cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Recent urbanization in China is correlated with a Westernized microbiome encoding increased virulence and antibiotic resistance genes
Creators: name: Howard, Annie Green
name: Gordon-Larsen, Penny
Publisher: name: BioMed Central
Year: 2017

description: Abstract Background Urbanization is associated with an increased risk for a number of diseases, including obesity, diabetes, and cancer, which all also show associations with the microbiome. While microbial community composition has been shown to vary across continents and in traditional versus Westernized societies, few studies have examined urban-rural differences in neighboring communities within a single country undergoing rapid urbanization. In this study, we compared the gut microbiome, plasma metabolome, dietary habits, and health biomarkers of rural and urban people from a single Chinese province. Results We identified significant differences in the microbiota and microbiota-related plasma metabolites in rural versus recently urban subjects from the Hunan province of China. Microbes with higher relative abundance in Chinese urban samples have been associated with disease in other studies and were substantially more prevalent in the Human Microbiome Project cohort of American subjects. Furthermore, using whole metagenome sequencing, we found that urbanization was associated with a loss of microbial diversity and changes in the relative abundances of Viruses, Archaea, and Bacteria. Gene diversity, however, increased with urbanization, along with the proportion of reads associated with antibiotic resistance and virulence, which were strongly correlated with the presence of Escherichia and Shigella. Conclusions Our data suggest that urbanization has produced convergent evolution of the gut microbial composition in American and urban Chinese populations, resulting in similar compositional patterns of abundant microbes through similar lifestyles on different continents, including a loss of potentially beneficial bacteria and an increase in potentially harmful genes via increased relative abundance of Escherichia and Shigella.
Atelier 1 : Ouvre ta recherche
Creators: name: AZILAN, Innocent
Publisher: name: Zenodo
Year: 2023
Subjects: Open Science
Open Access
Togo
Ouvre Ta Recherche

description: Cet atelier (le premier) s'inscrit dans une série de 3 ateliers "Ouvre Ta Recherche", animé par le doctorant Innocent AZILAN, à l'endroit des doctorants, masterants et nouveaux chercheurs de l'Université de Lomé. Ces ateliers portent sur plusieurs thématiques, dont la documentation, la publicisation de la recherche, l'ouverture de la recherche et l'invisibilité des productions scientifiques à l'Université de Lomé.
title: Arbre_8
Creators: name: Clemence OBERHAUSER
name: Galinand, Cyrille
name: Université Paris1 Panthéon-Sorbonne
Publisher: name: Archeovision
Year: 2023
Subjects: subject: arborglyphe

description: arborglyphe
description: 1 fichier 3D (ply), 1 fichier image (jpg)
FMLRC: Hybrid long read error correction using an FM-index
Creators: name: Wang, Jeremy R
name: McMillan, Leonard
name: Holt, James
name: Jones, Corbin
Publisher: name: BioMed Central
Year: 2018

description: Abstract Background Long read sequencing is changing the landscape of genomic research, especially de novo assembly. Despite the high error rate inherent to long read technologies, increased read lengths dramatically improve the continuity and accuracy of genome assemblies. However, the cost and throughput of these technologies limits their application to complex genomes. One solution is to decrease the cost and time to assemble novel genomes by leveraging “hybrid” assemblies that use long reads for scaffolding and short reads for accuracy. Results We describe a novel method leveraging a multi-string Burrows-Wheeler Transform with auxiliary FM-index to correct errors in long read sequences using a set of complementary short reads. We demonstrate that our method efficiently produces significantly more high quality corrected sequence than existing hybrid error-correction methods. We also show that our method produces more contiguous assemblies, in many cases, than existing state-of-the-art hybrid and long-read only de novo assembly methods. Conclusion Our method accurately corrects long read sequence data using complementary short reads. We demonstrate higher total throughput of corrected long reads and a corresponding increase in contiguity of the resulting de novo assemblies. Improved throughput and computational efficiency than existing methods will help better economically utilize emerging long read sequencing technologies.
title: Investigation of the Apparent Diffusion Coefficient and Diffusion Kurtosis Image Distortion using Readout Segmented Echo Planar Imaging
Creators: name: Iwase, Daisuke
Publisher: name: European Congress of Radiology
Year: 2015
Subjects: subject: Head and neck
subject: MR-Diffusion/Perfusion
subject: Imaging sequences
subject: Image verification

description: Aims and objectives Methods and materials Results Conclusion Personal information References
description: Aims and objectives: Conventional diffusion-weighted images (DWIs) are obtained with the assumption that water molecules follow a Gaussian distribution. However, most water molecules in vivo follow a non-Gaussian distribution. Q-space imaging (QSI) analysis is a method...
title: Echogenic Breast Lesions: Always Benign?
Creators: name: Uceda, David
Publisher: name: European Congress of Radiology
Year: 2015
Subjects: subject: Neoplasia
subject: Haemorrhage
subject: Abscess
subject: Outcomes analysis
subject: Biopsy
subject: Ultrasound
subject: Management
subject: Breast

