cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Computational exploration and design of a multi-epitopes vaccine construct against Chlamydia psittaci
Creators: name: Alsubaiyel, Amal M.
name: Bukhari, Sarah I.
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Information Systems not elsewhere classified
subject: Infectious Diseases
subject: FOS: Health sciences

description: Chlamydia psittaci is an intracellular pathogen and causes variety of deadly infections in humans. Antibiotics are effective against C. psittaci however high percentage of resistant strains have been reported in recent times. As there is no licensed vaccine, we used in-silico techniques to design a multi-epitopes vaccine against C. psittaci. Following a step-wise protocol, the proteome of available 26 strains was retrieved and filtered for subcellular localized proteins. Five proteins were selected (2 extracellular and 3 outer membrane) and were further analyzed for B-cell and T-cell epitopes prediction. Epitopes were further checked for antigenicity, solubility, stability, toxigenicity, allergenicity, and adhesive properties. Filtered epitopes were linked via linkers and the 3D structure of the designed vaccine construct was predicted. Binding of the designed vaccine with immune receptors: MHC-I, MHC-II, and TLR-4 was analyzed, which resulted in docking energy scores of −4.37 kcal/mol, −0.20 kcal/mol and −22.38 kcal/mol, respectively. Further, the docked complexes showed stable dynamics with a maximum value of vaccine-MHC-I complex (7.8 Å), vaccine-MHC-II complex (6.2 Å) and vaccine-TLR4 complex (5.2 Å). As per the results, the designed vaccine construct reported robust immune responses to protect the host against C. psittaci infections. In the study, the C. psittaci proteomes were considered in pan-genome analysis to extract core proteins. The pan-genome analysis was conducted using bacterial pan-genome analysis (BPGA) software. The core proteins were checked further for non-redundant proteins using a CD-Hit server. Surface localized proteins were investigated using PSORTb v 3.0. The surface proteins were BLASTp against Virulence Factor Data Base (VFDB) to predict virulent factors. Antigenicity prediction of the shortlisted proteins was further done using VAXIGEN v 2.0. The epitope mapping was done using the immune epitope database (IEDB). A multi-epitopes vaccine was built and a 3D structure was generated using 3Dprot online server. The docking analysis of the designed vaccine with immune receptors was carried out using PATCHDOCK. Molecular dynamics and post-simulation analyses were carried out using AMBER v20 to decipher the dynamics stability and intermolecular binding energies of the docked complexes. Communicated by Ramaswamy H. Sarma
sj-docx-1-jbr-10.1177_07487304231202561 – Supplemental material for The Molecular Circadian Clock Is a Target of Anti-cancer Translation Inhibitors
Creators: name: Berthier, Alexandre
name: Gheeraert, Céline
name: Johanns, Manuel
name: Vinod, Manjula
name: Staels, Bart
name: Eeckhoute, Jérôme
name: Lefebvre, Philippe
Publisher: name: SAGE Journals
Year: 2023
Subjects: Endocrinology
Biological Sciences not elsewhere classified
Neuroscience

description: Supplemental material, sj-docx-1-jbr-10.1177_07487304231202561 for The Molecular Circadian Clock Is a Target of Anti-cancer Translation Inhibitors by Alexandre Berthier, Céline Gheeraert, Manuel Johanns, Manjula Vinod, Bart Staels, Jérôme Eeckhoute and Philippe Lefebvre in Journal of Biological Rhythms
Three-dimensional Global Simulations of Type-II Planet-disk Interaction with a Magnetized Disk Wind: I. Magnetic Flux Concentration and Gap Properties
Creators: name: Aoyama, Yuhiko
name: Bai, Xuening
Publisher: name: arXiv
Year: 2023
Subjects: subject: Earth and Planetary Astrophysics (astro-ph.EP)
subject: FOS: Physical sciences

description: Giant planets embedded in protoplanetary disks (PPDs) can create annulus density gaps around their orbits in the type-II regime, potentially responsible for the ubiquity of annular substructures observed in PPDs. Despite of substantial amount of works studying type-II planet migration and gap properties, they are almost exclusively conducted under the viscous accretion disk framework. However, recent studies have established magnetized disk winds as the primary driving disk accretion and evolution, which can co-exist with turbulence from the magneto-rotational instability (MRI) in the outer PPDs. We conduct a series of 3D global non-ideal magneto-hydrodynamic (MHD) simulations of type-II planet-disk interaction applicable to the outer PPDs. Our simulations properly resolve the MRI turbulence and accommodate the MHD disk wind. We found that the planet triggers the poloidal magnetic flux concentration around its orbit. The concentrated magnetic flux strongly enhances angular momentum removal in the gap, which is along the inclined poloidal field through a strong outflow emanating from the disk surface outward of the planet gap. The resulting planet-induced gap shape is more similar to an inviscid disk, while being much deeper, which can be understood from a simple inhomogeneous wind torque prescription. The corotation region is characterized by a fast trans-sonic accretion flow that is asymmetric in azimuth about the planet and lacking the horseshoe turns, and the meridional flow is weakened. The torque acting on the planet generally drives inward migration, though the migration rate can be affected by the presence of neighboring gaps through stochastic, planet-free magnetic flux concentration.
description: 42 pages, 24 figures, Accepted for publication in the Astrophysical Journal
Additional file 2 of Survey of adolescents’ needs and parents’ views on sexual health in juvenile idiopathic arthritis
Creators: name: Savel, Carine
name: Chausset, Aurélie
name: Berland, Pauline
name: Guiguet-Auclair, Candy
name: Cabane, Laura
name: Fautrel, Bruno
name: Gaudin, Philippe
name: Guillot, Pascale
name: Hayem, Gilles
name: Lafarge, Delphine
name: Merlin, Etienne
name: Pezière, Nadine
name: Sordet, Christelle
name: Trope, Sonia
name: Tournadre, Anne
name: Malochet, Sandrine
name: Cohen, Jean-David
Publisher: name: figshare
Year: 2023
Subjects: Medicine
Science Policy

