cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Analysis of problems and potentials for increasing pandemic resilience in public health administrations in Saxony-Anhalt, Germany : a mixed-methods approach
Creators: name: Samtlebe, Pascal
name: Niemann, Jana-Kristin
name: Markert, Jenny
name: Knöchelmann, Anja
name: Bernard, Marie
Publisher: name: Universitäts- und Landesbibliothek Sachsen-Anhalt
Year: 2024
Subjects: subject: 610

description: Introduction: The COVID-19 pandemic has shown the importance of resilient, modern, and well-equipped public health administrations from national to communal levels. In Germany, the surveillance, contact tracing, and local adaptions went through local health offices, revealing both their important role and also their lack of equipment and general preparation for health crises. Research on the mode of operation of the public health service (PHS), especially in a time of crisis, is rare. The present study aims to qualitatively and quantitatively assess problem areas, conflict potentials, and challenges that have become apparent for the PHS of Saxony-Anhalt during the pandemic. It focuses on the individual insight of employees of the PHS of Saxony-Anhalt and its 14 health offices to derive concrete needs and fields of action for increasing pandemic preparedness. Furthermore, the prospective personnel and resource-based requirements as well as the necessary structural and organisational changes of the public health departments are to be considered. Methods and analysis: The study will follow a sequential mixed-methods approach. Introductory expert interviews (n=12) with leading staff of Saxony-Anhalt’s PHS will be conducted, followed by focus group interviews (n=4) with personnel from all departments involved in the pandemic response. Thereafter, a quantitative survey will be carried out to validate and complement the results of the qualitative phase. Ethics and dissemination: Ethical approval was obtained by the Martin-Luther-Universität Halle-Wittenberg ethics commission (Ref number 2023-102). The authors will submit the results of the study to relevant peer-reviewed journals and give national and international oral presentations to researchers, members of the PHS, and policymakers.
Additional file 4 of The diagnostic value of lower glucose consumption for IDH1 mutated gliomas on FDG-PET
Creators: name: Liu, Feng-Min
name: Gao, Yu-fei
name: Kong, Yanyan
name: Guan, Yihui
name: Zhang, Jinsen
name: Li, Shuai-Hong
name: Ye, Dan
name: Wen, Wenyu
name: Zuo, Chuantao
name: Hua, Wei
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Additional file 4.
BindingDB Entry 12155: PHENYL AZEPINES AS RIPK1 INHIBITORS AND METHODS OF USE THEREOF
Creators: name: BindingDB
Publisher: name: BindingDB
Year: 2024
Subjects: Receptor-interacting serine/threonine-protein kinase 1, Merck Sharp & Dohme, Affinity

description: Small molecule binding data for protein Receptor-interacting serine/threonine-protein kinase 1, Uniprot Q13546
Additional file 1 of The diagnostic value of lower glucose consumption for IDH1 mutated gliomas on FDG-PET
Creators: name: Liu, Feng-Min
name: Gao, Yu-fei
name: Kong, Yanyan
name: Guan, Yihui
name: Zhang, Jinsen
name: Li, Shuai-Hong
name: Ye, Dan
name: Wen, Wenyu
name: Zuo, Chuantao
name: Hua, Wei
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Additional file 1 Supplementary Table 1: Characteristic of patient population subjected to pathological evaluation, related to Fig. 1.
There is no 'velocity kick' memory in electrodynamics
Creators: name: Herdegen, Andrzej
Publisher: name: arXiv
Year: 2023
Subjects: subject: Classical Physics (physics.class-ph)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Mathematical Physics (math-ph)
subject: FOS: Physical sciences
subject: 81V10

description: The memory effect in electrodynamics, as discovered in 1981 by Staruszkiewicz, and also analysed later, consists of adiabatic shift of the position of a test particle. The proposed 'velocity kick' memory effect, supposedly discovered recently, is in contradiction to these findings. We show that the 'velocity kick' memory is an artefact resulting from an unjustified interchange of limits. This example is a warning against drawing uncritical conclusions for spacetime fields, from their asymptotic behavior.
description: 5 pages, minor corrections, comments added
BindingDB Entry 12154: BIVALENT LIGANDS TO UNDERSTAND DIMERIZATION OF THE MU OPIOID RECEPTOR AND THE CHEMOKINE RECEPTOR CCR5 IN NEUROLOGICAL DISORDERS
Creators: name: BindingDB
Publisher: name: BindingDB
Year: 2024
Subjects: C-C chemokine receptor type 5 and Protein MOR1, Virginia Commonwealth University, Affinity