description: Learning objectives Background Findings and procedure details Conclusion Personal information References
description: Learning objectives: To analyze the clinical and radiological findings of echogenic breast lesions and its malignancy or benignity which were proved by biopsy in suspicious cases or with radiological follow-up in the remaining...
Quantum Electrodynamics is Crucial for Plasmonic Resonance of Metallic Nanostructures
Creators: name: Zhang, Mingliang
name: Xiang, Hongping
name: Zhang, Xu
name: Lu, Gang
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Plasmonic resonance of a metallic nanostructure results from coherent motion of its conduction electrons driven by incident light. At the resonance, the induced dipole in the nanostructure is proportional to the number of the conduction electrons, hence $10^{7}$ times larger than that in an atom. The interaction energy between the induced dipole and fluctuating virtual field of the incident light can reach a few tenths of an eV. Therefore, the classical electromagnetism dominating the field becomes inadequate. We argue that quantum electrodynamics (QED) should be used instead as the fundamental theory to describe the virtual field and its interaction with the electrons. Based on QED, we derive analytic expressions for the plasmonic resonant frequency, which depends on three easily accessible material parameters. The analytic theory reproduces very well the experimental data, and can be used for rational design of materials.
description: 6 pages, 4 figures
Pinned vortex hopping in a neutron star crust
Creators: name: Haskell, Brynmor
name: Melatos, Andrew
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: The motion of superfluid vortices in a neutron star crust is at the heart of most theories of pulsar glitches. Pinning of vortices to ions can decouple the superfluid from the crust and create a reservoir of angular momentum. Sudden large scale unpinning can lead to an observable glitch. In this paper we investigate the scattering of a free vortex off a pinning potential and calculate its mean free path, in order to assess whether unpinned vortices can skip multiple pinning sites and come close enough to their neighbours to trigger avalanches, or whether they simply hop from one pinning site to another giving rise to a more gradual creep. We find that there is a significant range of parameter space in which avalanches can be triggered, thus supporting the hypothesis that they may lie at the origin of pulsar glitches. For realistic values of the pinning force and superfluid drag parameters we find that avalanches are more likely in the higher density regions of the crust where pinning is stronger. Physical differences in stellar parameters, such as mass and temperature, may lead to a switch between creep-like motion and avalanches, explaining the different characteristics of glitching pulsars.
description: Submitted to MNRAS
Learning Structured Neural Semantic Parsers
Creators: name: Yin, Pengcheng
Publisher: name: Carnegie Mellon University
Year: 2023
Subjects: Natural Language Processing

description: Semantic parsing, the task of translating user-issued natural language (NL) utterances (e.g., Flights from Pittsburgh to New York) into formal meaning representations (MRs, e.g., an SQL database query or a Python program), has become an important direction in developing natural language interfaces to computational systems. Recent years have witnessed the burgeoning of applying neural network-based semantic parsers in various tasks and domains. However, meaning representations typically exhibit strong syntactic structure, and are defined following domain-specific structured knowledge schemas (e.g., a database schema or Python API specification), which is not easily captured by standard neural sequence transduction models. Neural semantic parsers are also data-hungry, requiring non-trivial manual annotation effort by domain experts. These issues limit the scope of applications supported by a neural semantic parser, impeding the progress of applying the system to broader scenarios, especially those with diverse and complex structure of meaning representations. In this thesis, we explore developing neural semantic parsing models that could better capture the structure in various types of logical formalisms and knowledge schemas, while providing approaches to mitigate the cost of labeled data acquisition. The dissertation consists of three parts. The first part introduces a general-purpose parsing model with built-in syntactic knowledge of the grammatical structure of meaning representations. Next, in the second part, we investigate approaches to encode structured information in domain knowledge schemas (e.g., database tables) useful to understand user-issued utterances. Specifically, we focus on grounding elements in the schema (e.g., columns like departure_city in database tables, or functions like GetFlight(from=GetCityByName(·)) in API specifications) to their corresponding NL constituents (e.g., from Pittsburgh) in utterances. Finally, in the third part, we aim to improve the data efficiency of semantic parsers via semisupervised learning, while developing machine-assisted approaches to accelerate training data acquisition.
Drivers and actions that determine the choice of young farmers in Costa Rica to stay on the family farm
Creators: name: Rodriguez-Lizano, Victor
name: Montero-Vega, Mercedes
name: Sibelet, Nicole
Publisher: name: The International Journal of Sociology of Agriculture and Food
Year: 2022

description: Succession is essential for the existence and development of family farms and rural areas; however, the generalized aging of farmers is occurring worldwide. The main objective of this research is to analyse the motivations that determine young farmers’ choice to remain on the family farm, and their relation to the Generational Integration Process. Traditionally, succession analysis focuses on how socioeconomic conditions influence the probability of a farm being successfully passed on to the following generation. Other approaches focus on the Generational Integration Process (GIP), which is the ability of distinct generations to relate as a family, with the goal of passing on the farm through specific actions involving the participation of both successors and incumbent. The field work was carried out in Zarcero, a horticultural canton in Costa Rica, where 20 semi-structured interviews were conducted with young famers (under the age of 35). Results indicate that the main reasons for staying on the family farm are related to self-management, a feeling of belonging, and family ties. This study generated a tentative framework to consistently analyse the Generational Integration Process and shows the complex nature of family farm succession by highlighting the multiple links between different motivations.
description: The International Journal of Sociology of Agriculture and Food, Vol. 28 No. 2 (2022): Regular Issue
Hypergeometric $τ$ Functions of the $q$-Painlevé Systems of Types $A_4^{(1)}$ and $(A_1+A_1')^{(1)}$
Creators: name: Nakazono, Nobutaka
Publisher: name: arXiv
Year: 2016
Subjects: subject: Exactly Solvable and Integrable Systems (nlin.SI)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences

description: We consider $q$-Painlevé equations arising from birational representations of the extended affine Weyl groups of $A_4^{(1)}$- and $(A_1+A_1)^{(1)}$-types. We study their hypergeometric solutions on the level of $τ$ functions.
title: Part I - Revising the sellar and parasellar region: normal anatomy
Creators: name: Oliveira, Carlos Miguel
Publisher: name: European Congress of Radiology
Year: 2015
Subjects: subject: Neuroradiology brain
subject: Anatomy
subject: CT
subject: MR
subject: Diagnostic procedure
subject: Normal variants
subject: Congenital
subject: Pathology

description: Learning objectives Background Findings and procedure details Conclusion Personal information References
description: Learning objectives: Our objective is to provide an insight of the sellar and parasellar regions normal anatomy, on both CT and...
β2-adrenoceptor signaling regulates invadopodia formation to enhance tumor cell invasion
Creators: name: Bear, James
name: Chan, Keefe T
Publisher: name: BioMed Central
Year: 2015

description: Abstract Introduction For efficient metastatic dissemination, tumor cells form invadopodia to degrade and move through three-dimensional extracellular matrix. However, little is known about the conditions that favor invadopodia formation. Here, we investigated the effect of β-adrenoceptor signaling - which allows cells to respond to stress neurotransmitters - on the formation of invadopodia and examined the effect on tumor cell invasion. Methods To characterize the molecular and cellular mechanisms of β-adrenergic signaling on the invasive properties of breast cancer cells, we used functional cellular assays to quantify invadopodia formation and to evaluate cell invasion in two-dimensional and three-dimensional environments. The functional significance of β-adrenergic regulation of invadopodia was investigated in an orthotopic mouse model of spontaneous breast cancer metastasis. Results β-adrenoceptor activation increased the frequency of invadopodia-positive tumor cells and the number of invadopodia per cell. The effects were selectively mediated by the β2-adrenoceptor subtype, which signaled through the canonical Src pathway to regulate invadopodia formation. Increased invadopodia occurred at the expense of focal adhesion formation, resulting in a switch to increased tumor cell invasion through three-dimensional extracellular matrix. β2-adrenoceptor signaling increased invasion of tumor cells from explanted primary tumors through surrounding extracellular matrix, suggesting a possible mechanism for the observed increased spontaneous tumor cell dissemination in vivo. Selective antagonism of β2-adrenoceptors blocked invadopodia formation, suggesting a pharmacological strategy to prevent tumor cell dissemination. Conclusion These findings provide insight into conditions that control tumor cell invasion by identifying signaling through β2-adrenoceptors as a regulator of invadopodia formation. These findings suggest novel pharmacological strategies for intervention, by using β-blockers to target β2-adrenoceptors to limit tumor cell dissemination and metastasis.
The State of Thematic Analysis in HCI for Healthcare: A Scoping Review Protocol
Creators: name: Bowman, Robert
name: Nadal, Camille
name: Thieme, Anja
name: Morrissey, Kellie
name: Doherty, Gavin
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Health Information Technology
subject: Physical Sciences and Mathematics
subject: Medicine and Health Sciences
subject: Graphics and Human Computer Interfaces
subject: Computer Sciences

description: Scoping review protocol developed using the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR). The review intends to map the use of thematic analysis in human-computer interaction (HCI) research for healthcare.
title: Study of clear cell renal cell carcinoma and renal angiomyolipoma with minimal fat by applying intravoxel incoherent motion diffusion weighted imaging: a preliminary study
Creators: name: Li, Jie
Publisher: name: European Congress of Radiology
Year: 2015
Subjects: subject: Kidney
subject: MR-Diffusion/Perfusion
subject: Colonography MR

description: Aims and objectives Methods and materials Results Conclusion Personal information References
description: Aims and objectives: To characterize Intravoxel Incoherent Motion Diffusion Weighted Imaging (IVIM) in the study of clear cell renal cell carcinoma (CCRCC) and renal angiomyolipoma with minimal fat...
title: Stenosis of Aortic Annulus with Age and Evaluation of Annular Area Before TAVI: A Coronary CTA Study
Creators: name: Öztürker, Coşkun
Publisher: name: European Congress of Radiology
Year: 2015
Subjects: subject: Arteriosclerosis
subject: Contrast agent-intravenous
subject: CT-Angiography
subject: Cardiac

