cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Additional file 1 of Factors that influence mental health of university and college students in the UK: a systematic review
Creators: name: Campbell, Fiona
name: Blank, Lindsay
name: Cantrell, Anna
name: Baxter, Susan
name: Blackmore, Christopher
name: Dixon, Jan
name: Goyder, Elizabeth
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Science Policy
subject: 111714 Mental Health
subject: FOS: Health sciences

description: Additional file 1.
Encoding Event-Based Data With a Hybrid SNN Guided Variational Auto-encoder in Neuromorphic Hardware
Creators: name: Stewart, Kenneth
name: Danielescu, Andreea
name: Shea, Timothy
name: Neftci, Emre
Publisher: name: arXiv
Year: 2021
Subjects: subject: Neural and Evolutionary Computing (cs.NE)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Neuromorphic hardware equipped with learning capabilities can adapt to new, real-time data. While models of Spiking Neural Networks (SNNs) can now be trained using gradient descent to reach an accuracy comparable to equivalent conventional neural networks, such learning often relies on external labels. However, real-world data is unlabeled which can make supervised methods inapplicable. To solve this problem, we propose a Hybrid Guided Variational Autoencoder (VAE) which encodes event based data sensed by a Dynamic Vision Sensor (DVS) into a latent space representation using an SNN. These representations can be used as an embedding to measure data similarity and predict labels in real-world data. We show that the Hybrid Guided-VAE achieves 87% classification accuracy on the DVSGesture dataset and it can encode the sparse, noisy inputs into an interpretable latent space representation, visualized through T-SNE plots. We also implement the encoder component of the model on neuromorphic hardware and discuss the potential for our algorithm to enable real-time learning from real-world event data.
description: Published in NICE 2022
Additional file 1 of Ethnobotanical investigation of medicinal plants in Buska Mountain range, Hamar district, Southwestern Ethiopia
Creators: name: Bekele, Melese
name: Woldeyes, Feleke
name: Lulekal, Ermias
name: Bekele, Tamrat
name: Demissew, Sebsebe
Publisher: name: figshare
Year: 2022
Subjects: subject: Ecology
subject: FOS: Biological sciences
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: Science Policy
subject: Plant Biology

description: Additional file 1. Medicinal plants used for the treatment of human diseases. The file lists plant species used to treat human ailments, scientific and local name of plant species, plant part used, voucher number, methods of preparation and application.
Quantum walks and quantum search on graphene lattices
Creators: name: Foulger, Iain
name: Gnutzmann, Sven
name: Tanner, Gregor
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantum walks have been very successful in the development of search algorithms in quantum information, in particular in the development of spatial search algorithms. However, the construction of continuous-time quantum search algorithms in two-dimensional lattices has proved difficult, requiring additional degrees of freedom. Here, we demonstrate that continuous-time quantum walk search is possible in two-dimensions by changing the search topology to a graphene lattice, utilising the Dirac point in the energy spectrum. This is made possible by making a change to standard methods of marking a particular site in the lattice. Various ways of marking a site are shown to result in successful search protocols. We further establish that the search can be adapted to transfer probability amplitude across the lattice between specific lattice sites thus establishing a line of communication between these sites.
description: 16 pages, 15 figures
Architektonische Planungsprinzipien als Grundlage für eine holzbauadäquate Gebäudetechnik
Creators: name: Koppelhuber, Daniela
Publisher: name: Zenodo
Year: 2020
Subjects: BIGWOOD INTERREG
timber constructions
multi-storey timber buildings
BIM
Planung
susatinability

description: Architektonische Planungsprinzipien als Grundlage
 für eine holzbauadäquate Gebäudetechnik
58. Disease modifying anti-rheumatic drug (DMARD) therapy laboratory monitoring for toxicity in rheumatology patients
Creators: name: Raashid Luqmani1
name: Krystie Driver1
name: Escudero1, Alexa
name: Mirza1, Maria
name: Paddon1, Kevin
name: Shine1, Brian
name: Soni1, Anushka
Publisher: name: Zenodo
Year: 2022
Subjects: Vasculitis
ANCA
Abstracts
Giant Cell Arthritis
MPA
GPA
EGPA
Takayasu
IgA vasculitis