description: Small molecule binding data for protein C-C chemokine receptor type 5 and Protein MOR1, Uniprot P51681
Medication Adherence in Adolescents with HIV: The Impact of Body Dissatisfaction
Creators: name: Woods, Amanda
Publisher: name: Georgia State University
Year: 2010

description: Human immune deficiency virus (HIV) and Acquire immune deficiency syndrome (AIDS) is a worldwide epidemic that impacts individuals physically, socially, and psychologically, and the rates of HIV/AIDS in youth are rising. Antiretroviral treatments have drastically prolonged life in individuals with HIV/AIDS; however, this type of treatment requires strict medication adherence. Many psychosocial factors impacting antiretroviral adherence have been explored, yet very little has been investigated regarding body image. This study investigated the potential impact of body dissatisfaction on antiretroviral medication adherence in adolescents with HIV. Seventy five male and female youth were administered questionnaires on the constructs of body dissatisfaction and medication adherence. Results support the hypothesis that body dissatisfaction negatively impacts medication adherence; yet, its effect in this sample was small (R2 = .06; F(1,61) =3.87, p =.05). Additionally, it was predicted that gender would moderate the nature of the relation between body dissatisfaction and medication adherence, given the disparate societal presentations of ideal body types among genders. However, within the current sample, gender did not have an effect on this relation. Furthermore, this study was interested in exploring if body dissatisfaction within a population of HIV-infected youth was best explained by specific body dissatisfaction with areas of the body associated with lipodystrophy or lipoatrophy syndromes. Due to a very small presentation of these syndromes in the final sample (n = 4), it was not surprising that body dissatisfaction was not best explained through specific dissatisfaction with these body parts. However, dissatisfaction with muscularity in general, was predictive of general body dissatisfaction regardless of gender. A discussion of these findings is included. This study is one of the first of its kind to explore the potential detrimental effects of body dissatisfaction in HIV infected youth.
An indacenopicene-based buckybowl catcher for recognition of fullerenes
Creators: name: Scholz, Barbara
name: Oshchepkov, Alexander S.
name: Papaianina, Olena
name: Ruppenstein, Cordula
name: Akhmetov, Vladimir A.
name: Sharapa, Dmitry I.
name: Amsharov, Konstantin
name: Pérez-Ojeda, M. Eugenia
Publisher: name: Universitäts- und Landesbibliothek Sachsen-Anhalt
Year: 2023
Subjects: subject: 540

description: A novel buckybowl catcher with an extended π-surface has been synthesized via cross-coupling of two bowl shaped bromoindacenopicene moieties with a tolyl linker. The obtained catcher has been unambiguously characterized by 2D-NMR and mass spectrometry. DFT calculations indicate that the curved shape of the receptor moieties is favourable for binding fullerenes. Effective binding was confirmed for interactions with C60 and C70 utilizing NMR spectroscopy and isothermal titration calorimetry (ITC). The resulting binding values show a higher affinity of the catcher towards C70 over C60. The designed catcher demonstrated the fundamental possibility of creating sensors for spherical aromaticity.
Additional file 3 of The diagnostic value of lower glucose consumption for IDH1 mutated gliomas on FDG-PET
Creators: name: Liu, Feng-Min
name: Gao, Yu-fei
name: Kong, Yanyan
name: Guan, Yihui
name: Zhang, Jinsen
name: Li, Shuai-Hong
name: Ye, Dan
name: Wen, Wenyu
name: Zuo, Chuantao
name: Hua, Wei
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Additional file 3.
Introduction to Feature selection for bioinformaticians using R
Creators: name: Yasset Perez-Riverol
Publisher: name: figshare
Year: 2016
Subjects: subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: 80301 Bioinformatics Software

description: Bioinformatics is becoming more and more a Data Mining field. Every passing day, Genomics and Proteomics yield bucketloads of multivariate data (genes, proteins, DNA, identified peptides, structures), and every one of these biological data units is described by a number of features: length, physicochemical properties, scores, etc. Careful consideration of which features to select when trying to reduce the dimensionality of a specific dataset is, therefore, critical if one wishes to analyze and understand their impact on a model, or to identify what attributes produce a specific biological effect.
For instance, considering a predictive model C1A1 + C2A2 + C3A3 … CnAn = S, where Ci are constants, Ai are features or attributes and S is the predictor output (retention time, toxicity, score, etc). It is essential to identify which of those features (A1, A2 and A3…An) are most relevant to the model and to understand how they correlate with S, as working with such a subset will enable the researcher to discard a lot of irrelevant and redundant information.