description: Supplementary Material 2
sj-docx-1-tam-10.1177_17588359231200463 – Supplemental material for Tumor response assessment by measuring the single largest lesion per organ in advanced non-small cell lung cancer patients treated with PD-1/PD-L1 inhibitor
Creators: name: He, Li-Na
name: Chen, Tao
name: Fu, Sha
name: Jiang, Yongluo
name: Zhang, Xuanye
name: Chen, Chen
name: Du, Wei
name: Luo, Linfeng
name: Li, Anlin
name: Wang, Yixing
name: Yu, Hui
name: Zhou, Yixin
name: Wang, Yuhong
name: Yang, Yunpeng
name: Huang, Yan
name: Zhao, Hongyun
name: Fang, Wenfeng
name: Zhang, Li
name: Hong, Shaodong
Publisher: name: SAGE Journals
Year: 2023
Subjects: Oncology and Carcinogenesis not elsewhere classified
Aged Health Care
Pharmacology and Pharmaceutical Sciences not elsewhere classified
Respiratory Diseases

description: Supplemental material, sj-docx-1-tam-10.1177_17588359231200463 for Tumor response assessment by measuring the single largest lesion per organ in advanced non-small cell lung cancer patients treated with PD-1/PD-L1 inhibitor by Li-Na He, Tao Chen, Sha Fu, Yongluo Jiang, Xuanye Zhang, Chen Chen, Wei Du, Linfeng Luo, Anlin Li, Yixing Wang, Hui Yu, Yixin Zhou, Yuhong Wang, Yunpeng Yang, Yan Huang, Hongyun Zhao, Wenfeng Fang, Li Zhang and Shaodong Hong in Therapeutic Advances in Medical Oncology
Effect of mutations on the folding and stability of γD-crystallin protein
Creators: name: Ghosh, Deepshikha
name: Sojitra, Kandarp Ashokbhai
name: Biswas, Anushka
name: Agarwal, Manish
name: Radhakrishna, Mithun
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Physical Sciences not elsewhere classified
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Information Systems not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Computational Biology

description: Interprotein interactions between the partially unfolded states of γD-crystallin (γD-crys) protein are known to cause cataracts. Therefore, understanding the unfolding pathways of native γD-crys is extremely crucial to delineate their aggregation mechanism. In this study, we have performed extensive all-atom Molecular Dynamics simulations with explicit solvent to understand the role of the critical residues that drive the stability of the motifs and domains of γD-crys in its wild type and mutant forms. Our findings show that while the individual motifs of wild type are not stable in the native form, the individual domains remain structurally stable at 425K. This enhanced stability of the domain was attributed to the hydrophobic interactions between the motifs. Single and double point mutations of the domains with negatively charged aspartic and glutamic acid amino acid residues (I3E, W42D, W42E, I3D/W42D, I3E/W42E, and L92D/W157D) decreases the structural stability, leading to unfolding of individual domains of γD-crys. We believe that our study sheds light on the weakest links of γD-crys, along with the role of interactions stabilizing the domains. Further, this study bolsters and provides a better understanding of the domain swapping mechanism of aggregation of γD-crys. Communicated by Ramaswamy H. Sarma
title: Fishing vessel research and development in Newfoundland
Creators: name: Cumming, D.
Publisher: name: National Research Council of Canada. Institute for Marine Dynamics
publisherIdentifier: https://ror.org/04mte1k06
publisherIdentifierScheme: ror
Year: 1989
Subjects: subject: fishing vessel
subject: research and development

description: This report consists of a formal submission related to fishing vessel research and development to the Ocean Studies Task Force; Working Group 7, Fishing Technology and Harvesting.
sj-doc-1-tde-10.1177_26350106231205029 – Supplemental material for Impact of Fatigue and Its Influencing Factors on Diabetes Self-Management in Adults With Type 2 Diabetes: A Structural Equation Modeling Analysis
Creators: name: Kuo, Hsuan-Ju
name: García, Alexandra A.
name: Huang, Ya-Ching
name: Zuñiga, Julie A.
name: Benner, Aprile D.
name: Cuevas, Heather
name: Fan, Kang-Chih
name: Hsu, Chih-Yao
Publisher: name: SAGE Journals
Year: 2023
Subjects: Endocrinology
Nursing not elsewhere classified
Nutrition and Dietetics not elsewhere classified
Public Health and Health Services not elsewhere classified
Sociological Methodology and Research Methods

description: Supplemental material, sj-doc-1-tde-10.1177_26350106231205029 for Impact of Fatigue and Its Influencing Factors on Diabetes Self-Management in Adults With Type 2 Diabetes: A Structural Equation Modeling Analysis by Hsuan-Ju Kuo, Alexandra A. García, Ya-Ching Huang, Julie A. Zuñiga, Aprile D. Benner, Heather Cuevas, Kang-Chih Fan and Chih-Yao Hsu in The Science of Diabetes Self-Management and Care
Additional file 1 of Association of free-living diet composition with plasma lipoprotein(a) levels in healthy adults
Creators: name: Matveyenko, Anastasiya
name: Seid, Heather
name: Kim, Kyungyeon
name: Ramakrishnan, Rajasekhar
name: Thomas, Tiffany
name: Matienzo, Nelsa
name: Reyes-Soffer, Gissette
Publisher: name: figshare
Year: 2023
Subjects: Biochemistry
Medicine
Biological Sciences not elsewhere classified
Science Policy