description: Background/ Objectives: Review of blood results for monitoring DMARDs is performed manually in our department and subject to human error with up to 200 starters per month. In the last 6 months at least 3 patients have had abnormalities which were missed, highlighting a significant clinical risk. The aim of the project was to develop, test and implement an automated algorithm to detect and act on significant blood abnormalities in patients starting DMARD therapy for a range of rheumatic diseases, including vasculitis. Methods: We created a system to automatically analyse laboratory results supplied by our laboratory according to threshold values recommended by the British Society for Rheumatology (BSR). We imported data into a specifically designed database to provide analyses based on BSR guidelines. The data are immediately ready for review by a clinician, grouped as: normal, mildly abnormal (exceeding the upper or lower limit of normal for our laboratory), missing (individual values not recorded), or abnormal (outside the threshold values advised by the BSR); records with consecutive results showing a trend towards abnormality are also recorded. The clinician has the responsibility to review all records and endorse them after taking appropriate action where required. Results: We tested the system on 2 cohorts of 100 and 227 sets of blood tests respectively and confirmed that it is more rapid and robust than a manual process. We compared each record with a manual evaluation of the data on a spreadsheet. We identified more abnormalities using the new system than were found on manual inspection (29% vs 10%, Chi square P<0.001). The manual inspection took 3 hours to prepare the data for evaluation; the new system performed the same task in under 1 minute. Table 1 shows the summary data for 100 test records, assessed manually and then using the algorithm, followed by real data using 1347 records from 395 patients initiating DMARDs (requiring action on 0.67% of all records: 2 missing results and 7 significantly abnormal results; in a further 7.4%, trending values were detected). Subsequent manual inspection of the test records defined as abnormal by the algorithm confirmed that the new system had correctly identified abnormalities in every case. Conclusions: We have developed a blood monitoring system for patients initiating DMARDs, capable of processing up to 10,000 results per session. The system is practical, more efficient, and more accurate than a manual process for DMARD monitoring for any patients receiving immunosuppressive therapies. Disclosures: None Table 1. Analysis of blood results
57. Drug Associated ANCA Vasculitis: A Single Center Experience
Creators: name: Jeyabalan1, Anushya
name: Pravarut Nithagon1
name: Zonozi1, Reza
name: Wallace2, Zach
name: Pendergraft3, William
name: Tillyer1, Emma
name: Laliberte1, Karen
name: Niles1, John
Publisher: name: Zenodo
Year: 2022
Subjects: Vasculitis
ANCA
Abstracts
Giant Cell Arthritis
MPA
GPA
EGPA
Takayasu
IgA vasculitis

description: Background/ Objectives: The trigger that induces antineutrophil cytoplasmic antibodies (ANCA) that lead to systemic vasculitis is largely unknown. Over the years, there have been associations noted between certain drugs and ANCA associated vasculitis; primarily hydralazine, propylthiouracil (PTU), methimazole, cocaine adulterated with levamisole, minocycline, and more recently, allopurinol. The aim of this study was to further elucidate the characteristics of the correlation between these drugs and detection of ANCA. Methods: We conducted a retrospective analysis of 3997 patients from 1989-2021 with a newly detected ANCA test for myeloperoxidase (MPO) and/or proteinase-3 (PR3) antibodies at the Massachusetts General Hospital (MGH) ANCA laboratory. For each new ANCA-positive patient, a limited discussion was held with the ordering clinician to review implications of the positive test and to identify exposure to any suspected culprit drugs at the time of positive ANCA test. Electronic medical records of cases managed at MGH were also reviewed. Results: Of the 3997 patients (mean age: 73 years, 60% female) with a newly positive ANCA test from 1989 to 2021, 434 patients (mean age: 68 years, 63% female) were found to have exposure to one or more culprit drugs prior to detection of ANCA, representing 11% of the total cohort. Hydralazine exposure was noted in 149/434 (34.3%) of patients, cocaine/levamisole exposure in 107/149 (24.7%) patients, with the remainder of patients with PTU (50/434, 11.5%), minocycline (46/434, 10.6%) and methimazole (14/434, 3.2%) exposure. We found 68 of 434 patients (15.7%) were treated with allopurinol prior to a positive ANCA test. MPO-ANCA positivity was a predominant feature in the drug-associated cohort, representing 378/434 (87%) of drug associated cases. The median MPO titer in the drug-associated cohort was 5 times higher compared to the median MPO titer of the total ANCA positive cohort. The median MPO titer of the hydralazine group was 15 times higher compared to the entire cohort. 34 of 59 patients (57.6%) with double positive MPO and PR3-ANCA had a culprit drug exposure prior to ANCA detection. Conclusions: The true prevalence of drug-associated cases is likely underrepresented as medication exposure at the time of a positive ANCA test were unknown in many cases. Our data suggest that patients with high MPO-ANCA titers and/or double positive MPO and PR3-ANCA should be investigated for any of these likely culprit drugs. Disclosures: None
Additional file 1 of Psychometric properties and measurement invariance of the Vaccination Attitudes Examination Scale (VAX) in a Spanish sample
Creators: name: Espejo, Begoña
name: Checa, Irene
name: Martín-Carbonell, Marta
Publisher: name: figshare
Year: 2022
Subjects: subject: Medicine
subject: Biotechnology
subject: Sociology
subject: FOS: Sociology
subject: Immunology
subject: FOS: Clinical medicine
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Science Policy

description: Additional file 1. Items of the Vaccine Attitudes Examination (VAX) scale in Spanish.
Adiabatic approximation for the motion of Ginzburg-Landau vortex filament
Creators: name: Zhang, Jingxuan
Publisher: name: arXiv
Year: 2021
Subjects: subject: Analysis of PDEs (math.AP)
subject: FOS: Mathematics
subject: 35Q55 (Primary) 37K40 (Secondary)

description: In this paper, we consider the concentration property of solutions to the dispersive Ginzburg-Landau (or Gross-Pitaevskii) equation in three dimensions. On a spatial domain, it has long been conjectured that such a solution concentrates near some curve evolving according to the binormal curvature flow, and conversely, that a curve moving this way can be realized in a suitable sense by some solution to the dispersive Ginzburg-Landau equation. Some partial results are known with rather strong symmetry assumptions. Our main theorems here provide affirmative answer to both conjectures under certain small curvature assumption. The results are valid for small but fixed material parameter in the equation, in contrast to the general practice to take this parameter to its zero limit. The advantage is that we can retain precise description of the vortex filament structure. The results hold on a long but finite time interval, depending on the curvature assumption.
description: 26 pp
ADBSat: Methodology of a novel panel method tool for aerodynamic analysis of satellites
Creators: name: Sinpetru, Luciana A.
name: Crisp, Nicholas H.
name: Mostaza-Prieto, David
name: Livadiotti, Sabrina
name: Roberts, Peter C. E.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Space Physics (physics.space-ph)
subject: FOS: Physical sciences

