cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Ectopic PU.1 Expression Provides Chimeric Antigen Receptor (CAR) T Cells with Innate Cell Capacities Including IFN-β Release
Creators: name: Harrer, Dennis Christoph
name: Eder, Matthias
name: Barden, Markus
name: Pan, Hong
name: Herr, Wolfgang
name: Abken, Hinrich
Publisher: name: Universität Regensburg
Year: 2024
Subjects: subject: transcription factor; CAR; T cell
subject: 610 Medizin

description: Chimeric antigen receptor (CAR) T cell therapy has achieved extraordinary success in
eliminating B cell malignancies; however, so far, it has shown limited efficacy in the treatment of
solid tumors, which is thought to be due to insufficient CAR T cell activation. We hypothesized
that the transcription factor PU.1, a master regulator of innate cell functionality, may augment proinflammatory
CAR T cell activation. T cells were engineered with a CEA-specific CAR together
with the constitutive expression of PU.1. CAR-redirected T cell activation was recorded for canonical
functionality in vitro under conditions of prolonged repetitive antigen exposure. Ectopic PU.1
expression in CAR T cells upregulated the costimulatory receptors CD40, CD80, CD86, and CD70,
which, unexpectedly, did not augment effector functions but hampered the upregulation of 4-1BB,
decreased IL-2 production, reduced CAR T cell proliferation, and impaired their cytotoxic capacities.
Under “stress” conditions of repetitive engagement of cognate tumor cells, CAR T cells with ectopic
PU.1 showed reduced persistence, and finally failed to control the growth of cancer cells. Mechanistically,
PU.1 caused CAR T cells to secrete IFN-β, a cytokine known to promote CAR T cell attrition
and apoptosis. Collectively, PU.1 can polarize the functional capacities of CAR T cells towards
innate cells.
Bandakia kulluensis Panesar 2004
Creators: name: Pešić, Vladimir
name: Chatterjee, Tapas
name: Bordoloi, Sabitry
Publisher: name: Zenodo
Year: 2010
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Arachnida
Trombidiformes
Anisitsiellidae
Bandakia
Bandakia kulluensis

description: Bandakia kulluensis Panesar, 2004
Records from the study area: Himachal Pradesh—Panesar (2004).
Habitat: Mosses of a waterfall.
Distribution: India.
description: Published as part of Pešić, Vladimir, Chatterjee, Tapas & Bordoloi, Sabitry, 2010, A checklist of the water mites (Acari: Hydrachnidia) of India, with new records and description of one new species, pp. 1-54 in Zootaxa 2617 (1) on page 8, DOI: 10.11646/zootaxa.2617.1.1, http://zenodo.org/record/197964
Constraints on anomalous quartic gauge couplings via $Zγjj$ production at the LHC
Creators: name: Yang, Ji-Chong
name: Guo, Yu-Chen
name: Yue, Chong-Xing
name: Fu, Qing
Publisher: name: arXiv
Year: 2021
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: In this paper, we investigate the contributions of anomalous quartic gauge couplings (aQGCs) to $Zγjj$ production at the Large Hadron Collider (LHC) in the context of Standard Model effective theory (SMEFT). When energy scale is large, the validity of SMEFT becomes an important issue. To ensure the validity, the unitarity bound is applied in a model independent approach, which is found to have significant suppressive effects on the signals of $O_{M_i}$ operators. The kinematic and polarization features of the aQGC signals are also studied. The polarization effect is useful to highlight the signals of $O_{T_i}$ operators. The sensitivity estimates on dimension-8 operators with unitarity bounds at $\sqrt{s}=14$ TeV are obtained.
description: 25 pages, 6 figures
Spin-orbit torque control of spin waves in a ferromagnetic waveguide
Creators: name: Nikitchenko, Andrei I.
name: Pertsev, Nikolay A.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Spin-orbit torque (SOT) created by a spin current injected into a ferromagnet by an adjacent heavy metal represents an efficient tool for the excitation and manipulation of spin waves. Here we report the micromagnetic simulations describing the influence of SOT on the propagation of spin waves in the $\mathrm{W}/\mathrm{CoFeB}/\mathrm{MgO}$ nanostructure having voltage-controlled magnetic anisotropy (VCMA). The simulations show that two spin waves travelling in the opposite directions can be generated in the center of the $\mathrm{CoFeB}$ waveguide via the modulation of VCMA induced by a microwave voltage locally applied to the $\mathrm{MgO}$ nanolayer. The amplitudes of these waves exponentially decrease with the propagation distance with similar decay lengths of about 2.5 $μ$m. In the presence of a direct electric current injected into the $\mathrm{W}$ film beneath the waveguide center, the decay lengths of two spin waves change in the opposite way owing to different directions of the electric currents flowing in the underlying halves of the $\mathrm{W}$ layer. Remarkably, above the critical current density $J_\mathrm{W} \approx 2 \times 10^{10}$ A m$^{-2}$, SOT provides the amplification of the spin wave propagating in one half of the waveguide and strongly accelerates the attenuation of the wave travelling in the other half. As a result, a long-distance spin-wave propagation takes place in a half of the $\mathrm{CoFeB}$ waveguide only. Furthermore, by reversing the polarity of the dc voltage applied to the heavy-metal layer one can change the propagation area and switch the travel direction of the spin wave in the ferromagnetic waveguide. Thus, the $\mathrm{W}/\mathrm{CoFeB}/\mathrm{MgO}$ nanostructure can be employed as an electrically controlled magnonic device converting the electrical input signal into a spin signal, which can be transmitted to one of two outputs of the device.
description: 10 pages, 10 figures
Poised PABP–RNA hubs implement signal-dependent mRNA decay in development
Creators: name: Modic, Miha
name: Kuret, Klara
name: Steinhauser, Sebastian
name: Faraway, Rupert
name: van Genderen, Emiel
name: de Los Mozos, Igor Ruiz
name: Novljan, Jona
name: Vičič, Žiga
name: Lee, Flora CY
name: Berge, Derk ten
name: Luscombe, Nicholas M
name: Ule, Jernej
Publisher: name: The Francis Crick Institute
Year: 2024
Subjects: classificationCode: Tumour Biology
subject: Tumour Biology
classificationCode: Stem Cells
subject: Stem Cells
classificationCode: Ecology,Evolution & Ethology
subject: Ecology,Evolution & Ethology
classificationCode: Gene Expression
subject: Gene Expression
classificationCode: Genetics & Genomics
subject: Genetics & Genomics
classificationCode: Computational & Systems Biology
subject: Computational & Systems Biology
classificationCode: Neurosciences
subject: Neurosciences
subject: FOS: Clinical medicine
classificationCode: Biochemistry & Proteomics
subject: Biochemistry & Proteomics