description: Aims and objectives Methods and materials Results Conclusion Personal information References
description: Aims and objectives: Aortic stenosis is a common disease of heart valves, particularly in elderly patients. The primary treatment method in symptomatic patients is surgical valve implantation. Transcatheter aortic valve implantation (TAVI) is the successfully-applied...
title: Assessment of paraaortic lymph node metastasis in patients with perihilar cholangiocarcinoma; a comparison between contrast-enhanced computed tomography and F-18 fluorodeoxyglucose-positron emission tomography/computed tomography
Creators: name: Furuhashi, Naohiro
Publisher: name: European Congress of Radiology
Year: 2015
Subjects: subject: Metastases
subject: Cancer
subject: Staging
subject: Contrast agent-intravenous
subject: PET-CT
subject: CT
subject: Lymph nodes
subject: Biliary Tract / Gallbladder
subject: Abdomen

description: Aims and objectives Methods and materials Results Conclusion Personal information References
description: Aims and objectives: The only curative therapy for perihilar cholangiocarcinoma is margin negative resection. It is important to evaluate paraaortic lymph node (PALN) metastasis to decide the indication for surgery because it corresponds to distal metastasis on the...
Associations of coronary artery calcified plaque density with mortality in type 2 diabetes: the Diabetes Heart Study
Creators: name: Raffield, Laura M
Publisher: name: BioMed Central
Year: 2018

description: Abstract
                Background
                Coronary artery calcified plaque (CAC) is strongly predictive of cardiovascular disease (CVD) events and mortality, both in general populations and individuals with type 2 diabetes at high risk for CVD. CAC is typically reported as an Agatston score, which is weighted for increased plaque density. However, the role of CAC density in CVD risk prediction, independently and with CAC volume, remains unclear.
                Methods
                We examined the role of CAC density in individuals with type 2 diabetes from the family-based Diabetes Heart Study and the African American-Diabetes Heart Study. CAC density was calculated as mass divided by volume, and associations with incident all-cause and CVD mortality [median follow-up 10.2 years European Americans (n = 902, n = 286 deceased), 5.2 years African Americans (n = 552, n = 93 deceased)] were examined using Cox proportional hazards models, independently and in models adjusted for CAC volume.
                Results
                In European Americans, CAC density, like Agatston score and volume, was consistently associated with increased risk of all-cause and CVD mortality (p ≤ 0.002) in models adjusted for age, sex, statin use, total cholesterol, HDL, systolic blood pressure, high blood pressure medication use, and current smoking. However, these associations were no longer significant when models were additionally adjusted for CAC volume. CAC density was not significantly associated with mortality, either alone or adjusted for CAC volume, in African Americans.
                Conclusions
                CAC density is not associated with mortality independent from CAC volume in European Americans and African Americans with type 2 diabetes.
Anticipating regime shifts in gene expression: The case of an autoactivating positive feedback loop
Creators: name: Sharma, Yogita
name: Dutta, Partha Sharathi
name: Gupta, A. K.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Adaptation and Self-Organizing Systems (nlin.AO)
subject: FOS: Physical sciences

description: Considerable evidence suggests that anticipating sudden shifts from one state to another in bistable dynamical systems is a challenging task, examples include ecosystems, financial markets, complex diseases, etc. In this paper, we investigate the effects of additive, multiplicative and cross correlated stochastic perturbations on determining regime shifts in a bistable gene regulatory sys- tem, which gives rise to two distinct states of low and high concentrations of protein. We obtain the stationary probability density and mean first passage time of the system. We show that increasing additive(multiplicative) noise intensity induces regime shift from a low(high) to a high(low) pro- tein concentration state. However, an increase in cross correlation intensity always induces regime shifts from high to low protein concentration state. For both bifurcation (often called tipping point) and noise induced (called stochastic switching) regime shifts, we further explore the robustness of recently developed critical slowing down based early warning signal (EWS) indicators (e.g., rising variance and lag-1 autocorrelation) on our simulated time series data. We identify that using EWS indicators, prediction of an impending bifurcation induced regime shift is relatively easier than that of a noise induced regime shift in the considered system. Moreover, the success of EWS indicators also strongly depends upon the nature of noise. Our results establish the key fact that finding more robust indicator to forewarn regime shifts for a broader class complex natural systems is still in its infancy and demands extensive research.
The Triple A Process ( AmbientAminAbsorption ) Optimization of Biogas Upgrading based on Chemical Scrubbing with Amino Acid Salts for Scalable Expansion of Biomethane Production
Creators: name: Song, Jianing
name: Schmid, Marc Oliver
name: Güsewell, Joshua
name: Eltrop, Ludger
Publisher: name: Zenodo
Year: 2023
Subjects: Biogas, Biogas Gas Cleaning, Ambient Amino Absorption, Chemical Scrubbing