description: ADBSat is a novel software that determines the aerodynamic properties of any body in free-molecular flow. Its main advantage is the fast approximation of the aerodynamics of spacecraft in the lower end of the low-Earth orbit altitude range. It is a novel implementation of a panel method, where the body is represented as a set of fundamental elements and the sum of their individual aerodynamic properties makes up the properties of the whole. ADBSat's approach treats the shape as a set of flat triangular plates. These are read from a CAD geometry file in the Wavefront format, which can be created with most common CAD programs. A choice of gas-surface interaction models is available to represent the physics of free-molecular flow under different conditions. Its modular design means that other models can be easily and quickly implemented. It also benefits from a new shading algorithm for fast determination of elemental flow exposure. An example case is presented to show the capability and functionality of the program.
description: 30 pages, 9 figures. Submitted to Computer Physics Communications
Additional file 1 of De novo disruptive heterozygous MMP21 variants are potential predisposing genetic risk factors in Chinese Han heterotaxy children
Creators: name: Qin, Xi-ji
name: Xu, Meng-meng
name: Ye, Jia-jun
name: Niu, Yi-wei
name: Wu, Yu-rong
name: Xu, Rang
name: Li, Fen
name: Fu, Qi-hua
name: Chen, Sun
name: Sun, Kun
name: Xu, Yue-juan
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Table S1. Primers used for Sanger sequencing validation of MMP21 variants, mutagenesis of mutant MMP21 vectors, RT-qPCR, and construction of in situ hybridization probes.
55. The Birmingham Vasculitis Activity Score (BVAS) Ontology
Creators: name: Mcglinn1, Kris
name: Stephens1, Gaye
name: Raashid Luqmani2
name: Scott1, Jennifer
name: Hooshafza1, Sepideh
name: O'Sullivan1, Declan
Publisher: name: Zenodo
Year: 2022
Subjects: Vasculitis
ANCA
Abstracts
Giant Cell Arthritis
MPA
GPA
EGPA
Takayasu
IgA vasculitis

description: Background: The Birmingham Vasculitis Activity Score (BVAS) is a validated tool for assessment of disease activity in patients with different forms of vasculitis. It is used as an internationally recognised tool in vasculitis clinical trials, real world data collections, registries and in routine clinical practice. While BVAS is standardised, there is no standard approach to representing BVAS data within registries and currently no machine-readable digital description of the BVAS standard. The Web of Data is an initiative to make data open and interconnected, stored and shared across the World Wide Web using web technologies. An ontological description of BVAS, based on these technologies, will therefore serve two purposes. The first is to provide a structure for storing and publishing BVAS data in a way that can be queried over the web, thus supporting semantic interoperability between registries for the purpose of doing analysing federated data SNOMED-CT. Efforts are currently underway to make vasculitis registries across Europe and Australia interoperable and machine readable. These make it possible to add additional semantics using standard classifications, thereby allowing automated and standardised mapping of BVAS data to the pattern of organ involvement in patients with vasculitis. Methods: The ontology was developed using a standard methodology using freely available and open-source tools. In addition, a set of R2RML mappings have been developed for uplifting Anti-neutrophil cytoplasmic antibody (ANCA) associated vasculitis (AAV) BVAS data into Resource Description Framework (RDF), along with a set of samples SPARQL queries for querying this data. Conclusion: This ontology will support exposure of BVAS data in a machine readable and FAIR manner. Disclosure: None.
Knowledge Triggering, Extraction and Storage via Human-Robot Verbal Interaction
Creators: name: Grassi, Lucrezia
name: Recchiuto, Carmine Tommaso
name: Sgorbissa, Antonio
Publisher: name: arXiv
Year: 2021
Subjects: subject: Robotics (cs.RO)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: This article describes a novel approach to expand in run-time the knowledge base of an Artificial Conversational Agent. A technique for automatic knowledge extraction from the user's sentence and four methods to insert the new acquired concepts in the knowledge base have been developed and integrated into a system that has already been tested for knowledge-based conversation between a social humanoid robot and residents of care homes. The run-time addition of new knowledge allows overcoming some limitations that affect most robots and chatbots: the incapability of engaging the user for a long time due to the restricted number of conversation topics. The insertion in the knowledge base of new concepts recognized in the user's sentence is expected to result in a wider range of topics that can be covered during an interaction, making the conversation less repetitive. Two experiments are presented to assess the performance of the knowledge extraction technique, and the efficiency of the developed insertion methods when adding several concepts in the Ontology.
description: 19 pages, 7 figures, submitted to Robotics and Autonomous Systems
Identification-Detection Group Testing Protocols for COVID-19 at High Prevalence
Creators: name: Chiani, Marco
name: Liva, Gianluigi
name: Paolini, Enrico
Publisher: name: arXiv
Year: 2021
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Populations and Evolution (q-bio.PE)
subject: FOS: Physical sciences
subject: FOS: Biological sciences