description: Signaling pathways drive cell fate transitions largely by changing gene expression. However, the mechanisms for rapid and selective transcriptome rewiring in response to signaling cues remain elusive. Here we use deep learning to deconvolve both the sequence determinants and the trans-acting regulators that trigger extracellular signal-regulated kinase (ERK)–mitogen-activated protein kinase kinase (MEK)-induced decay of the naive pluripotency mRNAs. Timing of decay is coupled to embryo implantation through ERK–MEK phosphorylation of LIN28A, which repositions pLIN28A to the highly A+U-rich 3′ untranslated region (3′UTR) termini of naive pluripotency mRNAs. Interestingly, these A+U-rich 3′UTR termini serve as poly(A)-binding protein (PABP)-binding hubs, poised for signal-induced convergence with LIN28A. The multivalency of AUU motifs determines the efficacy of pLIN28A–PABP convergence, which enhances PABP 3′UTR binding, decreases the protection of poly(A) tails and activates mRNA decay to enable progression toward primed pluripotency. Thus, the signal-induced convergence of LIN28A with PABP–RNA hubs drives the rapid selection of naive mRNAs for decay, enabling the transcriptome remodeling that ensures swift developmental progression.
On Perfectness of Annihilating-Ideal Graph of $\mathbb{Z}_n$
Creators: name: Saha, Manideepa
name: Biswas, Sucharita
name: Das, Angsuman
Publisher: name: arXiv
Year: 2021
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: 05C25, 05C17

description: The annihilating-ideal graph of a commutative ring $R$ with unity is defined as the graph $\mathbb{AG}(R)$ with the vertex set is the set of all non-zero ideals with non-zero annihilators and two distinct vertices $I$ and $J$ are adjacent if and only if $IJ = 0$. Nikandish {\it et.al.} proved that $\mathbb{AG}(\mathbb{Z}_n)$ is weakly perfect. In this short paper, we characterize $n$ for which $\mathbb{AG}(\mathbb{Z}_n)$ is perfect.
description: 9 pages, 0 figures
Random-Player Maker-Breaker games
Creators: name: Krivelevich, Michael
name: Kronenberg, Gal
Publisher: name: arXiv
Year: 2015
Subjects: subject: Combinatorics (math.CO)
subject: Probability (math.PR)
subject: FOS: Mathematics
subject: 05C80, 05D40

description: In a $(1:b)$ Maker-Breaker game, a primary question is to find the maximal value of $b$ that allows Maker to win the game (that is, the critical bias $b^*$). Erdős conjectured that the critical bias for many Maker-Breaker games played on the edge set of $K_n$ is the same as if both players claim edges randomly. Indeed, in many Maker-Breaker games, "Erdős Paradigm" turned out to be true. Therefore, the next natural question to ask is the (typical) value of the critical bias for Maker-Breaker games where only one player claims edges randomly. A random-player Maker-Breaker game is a two-player game, played the same as an ordinary (biased) Maker-Breaker game, except that one player plays according to his best strategy and claims one element in each round, while the other plays randomly and claims $b$ elements. In fact, for every (ordinary) Maker-Breaker game, there are two different random-player versions; the $(1:b)$ random-Breaker game and the $(m:1)$ random-Maker game. We analyze the random-player version of several classical Maker-Breaker games such as the Hamilton cycle game, the perfect-matching game and the $k$-vertex-connectivity game (played on the edge sets of $K_n$). For each of these games we find or estimate the asymptotic values of $b$ that allow each player to typically win the game. In fact, we provide the "smart" player with an explicit winning strategy for the corresponding value of $b$.
description: Jonas Groschwitz and Tibor Szabo worked independently on several of the problems presented in this paper, and obtained similar results. Their work is presented in the following Arxiv postings: arXiv:1507.06688, arXiv:1602.04628. arXiv admin note: text overlap with arXiv:1408.5684
Maternal adverse childhood experiences on child growth and development in rural Pakistan: An observational cohort study
Creators: name: Maselko, Joanna
name: Scherer, Elissa
name: Bates, Lisa
name: Chung, Esther O.
name: Sikander, Siham
name: Zalla, Lauren C.
name: Hagaman, Ashley
name: LeMasters, Katherine
name: Staley, Brooke S.
Publisher: name: Public Library of Science
Year: 2023