description: The production structure of raw biogas in Germany is closely connected with the agricultural structure. As a result, it is characterized by smaller biogas plants (BGAs), which are in a performance class > 250 m³/h STP methane. There are similar economies of scale for the costs of common processing technologies, which are especially small for large factories. The biomethane processing plants therefore have an average capacity of 630 m³ N/h. Therefore, there is a need for new, low-cost, small-scale gas upgrading technologies that can also be easily integrated into farm effluent and circulation systems, that is the aim of this study. To achieve this goal, a biogas upgrading process, based on chemical purification (amino acid salts-scrubber), must be optimized at first in the laboratory stud and then upscaled to pilot plant.
 The aim of the Triple-A project is to develop a novel robust and small-scale upgrading process. The so-called Triple-A technology uses amino acids (amine) under ambient conditions for chemical gas scrubbing (absorption). The concept and the scrubbing agent used result in advantages that have positive impacts on the operational process, the economic efficiency, and the implementation potential of the technology: (1) The scrubbing agent should be self-extractable from common biogas substrates such as silages and recycled after consumption in the digester and used for local bioeconomic cycles with short distances. (2) The process flow at ambient conditions allows a simple design with low requirements for plant components, safety and professional operation, low energy demand and thus high potential to reduce costs. (3) These characteristics allow a well scalable and cost-optimized operation for upgrading capacities smaller 250 m³ i.N. h.
 Next to the problem and concept of the process as well as the corresponding research, the results of the first screening of solvents and the initial operating an established continuously operating plant will be presented. Also, different possible models for the construction of reactors of pilot plant will be introduced.
title: Dinamic X-Rays shallowing study (VFSS): the comparison between inter-observer evaluations.
Creators: name: Malta, Bruna
Publisher: name: European Congress of Radiology
Year: 2015
Subjects: subject: Gastrointestinal tract
subject: Fluoroscopy
subject: Dynamic swallowing studies
subject: Eating disorders

description: Aims and objectives Methods and materials Results Conclusion Personal information References
description: Aims and objectives: The aim of this study is to check the range of reliability and inter-observer agreement in the interpretation of some predetermined parameters by a pattern of reporting of the Dinamic X-Rays Shallowing study...
title: Pancreas Divisum: Anatomical Etiology of Recurrent Pancreatitis
Creators: name: Turan, Aynur
Publisher: name: European Congress of Radiology
Year: 2015
Subjects: subject: Congenital
subject: Diagnostic procedure
subject: MR
subject: Anatomy
subject: Abdomen

description: Learning objectives Background Findings and procedure details Conclusion Personal information References
description: Learning objectives: Present the magnetic resonance imaging (MRI) features of the pancreas divisum Review other diagnostic techniques for this entity Make differential diagnosis between different etiologies of non-biliary...
Comparison of strategies for identification of regulatory quantitative trait loci of transcript expression traits
Creators: name: North, Kari
name: Li, Xia
name: Franceschini, Nora
Publisher: name: BioMed Central Ltd
Year: 2007

description: Abstract In order to identify regulatory genes, we determined the heritability of gene transcripts, performed linkage analysis to identify quantitative trait loci (QTLs), and evaluated the evidence for shared genetic effects among transcripts with co-localized QTLs in non-diseased participants from 14 CEPH (Centre d'Etude du Polymorphisme Humain) Utah families. Seventy-six percent of transcripts had a significant heritability and 54% of them had LOD score ≥ 1.8. Bivariate genetic analysis of 15 transcripts that had co-localized QTLs on 4q28.2-q31.1 identified significant genetic correlation among some transcripts although no improvement in the magnitude of LOD scores in this region was noted. Similar results were found in analysis of 12 transcripts, that had co-localized QTLs in the 13q34 region. Principal-component analyses did not improve the ability to identify chromosomal regions of co-localized gene expressions.
Engagement Workshops (EWs) contributions to the SPIs for OOSC
Creators: name: Rivera, Miriam
name: Toran, Raul
Publisher: name: Zenodo
Year: 2022
Subjects: ENJOI
SPIs
Engagement Workshops

description: This deliverable has the objective to draft a working list of Standards, Principles and Indicators (SPIs) for an Outstanding Open Science Communication (OOSC) integrating the results and feedback coming from the four ENJOI Engagement Workshops (EWs). This working list of SPIs goes to substitute the previous one released with the Inception report described in D2.1 since it includes the science communication producers’ and users’ significant feedback and views. Recommendations and contributions collected during the four Ews will also subsequently be condensed in the ENJOI Manifesto for OOSC.
description: ENJOI WP2. Identification of Standards, Principles and Indicators (SPIs) and methodological approach for qualitative analysis of Outstanding Open Science Communication (OOSC)
Three Point Functions in the N=4 Orthogonal Coset Theory
Creators: name: Ahn, Changhyun
name: Kim, Hyunsu
name: Paeng, Jinsub
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We construct the lowest higher spin-2 current in terms of the spin-1 and the spin-1/2 currents living in the orthogonal SO(N+4)/[SO(N) x SO(4)] Wolf space coset theory for general N. The remaining fifteen higher spin currents are determined. We obtain the three-point functions of bosonic (higher) spin currents with two scalars for finite N and k (the level of the spin-1 current). By multiplying SU(2) x U(1) into the above Wolf space coset theory, the other fifteen higher spin currents together with the above lowest higher spin-2 current are realized in the extension of the large N=4 linear superconformal algebra. Similarly, the three-point functions of bosonic (higher) spin currents with two scalars for finite N and k are obtained. Under the large N 't Hooft limit, the two types of three-point functions in the nonlinear and linear versions coincide as in the unitary coset theory found previously.
description: 70 pages. arXiv admin note: text overlap with arXiv:1506.00357
title: The added value of cardio-RM in patients with suspected myocarditis.
Creators: name: Malta, Bruna
Publisher: name: European Congress of Radiology
Year: 2015
Subjects: subject: Cardiac
subject: Computer applications
subject: Cardiovascular system
subject: MR
subject: Diagnostic procedure
subject: Imaging sequences
subject: Ischaemia / Infarction