description: Group testing allows saving chemical reagents, analysis time, and costs, by testing pools of samples instead of individual samples. We introduce a class of group testing protocols with small dilution, suited to operate even at high prevalence ($5\%-10\%$), and maximizing the fraction of samples classified positive/negative within the first round of tests. Precisely, if the tested group has exactly one positive sample then the protocols identify it without further individual tests. The protocols also detect the presence of two or more positives in the group, in which case a second round could be applied to identify the positive individuals. With a prevalence of $5\%$ and maximum dilution 6, with 100 tests we classify 242 individuals, $92\%$ of them in one round and $8\%$ requiring a second individual test. In comparison, the Dorfman's scheme can test 229 individuals with 100 tests, with a second round for $18.5\%$ of the individuals.
description: 11 pages, 4 figures
Glory is Back. Om den første tildelingen av den norske «Medaljen for edel dåd» til sovjetiske sjømenn
Creators: name: Petrov, Alexander
Publisher: name: figshare
Year: 2020
Subjects: subject: History
subject: 160607 International Relations
subject: FOS: Political science

description: En av de norske medaljene «For ædel daad» som ble tildelt en gruppe sjømenn fra Sovjetunionen i 1935, befinner seg i samlingen til Vladimir Galanov i den russiske byen Smolensk. Sjømenn fra Sovjetunionen ble tildelt slike medaljer i hvert fall tre ganger: i 1935 ble en gruppe på 9 sjømenn hedret, i 1939 ble 19 sjømenn tildelt medalje, og i 1977 fikk en sovjetisk sjømann medaljen. 
Avoiding bias when inferring race using name-based approaches
Creators: name: Kozlowski, Diego
name: Murray, Dakota S.
name: Bell, Alexis
name: Hulsey, Will
name: Larivière, Vincent
name: Monroe-White, Thema
name: Sugimoto, Cassidy R.
Publisher: name: arXiv
Year: 2021
Subjects: subject: Computers and Society (cs.CY)
subject: Information Retrieval (cs.IR)
subject: Physics and Society (physics.soc-ph)
subject: FOS: Computer and information sciences
subject: FOS: Physical sciences

description: Racial disparity in academia is a widely acknowledged problem. The quantitative understanding of racial based systemic inequalities is an important step towards a more equitable research system. However, because of the lack of robust information on authors' race, few large scale analyses have been performed on this topic. Algorithmic approaches offer one solution, using known information about authors, such as their names, to infer their perceived race. As with any other algorithm, the process of racial inference can generate biases if it is not carefully considered. The goal of this article is to assess the extent to which algorithmic bias is introduced using different approaches for name based racial inference. We use information from the U.S. Census and mortgage applications to infer the race of U.S. affiliated authors in the Web of Science. We estimate the effects of using given and family names, thresholds or continuous distributions, and imputation. Our results demonstrate that the validity of name based inference varies by race/ethnicity and that threshold approaches underestimate Black authors and overestimate White authors. We conclude with recommendations to avoid potential biases. This article lays the foundation for more systematic and less biased investigations into racial disparities in science.
Additional file 1 of Translation of a tissue epigenetic signature to circulating free DNA suggests BCAT1 as a potential noninvasive diagnostic biomarker for lung cancer
Creators: name: Palanca-Ballester, Cora
name: Hervas, David
name: Villalba, Maria
name: Valdes-Sanchez, Teresa
name: Garcia, Diana
name: Alcoriza-Balaguer, Maria Isabel
name: Benet, Marta
name: Martinez-Tomas, Raquel
name: Briones-Gomez, Andres
name: Galbis-Caravajal, Jose
name: Calvo, Alfonso
name: Juan, Oscar
name: Lahoz, Agustin
name: Cases, Enrique
name: Sandoval, Juan
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Table S1. Clinical diagnostic of samples.
56. Different epidemiologic profiles of systemic vasculitis between two referral centers from Brazil and Peru
Creators: name: De Souza1, Alexandre Wagner Silva
name: Zarur1, Eduarda
name: Victor R. Pimentel-Quiroz2, 3
name: Sanchez-Torres2, Alfredo
name: Manuel Ugarte-Gil2, 3
name: Sato1, Emília Inoue
Publisher: name: Zenodo
Year: 2022
Subjects: Vasculitis
ANCA
Abstracts
Giant Cell Arthritis
MPA
GPA
EGPA
Takayasu
IgA vasculitis