There are two main approaches to this selection process:
Filter approaches: you select the features first, then you use this subset to execute classification or clustering algorithms, etc;Embedded or Wrapper approaches a classification algorithm is applied to the raw dataset in order to identify the most relevant features.One of the simplest and most powerful filter approaches is the use of correlation matrix filters. In regression and data mining problems, variables may be highly correlated with one another or "redundant". For example in cheminformatics, aromatic rings, bond counts and carbon atom counts can be very tightly correlated. If so, any one of these variables could be used as a proxy for all the others. It is best to choose the feature which is most likely to be the direct cause of toxicity, absorption or a specific response distribution.
In this blog post we presented some advance techniques to perform feature selection in bioinformatics.
Consistent first order action functional for gauge theories
Creators: name: Gallagher, Priidik
name: Koivisto, Tomi S.
name: Marzola, Luca
name: Varrin, Ludovic
name: Zlosnik, Tom
Publisher: name: arXiv
Year: 2023
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: A novel first order action principle has been proposed as the possible foundation for a more fundamental theory of General Relativity and the Standard Model. It is shown in this article that the proposal consistently incorporates gravity and matter fields, and guides to a new and robust path towards unification of fundamental interactions.
description: 6 pages and references
BindingDB Entry 12153: NITROGEN-CONTAINING HETEROCYCLIC POLYCYCLIC COMPOUND, PREPARATION METHOD THEREFOR, AND APPLICATION THEREOF
Creators: name: BindingDB
Publisher: name: BindingDB
Year: 2024
Subjects: Cytochrome P450 1A2, Cytochrome P450 2C19, Cytochrome P450 2C9, and Cytochrome P450 2D6, Shanghai Hansoh Biomedical Co., Affinity

description: Small molecule binding data for protein Cytochrome P450 1A2, Cytochrome P450 2C19, Cytochrome P450 2C9, and Cytochrome P450 2D6, Uniprot P05177, P10635, P11712, and P33261
Gravitational Aharonov-Bohm Effect
Creators: name: Chiao, RY
name: Inan, NA
name: Scheibner, M
name: Sharping, J
name: Singleton, DA
name: Tobar, ME
Publisher: name: arXiv
Year: 2023
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Atomic Physics (physics.atom-ph)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: We investigate the gravitational Aharonov-Bohm effect, by placing a quantum system in free-fall around a gravitating body {\it e.g.} a satellite orbiting the Earth. Since the system is in free-fall, by the equivalence principle, the quantum system is locally in flat, gravity-free space-time - it is screened from the gravitational field. For a slightly elliptical orbit, the gravitational potential will change with time. This leads to the energy levels of the quantum system developing side bands which is the signature for this version of the Aharonov-Bohm effect. This contrasts with the normal signature of the Aharonov-Bohm effect of shifting of interference fringes.
description: Published version
Open Access an der TH Köln und darüber hinaus
Creators: name: Lukas, Florian
Publisher: name: Zenodo
Year: 2024

description: The presentation presents some thoughts on the Open Access principle. The focus is on accessibility to publications and obstacles. Especially with regard to countries of the "Global South", a fairer and more barrier-free scientific exchange is desirable, as this ultimately benefits everyone. One possibility would certainly be to revise the publication system in general. Large research institutions such as the TH Köln can help with this.
Plug-and-Play Latent Feature Editing for Orientation-Adaptive Quantitative Susceptibility Mapping Neural Networks
Creators: name: Gao, Yang
name: Xiong, Zhuang
name: Shan, Shanshan
name: Liu, Yin
name: Rong, Pengfei
name: Li, Min
name: Wilman, Alan H
name: Pike, G. Bruce
name: Liu, Feng
name: Sun, Hongfu
Publisher: name: arXiv
Year: 2023
Subjects: subject: Image and Video Processing (eess.IV)
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: Quantitative susceptibility mapping (QSM) is a post-processing technique for deriving tissue magnetic susceptibility distribution from MRI phase measurements. Deep learning (DL) algorithms hold great potential for solving the ill-posed QSM reconstruction problem. However, a significant challenge facing current DL-QSM approaches is their limited adaptability to magnetic dipole field orientation variations during training and testing. In this work, we propose a novel Orientation-Adaptive Latent Feature Editing (OA-LFE) module to learn the encoding of acquisition orientation vectors and seamlessly integrate them into the latent features of deep networks. Importantly, it can be directly Plug-and-Play (PnP) into various existing DL-QSM architectures, enabling reconstructions of QSM from arbitrary magnetic dipole orientations. Its effectiveness is demonstrated by combining the OA-LFE module into our previously proposed phase-to-susceptibility single-step instant QSM (iQSM) network, which was initially tailored for pure-axial acquisitions. The proposed OA-LFE-empowered iQSM, which we refer to as iQSM+, is trained in a self-supervised manner on a specially-designed simulation brain dataset. Comprehensive experiments are conducted on simulated and in vivo human brain datasets, encompassing subjects ranging from healthy individuals to those with pathological conditions. These experiments involve various MRI platforms (3T and 7T) and aim to compare our proposed iQSM+ against several established QSM reconstruction frameworks, including the original iQSM. The iQSM+ yields QSM images with significantly improved accuracies and mitigates artifacts, surpassing other state-of-the-art DL-QSM algorithms.
description: 13pages, 9figures
BindingDB Entry 12152: SUBSTITUTED HYDANTOIN COMPOUNDS, METHODS FOR PREPARATION THEREOF AND USE THEREOF IN THE TREATMENT AND/OR PREVENTION OF A CORONA VIRUS DISEASE
Creators: name: BindingDB
Publisher: name: BindingDB
Year: 2024
Subjects: Replicase polyprotein 1ab, Affinity