description: Maternal adverse childhood experiences (ACEs) have significant impacts on the next generation with links to negative birth outcomes, impaired cognitive development, and increased socioemotional problems in children. However, not all types or levels of adversity are similarly deleterious and research from diverse contexts is needed to better understand why and how intergenerational transmission of adversity occurs. We examined the role of maternal ACEs on children’s growth, cognitive, and socioemotional development at 36 months postpartum in rural Pakistan. We used data from 877 mother-child dyads in the Bachpan Cohort, a birth cohort study. Maternal ACEs were captured using an adapted version of the ACE-International Questionnaire. Outcomes at 36 months of age included child growth using the WHO growth z-scores, fine motor and receptive language development assessed with the Bayley Scales of Infant and Toddler Development, and socioemotional and behavioral development measured with the Ages and Stages Questionnaire: Socioemotional and Strengths and Difficulties Questionnaire. To estimate the associations between maternal ACEs and child outcomes, we used multivariable generalized linear models with inverse probability weights to account for sampling and loss to follow-up. Over half of mothers in our sample (58%) experienced at least one ACE. Emotional abuse, physical abuse, and emotional neglect were the most commonly reported ACEs. We found null relationships between the number of maternal ACEs and child growth. Maternal ACEs were associated with higher fine motor and receptive language development and worse socioemotional and behavioral outcomes. Maternal ACE domains had similarly varying relationships with child outcomes. Our findings highlight the complexity of intergenerational associations between maternal ACEs and children’s growth and development. Further work is necessary to examine these relationships across cultural contexts and identify moderating factors to mitigate potential negative intergenerational effects.
Counting special Lagrangian classes and semistable Mukai vectors for K3 surfaces
Creators: name: Athreya, Jayadev S.
name: Fan, Yu-Wei
name: Lee, Heather
Publisher: name: arXiv
Year: 2021
Subjects: subject: Algebraic Geometry (math.AG)
subject: Differential Geometry (math.DG)
subject: Geometric Topology (math.GT)
subject: Symplectic Geometry (math.SG)
subject: FOS: Mathematics

description: Motivated by the study of the growth rate of the number of geodesics in flat surfaces with bounded lengths, we study generalizations of such problems for K3 surfaces. In one generalization, we give a result regarding the upper bound on the asymptotics of the number of classes of irreducible special Lagrangians in K3 surfaces with bounded period integrals. In another generalization, we give the exact leading term in the asymptotics of the number of Mukai vectors of semistable coherent sheaves on algebraic K3 surfaces with bounded central charges, with respect to generic Bridgeland stability conditions.
description: Minor revision in response to the referee report
Microbial community function and bacterial pathogen composition in pit latrines in peri-urban Malawi
Creators: name: Chigwechokha, Petros
name: Brown, Joe
name: Capone, Drew
name: de los Reyes III, Francis L.
name: Smith, Savanna K.
name: Risk, Benjamin B.
name: Holm, Rochelle H.
name: Tilley, Elizabeth
Publisher: name: Public Library of Science
Year: 2023

description: Despite the widespread global reliance on pit latrines as improved sanitation systems, the decomposition of waste within pit latrines is poorly understood. One area needing elucidation is the characterization and function of microbial communities within pit latrines. To address this gap, we characterized the microbial communities of 55 lined pit latrines at three sampling layers from two communities in peri-urban Malawi. The microbial communities of the fecal sludge samples were analyzed for beta diversity, pathogen presence, and functional profiling. Household surveys were conducted and used to compare microbial community patterns to household characteristics and pit latrine use patterns. Compared to activated sludge, anaerobic digestion in municipal wastewater systems, and human gut microbiomes, pit latrines were found to contain unique microbial communities. While the microbial community composition as a whole did not vary by sampling depth, pathogen composition varied by sampling depth, location, and household water source. The inferred microbial function also varied by depth (e.g., increase in methanogens and decrease in aerobes with depth). The richness of lined pit latrines determined from surface samples from eight latrines was found to be representative for a given area. Samples from middle and lower depths collected using a Gulper pump did not provide more information on richness, a result that informs future sampling designs. These findings are important for improving waste-based epidemiology (WBE) approaches to understand community health and waste degradation characterization of lined pit latrines.
Entscheidungsbaum: Video-Uploads auf Video-Plattformen
Creators: name: Vettermann, Oliver
Publisher: name: Zenodo
Year: 2023
Subjects: Datenschutzrecht
Rechtsgrundlagen
Flowchart
Handreichung
Verantwortlichkeit
Forschungsdatenmanagement

