (ZnSO4) on cobs of Zea mays cultivated under field conditions. Supplementary figure 3. Effect of ZnONPs and salt precursor (ZnSO4) on microbial counts of soil samples of Zea mays (var. PMH-1) cultivated under field conditions.
Dissemination of a Highly Virulent Pathogen: Tracking The Early Events That Define Infection
Creators: name: Wagner, Nikki J.
name: Miller, Virginia L.
name: Gonzalez, Rodrigo J.
name: Weening, Eric H.
name: Lane, M. Chelsea
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2015

description: The series of events that occurs immediately after pathogen entrance into the body is largely speculative. Key aspects of these events are pathogen dissemination and pathogen interactions with the immune response as the invader moves into deeper tissues. We sought to define major events that occur early during infection of a highly virulent pathogen. To this end, we tracked early dissemination of Yersinia pestis, a highly pathogenic bacterium that causes bubonic plague in mammals. Specifically, we addressed two fundamental questions: (1) do the bacteria encounter barriers in disseminating to draining lymph nodes (LN), and (2) what mechanism does this nonmotile bacterium use to reach the LN compartment, as the prevailing model predicts trafficking in association with host cells. Infection was followed through microscopy imaging in addition to assessing bacterial population dynamics during dissemination from the skin. We found and characterized an unexpected bottleneck that severely restricts bacterial dissemination to LNs. The bacteria that do not pass through this bottleneck are confined to the skin, where large numbers of neutrophils arrive and efficiently control bacterial proliferation. Notably, bottleneck formation is route dependent, as it is abrogated after subcutaneous inoculation. Using a combination of approaches, including microscopy imaging, we tested the prevailing model of bacterial dissemination from the skin into LNs and found no evidence of involvement of migrating phagocytes in dissemination. Thus, early stages of infection are defined by a bottleneck that restricts bacterial dissemination and by neutrophil-dependent control of bacterial proliferation in the skin. Furthermore, and as opposed to current models, our data indicate an intracellular stage is not required by Y. pestis to disseminate from the skin to draining LNs. Because our findings address events that occur during early encounters of pathogen with the immune response, this work can inform efforts to prevent or control infection.
Comments on the T-dual of the gravity dual of D5-branes on $S^3$
Creators: name: Araujo, Thiago R.
name: Nastase, Horatiu
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We consider an abelian T-duality on a deformation of the gravitational solution of \cite{Maldacena2001}, which is the gravity dual of $N_c$ D5-branes wrapping a three-cycle inside a manifold that admits a $G_2$ structure. Performing the T-duality we find $N_c$ D$4$-branes wrapping a two-cycle with non-trivial antisymmetric fields in the NS-NS and RR sector. We study some aspects of its dual field theory and we compare with the original solution.
description: 26 pages
Additional file 3 of How much does effective health facility inspection cost? An analysis of the economic costs of Kenya’s Joint Health Inspection innovations
Creators: name: Chege, Timothy
name: Wafula, Francis
name: Tama, Eric
name: Khayoni, Irene
name: Ogira, Dosila
name: Gitau, Njeri
name: Goodman, Catherine
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Science Policy
subject: 110309 Infectious Diseases
subject: FOS: Health sciences

description: Additional file 3. Economic and financial costs of JHI pilot by phase and funder (2017 USD).
WISE photometry for 400 million SDSS sources
Creators: name: Lang, Dustin
name: Hogg, David W.
name: Schlegel, David J.
Publisher: name: arXiv
Year: 2014
Subjects: subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: We present photometry of images from the Wide-Field Infrared Survey Explorer (WISE; Wright et al. 2010) of over 400 million sources detected by the Sloan Digital Sky Survey (SDSS; York et al. 2000). We use a "forced photometry" technique, using measured SDSS source positions, star-galaxy separation and galaxy profiles to define the sources whose fluxes are to be measured in the WISE images. We perform photometry with The Tractor image modeling code, working on our "unWISE" coaddds and taking account of the WISE point-spread function and a noise model. The result is a measurement of the flux of each SDSS source in each WISE band. Many sources have little flux in the WISE bands, so often the measurements we report are consistent with zero. However, for many sources we get three- or four-sigma measurements; these sources would not be reported by the WISE pipeline and will not appear in the WISE catalog, yet they can be highly informative for some scientific questions. In addition, these small-signal measurements can be used in stacking analyses at catalog level. The forced photometry approach has the advantage that we measure a consistent set of sources between SDSS and WISE, taking advantage of the resolution and depth of the SDSS images to interpret the WISE images; objects that are resolved in SDSS but blended together in WISE still have accurate measurements in our photometry. Our results, and the code used to produce them, are publicly available at http://unwise.me.