description: Background: Little is known about the epidemiologic features of systemic vasculitis in South American countries. This study aims to compare the prevalence of systemic vasculitides in two vasculitis referral centers from Brazil and Peru. Methods: This is a descriptive cross-sectional study performed in two vasculitis referral centers from Brazil and Peru. All patients above 18 years of age with at least 6 months of follow-up and who met classification or diagnosis criteria for the most common systemic vasculitides were included in the study. Demographic data were also collected. Results: A total of 562 patients with systemic vasculitis were analyzed, 345 (61.4%) of them from Brazil and 217 (38.6%) from Peru. The frequency of Behçet’s disease (37.9% vs. 1.8%; p < 0.0001), Takayasu arteritis (TAK) (25.2% vs. 6.9%; p < 0.0001), and giant cell arteritis (9.8% vs. 0.9%; p < 0.0001) was significantly higher in the Brazilian center compared to the Peruvian center. On the other hand, the frequency of microscopic polyangiitis (MPA) (67.3% vs. 2.8%; p < 0.0001) and renal-limited vasculitis (2.8% vs. 0.0%; p = 0.009) was significantly higher in the Peruvian center. No significant differences were found between both centers concerning granulomatosis with polyangiitis (GPA) (13.0% vs. 14.8%; p = 0.567), polyarteritis nodosa (4.0% vs. 1.8%; p = 0.146), cryoglobulinemic vasculitis (3.1% vs. 0.9%; p = 0.081), eosinophilic granulomatosis with polyangiitis (2.8% vs. 2.3%; p = 0.670), IgA vasculitis (0.5% vs. 0.0; p = 0.850) and urticarial vasculitis (0.2 vs. 0.5%; p = 0.740). At diagnosis, Brazilian patients with TAK, GPA and MPA were younger than Peruvian patients. No differences were found regarding the age at disease presentation for the other systemic vasculitides (Table 1). The female gender is predominant amongst patients with systemic vasculitis from both countries. Conclusions: Significant epidemiologic differences in the frequency of systemic vasculitis are observed between a vasculitis referral center from Brazil and from Peru. MPA is the most frequent vasculitis in the Peruvian center while BD and TAK are the most common forms of vasculitis in the Brazilian center. Further studies are needed to unravel if these differences are due to genetic and/or environmental factors. Disclosures: None. Table 1. Demographics features of vasculitis patients from Brazil and Peru.
Gauge Invariant 1PI Effective Superstring Field Theory: Inclusion of the Ramond Sector
Creators: name: Sen, Ashoke
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We construct off-shell amplitudes in heterotic and type II string theories involving arbitrary combination of Ramond and Neveu-Schwarz sector external states. We also construct the equations of motion of a gauge invariant 1PI effective field theory which reproduces these off-shell amplitudes. Using this construction we prove that the renormalized physical masses do not depend on the choice of local coordinate system and locations of picture changing operators used in defining the off-shell amplitudes. We also use this formalism to examine the conditions under which space-time supersymmetry is unbroken in the quantum theory.
description: LaTeX file, 35 pages; v2: minor additions
54. FAIRVASC: A semantic web approach to rare disease registry integration
Creators: name: Mcglinn1, Kris
name: Rutherford2, Matthew
name: Gisslander3, Karl
name: Hederman1, Lucy
name: Little1, Mark A.
name: O'Sullivan1, Declan
Publisher: name: Zenodo
Year: 2022
Subjects: Vasculitis
ANCA
Abstracts
Giant Cell Arthritis
MPA
GPA
EGPA
Takayasu
IgA vasculitis

description: Background: Rare disease data is often fragmented within multiple heterogeneous siloed regional disease registries, each containing a small number of cases. These data are particularly sensitive, as low subject counts make the identification of patients more likely, meaning registries are not inclined to share subject level data outside their registries. At the same time access to multiple rare disease datasets is important as it will lead to new research opportunities and analysis over larger cohorts. Methods: To enable this, two major challenges must therefore be overcome. The first is to integrate data at a semantic level, so that it is possible to query over registries and return results which are comparable. The second is to enable queries which do not take subject level data from the registries. Results: To meet the first challenge, this paper we present the FAIRVASC ontology to manage data related to the rare disease anti-neutrophil cytoplasmic antibody (ANCA) associated vasculitis (AAV), which is based on the harmonisation of terms in seven European data registries. It has been built upon a set of key clinical questions developed by a team of experts in vasculitis selected from the registry sites and makes use of several standard classifications, such as Systematized Nomenclature of Medicine - Clinical Terms (SNOMED-CT) and Orphacode. It also presents the method for adding semantic meaning to AAV data across the registries using the declarative Relational to Resource Description Framework Mapping Language (R2RML). To meet the second challenge, a federated querying approach is presented for accessing aggregated and pseudonymized data, and which supports analysis of AAV data in a manner that protects patient privacy. For additional security, the federated querying approach is augmented with a method for auditing queries (and the uplift process) using the provenance ontology (PROV-O) to track when queries and changes occur and by whom. Conclusions: The main contribution of this work is the successful application of semantic web technologies and federated queries to provide a novel infrastructure that can readily incorporate additional registries, thus providing simultaneous access to harmonised data relating to unprecedented numbers of patients with rare disease from nearly 10,000 patients with vasculitis, while also meeting data privacy and security concerns. Disclosures: None
Additional file 2 of Translation of a tissue epigenetic signature to circulating free DNA suggests BCAT1 as a potential noninvasive diagnostic biomarker for lung cancer
Creators: name: Palanca-Ballester, Cora
name: Hervas, David
name: Villalba, Maria
name: Valdes-Sanchez, Teresa
name: Garcia, Diana
name: Alcoriza-Balaguer, Maria Isabel
name: Benet, Marta
name: Martinez-Tomas, Raquel
name: Briones-Gomez, Andres
name: Galbis-Caravajal, Jose
name: Calvo, Alfonso
name: Juan, Oscar
name: Lahoz, Agustin
name: Cases, Enrique
name: Sandoval, Juan
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Table S2. Assays primers and conditions.
Semiclassical and quantum features of the Bianchi I cosmology in the polymer representation
Creators: name: Giovannetti, E.
name: Montani, G.
name: Schiattarella, S.
Publisher: name: arXiv
Year: 2021
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We analyze the Bianchi I cosmology in the presence of a massless scalar field and describe its dynamics via a semiclassical and quantum polymer approach. We study the morphology of the Big Bounce by adopting three different sets of configurational variables: the Ashtekar connections, a set of anisotropic volume-like coordinates and the Universe volume plus two anisotropy coordinates (the latter two sets of variables would coincide in the case of an isotropic Universe). In the semiclassical analysis we demonstrate that the value of the critical matter energy density depends on the Cauchy problem for the dynamics when adopting the Ashtekar connections or the anisotropic volume-like coordinates. On the contrary, when the Universe volume is considered as a configurational coordinate, we are able to derive a polymer-modified Friedmann equation for the Bianchi I model, from which the expression of the critical energy density can be derived. This analysis shows that the Big Bounce has universal features only when the Universe volume is defined on the polymer lattice. Then, a cosmological constant is included in the Ashtekar connections' formulation and some interesting results are mentioned making a comparison between the synchronous dynamics and that one when the scalar field is taken as a relational time. From a pure quantum point of view, we investigate the Bianchi I dynamics in terms of the Ashtekar connections. We apply the ADM reduction of the variational principle and then we quantize the system. We study the resulting Schrödinger dynamics, stressing that the behavior of the wave packet peak over time singles out common features with the semiclassical trajectories, confirming the non-universal character of the emerging Big Bounce also on a quantum level.
Efficient Rotation-Scaling-Translation Parameters Estimation Based on Fractal Image Model
Creators: name: Uss, M.
name: Vozel, B.
name: Lukin, V.
name: Chehdi, K.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Computer and information sciences