description: Additional file 1.
Supplemental Material - A Mother’s Voice: The Construction of Maternal Identity Following Perinatal Loss
Creators: name: Rossen, Larissa
name: Opie, Jessica E.
name: O’Dea, Gypsy
Publisher: name: SAGE Journals
Year: 2023
Subjects: Psychology not elsewhere classified

description: Supplemental Material for A Mother’s Voice: The Construction of Maternal Identity Following Perinatal Loss by Larissa Rossen, Jessica E. Opie, and Gypsy O’Dea in OMEGA - Journal of Death and Dying
sj-docx-1-oss-10.1177_01708406231203295 – Supplemental material for Prefiguring Alternative Organizing: Confronting marginalization through projective cultural adjustment and tempered autonomy
Creators: name: Bhatt, Babita
name: Qureshi, Israr
name: Shukla, Dhirendra M.
name: Hota, Pradeep K.
Publisher: name: SAGE Journals
Year: 2023
Subjects: subject: Organisation and Management Theory
subject: Sociology
subject: FOS: Sociology

description: Supplemental material, sj-docx-1-oss-10.1177_01708406231203295 for Prefiguring Alternative Organizing: Confronting marginalization through projective cultural adjustment and tempered autonomy by Babita Bhatt, Israr Qureshi, Dhirendra M. Shukla and Pradeep K. Hota in Organization Studies
Layer specific fMRI
Creators: name: Renzo (Laurentius) Huber
Publisher: name: F1000 Research Limited
Year: 2018

description: The new research field of layer fMRI opens up a whole new window to investigate brain connectivity.
This NIH fMRI summer talk provides a broad overview of the most important limits of layer-fMRI.
Biggest challenges of signal interpretation and analysis are discussed.

We confirm we have permission to use images from participants included in this presentation
sj-docx-1-sci-10.1177_00368504231200626 - Supplemental material for Nickel-related hypersensitivity reactions following endovascular interventions: A review of current evidence
Creators: name: Tjen, Vanessa H
name: Yang, Paul Zichu
Publisher: name: SAGE Journals
Year: 2023
Subjects: Biological Sciences not elsewhere classified

description: Supplemental material, sj-docx-1-sci-10.1177_00368504231200626 for Nickel-related hypersensitivity reactions following endovascular interventions: A review of current evidence by Vanessa H Tjen and Paul Zichu Yang in Science Progress
Additional file 1 of Effects of a novel, non-invasive pre-hatch application of probiotic for broilers on development of cecum microbiota and production performance
Creators: name: Villumsen, Kasper Rømer
name: Sandvang, Dorthe
name: Vestergård, Gisle
name: Olsen, Mia Son Räfle
name: Juul, Johanne
name: Dencker, Morten
name: Kudsk, Johannes
name: Poulsen, Louise Ladefoged
Publisher: name: figshare
Year: 2023
Subjects: subject: Space Science
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Physiology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: Computational Biology

description: Additional file 1. Figure S1. Rarefaction curves for all included cecal samples. Sample sizes after filtering range from 8242 to 187753 reads.
Heterocyclic compounds with different moieties: synthesis and evaluation of biological activities assisted with the computational study
Creators: name: Kısa, Dursun
name: Koç, Esra
name: Topcu, Kübra Sena Baş
name: İmamoğlu, Rizvan
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biochemistry
Cell Biology
Pharmacology
Biotechnology
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified
Hematology

description: In the present work, heterocyclic compounds containing different moieties, such as pyrazole and thiophene, were synthesized and screened for inhibitory potency against medicinal enzymes and bacterial and cancer (breast and cervical) cell lines. The synthesized compounds have exhibited inhibitory capability against the studied enzymes. Among substances, C3 compound showed AChE and BChE inhibitory potency with the lowest IC50 value of 3.72 ± 0.57 and 1.66 ± 0.22 µM, respectively, in comparison to the standard tacrine. These analogs indicated varying degrees of tyrosinase inhibitory potencies ranging from 1.12 ± 0.50 to 7.70 ± 0.88 µM, and substance C4 was more potent against the enzyme than the reference compound, kojic acid. All four compounds have IC50 values between 37.11 ± 1.56–124.8 ± 2.09 µM for α-glucosidase. It was found that compound C1 exhibited a better antiproliferative activity compared to other substances, with IC50 values at 5.068 and 6.460 µg mL−1 for MCF-7 and HeLa cells, respectively. C1 and C2 compounds had good inhibitory ability against E. faecalis with a MIC value (16 µg mLˉˡ). Molecular docking analysis showed that C3 has the lowest binding score against α-glucosidase (-8.617 kcal/mol). Communicated by Ramaswamy H. Sarma
Enzyme inhibitory potential of some indole Schiff bases on acetylcholinesterase and human carbonic anhydrase isoforms I and II enzymes: an in vitro and molecular docking study
Creators: name: Akman, Ebru
name: Sirinzade, Hanif
name: Ozguven, Serap Yilmaz
name: Dilek, Esra
name: Suzen, Sibel
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Pharmacology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified

description: In this study, the in vitro effects of some indole Schiff bases on acetylcholinesterase and human carbonic anhydrase isoforms I and II were investigated. A series of N-methylindole hydrazide/hydrazone derivatives (1a-1t) were tested on these enzymes. The interactions of the synthesized indole derivatives with target enzymes were studied by molecular docking methodology. The results revealed that indole derivative Schiff base compounds inhibited the enzymes significantly. Ki values for hCAI isoenzyme were determined to be in the range of 36.18 ± 3.07–224.29 ± 5.78 nM; for the hCAII isoenzyme in the range of 31.30 ± 2.63–201.64 ± 7.25 nM; for acetylcholinesterase in the range of 6.82 ± 0.72–110.30 ± 9.26 nM. Compared to the control compound Acetazolamide (AZA), 1k and 1p were found to have the best inhibitory effect for hCAI; 1p was found to be the best inhibitory effect for hCAII. Compared to the control compound Tacrine (TAC), 1s showed the best inhibitory effect for AChE. In vitro results were verified with the results obtained by docking studies and interactions with enzymes were demonstrated. Communicated by Ramaswamy H. Sarma
On the monotonicity of the Hilbert functions for 4-generated pseudo-symmetric monomial curves
Creators: name: Şahin, Nil
Publisher: name: arXiv
Year: 2023
Subjects: subject: Commutative Algebra (math.AC)
subject: FOS: Mathematics
subject: 13H10, 14H20

description: In this article we solve the conjecture "Hilbert function of the local ring for a 4 generated pseudo-symmetric numerical semigroup $\langle n_1,n_2,n_3,n_4 \rangle$ is always non-decreasing when $ n_1 < n_2 < n_3 < n_4$". We give a complete characterization to the standard bases when the tangent cone is not Cohen-Macaulay by showing that the number of elements in the standard basis depends on some parameters $s_j$ 's we define. Since the tangent cone is not Cohen-Macaulay, non-decreasingness of the Hilbert fuction was not guaranteed, we proved the non-decreasingness from our explicit Hilbert Function computation.
Generalized second law of thermodynamics for the matter creation scenario and emergence of phantom regime
Creators: name: Cárdenas, Víctor H.
name: Cruz, Miguel
name: Lepe, Samuel
Publisher: name: arXiv
Year: 2023
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: This work is focused on the exploration of the thermodynamics foundations of the matter creation scenario when a generalized form of the second law of thermodynamics for this scheme is implemented. In this scenario we consider an expanding cosmology in which the created matter is trapped by the apparent horizon. The scheme leads to phantom evolution but at first glance it lacks of physical consistency. However, the inclusion of chemical potential into the description solves the thermodynamics issues of the model and determines the behavior of the cosmic fluid, in other words, the cosmic fluid now can behave as phantom dark energy or as quintessence one.
description: 7 pages, no figures. Accepted for publication in EPJ Plus
Porting And Evolution Of Thetis On The Curie Supercomputer
Creators: name: N. Audiffren
Publisher: name: Zenodo
Year: 2013
Subjects: simulation, hybrid, Hypre library, Curie Tier-0, POSIX VTK, HDF5 I/O

description: It has already been shown that the numerical tool Thétis based on the resolution of the Navier-Stokes

equation for multiphase flows gives accurate results for coastal applications, e.g. wave breaking, tidal

bore propagation, tsunamis generation, swash flows, etc. [1,2,3,4,5,6]. In this study our goal is to

improve the time and memory consumption in the set-up phase of the simulation (partitioning and

building the computational mesh), examining the eventual benefits of an hybrid approach of the Hypre

library, and doing fine tuning in implementation of the code on Curie Tier-0. We also implement

parallel POSIX VTK and HDF5 I/O. Thétis is now able to run efficiently up to 1 billion mesh nodes at

16384 cores on CURIE in a production context.
Cluster-size decay in supercritical long-range percolation
Creators: name: Jorritsma, Joost
name: Komjáthy, Júlia
name: Mitsche, Dieter
Publisher: name: arXiv
Year: 2023
Subjects: subject: Probability (math.PR)
subject: FOS: Mathematics
subject: 60C05, 60K35

description: We study the cluster-size distribution of supercritical long-range percolation on $\mathbb{Z}^d$, where two vertices $x,y\in\mathbb{Z}^d$ are connected by an edge with probability $\mathrm{p}(\|x-y\|):=p\min(1,β\|x-y\|)^{-dα}$ for parameters $p\in(0, 1]$, $α>1$, and $β>0$. We show that when $α>1+1/d$, and either $β$ or $p$ is sufficiently large, the probability that the origin is in a finite cluster of size at least $k$ decays as $\exp\big(-Θ(k^{(d-1)/d})\big)$. This corresponds to classical results for nearest-neighbor Bernoulli percolation on $\mathbb{Z}^d$, but is in contrast to long-range percolation with $α<1+1/d$, when the exponent of the stretched exponential decay changes to $2-α$. This result, together with our accompanying paper, establishes the phase diagram of long-range percolation with respect to cluster-size decay. Our proofs rely on combinatorial methods that show that large delocalized components are unlikely to occur. As a side result we determine the asymptotic growth of the second-largest connected component when the graph is restricted to a finite box.
description: 36 pages, minor revision: to appear in Electronic Journal of Probability
Gapped boundary of (4+1)d beyond-cohomology bosonic SPT phase
Creators: name: Yang, Xinping
name: Cheng, Meng
Publisher: name: arXiv
Year: 2023
Subjects: subject: Strongly Correlated Electrons (cond-mat.str-el)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In this work we study gapped boundary states of $\mathbb{Z}_N$ bosonic symmetry-protected topological (SPT) phases in 4+1d, which are characterized by mixed $\mathbb{Z}_N$-gravity response, and the closely related phases protected by $C_N$ rotation symmetry. We show that if $N\notin \{2,4,8,16\}$, any symmetry-preserving boundary theory is necessarily gapless for the root SPT state. We then propose a (3+1)$d$ $\mathbb{Z}_2$ gauge theory coupled to fermionic matter as a candidate boundary theory for $N=2,4,8,16$, where the anomalous symmetry is implemented by invertible topological defects obtained from gauging (2+1)$d$ chiral topological superconductors. For the $C_N$ case, we present an explicit construction for the boundary states for $N=2,4,8,16$, and argue that the construction fails for other values of $N$.
description: 15 pages, 4 figures; v2: added discussions on the group structure of SPT phases, and more on the $N=3$ case. More references added; v3: published. More details on the (4+1)$d$ $\mathbb{Z}_N$ SPT classification
Additional file 1 of Metabolomics and biomarkers for lupus nephritis – a systematic review
Creators: name: Barone, Felippe Pereira
name: Lourenço, Silvia Vanessa
name: Azevedo, Luiz Sergio
name: de Souza, Mayara Nanci
name: Coutinho-Camillo, Claudia Malheiros
name: Florezi, Giovanna Piacenza
Publisher: name: figshare
Year: 2023
Subjects: subject: Biochemistry
subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Physiology
subject: Biotechnology
subject: Chemical Sciences not elsewhere classified
subject: Ecology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Cancer