description: Dieser Entscheidungsbaum dient dazu, die Handreichung zu datenschutzrechtlichen Aspekten beim Upload von Konferenz-Videos auf nationalen oder gängigen Video-Plattformen zu unterstützen und einen Überblick über die zu absolvierenden Fragen zu ermöglichen. Dabei erhebt der Entscheidungsbaum kein Versprechen auf Vollständigkeit. Für detailliertere Hinweise (z.B. zur automatisierten Entscheidungsfindung) sei auf die ausführliche Handreichung bei NFDI4culture verwiesen. Im Übrigen ersetzt das Ergebnis der Prüfung keine juristische Beurteilung im Einzelfall, sondern dient lediglich der Sensibilisierung für Kernpunkte beim Datenschutz in Wissenschaft und Forschung.
description: Diese Handreichung entstand im Rahmen des DFG-geförderten Forschungsprojektes NFDI4culture, Projektnummer 441958017.
X-ray coherent pulsations during a sub-luminous accretion disk state of the transitional millisecond pulsar XSS J12270-4859
Creators: name: Papitto, A.
name: de Martino, D.
name: Belloni, T. M.
name: Burgay, M.
name: Pellizzoni, A.
name: Possenti, A.
name: Torres, D. F.
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We present the first detection of X-ray coherent pulsations from the transitional millisecond pulsar XSS J12270-4859, while it was in a sub-luminous accretion disk state characterized by a 0.5-10 keV luminosity of 5E33 erg/s (assuming a distance of 1.4 kpc). Pulsations were observed by XMM-Newton at an rms amplitude of (7.7 +/- 0.5)% with a second harmonic stronger than the the fundamental frequency, and were detected when the source is neither flaring nor dipping. The most likely interpretation of this detection is that matter from the accretion disk was channelled by the neutron star magnetosphere and accreted onto its polar caps. According to standard disk accretion theory, for pulsations to be observed the mass in-flow rate in the disk was likely larger than the amount of plasma actually reaching the neutron star surface; an outflow launched by the fast rotating magnetosphere then probably took place, in agreement with the observed broad-band spectral energy distribution. We also report about the non-detection of X-ray pulsations during a recent observation performed while the source behaved as a rotationally-powered radio pulsar.
description: Accepted for publication in MNRAS Letters. 5 pages, including 3 figures and 1 table. Corrected a typo in the uncertainty affecting the spin frequency
J-PLUS: Detecting and studying extragalactic globular clusters -- the case of NGC 1023
Creators: name: Silva, Danielle de Brito
name: Coelho, Paula
name: Cortesi, Arianna
name: Bruzual, Gustavo
name: C., Gladis Magris
name: Chies-Santos, Ana L.
name: Hernandez-Jimenez, Jose A.
name: Ederoclite, Alessandro
name: Roman, Izaskun San
name: Varela, Jesús
name: Forbes, Duncan A.
name: Jiménez-Teja, Yolanda
name: Cenarro, Javier
name: Cristóbal-Hornillos, David
name: Hernández-Monteagudo, Carlos
name: López-Sanjuan, Carlos
name: Marín-Franch, Antonio
name: Moles, Mariano
name: Ramió, Héctor Vázquez
name: Dupke, Renato
name: 2, Laerte Sodré Jr.
name: Angulo, Raul E.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: Extragalactic globular clusters (GCs) are key objects for studying the history of galaxies. The arrival of wide-field surveys such as the Javalambre Photometric Local Universe Survey (J-PLUS) offers new possibilities for the study of these systems. We perform the first study of GCs in J-PLUS to recover information about the history of NGC 1023 taking advantage of wide-field images and 12 filters. We develop the semiautomatic pipeline GCFinder that detects GC candidates in J-PLUS images and can also be adapted to similar surveys. We study the stellar population properties of a sub-sample of GC candidates using spectral energy distribution (SED) fitting. We find 523 GC candidates in NGC 1023, of which $\sim$300 are new. We identify subpopulations of GC candidates, where age and metallicity distributions have multiple peaks. By comparing our results with simulations, we report a possible broad age-metallicity relation, evidence that NGC 1023 experienced accretion events in the past. The dominating age peak is at $10^{10}$ yr. We report a correlation between masses and ages that suggests that massive GC candidates are more likely to survive the turbulent history of the host galaxy. Modeling the light of NGC 1023, we find two spiral-like arms and detect a displacement of the galaxy's photometric center with respect to the outer isophotes and center of GC distribution ($\sim$700 pc and $\sim$1600 pc, respectively), which could be the result of ongoing interaction between NGC 1023 and NGC 1023A. By studying the GC system of NGC 1023 with J-PLUS we showcase the power of multi-band surveys for this kind of study and find evidence of a complex accretion history of the host galaxy.
description: Published in A&A, 2022
Nanoparticle display of prefusion coronavirus spike elicits S1-focused cross-reactive antibody response against diverse coronavirus subgenera
Creators: name: McLellan J.S.
name: Palandjian C.
name: Hutchinson G.B.
name: Corbett-Helaire K.S.
name: Ziwawo C.T.
name: Wang N.
name: Abiona O.M.
name: Ellis D.
name: Kanekiyo M.
name: Fritch E.J.
name: Werner A.P.
name: King N.P.
name: Baker D.
name: Boyoglu-Barnum S.
name: West A.
name: Leist S.R.
name: Ueda G.
name: Wrapp D.
name: Tsybovsky Y.
name: Baric R.S.
name: Graham B.S.
Publisher: name: Nature Research
Year: 2023