description: Small molecule binding data for protein Replicase polyprotein 1ab, Uniprot A0A679G4D8, A0A6B9V049, A0A6B9VP19, A0A6V7ALW7, and P0DTD1
Discretized Distributed Optimization over Dynamic Digraphs
Creators: name: Doostmohammadian, Mohammadreza
name: Jiang, Wei
name: Liaquat, Muwahida
name: Aghasi, Alireza
name: Zarrabi, Houman
Publisher: name: arXiv
Year: 2023
Subjects: subject: Optimization and Control (math.OC)
subject: Machine Learning (cs.LG)
subject: Systems and Control (eess.SY)
subject: Signal Processing (eess.SP)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences
subject: FOS: Electrical engineering, electronic engineering, information engineering

description: We consider a discrete-time model of continuous-time distributed optimization over dynamic directed-graphs (digraphs) with applications to distributed learning. Our optimization algorithm works over general strongly connected dynamic networks under switching topologies, e.g., in mobile multi-agent systems and volatile networks due to link failures. Compared to many existing lines of work, there is no need for bi-stochastic weight designs on the links. The existing literature mostly needs the link weights to be stochastic using specific weight-design algorithms needed both at the initialization and at all times when the topology of the network changes. This paper eliminates the need for such algorithms and paves the way for distributed optimization over time-varying digraphs. We derive the bound on the gradient-tracking step-size and discrete time-step for convergence and prove dynamic stability using arguments from consensus algorithms, matrix perturbation theory, and Lyapunov theory. This work, particularly, is an improvement over existing stochastic-weight undirected networks in case of link removal or packet drops. This is because the existing literature may need to rerun time-consuming and computationally complex algorithms for stochastic design, while the proposed strategy works as long as the underlying network is weight-symmetric and balanced. The proposed optimization framework finds applications to distributed classification and learning.
BindingDB Entry 12151: PYRIDOPYRIMIDINES AND METHODS OF THEIR USE
Creators: name: BindingDB
Publisher: name: BindingDB
Year: 2024
Subjects: 1-phosphatidylinositol 3-phosphate 5-kinase, Kineta, Affinity

description: Small molecule binding data for protein 1-phosphatidylinositol 3-phosphate 5-kinase, Uniprot Q9Y2I7
V: Excavations at Warrington Friary 2000
Creators: name: Heawood, Richard
name: Howard-Davis, Christine L E
name: Boylston, Anthea
name: Weston, D
Publisher: name: Archaeology Data Service
Year: 2018

description: Journal of the Chester Archaeological Society, 77, 131-185
description: Excavation on the site of the Augustinian friary at Warrington found evidence of five phases of activity, beginning in the Roman period. Remains of this date included three pits, and two extensive deposits which produced 353 sherds of Romano-British pottery; it is suggested that the pottery was being made or distributed in the immediate vicinity. The first church of the Augustinian friars was probably built soon after 1261, and the sandstone foundations of the north wall and internal column plinths of the nave were revealed. The most distinctive feature of the church was the large, almost square north transept; the excavation showed this to be a later addition, probably built by c. 1350. The church was retained for the use of the townspeople when the friary was dissolved in 1539, and the removal of the floor covering may have followed soon afterwards, whilst the north transept is likely to have been taken down before the end of the sixteenth century; the nave was demolished by the mid- to late seventeenth century. In total, 106 partial or complete articulated inhumations were excavated. Thirty-seven burials were identified as predating the Dissolution, including two in partially surviving coffins, dated by dendrochronology to the late thirteenth or early fourteenth centuries. It is clear that the site was used for burial until the eighteenth century. Includes separately authored reports on:
Active elastic metamaterials with equidistant solely resonant bandgaps
Creators: name: Ba'ba'a, Hasan B. Al
Publisher: name: arXiv
Year: 2023
Subjects: subject: Applied Physics (physics.app-ph)
subject: FOS: Physical sciences