description: Aims and objectives Methods and materials Results Conclusion Personal information References
description: Aims and objectives: The aim of this study is to test the added value of cardio-RM in the diagnostic classification and in the clinical management of patients suspected for myocarditis,through the use of standardized protocol aimed to assess global and segmental...
Supplemental materials for the Data Protection Record of Processing Activities and Privacy Notice generator toolkit by EMBL’s European Bioinformatics Institute
Creators: name: Gonzalez-Ferreiro, Montserrat
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Business
subject: Engineering
subject: Law
subject: FOS: Law
subject: data protection
subject: GDPR
subject: intergovernmental organisation
subject: personal data
subject: privacy notice
subject: record of processing activities
subject: research infrastructures

description: Data Protection Record of Processing Activities and Privacy Notice generator toolkit by EMBL’s European Bioinformatics Institute
Engagement Workshops (EWs) contributions to the SPIs for OOSC
Creators: name: Catanzaro, M.
name: Rivera, M.
name: Toran, R.
Publisher: name: Zenodo
Year: 2022
Subjects: ENJOI
SPIs
Engagement Workshops

description: * New version available * This deliverable has the objective to draft a working list of Standards, Principles and Indicators (SPIs) for an Outstanding Open Science Communication (OOSC) integrating the results and feedback coming from the four ENJOI Engagement Workshops (EWs). This working list of SPIs goes to substitute the previous one released with the Inception report described in D2.1 since it includes the science communication producers’ and users’ significant feedback and views. Recommendations and contributions collected during the four Ews will also subsequently be condensed in the ENJOI Manifesto for OOSC.
description: ENJOI WP2. Identification of Standards, Principles and Indicators (SPIs) and methodological approach for qualitative analysis of Outstanding Open Science Communication (OOSC)
Direct and indirect genetic effects on triglycerides through omics and correlated phenotypes
Creators: name: Justice, Anne E
name: Graff, Misa
name: Tao, Ran
name: Fernández-Rhodes, Lindsay
name: Howard, Annie G
name: North, Kari E
Publisher: name: BioMed Central
Year: 2018

description: Abstract
              Even though there has been great success in identifying lipid-associated single-nucleotide polymorphisms (SNPs), the mechanisms through which the SNPs act on each trait are poorly understood. The emergence of large, complex biological data sets in well-characterized cohort studies offers an opportunity to investigate the genetic effects on trait variability as a way of informing the causal genes and biochemical pathways that are involved in lipoprotein metabolism. However, methods for simultaneously analyzing multiple omics, environmental exposures, and longitudinally measured, correlated phenotypes are lacking. The purpose of our study was to demonstrate the utility of the structural equation modeling (SEM) approach to inform our understanding of the pathways by which genetic variants lead to disease risk. With the SEM method, we examine multiple pathways directly and indirectly through previously identified triglyceride (TG)-associated SNPs, methylation, and high-density lipoprotein (HDL), including sex, age, and smoking behavior, while adding in biologically plausible direct and indirect pathways. We observed significant SNP effects (P < 0.05 and directionally consistent) on TGs at visit 4 (TG4) for five loci, including rs645040 (DOCK7), rs964184 (ZPR1/ZNF259), rs4765127 (ZNF664), rs1121980 (FTO), and rs10401969 (SUGP1). Across these loci, we identify three with strong evidence of an indirect genetic effect on TG4 through HDL, one with evidence of pleiotropic effect on HDL and TG4, and one variant that acts on TG4 indirectly through a nearby methylation site. Such information can be used to prioritize candidate genes in regions of interest, inform mechanisms of action of methylation effects, and highlight possible genes with pleiotropic effects.
Seismic evidence for a weak radial differential rotation in intermediate-mass core helium burning stars
Creators: name: Deheuvels, S.
name: Ballot, J.
name: Beck, P. G.
name: Mosser, B.
name: Østensen, R.
name: García, R. A.
name: Goupil, M. J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: The detection of mixed modes that are split by rotation in Kepler red giants has made it possible to probe the internal rotation profiles of these stars, which brings new constraints on the transport of angular momentum in stars. Mosser et al. (2012) have measured the rotation rates in the central regions of intermediate-mass core helium burning stars (secondary clump stars). Our aim was to exploit& the rotational splittings of mixed modes to estimate the amount of radial differential rotation in the interior of secondary clump stars using Kepler data, in order to place constraints on angular momentum transport in intermediate-mass stars. We selected a subsample of Kepler secondary clump stars with mixed modes that are clearly rotationally split. By applying a thorough statistical analysis, we showed that the splittings of both gravity-dominated modes (trapped in central regions) and p-dominated modes (trapped in the envelope) can be measured. We then used these splittings to estimate the amount of differential rotation by using inversion techniques and by applying a simplified approach based on asymptotic theory (Goupil et al. 2013). We obtained evidence for a weak radial differential rotation for six of the seven targets that were selected, with the central regions rotating $1.8\pm0.3$ to $3.2\pm1.0$ times faster than the envelope. The last target was found to be consistent with a solid-body rotation. This demonstrates that an efficient redistribution of angular momentum occurs after the end of the main sequence in the interior of intermediate-mass stars, either during the short-lived subgiant phase, or once He-burning has started in the core. In either case, this should bring constraints on the angular momentum transport mechanisms that are at work.
description: 16 pages, 8 figures, accepted in A&A
title: Scrotal ultrasound sonoelastography in male fertility diagnosis
Creators: name: Zhukov, Oleg
Publisher: name: European Congress of Radiology
Year: 2015
Subjects: subject: Genital / Reproductive system male
subject: Elastography
subject: Diagnostic procedure
subject: Tissue characterisation