description: Multivalent antigen display is a fast-growing area of interest toward broadly protective vaccines. Current nanoparticle-based vaccine candidates demonstrate the ability to confer antibody-mediated immunity against divergent strains of notably mutable viruses. In coronaviruses, this work is predominantly aimed at targeting conserved epitopes of the receptor binding domain. However, targeting conserved non-RBD epitopes could limit the potential for antigenic escape. To explore new potential targets, we engineered protein nanoparticles displaying coronavirus prefusion-stabilized spike (CoV_S-2P) trimers derived from MERS-CoV, SARS-CoV-1, SARS-CoV-2, hCoV-HKU1, and hCoV-OC43 and assessed their immunogenicity in female mice. Monotypic SARS-1 nanoparticles elicit cross-neutralizing antibodies against MERS-CoV and protect against MERS-CoV challenge. MERS and SARS nanoparticles elicit S1-focused antibodies, revealing a conserved site on the S N-terminal domain. Moreover, mosaic nanoparticles co-displaying distinct CoV_S-2P trimers elicit antibody responses to distant cross-group antigens and protect male and female mice against MERS-CoV challenge. Our findings will inform further efforts toward the development of pan-coronavirus vaccines.
Additional file 1 of Scatter-hoarding birds disperse seeds to sites unfavorable for plant regeneration
Creators: name: Sorensen, Marjorie C.
name: Mueller, Thomas
name: Donoso, Isabel
name: Graf, Valentin
name: Merges, Dominik
name: Vanoni, Marco
name: Fiedler, Wolfgang
name: Neuschulz, Eike Lena
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Ecology
subject: Plant Biology

description: Additional file 1. Containing figures S1 and S2, showing revisitation densities of all tagged birds and movements of one juvenile bird, respectively.
IPBES invasive alien species assessment, data management report for Chapter 3. Section 3.2.2.2: Human migration
Creators: name: Vandvik, Vigdis
name: Eycott, Amy E.
Publisher: name: Zenodo
Year: 2023
Subjects: Data management report

description: Section 3.2.2.2 assesses the role of human migration as drivers of biological invasions. The experts conducted a systematic review to report on the existing knowledge on this driver. This systematic review consists in the main source of evidence for the section.
Sparse Coding with Earth Mover's Distance for Multi-Instance Histogram Representation
Creators: name: Zhang, Mohua
name: Peng, Jianhua
name: Liu, Xuejie
name: Wang, Jim Jing-Yan
Publisher: name: arXiv
Year: 2015
Subjects: subject: Machine Learning (cs.LG)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences

description: Sparse coding (Sc) has been studied very well as a powerful data representation method. It attempts to represent the feature vector of a data sample by reconstructing it as the sparse linear combination of some basic elements, and a $L_2$ norm distance function is usually used as the loss function for the reconstruction error. In this paper, we investigate using Sc as the representation method within multi-instance learning framework, where a sample is given as a bag of instances, and further represented as a histogram of the quantized instances. We argue that for the data type of histogram, using $L_2$ norm distance is not suitable, and propose to use the earth mover's distance (EMD) instead of $L_2$ norm distance as a measure of the reconstruction error. By minimizing the EMD between the histogram of a sample and the its reconstruction from some basic histograms, a novel sparse coding method is developed, which is refereed as SC-EMD. We evaluate its performances as a histogram representation method in tow multi-instance learning problems --- abnormal image detection in wireless capsule endoscopy videos, and protein binding site retrieval. The encouraging results demonstrate the advantages of the new method over the traditional method using $L_2$ norm distance.
Design for empowerment: Supporting the self-management of people living with a chronic condition (lymphoedema) by design
Creators: name: Kopanoglu, Teksin
Publisher: name: Cardiff Metropolitan University
Year: 2023
Subjects: Design practice and methods
Design not elsewhere classified
Industrial and product design
Interaction and experience design
Service design
Social design