description: This paper deals with area-based subpixel image registration under rotation-isometric scaling-translation transformation hypothesis. Our approach is based on a parametrical modeling of geometrically transformed textural image fragments and maximum likelihood estimation of transformation vector between them. Due to the parametrical approach based on the fractional Brownian motion modeling of the local fragments texture, the proposed estimator MLfBm (ML stands for "Maximum Likelihood" and fBm for "Fractal Brownian motion") has the ability to better adapt to real image texture content compared to other methods relying on universal similarity measures like mutual information or normalized correlation. The main benefits are observed when assumptions underlying the fBm model are fully satisfied, e.g. for isotropic normally distributed textures with stationary increments. Experiments on both simulated and real images and for high and weak correlation between registered images show that the MLfBm estimator offers significant improvement compared to other state-of-the-art methods. It reduces translation vector, rotation angle and scaling factor estimation errors by a factor of about 1.75...2 and it decreases probability of false match by up to 5 times. Besides, an accurate confidence interval for MLfBm estimates can be obtained from the Cramer-Rao lower bound on rotation-scaling-translation parameters estimation error. This bound depends on texture roughness, noise level in reference and template images, correlation between these images and geometrical transformation parameters.
description: 42 pages, 8 figures, 7 tables. Journal paper
Synthesis and phtoluminescence [sic] study of microporous metal organic frameworks (MMOFs) for sensing and detection of nitroexplosives and aromatic compounds
Creators: name: Pramanik, Sanhita
Publisher: name: No Publisher Supplied
Year: 2011