description: Elastic metamaterials are man-made structures with properties that transcend naturally occurring materials. One predominant feature of elastic metamaterials is locally resonant bandgaps, i.e., frequency ranges at which wave propagation is blocked. Locally resonant bandgaps appear at relatively low frequency and arise from the existence of periodically placed mechanical local resonators. Typically, elastic metamaterials exhibit both locally resonant and Bragg-scattering bandgaps, which can generally be different in width and frequency ranges. This paper proposes two designs of active elastic metamaterials that only exhibit locally resonant bandgaps, which are infinite in number, evenly spaced in the frequency spectrum, and identical in width. The mathematical model is established using the transfer matrix method and synthesis of locally resonant bandgaps is achieved via an active elastic support with carefully designed frequency-dependent stiffness. A single unit cell of each proposed metamaterials is thoroughly studied, and its dispersion relation is derived analytically, along with the periodically repeating bandgap limits and widths. Following the dispersion analysis and bandgap parametric studies, finite arrays of the proposed metamaterials are considered, and their frequency response is calculated to verify the analytical predictions from dispersion analyses.
I: The late prehistoric and Romano-British settlement of the Mersey basin: a study in marginality
Creators: name: Nevell, Michael D
Publisher: name: Archaeology Data Service
Year: 2018

description: Journal of the Chester Archaeological Society, 78, 1-21
description: The paper presents an overview of some attempts to provide a theoretical framework for both the location and interpretation of the number of late prehistoric and Romano-British rural sites within the Mersey Basin region, centred around the theme of marginality. It uses the body of archaeological evidence for the period to look at the issues of climatic and social marginality. The debate on the rural settlement of these periods is focused on the social hierarchy and material culture of the area and whether this was distinctive, both before and after the Roman conquest.
BindingDB Entry 12150: 1,3,4-OXADIAZOLE THIOCARBONYL COMPOUNDS AS HISTONE DEACETYLASE 6 INHIBITOR, AND PHARMACEUTICAL COMPOSITION COMPRISING THE SAME
Creators: name: BindingDB
Publisher: name: BindingDB
Year: 2024
Subjects: Histone deacetylase 6, Chong Kun Dang Pharmaceutical, Affinity

description: Small molecule binding data for protein Histone deacetylase 6, Uniprot Q9UBN7
Additional file 6 of The diagnostic value of lower glucose consumption for IDH1 mutated gliomas on FDG-PET
Creators: name: Liu, Feng-Min
name: Gao, Yu-fei
name: Kong, Yanyan
name: Guan, Yihui
name: Zhang, Jinsen
name: Li, Shuai-Hong
name: Ye, Dan
name: Wen, Wenyu
name: Zuo, Chuantao
name: Hua, Wei
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Additional file 6.
MAM-E: Mammographic synthetic image generation with diffusion models
Creators: name: Montoya-del-Angel, Ricardo
name: Sam-Millan, Karla
name: Vilanova, Joan C
name: Martí, Robert
Publisher: name: arXiv
Year: 2023
Subjects: subject: Image and Video Processing (eess.IV)
subject: Computer Vision and Pattern Recognition (cs.CV)
subject: FOS: Electrical engineering, electronic engineering, information engineering
subject: FOS: Computer and information sciences

description: Generative models are used as an alternative data augmentation technique to alleviate the data scarcity problem faced in the medical imaging field. Diffusion models have gathered special attention due to their innovative generation approach, the high quality of the generated images and their relatively less complex training process compared with Generative Adversarial Networks. Still, the implementation of such models in the medical domain remains at early stages. In this work, we propose exploring the use of diffusion models for the generation of high quality full-field digital mammograms using state-of-the-art conditional diffusion pipelines. Additionally, we propose using stable diffusion models for the inpainting of synthetic lesions on healthy mammograms. We introduce MAM-E, a pipeline of generative models for high quality mammography synthesis controlled by a text prompt and capable of generating synthetic lesions on specific regions of the breast. Finally, we provide quantitative and qualitative assessment of the generated images and easy-to-use graphical user interfaces for mammography synthesis.
description: 10 pages + 2 pages of references, 6 figures
BindingDB Entry 12149: "Cyclopenta[c]pyrrol Negative Allosteric Modulators of NR2B"
Creators: name: BindingDB
Publisher: name: BindingDB
Year: 2024
Subjects: Potassium voltage-gated channel subfamily H member 2, Novartis, Affinity