description: This PhD thesis explores `empowerment` from the patient perspective and presents design guidelines to support the empowerment of people living with a chronic condition, lymphoedema.
 Lymphoedema is a chronic condition that causes oedema/swelling of a part of body, commonly the arm(s) or the leg(s). It requires a daily management routine to avoid progression of the symptoms. People Living with Lymphoedema (PLWL) find continuously self-managing their condition challenging, and usually require comprehensive support. Patient empowerment is commonly set as an objective by healthcare organisations, to sustain their limited resources while maintaining patients’ increased quality of life. Designed products and services have the potential to facilitate or inhibit this empowerment. This thesis investigates the research question `How might we design to support the empowerment of people living with lymphoedema?`. An iterative design research process was followed. First, following a systematic literature review, qualitative studies on lymphoedema experience were synthesised with theoretical models on health behaviour. Then, primary studies including observations, interviews, cultural probes and a co-making workshop were conducted. Design probes were developed and utilised to explore the past (how it was), present (how it is) and future (how it might be) of self-management with study participants who had lymphoedema.
 The results presented empowerment as a multidimensional journey. Provided support should be tailored to address the stage-specific needs of patients in their empowerment journey. Design guidelines are presented to facilitate empowerment by providing the right support at the right time for the individuals. This journey-based approach to patient empowerment can further contribute to the research on personalisation of adaptive products for health and wellbeing. Although this thesis focuses particularly on patients with lymphoedema, similarities with experiences of patients with other chronic conditions were recognised, opening up possibilities for future research on design for other life-changing conditions and journeys.
Absorption of hybrid fibre modes by Cs atoms in quadrupole transitions
Creators: name: Bougouffa, Smail
name: Babiker, Mohamed
Publisher: name: arXiv
Year: 2021
Subjects: subject: Optics (physics.optics)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We evaluate the rate of the absorption of an optical nanofiber mode by a Cs atom in an electric quadrupole transition. With the Cs atom localized near the outer surface of the optical nano-fiber, an interaction occurs between the atomic quadrupole tensor components and the gradients of the vector components of the electric field of a hybrid fiber mode. The absorption rate is evaluated as a function of the radial position of the atom from the fiber axis, assuming a specific value of the laser power and we use experimentally accessible parameters. We find that the absorption of the hybrid modes by the Cs atom decreases as the atom recedes away from the fiber axis and formally vanishes at sufficiently large radial distances. Close to the fiber, however, the absorption rate for the input power chosen can be two orders of magnitude larger than the quadrupole de-excitation rate despite the moderate power used.
description: 14 pages, 8 figures
Fracpairs and fractions over a reduced commutative ring
Creators: name: Bergstra, Jan A.
name: Ponse, Alban
Publisher: name: arXiv
Year: 2014
Subjects: subject: Rings and Algebras (math.RA)
subject: FOS: Mathematics
subject: B.2.0; F.4.1
subject: 13B30, 16S85

description: In the well-known construction of the field of fractions of an integral domain, division by zero is excluded. We introduce "fracpairs" as pairs subject to laws consistent with the use of the pair as a fraction, but do not exclude denominators to be zero. We investigate fracpairs over a reduced commutative ring (a commutative ring that has no nonzero nilpotent elements) and provide these with natural definitions for addition, multiplication, and additive and multiplicative inverse. We find that modulo a simple congruence these fracpairs constitute a "common meadow", which is a commutative monoid both for addition and multiplication, extended with a weak additive inverse, a multiplicative inverse except for zero, and an additional element "a" that is the image of the multiplicative inverse on zero and that propagates through all operations. Considering "a" as an error-value supports the intuition. The equivalence classes of fracpairs thus obtained are called common cancellation fractions (cc-fractions), and cc-fractions over the integers constitute a homomorphic pre-image of the common meadow Qa, the field Q of rational numbers expanded with an a-totalized inverse. Moreover, the initial common meadow is isomorphic to the initial algebra of cc-fractions over the integer numbers. Next, we define canonical term algebras for cc-fractions over the integers and some meadows that model the rational numbers expanded with a totalized inverse, and provide some negative results concerning their associated term rewriting properties. Then we consider reduced commutative rings in which the sum of two squares plus one cannot be a zero divisor: by extending the equivalence relation on fracpairs we obtain an initial algebra that is isomorphic to Qa. Finally, we express negative conjectures concerning alternative specifications for these (concrete) datatypes.
description: 25 pages, 8 tables
A chain theorem for sequentially $3$-rank-connected graphs with respect to vertex-minors
Creators: name: Lee, Duksang
name: Oum, Sang-il
Publisher: name: arXiv
Year: 2021
Subjects: subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: G.2.2
subject: 05C40, 05C50, 05C83

description: Tutte (1961) proved the chain theorem for simple $3$-connected graphs with respect to minors, which states that every simple $3$-connected graph $G$ has a simple $3$-connected minor with one edge fewer than $G$, unless $G$ is a wheel graph. Bouchet (1987) proved an analog for prime graphs with respect to vertex-minors. We present a chain theorem for higher connectivity with respect to vertex-minors, showing that every sequentially $3$-rank-connected graph $G$ has a sequentially $3$-rank-connected vertex-minor with one vertex fewer than $G$, unless $|V(G)|\leq 12$.
description: 22 pages
NBL1 Reduces Corneal Fibrosis and Scar Formation after Wounding
Creators: name: Mei, Hua
name: Liu, Emily
name: Tsai, Chi-Hao
name: Lu, Krystal Lynn
name: Phan, Andrew
Publisher: name: MDPI
Year: 2023