description: Due to the increased terrorist activity worldwide and the use of modern bombs in those attacks, the development of a new method capable of rapidly and cost-efficiently detecting trace vapor of explosives is highly desirable. Chemical explosives composed of a diverse group of compounds, including nitroaromatics, nitramines, nitrate esters as well as some inorganic/organic nitrates and peroxides. Current methodologies include use of well trained dogs and sophisticated instrumentation such as gas chromatography coupled with a mass spectrometer, nuclear quadruple resonance, ionization mass spectrometry (IMS). These methods are highly sensitive and selective, but often expensive, not always easily accessible, and require intense training for operation. As a complementary method, chemical sensors can provide new ways to the rapid detection of ultra trace explosives, and can be easily incorporated into inexpensive and portable microelectronic devices. Fluorescence based sensors utilizing conjugated polymers have attracted enormous attention in the recent years for their excellent performance. In this thesis, a systematic study was performed in a series of luminescent MMOFs and their behavior upon exposure to the vapor of different analytes. For example, [Zn2(oba)2(bpy)]∙DMA, one of the MMOFs made of paddle-wheel SBU, selectively responds to nitroaromatics (with electron-withdrawing groups) and other aromatic compounds, like benzene, toluene (with electron-donating groups) via fluorescent quenching and enhancement respectively. The study also shows that nitro-containing non-aromatic analytes (nitroaliphatics) make negligible effect on the fluorescence of [Zn2(oba)2(bpy)]∙DMA . The results demonstrate the exceptional ability of this particular MMOF to selectively detect explosives of different types (e.g. aromatic DNT vs. non-aromatic or aliphatic DMNB). Another series of highly luminescent MMOFs made of the same metal center (Zn) and similar ligands (bpdc, bpy, 2,2′dmbpy and bpe) but different structures have also been investigated. Photoluminescence studies show that the guest-free samples of these compounds also exhibit quenching or enhancement phenomena, when exposed to the vapors of two different types of analyte molecules having electron rich and electron deficient functional groups. The origin of such effect can be well understood and explained based on molecular orbital and band structure calculations, as well as the comparison of their redox potentials. In addition, synthesis and characterization of some new MMOFs, composed of V-shaped dicarboxylic acid and selected diamine ligands are briefly discussed. Clearly, ligands play an important role in the crystal structure formation as well as pore characteristics of the resultant MMOFs.
Observed versus Simulated Halo c-Mvir Relations
Creators: name: Leier, Dominik
name: Ferreras, Ignacio
name: Negri, Andrea
name: Saha, Prasenjit
Publisher: name: arXiv
Year: 2021
Subjects: subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The concentration - virial mass relation is a well-defined trend that reflects the formation of structure in an expanding Universe. Numerical simulations reveal a marked correlation that depends on the collapse time of dark matter halos and their subsequent assembly history. However, observational constraints are mostly limited to the massive end via X-ray emission of the hot diffuse gas in clusters. An alternative approach, based on gravitational lensing over galaxy scales, revealed an intriguingly high concentration at Milky Way-sized halos. This letter focuses on the robustness of these results by adopting a bootstrapping approach that combines stellar and lensing mass profiles. We also apply the identical methodology to simulated halos from EAGLE to assess any systematic. We bypass several shortcomings of ensemble type lens reconstruction and conclude that the mismatch between observed and simulated concentration-to-virial-mass relations are robust, and need to be explained either invoking a lensing-related sample selection bias, or a careful investigation of the evolution of concentration with assembly history. For reference, at a halo mass of $10^{12} M_\odot$, the concentration of observed lenses is $c_{12}\sim 40\pm 5$, whereas simulations give $c_{12}\sim 15\pm1$.
description: 5 pages, 3 figures, 2 tables, accepted for publication in MNRAS Letters
A quantum dimer model for the pseudogap metal
Creators: name: Punk, Matthias
name: Allais, Andrea
name: Sachdev, Subir
Publisher: name: arXiv
Year: 2015
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We propose a quantum dimer model for the metallic state of the hole-doped cuprates at low hole density, $p$. The Hilbert space is spanned by spinless, neutral, bosonic dimers and spin $S=1/2$, charge $+e$ fermionic dimers. The model realizes a `fractionalized Fermi liquid' with no symmetry-breaking and small hole pocket Fermi surfaces enclosing a total area determined by $p$. Exact diagonalization, on lattices of sizes up to $8 \times 8$, shows anisotropic quasiparticle residue around the pocket Fermi surfaces. We discuss the relationship to experiments.
description: 9+10 pages, 17 figures
Project of the underwater system for chemical threat detection
Creators: name: Silarski, M.
name: Hunik, D.
name: Moskal, P.
name: Smolis, M.
name: Tadeja, S.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: In this article we describe a novel method for the detection of explosives and other hazardous substances in the marine environment using neutron activation. Unlike the other considered methods based on this technique we propose to use guides forneutron and gamma quanta which speeds up and simplifies identification. Moreover, it may provide a determination of the density distribution of a dangerous substance. First preliminary results of Monte Carlo simulations dedicated for design of a device exploiting this method are also presented.
description: 9 pages, 6 figures
D3.2 The SENTINEL digital core: Full-featured version
Creators: name: Bouklas, Kostas
name: Tsantekidis, Marinos
name: Karantjias Thanos
name: Poulios, Konstantinos
Publisher: name: Zenodo
Year: 2022
Subjects: sentinelh2020
euprojects
compliance
smes
dataprotection
security
deliverables
platform

description: This deliverable accompanies the first version of the SENTINEL integrated platform. Continuing the work from the MVP reported during the M12 technical review and following the same methodology (i.e., the Lean start-up methodology), the SENTINEL project aims to present the first integrated platform with close to final functionality on module level and system level without excluding further functionalities being added in the rest of the projects duration. This deliverable has been developed within the scope of ‘WP3 – The SENTINEL digital core’, under Grant Agreement No. 101021659.
31. Frequency of Immune Checkpoint Inhibitor-Induced Polymyalgia Rheumatica
Creators: name: Kato1, Koki
name: Mizuno1, Tomohiro
name: Takenao Koseki1
name: Ito1, Yoshimasa
name: Takahashi1, Kazuo
name: Naotake Tsuboi1
name: Yamada1, Shigeki
Publisher: name: Zenodo
Year: 2022
Subjects: Vasculitis
ANCA
Abstracts
Giant Cell Arthritis
MPA
GPA
EGPA
Takayasu
IgA vasculitis

description: Background: Immune checkpoint inhibitors (ICPIs) induce immune-related adverse events (irAEs) such as skin disorders, gastrointestinal disorders, thyroid dysfunction, type 1 diabetes mellitus, lupus nephritis, and vasculitides. Information on ICPIs-induced vasculitides is limited, and predictors for this condition have not been identified. Therefore, we have examined the frequency of immune checkpoint inhibitor-induced vasculitides by analyzing the data recorded in the Japanese Adverse Drug Event Report (JADER). Methods: Data from April 2004 to March 2020 were extracted from JADER database, and vasculitides as an immune-related adverse event was defined according to the 2012 revised International Chapel Hill Consensus Conference Nomenclature of Vasculitides. The reporting odds ratio (ROR), which evaluates the AE signals according to previous reports. Adverse event signals were recognized as significant when the ROR estimates and lower limits of the corresponding 95% confidence intervals exceeded 1. Results: The use of nivolumab showed a significant signal for vasculitides. Furthermore, significant signals of Polymyalgia rheumatica (PMR) were detected in the patients treated with nivolumab, pembrolizumab, and ipilimumab. In addition, the frequencies of nivolumab- and pembrolizumab-induced PMR were higher in patients aged ≥70 years and female patients, respectively. PMR was reported in 38 patients treated with nivolumab; 31 (82%) of these were either in recovery or in remission. Further, PMR was reported in 17 patients treated with pembrolizumab; 13 (76%) of these were in recovery or remission, while three (18%) were not. PMR was reported in 12 patients treated with ipilimumab; seven (58%) of these were in recovery or remission. Conclusions: Careful monitoring for PMR is required when the patients are aged > 70 years and have been treated with nivolumab and when the patients are women and have been treated with pembrolizumab. Disclosures: None.
Additional file 1 of Exploring optimal Taxol® CYP725A4 activity in Saccharomyces cerevisiae
Creators: name: Nowrouzi, Behnaz
name: Lungang, Liang
name: Rios-Solis, Leonardo
Publisher: name: figshare
Year: 2022
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: Inorganic Chemistry