description: Small molecule binding data for protein Potassium voltage-gated channel subfamily H member 2, Uniprot Q12809
BindingDB Entry 12148: 6-CARBAMATE SUBSTITUTED HETEROARYL RING DERIVATIVES
Creators: name: BindingDB
Publisher: name: BindingDB
Year: 2024
Subjects: Son of sevenless homolog 1 [564-1049]/GTPase KRas [G12C], Medshine Discovery, Affinity

description: Small molecule binding data for protein Son of sevenless homolog 1 [564-1049]/GTPase KRas [G12C], Uniprot P01116 and Q07889
Test set of clinical meta-data for Local Control Challenge
Creators: name: Fuller, Clifton
name: Mohamed, Abdallah
name: Elhalawani, Hesham
Publisher: name: figshare
Year: 2016
Subjects: subject: 111208 Radiation Therapy
subject: FOS: Clinical medicine

description: This MD Anderson Cancer Center set of anonymized high-quality computed tomography (CT) scans with contrast represent a comparatively homogeneous, uniform cohort of 288 oropharynx cancer patients with detailed clinical history, consistent follow-up of > 2 years, known etiological/biological correlates (specifically, human papilloma virus status). Our major target is to assess/validate the radiomics workflow and predictive capacity of radiomics signatures from challenge participants.We imported the CT scans from the patients’ electronic medical records, that were performed before the initiation of the radiation treatment course. All the patients were treated using the IMRT modality. Some patients were simultaneously prescribed chemotherapy. We intended that the CT films would be as much representative of the original simulation CT scans that were used for treatment planning, in which no contrast was injected according to our institutional policy.Specifically, we posted around one-half of the CT scans from the dataset (138 patients), in DICOM-RT format, on the Kaggle in Class server system, as a “training set”. DICOM-RT files were fully anonymized, with expert physician segmenting primary tumor and lymph node as regions of interest, to eliminate segmentation-related uncertainty for challengers. The primary oropharyngeal tumor was segmented in red. Whereas, the metastatic cervical lymph nodes were segmented individually, rather than on the basis of the nodal level classification system. Both training and test sets include the following data for each DICOM-RT case:agegenderracetumor side and subsiteT-categoryN-categoryAJCC stagePathologic gradesmoking status (in pack-years)Challenge participants will also be able to download a “test" dataset, which includes the remaining randomly selected 150 patients' DICOM files and relevant clinical meta-data, with local control status blinded.Challenge participants will also be able to download a “test" dataset, which includes the remaining randomly selected half of the dataset, with local control status blinded.Challenge participants will also be able to download a “test" dataset, with the remaining random selected half of the dataset, which will have the local recurrence status blinded.
BindingDB Entry 12147: Quinazoline Derivatives, Pharmaceutical Compositions, and Therapeutic Uses Related to Nox Inhibition
Creators: name: BindingDB
Publisher: name: BindingDB
Year: 2024
Subjects: Cytochrome b-245 heavy chain and NADPH oxidase 4, Emory University, Affinity

description: Small molecule binding data for protein Cytochrome b-245 heavy chain and NADPH oxidase 4, Uniprot P04839 and Q9HBY0
Additional file 2 of The diagnostic value of lower glucose consumption for IDH1 mutated gliomas on FDG-PET
Creators: name: Liu, Feng-Min
name: Gao, Yu-fei
name: Kong, Yanyan
name: Guan, Yihui
name: Zhang, Jinsen
name: Li, Shuai-Hong
name: Ye, Dan
name: Wen, Wenyu
name: Zuo, Chuantao
name: Hua, Wei
Publisher: name: figshare
Year: 2021
Subjects: subject: Biochemistry
subject: Medicine
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Additional file 2.
title:  The Disappearing Disease
Creators: name: Weddington, Heather M.
Publisher: name: Old Dominion University
publisherIdentifier: https://ror.org/04zjtrb98
publisherIdentifierScheme: ROR
Year: 2011

description: This series of connected essays explores the aesthetic of fragmentation, not as a means to disrupt narrative, but as a means to stretch that narrative. It includes both lyric and traditional forms, along with a series of flash essays that puncture the present action with moments from the past. The essays vary tonally, from the serious to the comic, and though they are connected through first person narration, they are more connected thematically, through an exploration of sexuality, faith, idealism and its loss, and the ways in which gender is performed.
II: Some unusual Roman antefixes from Chester
Creators: name: Jones, Alison
Publisher: name: Archaeology Data Service
Year: 2018