description: Corneal scarring is a leading cause of blindness. Currently, there is no treatment to prevent and/or reduce corneal scar formation under pathological conditions. Our previous data showed that the NBL1 protein, also termed the DAN Family BMP (Bone morphogenetic protein) Antagonist, was highly expressed in corneal stromal cells upon wounding. Here, we examined the function of NBL1 in corneal wound healing. Mouse corneas were mechanically wounded, followed by a 2-week treatment using NBL1. Wounded corneas treated with vehicle or an Fc tag served as controls. Compared with the controls, NBL1 treatment facilitated wound re-epithelialization, partially restored the stromal thickness, and significantly reduced corneal scar formation. NBL1 treatment did not decrease immune cell infiltration, indicating that the anti-scarring effect was not dependent on immune suppression. We further examined the anti-fibrotic effect of NBL1 on human corneas. Pairs of human corneas were induced to form myofibroblasts (a key player in fibrosis and scarring) upon wounding and incubation in a medium containing TGF-β1. The OS corneas were treated with Fc as a control, and the OD corneas were treated with NBL1. Compared with the control, human corneas treated with NBL1 had significantly fewer myofibroblasts, which was consistent with these mouse data. A further study revealed that NBL1 treatment inhibited BMP canonical (phospho-Smad1/5) and no-canonical (phospho-p38) pathways in human corneas. Data show that NBL1 reduced corneal fibrosis and scar formation in mice and cultured human corneas. The underlying molecular mechanism is not certain because both anti-fibrotic Smad1/5 and pro-fibrotic p38 pathways were inhibited upon NBL1 treatment. Whether the p38 pathway dominates the Smad1/5 pathway during corneal fibrosis, leading to the anti-fibrotic effect of NBL1, needs further investigation.
Hadron Masses in Strong Magnetic Fields
Creators: name: Taya, Hidetoshi
Publisher: name: arXiv
Year: 2014
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: Hadron masses under strong magnetic fields are studied. In the presence of strong magnetic fields exceeding the QCD energy scale $ eB \gg Λ^2_{\rm QCD} $, ${\rm SU(3)}_{\rm flavor} \otimes {\rm SU(2)}_{\rm spin}$ symmetry of hadrons is explicitly broken so that the quark components of hadrons differ from those with zero or weak magnetic fields $ eB \lesssim Λ^2_{\rm QCD} $. Also, squeezing of hadrons by strong magnetic fields affects the hadron mass spectrum. We develop a quark model which appropriately incorporates these features and analytically calculate various hadron masses including mesons, baryons and those with strangeness.
description: 5 pages, 3 figures, 1 table. v2: discussion and figure improved, references added, version to be published in PRD
Energy-constrained LOCC-assisted quantum capacity of bosonic dephasing channel
Creators: name: Arqand, Amir
name: Memarzadeh, Laleh
name: Mancini, Stefano
Publisher: name: arXiv
Year: 2021
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We study the LOCC-assisted quantum capacity of bosonic dephasing channel with energy constraint on input states. We start our analysis by focusing on the energy-constrained squashed entanglement of the channel, which is an upper bound for the energy-constrained LOCC-assisted quantum capacity. As computing energy-constrained squashed entanglement of the channel is challenging due to a double optimization (over the set of density matrices and the isometric extensions of a squashing channel), we first derive an upper bound for it, and then we discuss how tight that bound is for energy-constrained LOCC-assisted quantum capacity of bosonic dephasing channel. We prove that the optimal input state is diagonal in the Fock basis. Furthermore, we prove that for a generic channel, the optimal squashing channel belongs to the set of symmetric quantum Markov chain inducer (SQMCI) channels of the channel system-environment output, provided that such a set is non-empty. With supporting arguments, we conjecture that this is instead the case for the bosonic dephasing channel. Hence, for it we analyze two explicit examples of squashing channels which are not SQMCI, but are symmetric. Through them, we derive explicit upper and lower bounds for the energy-constrained LOCC-assisted quantum capacity of the bosonic dephasing channel in terms of its quantum capacity with different noise parameters. As the difference between upper and lower bounds is at most of the order $10^{-1}$, we conclude that the bounds are tight. Hence we provide a very good estimation of the LOCC-assisted quantum capacity of the bosonic dephasing channel.
Additional file 1 of Characterisation and analysis of key studies used to restrict substances under REACH
Creators: name: Borchert, Flora
name: Beronius, Anna
name: Ågerstrand, Marlene
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: 59999 Environmental Sciences not elsewhere classified
subject: FOS: Earth and related environmental sciences
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Science Policy

description: Additional file 1: Table S1. Rationales for exclusion from analysis of RAC opinions. Table S2. Description of the selected RAC opinions. Table S3. Characterisation of key studies and comparison to the REACH registration database. Additional results to section 3.2 Characterisation of the key studies used for restrictions.
IPBES Invasive Alien Species Assessment, data management report for Chapter 3. Section 3.2.2.1: Regional and national changes in human population density
Creators: name: Blanchard, Ryan
Publisher: name: Zenodo
Year: 2023
Subjects: Data management report

description: Review of literature for the section 3.2.2.1 Regional and national changes in human population density focusing on the role of human population density as a driver of biological invasions for chapter 3 of IPBES thematic assessment of invasive alien species and their control. The experts conducted a semi-systematic review to report on the existing knowledge on this driver. This included references provided by experts and a snowball process based on following the citation network of shortlisted papers. This resulted in the data used as evidence for the section.
Opposing action of the FLR-2 glycoprotein hormone and DRL-1/FLR-4 MAP kinases balance p38-mediated growth and lipid homeostasis in C. elegans
Creators: name: Dowen R.H.
name: Park A.Y.
name: Torzone S.K.
name: Cohen N.R.
name: Breen P.C.
Publisher: name: Public Library of Science
Year: 2023