description: Additional file 1.
Better Understanding Differences in Attribution Methods via Systematic Evaluations
Creators: name: Rao, Sukrut
name: Böhle, Moritz
name: Schiele, Bernt
Publisher: name: arXiv
Year: 2023
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Artificial Intelligence (cs.AI)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Deep neural networks are very successful on many vision tasks, but hard to interpret due to their black box nature. To overcome this, various post-hoc attribution methods have been proposed to identify image regions most influential to the models' decisions. Evaluating such methods is challenging since no ground truth attributions exist. We thus propose three novel evaluation schemes to more reliably measure the faithfulness of those methods, to make comparisons between them more fair, and to make visual inspection more systematic. To address faithfulness, we propose a novel evaluation setting (DiFull) in which we carefully control which parts of the input can influence the output in order to distinguish possible from impossible attributions. To address fairness, we note that different methods are applied at different layers, which skews any comparison, and so evaluate all methods on the same layers (ML-Att) and discuss how this impacts their performance on quantitative metrics. For more systematic visualizations, we propose a scheme (AggAtt) to qualitatively evaluate the methods on complete datasets. We use these evaluation schemes to study strengths and shortcomings of some widely used attribution methods over a wide range of models. Finally, we propose a post-processing smoothing step that significantly improves the performance of some attribution methods, and discuss its applicability.
description: 35 pages, 36 figures, 2 tables, extended version of arXiv:2205.10435, IEEE Transactions on Pattern Analysis and Machine Intelligence
Studying How to Efficiently and Effectively Guide Models with Explanations
Creators: name: Rao, Sukrut
name: Böhle, Moritz
name: Parchami-Araghi, Amin
name: Schiele, Bernt
Publisher: name: arXiv
Year: 2023
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Artificial Intelligence (cs.AI)
subject: Machine Learning (cs.LG)
subject: FOS: Computer and information sciences

description: Despite being highly performant, deep neural networks might base their decisions on features that spuriously correlate with the provided labels, thus hurting generalization. To mitigate this, 'model guidance' has recently gained popularity, i.e. the idea of regularizing the models' explanations to ensure that they are "right for the right reasons". While various techniques to achieve such model guidance have been proposed, experimental validation of these approaches has thus far been limited to relatively simple and / or synthetic datasets. To better understand the effectiveness of the various design choices that have been explored in the context of model guidance, in this work we conduct an in-depth evaluation across various loss functions, attribution methods, models, and 'guidance depths' on the PASCAL VOC 2007 and MS COCO 2014 datasets. As annotation costs for model guidance can limit its applicability, we also place a particular focus on efficiency. Specifically, we guide the models via bounding box annotations, which are much cheaper to obtain than the commonly used segmentation masks, and evaluate the robustness of model guidance under limited (e.g. with only 1% of annotated images) or overly coarse annotations. Further, we propose using the EPG score as an additional evaluation metric and loss function ('Energy loss'). We show that optimizing for the Energy loss leads to models that exhibit a distinct focus on object-specific features, despite only using bounding box annotations that also include background regions. Lastly, we show that such model guidance can improve generalization under distribution shifts. Code available at: https://github.com/sukrutrao/Model-Guidance.
description: 41 pages, 38 figures, 4 tables, IEEE/CVF International Conference on Computer Vision (ICCV) 2023
Additional file 1 of LncRNA CYP4A22-AS1 promotes the progression of lung adenocarcinoma through the miR-205-5p/EREG and miR-34c-5p/BCL-2 axes
Creators: name: Dong, Liyao
name: Zhang, Lin
name: Zhao, Xinyun
name: Zou, Hongling
name: Lin, Sisi
name: Zhu, Xinping
name: Cao, Jili
name: Zhou, Chun
name: Yu, Zhihong
name: Zhu, Yongqiang
name: Chai, Kequn
name: Li, Mingqian
name: Li, Qun
Publisher: name: figshare
Year: 2023
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Supplementary Material 1
Progettare Materiali Didattici FAIR: L'esperienza di H2IOSC nella Gestione Condivisa di Oggetti Digitali Complessi
Creators: name: Pedonese, Giulia
name: Spadi, Alessia
name: Frontini, Francesca
Publisher: name: Zenodo
Year: 2024
Subjects: subject: training
subject: data management
subject: FAIR principles
subject: digital objects
subject: Digital humanities
subject: Linguistics
subject: FOS: Languages and literature
subject: data stewardship