description: Journal of the Chester Archaeological Society, 78, 23-47
description: Two Roman antefixes of apparently unique design were recovered from the fortress bath house site in Chester during excavations at the junction of Newgate and Pepper Street in 1963--4. One is almost complete and depicts the head of Jupiter Ammon; the other comprises a small fragment depicting a lion's head or mask. Together, they represent examples of a distinct group of antefixes that have been retrieved from a handful of sites within the city. None have been recovered from the legionary works depot at Holt, which produced ceramic building materials for the fortress from the late-first century AD. In comparing them with the more common inscribed antefixes of the Twentieth Legion, which are known from both Chester and Holt (where they were made), a number of questions concerning their distribution, dating and possible origin are considered.
Towards the Intuitive Understanding of Quantum World: Sonification of Rabi Oscillations, Wigner functions, and Quantum Simulators
Creators: name: Yamada, Reiko
name: Piñol, Eloy
name: Grandi, Samuele
name: Zakrzewski, Jakub
name: Lewenstein, Maciej
Publisher: name: arXiv
Year: 2023
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Recently, there has been considerable interest in "sonifying" scientific data; however, sonifying quantum processes using the newest quantum technologies, including Noise Intermediate Scale Quantum devices and quantum random number generators, is still an emerging area of research. Music technologists and composers employ the growing accessibility to diverse data from quantum mechanics as musical tools in the hope of generating new sound expressions. How different is the quantum world from the classical one, and is it possible to express the quantum world using sounds? Quantum phenomena are very different from those that we experience in our everyday lives. Thus, it is challenging to understand them intuitively. In this paper, we propose sonification as a method toward an intuitive understanding of various quantum mechanical phenomena, from Rabi oscillations and resonance fluorescence of a single atom through the generation of Schrödinger cat states in strong laser field physics to insulator-superfluid transition in quantum many-body systems. This paper illustrates various methods we experimented with in sonification and score representations of quantum data depending on the source data and performance settings.
description: 8 pages, 12 figures, presented at the 2nd International Symposium on Quantum Computing and Musical Creativity 2023; typos corrected
title: A Preliminary Comparative Study of Molecular Visualization Software for Education
Creators: name: Shen, Ruoming
Publisher: name: Old Dominion University Libraries
Year: 2022

description: Chemistry and biology are sciences vital for understanding metabolic processes, developing disease treatments, and improving environmental conditions. With extensive knowledge of biochemistry, we can take advantage of a material’s unique chemical composition and properties in various applications. Visualization software is essential for analyzing complex chemical and biological structures and predicting their interactions with each other. This paper presents a preliminary study of three open source molecular visualization software tools - Visual Molecular Dynamics (VMD), Jmol, and Mol*, and evaluates their strengths and deficiencies. This paper utilizes the March Molecule of the Month, Vascular Endothelial Growth Factor (VEGF), from the Protein Data Bank as a case study. The VEGF is a complex signaling protein that stimulates angiogenesis for building new blood vessels. All three tools handle VEGF well by providing a variety of visualization and analytical capabilities, with Jmol and Mol* better suited for educational purposes and VMD for research purposes. The paper also discusses the author’s interest and intent to contribute to the development of molecular visualization software in the future.
BindingDB Entry 12146: SMALL-MOLECULE INHIBITORS FOR BETA-CATENIN/BCELL LYMPHOMA 9 PROTEIN-PROTEIN INTERACTION
Creators: name: BindingDB
Publisher: name: BindingDB
Year: 2024
Subjects: Catenin beta -1 [E155A]/B-Cell CLL/Lymphoma 9 Protein [350-375]/Cadherin-1 [824-877], H. Lee Moffitt Cancer Center And Research Institute, Affinity

description: Small molecule binding data for protein Catenin beta -1 [E155A]/B-Cell CLL/Lymphoma 9 Protein [350-375]/Cadherin-1 [824-877]
BindingDB Entry 12145: ARYLAMINO DERIVATIVE ESTROGEN RECEPTOR MODULATOR AND USE THEREOF
Creators: name: BindingDB
Publisher: name: BindingDB
Year: 2024
Subjects: Cytochrome P450 1A2, Cytochrome P450 2C19, Cytochrome P450 2C9, Cytochrome P450 2D6, and Cytochrome P450 3A4, Xizang Haisco Pharmaceutical Co., Affinity

description: Small molecule binding data for protein Cytochrome P450 1A2, Cytochrome P450 2C19, Cytochrome P450 2C9, Cytochrome P450 2D6, and Cytochrome P450 3A4, Uniprot P05177, P08684, P10635, P11712, and P33261
Disentangling the Spectral Properties of the Hodge Laplacian: Not All Small Eigenvalues Are Equal
Creators: name: Grande, Vincent P.
name: Schaub, Michael T.
Publisher: name: arXiv
Year: 2023
Subjects: subject: Algebraic Topology (math.AT)
subject: Machine Learning (cs.LG)
subject: FOS: Mathematics
subject: FOS: Computer and information sciences