description: Aims and objectives Methods and materials Results Conclusion Personal information References
description: Aims and objectives: The aim of our study is to determine sonoelastography value in male reproductive function...
title: Pitfalls in cross-sectional neuroimaging: anatomy and artifacts simulating disease
Creators: name: Moore, Ryan
Publisher: name: European Congress of Radiology
Year: 2015
Subjects: subject: Neuroradiology brain
subject: Anatomy
subject: CT
subject: MR
subject: Education
subject: Education and training
subject: Ischaemia / Infarction

description: Learning objectives Background Findings and procedure details Conclusion Personal information References
description: Learning objectives: The most common anatomic and artifactual pitfalls in neuroimaging are...
title: Performance of low-dose, digital X-ray scanning (LODOX) compared to conventional radiography (CR) in the diagnostics of ureteral stones
Creators: name: Christe, Andreas
Publisher: name: European Congress of Radiology
Year: 2015
Subjects: subject: Abdomen
subject: Kidney
subject: Emergency
subject: Conventional radiography
subject: Experimental
subject: Radiation safety
subject: Calcifications / Calculi
subject: Dosimetric comparison

description: Aims and objectives Methods and materials Results Conclusion Personal information References
description: Aims and objectives: LODOX Statscan is a whole-body, low-dose X-ray scanner with digital enhancement and enlargement capabilities which was originally developed in the 1980′s in order to prevent smuggling of diamonds by mineworkers in South Africa. Ten years ago it...
“Effect of Modality in Evaluative Conditioning: Pictures vs. Words”
Creators: name: Münsterteicher, Marlen
name: Matthies, Nora
name: Wright, Jack
name: Dolic, Sandi
name: Gast, Vivian
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Psychiatry and Psychology
subject: Medicine and Health Sciences
subject: Life Sciences

description: As our "Experimentalpraktikum" we will research on the question wether the modality of the unconditioned stimuli (descriptions in words vs. pictures) has an effect on the evaluative conditioning of neutral stimuli.
Geometry of pointwise pseudo-slant warped product submanifolds in a Kähler manifold
Creators: name: Srivastava, S. K.
name: Sharma, A.
Publisher: name: arXiv
Year: 2016
Subjects: subject: Differential Geometry (math.DG)
subject: FOS: Mathematics
subject: 53C40, 53C42, 53C15

description: The purpose of this paper is to study pointwise pseudo-slant warped product submanifolds of a Kähler manifold $\widetilde{M}$. We derive the conditions of integrability and totally geodesic foliation for the distributions allied to the characterization of a pointwise pseudo-slant submanifold of $\widetilde{M}$. The necessary and sufficient conditions for isometrically immersed pointwise pseudo-slant submanfold of $\widetilde{M}$ to be a pointwise pseudo-slant warped product and a locally Riemannian product are obtained.
description: This paper has been withdrawn by the author due sign error
title: Dissecting Treg Heterogeneity in Human Cancer to find Novel Targets of Immunotheraphy
Creators: name: Alvisi, Giorgia
Publisher: name: The Open University
Year: 2022

description: T cell dysfunction in the tumor microenvironment (TME) mediated by the hyper-activation of inhibitory subpopulations such as regulatory T cells (Treg) represents a major obstacle to effective antitumor immunity and immunotherapy. The molecular mechanisms at the basis of the increased immunosuppressive capacity of Treg cells in the TME are currently not clear. Preclinical data shows that bulk Treg depletion improves T cell infiltration and its antitumor activity but simultaneously results in deleterious autoimmune responses. Targeting hyperactive Treg specifically present in the tumor would improve antitumor immunity while reducing toxicity. To this aim, we developed 30-parameter FACS to profile millions of single T cells from chemotherapy-naïve cancer patients. Computational algorithms applied to single-cell data identified T cell subsets preferentially enriched in tumors compared to adjacent normal lung tissue and peripheral blood. We found that the Interferon regulatory factor 4 (IRF4) defines a novel specific subpopulation of tumor infiltrating Tregs with superior immunosuppressive capacity. Integration of transcriptomic data and whole genome binding sites of transcription factors further revealed that IRF4, either alone or in combination with its partner BATF, directly controlled a molecular program responsible for Treg hyperproliferation and suppressive functions that included CTLA-4, ICOS, TNFRSF9 (4-1BB) and IL1R2. Accordingly, deletion of Irf4 exclusively in Tregs resulted in delayed tumor growth in mice while the abundance of IRF4+ Tregs correlated with poor prognosis in patients with multiple human cancers. We further identify mesenchyme homeobox 1 (MEOX1), a transcription factor novel to Treg biology, as sufficient to reprogram circulating Tregs to a tumor-infiltrating 4-1BB+ phenotype. MEOX1 activity sustains hyper-activated Treg gene expression and immunosuppression by favoring chromatin accessibility at sites regulated by AP-1/IRF4/BATF. Thus, Interfering with IRF4-dependent molecular program, which is shared by several solid tumors, may represent a novel immunotherapeutic approach capable to block immunosuppression in the tumor microenvironment.
ELISA – Developing a scale for Ecological Momentary Assessment of Life Satisfaction
Creators: name: Rein, Manuel
name: Vogelsmeier, Leonie
name: Bolsinova, Maria
Publisher: name: Open Science Framework
Year: 2022
Subjects: subject: Social and Behavioral Sciences