description: Additional file 1: Table S1. Schematic representation of strains in this study. Table S2. List of primers used in the study. Table S3. Sequence of genes in this study. Table S4. List of guide RNA sequences used in this study. Table S5. List of linkers used in this study. Table S6. Augmented definitive screening designs for optimising P450-reductase expressions, including controls. Table S7. Linear model formulas for response factors in definitive screening designs. Figure S1. The messy chromatogram from 2 mL of LRS6 strain culture in polypropylene-made deepwell microplates. Figure S2. Representative chromatograms of gene dosage study. Figure S3. Representative mass spectrum for LRS6 strain cultivated in shake flask. Figure S4. Representative chromatograms of the strains expressing self-sufficient CYP725A4, CYP725A4 only and parent taxadiene-producing LRS5, all cultivated in 5 mL of YPG in 10 mL glass tubes. Figure S5. Representative chromatograms for BN6, expressing Taxus CYP725A4 and POR in tandem, in different culture media. Figure S6. Marginal model plots for design of experiment (DoE) study for all predictors (Flavin Adenine Dinucleotide (FAD), Flavin Mononucleotide (FMN), Riboflavin, Hemin and δ-Aminolevulinic acid (ALA)) and their interactions on: Figure S7. DoE study results according to run number. Figure S8. Preliminary resting cell assay to test the effect of acid–base on side-product (OCT+ iso-OCT) to main product (T5α-ol) ratio. Figure S9. Representative chromatograms for the resting cell assays. Figure S10. Representative chromatograms for the resting cell assays with extracted ion of 288 m/z for confirming the identified diterpenoids. Figure S11. Representative mass spectra from resting cell assay experiment. Figure S12. Representative mass spectra from resting cell assay experiment.
بررسی و ساخت هیدروژل برمبنای ژلاتین و موسیلاژ بارهنگ شهری به روش کوآسرواسیون مرکب
Creators: name: سعید حمدی پور
name: میرخلیل پیروزی فرد
name: حامد همیشه کار
name: هادی الماسی
Publisher: name: figshare
Year: 2019
Subjects: subject: 30199 Analytical Chemistry not elsewhere classified
subject: FOS: Chemical sciences

description: هدف از این مطالعه بررسی امکان تشکیل کمپلکس توده ی مرکب بین ژلاتین و موسیلاژ بارهنگ شهری و بهینه سازی این کمپلکس در پی اچ و نسبت های مختلف پروتئین - پلی ساکارید است. در این تحقیق نسبت پروتئین به پلی ساکارید از 10 تا 90 و 90 تا 10و پی اچ از 2 تا 8 مورد ارزیابی قرار گرفت. کمپلکس تشکیل و آنالیزهای پتانسیل زتا، طیف سنجی تبدیل فوریه مادون قرمز، تعیین کدورت محلول و راندمان برای تایید تشکیل توده ی مرکب اندازه گیری شد در پی اچ کمتر از 5 تشکیل واکنش های الکترواستاتیک بدلیل بار مثبت پروتئین و بار منفی موسیلاژ امکانپذیر است. نتایج نشان میدهد با توجه به راندمان توده ی مرکب و کدورت محلول، شرایط بهینه تشکیل کمپلکس در نسبت 40 به 60 ژلاتین - موسیلاژ و پی اچ 3.55 میباشد. همچنین بررسی طیف تبدیل فوریه مادون قرمز و جا به جایی نوار جذبی مربوط به گروه های او اچ منفی و حذف نوارهای جذبی طیف شاخص ژلاتین و موسیلاژ در کمپلکس توده ی مرکب نیز دلیل دیگری برای تشکیل توده ی مرکب ژلاتین - موسیلاژ بود. از هیدروژل حاصل می توان در ریزپوشینه کردن ترکبات حساس مواد غذایی و دارویی و همچنین کنترل رهایش آنها استفاده کرد
Measuring Exciton Fine-Structure in Perovskite Nanocrystal Ensembles
Creators: name: Liu, Albert
Publisher: name: arXiv
Year: 2021
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Lead-halide perovskite nanocrystals (PNCs) exhibit unique optoelectronic properties, many of which originate from a purported bright-triplet exciton fine-structure. A major impediment to measuring this fine-structure is inhomogeneous spectral broadening, which has limited most experimental studies to single-nanocrystal spectroscopies. It is shown here that the linearly-polarized single-particle selection rules in PNCs are preserved in nonlinear spectroscopies of randomly-oriented ensembles. Simulations incorporating rotational-averaging demonstrate that techniques such as transient absorption and two-dimensional coherent spectroscopy are capable of resolving exciton fine-structure in PNCs, even in the presence of inhomogeneous broadening and orientation disorder.