description: La presentazione riassume la metodologia applicata dal progetto H2IOSC ai materiali di formazione diretti alla comunità italiana delle Social Sciences and Humanities. Dopo aver illustrato la strategia didattica del WP8 - "Training, Capacity Building, Engagement" la presentazione dettaglia le modalità di adattamento, creazione e gestione di materiali didattici intesi come oggetti digitali complessi attraverso l'applicazione della metodologia "FAIR-by-Design" sviluppata all'interno del progetto Skills4EOSC e l'utilizzo del "Minimal Metadata Set for Learning Resources" di Research Data Alliance. Infine, si presentano le piattaforme di training del progetto H2IOSC: il "Training Environment" per la gestione di eventi formativi e la "H2IOSC Library" per il deposito e il versionamento del materiale.

Progetto H2IOSC - Humanities and cultural Heritage Italian Open Science Cloud,  finanziato dall’Unione europea NextGenerationEU – PNRR M4C2 - Codice progetto IR0000029 - CUP B63C22000730005.
Hướng dẫn triển khai Khuyến nghị Tài nguyên Giáo dục Mở. Lĩnh vực hành động 4: Nuôi dưỡng sự sáng tạo các mô hình bền vững cho Tài nguyên Giáo dục Mở và giám sát tiến độ
Creators: name: Nghĩa, Lê Trung
Publisher: name: Zenodo
Year: 2024
Subjects: Khuyến nghị tài nguyên giáo dục mở
các mô hình bền vững

description: Đây là bản dịch tài liệu gốc tiếng Anh "Guidelines on the implementation of the OER Recommendation. Action Area 4: Nurturing the creation of sustainability models for OER and monitoring progress" do UNESCO xuất bản năm 2024, giấy phép CC BY-SA 3.0 IGO.
Qualquer amor já é um pouquinho de saúde: construindo laços entre Agentes Comunitários de Saúde e adolescentes
Creators: name: Federal University of Uberlândia
name: Dias, Nicole Geovana
name: Rodrigues Cardoso, Isabella
name: Mendes Vilela, Jéssica
name: Cristina Soares Panzo, Lívia
Publisher: name: Zenodo
Year: 2023
Subjects: subject: Gender studies
subject: Sexuality
subject: Adolescent Health
subject: Primary Care

description: Em um mundo diverso, adolescentes protagonizam e vivenciamexperiências únicas por meio da identidade de gênero e da sexualidade, mascompreender e acolher essas questões desafia profissionais de saúde.Portanto, ao reconhecer o papel crucial das/os agentes comunitários, apresente cartilha objetiva trazer um guia prático para fortalecer habilidades decomunicação, ferramentas de abordagem e conhecimento acerca de temáticassensíveis e fundamentais relacionadas à diversidade sexual e de gênero,possibilitando o diálogo respeitoso, inclusivo e empático e a assistênciaresolutiva, segura e acolhedora aos adolescentes.
Additional file 1 of PTBP1 plays an important role in the development of gastric cancer
Creators: name: Chu, Zewen
name: Zhu, Miao
name: Luo, Yuanyuan
name: Hu, Yaqi
name: Feng, Xinyi
name: Wang, Haibo
name: Sunagawa, Masataka
name: Liu, Yanqing
Publisher: name: figshare
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Supplementary File 1: Genotyping Report
Spin of Photons: Nature of Polarisation
Creators: name: Saito, Shinichi
Publisher: name: arXiv
Year: 2023
Subjects: subject: Optics (physics.optics)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Stokes parameters (${\bf S}$) in Poincaré sphere are very useful values to describe the polarisation state of photons. However, the fundamental principle of the nature of polarisation is not completely understood, yet, because we have no concrete consensus how to describe spin of photons, quantum-mechanically. Here, we have considered a monochromatic coherent ray of photons, described by a many-body coherent state, and tried to establish a fundamental basis to describe the spin state of photons, in connection with a classical description based on Stokes parameters. We show that a spinor description of the coherent state is equivalent to Jones vector for polarisation states, and obtain the spin operators (${\bf \hat{S}}$) of all components based on rotators in a $SU(2)$ group theory. Polarisation controllers such as phase-shifters and rotators are also obtained as quantum-mechanical operators to change the phase of the wavefunction for polarisation states. We show that the Stokes parameters are quantum-mechanical average of the obtained spin operators, ${\bf S} = \langle {\bf \hat{S}} \rangle $.
Dirac Equation for Photons: Origin of Polarisation
Creators: name: Saito, Shinichi
Publisher: name: arXiv
Year: 2023
Subjects: subject: Optics (physics.optics)
subject: Applied Physics (physics.app-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Spin is a fundamental degree of freedom, whose existence was proven by Dirac for an electron by imposing the relativity to quantum mechanics, leading to the triumph to derive the Dirac equation. Spin of a photon should be linked to polarisation, however, the similar argument for an electron was not applicable to Maxwell equations, which are already Lorentz invariant. Therefore, the origin of polarisation and its relationship with spin are not completely elucidated, yet. Here, we discuss propagation of coherent rays of photons in a graded-index optical fibre, which can be solved exactly using the Laguerre-Gauss or Hermite-Gauss modes in a cylindrical or a Cartesian coordinate. We found that the energy spectrum is massive with the effective mass as a function of the confinement and orbital angular momentum. The propagation is described by the one-dimensional ($1D$) non-relativistic Schrödinger equation, which is equivalent to the $2D$ space-time Klein-Gordon equation by a unitary transformation. The probabilistic interpretation and the conservation law require the factorisation of the Klein-Gordon equation, leading to the $2D$ Dirac equation with spin. We applied the Bardeen-Cooper-Schrieffer (BCS)-Bogoliubov theory of superconductivity to a coherent ray from a laser and identified a radiative Nambu-Anderson-Higgs-Goldstone mode for recovering the broken symmetry. The spin expectation value of a photon corresponds to the polarisation state in the Poincaré sphere, which is characterised by fixed phases after the onset of lasing due to the broken $SU(2)$ symmetry, and it is shown that its azimuthal angle is coming from the phase of the energy gap.
Macroscopic Singlet, Triplet, and Colour-Charged States of Coherent Photons
Creators: name: Saito, Shinichi
Publisher: name: arXiv
Year: 2023
Subjects: subject: Optics (physics.optics)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: A ray of photons, emitted from a laser source, is in a coherent state, where macroscopic number of photons are degenerate in the same quantum state. The coherent state has degrees of freedom for spin and orbital angular momentum, which allow an arbitrary superposition state among orthogonal states with varying their amplitudes and phases, described by a representation theory of Lie algebra and Lie group. Here, we experimentally demonstrate that we can construct generators of rotations for the quantum states of coherent photons, simply by combining widely available optical components, such as half- and quarter-wave plates and vortex lenses. We have found that a superposition state between vortexed and no-vortex states is characterised by the motion of the topological charge upon the rotation in the SU(3) states. We also realised singlet and triplet states by combining rays of photons with orthogonal polarisation states and vortexed states. This corresponds to realise an effective SU(4) state and we have confirmed the projection to an SU(2)$\times$SU(2) state upon passing through a polariser.
The Design and Implementation of a Bayesian Data Analysis Lesson for Pre-Service Mathematics and Science Teachers
Creators: name: Dogucu, Mine
name: Kazak, Sibel
name: Rosenberg, Joshua
Publisher: name: arXiv
Year: 2023
Subjects: subject: Other Statistics (stat.OT)
subject: FOS: Computer and information sciences