description: A well-known, psychometrically evaluated, and widely used instrument to assess the cognitive component of well-being (life satisfaction) on the trait level is the Satisfaction with Life Scale (Diener et al., 1985). However, to our knowledge no such instrument to assess life satisfaction as a state, i.e., momentary (life) satisfaction, exists to this date. While there are some studies that assessed momentary satisfaction or happiness with Ecological Momentary Assessment (de Vries et al., 2021; Magallón-Neri et al., 2018; van Agteren et al., 2021), they often utilized single-item measures whose psychometric properties were not evaluated. To fill this gap in the literature and to facilitate the research of inter- and intra-individual differences in well-being, the purpose of this study is to develop a brief, psychometrically sound questionnaire to measure momentary satisfaction in Ecological Momentary Assessment (EMA) studies.
title: Correlation between cognitive function and brain lesion volumes in patients with multiple sclerosis
Creators: name: Pourghorban, Ramin
Publisher: name: European Congress of Radiology
Year: 2015
Subjects: subject: Neuroradiology brain
subject: MR
subject: Diagnostic procedure
subject: Inflammation

description: Aims and objectives Methods and materials Results Conclusion Personal information References
description: Aims and objectives: Magnetic Resonance Imaging (MRI) plays a critical role in the diagnosis and follow-up of patients with multiple sclerosis (MS), but many aspects of MR Imaging has remained unrecognized yet, such as its relationship with various MS disabilities. One...
Inter-laboratory validation of the measurement of follicle stimulating hormone after various lengths of frozen storage
Creators: name: Young, Steven
Publisher: name: BioMed Central Ltd
Year: 2010

description: Abstract Background Serum follicle stimulating hormone (FSH) levels are used clinically to evaluate infertility, pituitary and gonadal disorders. With increased frequency of research collaborations across institutions, it is essential that inter-laboratory validation is addressed. Methods An inter-laboratory validation of three commercial FSH immunoassays was performed with human serum samples of varying frozen storage length (2 batches of 15 samples each) at -25 degree C. Percentage differences and Bland-Altman limits of agreement were calculated. Results The inter- and intra-laboratory consistency of FSH values with the same assay manufacturer was much higher after shorter-term storage (frozen for less than 11 months, mean percentage degradation less than 4%) than after long-term storage (2-3 years, mean percentage degradation = 23%). Comparing assay results from different manufacturers, there was similar overall long term degradation as seen with the same manufacturer (-25%), however the degradation was greater when the original FSH was greater than 20 mIU/mL relative to less than 10 mIU/mL (p < 0.001 trend test). Conclusion The findings suggest that degradation of serum samples stored between 11 months and 2-3 years at -25 degrees C can lead to unstable FSH measurements. Inter-laboratory variability due to frozen storage time and manufacturer differences in assay results should be accounted for when designing and implementing research or clinical quality control activities involving serum FSH at multiple study sites.
Summary for policymakers of the regional assessment report on biodiversity and ecosystem services for Europe and Central Asia of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services: Appendix 6.3: Agriculture (Chapter 6, Section 6.5.1)
Creators: name: IPBES
Publisher: name: Zenodo
Year: 2018
Subjects: Europe and Central Asia Assessment
IPBES
Supplementary material

description: Highlights for Table 6.6 on state and trends of nature’s contributions to people (NCP) delivery in Western and Central Europ
Measurement of van-der-Waals interaction by atom trajectory imaging
Creators: name: Thaicharoen, N.
name: Schwarzkopf, A.
name: Raithel, G.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: We study the repulsive van der Waals interaction of cold rubidium $70S_{1/2}$ Rydberg atoms by analysis of time-delayed pair correlation functions. After excitation, Rydberg atoms are allowed to accelerate under the influence of the van der Waals force. Their positions are then measured using a single-atom imaging technique. From the average pair correlation function of the atom positions we obtain the initial atom-pair separation and the terminal velocity, which yield the van der Waals interaction coefficient $C_{6}$. The measured $C_{6}$ value agrees well with calculations. The experimental method has been validated by simulations. The data hint at anisotropy in the overall expansion, caused by the shape of the excitation volume. Our measurement implies that the interacting entities are individual Rydberg atoms, not groups of atoms that coherently share a Rydberg excitation.