description: AAUnim: Pallseainsetecgonrafitremdtheavteallolhpemadeinntgalleavenldsanruertreiptiroensaenl tseidgcnoarlrsebctelyfo: re committing crucial resources to growth and reproduction; however, the pathways that perceive and respond to these inputs remain poorly understood. Here, we demonstrate that DRL-1 and FLR-4, which share similarity with mammalian mitogen-activated protein kinases, maintain lipid homeostasis in the C. elegans intestine. DRL-1 and FLR-4 function in a protein complex at the plasma membrane to promote development, as mutations in drl-1 or flr-4 confer slow growth, small body size, and impaired lipid homeostasis. To identify factors that oppose DRL-1/FLR-4, we performed a forward genetic screen for suppressors of the drl-1 mutant phenotypes and identified mutations in flr-2 and fshr-1, which encode the orthologues of follicle stimulating hormone and its putative G protein-coupled receptor, respectively. In the absence of DRL-1/FLR-4, neuronal FLR-2 acts through intestinal FSHR-1 and protein kinase A signaling to restrict growth. Furthermore, we show that opposing signaling through DRL-1 and FLR-2 coordinates TIR-1 oligomerization, which modulates downstream p38/ PMK-1 activity, lipid homeostasis, and development. Finally, we identify a surprising noncanonical role for the developmental transcription factor PHA-4/FOXA in the intestine where it restricts growth in response to impaired DRL-1 signaling. Our work uncovers a complex multi-tissue signaling network that converges on p38 signaling to maintain homeostasis during development.
Joint Species Distribution Modeling of Percentage Cover Data with Exclusive Competition for Space
Creators: name: Kettunen, Juho
name: Mehtätalo, Lauri
name: Tuittila, Eeva-Stiina
name: Korrensalo, Aino
name: Vanhatalo, Jarno
Publisher: name: arXiv
Year: 2021
Subjects: subject: Applications (stat.AP)
subject: FOS: Computer and information sciences

description: Joint species distribution models (JSDM) are among the most important statistical tools in community ecology. They are routinely used for inference and various prediction tasks, such as to build species distribution maps or biomass estimation over spatial areas. Existing JSDM's cannot, however, model mutual exclusion between species, which may happen in some species groups, such as mosses in the bottom layer of a peatland site. We tackle this deficiency in the context of modeling plant percentage cover data, where mutual exclusion arises from limited growing space and competition for light. We propose a hierarchical JSDM where multivariate latent Gaussian variable model describes species' niche preferences and Dirichlet-Multinomial distribution models the observation process and exclusive competition for space between species. We use both stationary and non-stationary multivariate Gaussian processes to model residual phenomena. We also propose a decision theoretic model comparison and validation approach to assess the goodness of JSDMs in four different types of predictive tasks. We apply our models and methods to a case study on modeling vegetation cover in a boreal peatland. Our results show that ignoring the interspecific interactions and competition for space significantly reduces models' predictive performance and leads to biased estimates for total percentage cover both for individual species and over all species combined. A model's relative predictive performance also depends on the model comparison methods highlighting that model comparison and assessment should resemble the true predictive task. Our results also demonstrate that the proposed joint species distribution model can be used to simultaneously infer interspecific correlations in niche preference as well as mutual exclusive competition for space and through that provide novel insight into ecological research.
description: 55 pages
Chemical Drug Design
Creators: name: Janet Smith
Publisher: name: Zenodo
Year: 2024

description: Drug discovery and development are intricate processes that traditionally involve numerous costly and time-consuming experimental steps. AI has emerged as a game-changer in this domain, offering a suite of tools and techniques that can significantly expedite the drug design process while reducing costs and enhancing success rates. AI-aided drug design leverages machine learning algorithms, deep learning models, molecular simulations, and big data analytics to streamline various stages of drug discovery, from target identification to lead optimization and pharmacokinetics evaluation.
Additional file 1 of Pregnancy loss and the risk of rheumatoid arthritis in Chinese women: findings from the China Kadoorie biobank
Creators: name: Hee, Jia Yi
name: Huang, Sha
name: Leong, Khai Pang
name: Chun, Li
name: Zhang, Yuxun Oswald
name: Gongye, Ruofan
name: Tang, Kun
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Physiology
subject: Biotechnology
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: Cancer
subject: Science Policy

description: Additional file 1.
A Survey of Word Reordering in Statistical Machine Translation: Computational Models and Language Phenomena
Creators: name: Bisazza, Arianna
name: Federico, Marcello
Publisher: name: arXiv
Year: 2015
Subjects: subject: Computation and Language (cs.CL)
subject: FOS: Computer and information sciences

description: Word reordering is one of the most difficult aspects of statistical machine translation (SMT), and an important factor of its quality and efficiency. Despite the vast amount of research published to date, the interest of the community in this problem has not decreased, and no single method appears to be strongly dominant across language pairs. Instead, the choice of the optimal approach for a new translation task still seems to be mostly driven by empirical trials. To orientate the reader in this vast and complex research area, we present a comprehensive survey of word reordering viewed as a statistical modeling challenge and as a natural language phenomenon. The survey describes in detail how word reordering is modeled within different string-based and tree-based SMT frameworks and as a stand-alone task, including systematic overviews of the literature in advanced reordering modeling. We then question why some approaches are more successful than others in different language pairs. We argue that, besides measuring the amount of reordering, it is important to understand which kinds of reordering occur in a given language pair. To this end, we conduct a qualitative analysis of word reordering phenomena in a diverse sample of language pairs, based on a large collection of linguistic knowledge. Empirical results in the SMT literature are shown to support the hypothesis that a few linguistic facts can be very useful to anticipate the reordering characteristics of a language pair and to select the SMT framework that best suits them.
description: 44 pages, to appear in Computational Linguistics