description: With the rise of the popularity of Bayesian methods and accessible computer software, teaching and learning about Bayesian methods are expanding. However, most educational opportunities are geared toward statistics and data science students and are less available in the broader STEM fields. In addition, there are fewer opportunities at the K-12 level. With the indirect aim of introducing Bayesian methods at the K-12 level, we have developed a Bayesian Data Analysis activity and implemented it with 35 mathematics and science pre-service teachers. In this manuscript, we describe the activity, the web app supporting the activity, and pre-service teachers' perceptions of the activity. Lastly, we discuss future directions for preparing K-12 teachers in teaching and learning about Bayesian methods.
Searching for anomalous quartic gauge couplings at muon colliders using principle component analysis
Creators: name: Dong, Yi-Fei
name: Mao, Ying-Chen
name: Yang, Ji-Chong
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: Searching for new physics~(NP) is one of the areas of high-energy physics that requires the most processing of large amounts of data. At the same time, quantum computing has huge potential advantages when dealing with large amounts of data. The principal component analysis~(PCA) algorithm may be one of the bridges connecting these two aspects. On the one hand, it can be used for anomaly detection, and on the other hand, there are corresponding quantum algorithms for PCA. In this paper, we investigate how to use PCA to search for NP. Taking the example of anomalous quartic gauge couplings in the tri-photon process at muon colliders, we find that PCA can be used to search for NP. Compared with the traditional event selection strategy, the expected constraints on the operator coefficients obtained by PCA based event selection strategy are even better.
description: correct one of the author names
Einstein-Podolsky-Rosen-Bohm experiments: a discrete data driven approach
Creators: name: De Raedt, Hans
name: Katsnelson, Mikhail I.
name: Jattana, Manpreet S.
name: Mehta, Vrinda
name: Willsch, Madita
name: Willsch, Dennis
name: Michielsen, Kristel
name: Jin, Fengping
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: FOS: Physical sciences

description: We take the point of view that building a one-way bridge from experimental data to mathematical models instead of the other way around avoids running into controversies resulting from attaching meaning to the symbols used in the latter. In particular, we show that adopting this view offers new perspectives for constructing mathematical models for and interpreting the results of Einstein-Podolsky-Rosen-Bohm experiments. We first prove new Bell-type inequalities constraining the values of the four correlations obtained by performing Einstein-Podolsky-Rosen-Bohm experiments under four different conditions. The proof is ``model-free'' in the sense that it does not refer to any mathematical model that one imagines to have produced the data. The constraints only depend on the number of quadruples obtained by reshuffling the data in the four data sets without changing the values of the correlations. These new inequalities reduce to model-free versions of the well-known Bell-type inequalities if the maximum fraction of quadruples is equal to one. Being model-free, a violation of the latter by experimental data implies that not all the data in the four data sets can be reshuffled to form quadruples. Furthermore, being model-free inequalities, a violation of the latter by experimental data only implies that any mathematical model assumed to produce this data does not apply. Starting from the data obtained by performing Einstein-Podolsky-Rosen-Bohm experiments, we construct instead of postulate mathematical models that describe the main features of these data. The mathematical framework of plausible reasoning is applied to reproducible and robust data, yielding without using any concept of quantum theory, the expression of the correlation for a system of two spin-1/2 objects in the singlet state. (truncated here)
description: Corrected typo's, minor corrections in appendix B.3, major correction in section 11.4.2
sj-docx-2-mpp-10.1177_23814683221116362 – Supplemental material for Use of Modeling to Inform Decision Making in North Carolina during the COVID-19 Pandemic: A Qualitative Study
Creators: name: Johnson, Karl
name: Biddell, Caitlin B.
name: Hassmiller Lich, Kristen
name: Swann, Julie
name: Delamater, Paul
name: Mayorga, Maria
name: Ivy, Julie
name: Smith, Raymond L.
name: Patel, Mehul D.
Publisher: name: SAGE Journals
Year: 2022
Subjects: subject: 111799 Public Health and Health Services not elsewhere classified
subject: FOS: Health sciences

description: Supplemental material, sj-docx-2-mpp-10.1177_23814683221116362 for Use of Modeling to Inform Decision Making in North Carolina during the COVID-19 Pandemic: A Qualitative Study by Karl Johnson, Caitlin B. Biddell, Kristen Hassmiller Lich, Julie Swann, Paul Delamater, Maria Mayorga, Julie Ivy, Raymond L. Smith and Mehul D. Patel in MDM Policy & Practice
Additional file 2 of PTBP1 plays an important role in the development of gastric cancer
Creators: name: Chu, Zewen
name: Zhu, Miao
name: Luo, Yuanyuan
name: Hu, Yaqi
name: Feng, Xinyi
name: Wang, Haibo
name: Sunagawa, Masataka
name: Liu, Yanqing
Publisher: name: figshare
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Chemical Sciences not elsewhere classified
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences

description: Supplementary File 2: Ptbp1 Cas9-KO Strategy
Dynamical symmetries of supersymmetric oscillators
Creators: name: Sinha, Akash
name: Ghosh, Aritra
name: Bagchi, Bijan
Publisher: name: arXiv
Year: 2023
Subjects: subject: Mathematical Physics (math-ph)
subject: High Energy Physics - Theory (hep-th)
subject: Classical Physics (physics.class-ph)
subject: FOS: Physical sciences

description: In this paper, we describe the dynamical symmetries of classical supersymmetric oscillators in one and two spatial (bosonic) dimensions. Our main ingredient is a generalized Poisson bracket which is defined as a suitable classical counterpart to commutators and anticommutators. In one dimension, i.e., in the presence of one bosonic and one fermionic coordinate, the Hamiltonian admits a $U(1,1)$ symmetry for which we explicitly compute the first integrals. It is found that suitable forms of the supercharges emerge in a natural way as fermionic conserved quantities. Following this, we describe classical supercharge operators based on the generalized Poisson bracket and subsequently define supersymmetry transformations. We perform a straightforward generalization to two spatial dimensions where the Hamiltonian has an overall $U(2,2)$ symmetry. We comment on plausible supersymmetric generalizations of the Pais-Uhlenbeck and isotonic oscillators, and also present the possibility of defining a generalized Nambu bracket within the classical formalism.
description: v2: Minor correction to section-(VA), references added; v3: Substantially revised, to appear in Physica Scripta; v4: Minor changes and one typo corrected
THE ROLE OF SPIRITUALITY IN SCIENCE AND NEW UZBEKISTAN
Creators: name: Abdiyev, Jenisbay
Publisher: name: Zenodo
Year: 2024

description: This article delves into the role of spirituality in shaping the trajectory of science and innovation in Uzbekistan. By exploring the historical significance of spirituality in the country, examining its impact on educational systems, and envisioning its role in nation-building, we aim to illuminate the transformative potential of embracing spirituality as a guiding force in the pursuit of progress.
Adapting UPSKILLS Modules to the University Curricula: CLARIN-IT Training Experience at the University of Ferrara
Creators: name: Pedonese, Giulia
Publisher: name: Zenodo
Year: 2024
Subjects: subject: training
subject: Linguistics
subject: FOS: Languages and literature
subject: Digital humanities

description:  

This presentation outlines the process of adapting and integrating CLARIN ERIC’s training materials into three language-focused university courses at the University of Ferrara. Our workflow draws on the training strategy developed in the Humanities and Heritage Italian Open Science Cloud (H2IOSC) project. It involves customising the UPSKILLS “Introduction to Language Data: Standards and Repositories” course to meet the specific needs of three English-to-Italian translation courses: English Language for Tourism, English Language for Translation and English Language and Linguistics for Humanities, Arts and Archaeology. By the end, we will present a practical example of how CLARIN services can enhance university teaching and teacher training and discuss its potential as a model for other educators interested in incorporating CLARIN into their curricula.
sj-doc-5-whe-10.1177_17455057221114274 – Supplemental material for Self-reported mental well-being of mothers with young children during the first wave of the COVID-19 pandemic in Germany: A mixed-methods study
Creators: name: Wandschneider, Lisa
name: Batram-Zantvoort, Stephanie
name: Alaze, Anita
name: Niehues, Vera
name: Spallek, Jacob
name: Razum, Oliver
name: Miani, Céline
Publisher: name: SAGE Journals
Year: 2022
Subjects: subject: 111402 Obstetrics and Gynaecology
subject: FOS: Clinical medicine

description: Supplemental material, sj-doc-5-whe-10.1177_17455057221114274 for Self-reported mental well-being of mothers with young children during the first wave of the COVID-19 pandemic in Germany: A mixed-methods study by Lisa Wandschneider, Stephanie Batram-Zantvoort, Anita Alaze, Vera Niehues, Jacob Spallek, Oliver Razum and Céline Miani in Women’s Health