description: The rich spectral information of the graph Laplacian has been instrumental in graph theory, machine learning, and graph signal processing for applications such as graph classification, clustering, or eigenmode analysis. Recently, the Hodge Laplacian has come into focus as a generalisation of the ordinary Laplacian for higher-order graph models such as simplicial and cellular complexes. Akin to the traditional analysis of graph Laplacians, many authors analyse the smallest eigenvalues of the Hodge Laplacian, which are connected to important topological properties such as homology. However, small eigenvalues of the Hodge Laplacian can carry different information depending on whether they are related to curl or gradient eigenmodes, and thus may not be comparable. We therefore introduce the notion of persistent eigenvector similarity and provide a method to track individual harmonic, curl, and gradient eigenvectors/-values through the so-called persistence filtration, leveraging the full information contained in the Hodge-Laplacian spectrum across all possible scales of a point cloud. Finally, we use our insights (a) to introduce a novel form of Hodge spectral clustering and (b) to classify edges and higher-order simplices based on their relationship to the smallest harmonic, curl, and gradient eigenvectors.
description: 5 pages, 4 figures, comments welcome
BindingDB Entry 12144: SUBSTITUTED QUINOLINE DERIVATIVES HAVING SOS1 INHIBITION ACTIVITIES AND USES THEREOF
Creators: name: BindingDB
Publisher: name: BindingDB
Year: 2024
Subjects: GTPase KRas (G12D) and Son of Sevenless Homolog 1 (SOS), Accutar Biotechnology, Affinity

description: Small molecule binding data for protein GTPase KRas (G12D) and Son of Sevenless Homolog 1 (SOS), Uniprot P01116 and Q07889
Additional file 1 of Identification of a small molecule as inducer of ferroptosis and apoptosis through ubiquitination of GPX4 in triple negative breast cancer cells
Creators: name: Ding, Yahui
name: Chen, Xiaoping
name: Liu, Can
name: Ge, Weizhi
name: Wang, Qin
name: Hao, Xin
name: Wang, Mengmeng
name: Chen, Yue
name: Zhang, Quan
Publisher: name: figshare
Year: 2021
Subjects: Biophysics
Biochemistry
Space Science
Cell Biology
Molecular Biology
Pharmacology
Chemical Sciences not elsewhere classified
Cancer

description: Additional file 1. NMR copies of compounds.
Efficient and robust second-harmonic generation in thin-film lithium niobate using modal phase matching
Creators: name: Hansen, Mikkel T.
name: Ulsig, Emil Z.
name: Labbe, Fabien
name: Madsen, Magnus L.
name: Ding, Yunhong
name: Rottwitt, Karsten
name: Volet, Nicolas
Publisher: name: arXiv
Year: 2023
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: A double-ridge waveguide is designed for efficient and robust second-harmonic generation (SHG) using the thin-film lithium-niobate-on-insulator (LNOI) platform. Perfect phase matching (PhM) is achieved between the fundamental waveguide mode at 1550 nm and a higher-order mode at the second harmonic. The fabrication tolerances of the PhM condition are simulated using a finite-difference method mode solver, and conversion efficiencies as high as 3.92/W are obtained for a 1-cm long waveguide. This design allows access to the largest element of the second-order nonlinear susceptibility tensor, and represents a scalable alternative to waveguides based on periodically-poled lithium niobate (PPLN). The design has the potential for generating pairs of entangled photons in the infrared C-band by spontaneous parametric down-conversion (SPDC).
Modelling wildland fire burn severity in California using a spatial Super Learner approach
Creators: name: Simafranca, Nicholas
name: Willoughby, Bryant
name: O'Neil, Erin
name: Farr, Sophie
name: Reich, Brian J
name: Giertych, Naomi
name: Johnson, Margaret
name: Pascolini-Campbell, Madeleine
Publisher: name: arXiv
Year: 2023
Subjects: subject: Machine Learning (cs.LG)
subject: Applications (stat.AP)
subject: FOS: Computer and information sciences
subject: 62-08, 62P12

description: Given the increasing prevalence of wildland fires in the Western US, there is a critical need to develop tools to understand and accurately predict burn severity. We develop a machine learning model to predict post-fire burn severity using pre-fire remotely sensed data. Hydrological, ecological, and topographical variables collected from four regions of California - the sites of the Kincade fire (2019), the CZU Lightning Complex fire (2020), the Windy fire (2021), and the KNP Fire (2021) - are used as predictors of the difference normalized burn ratio. We hypothesize that a Super Learner (SL) algorithm that accounts for spatial autocorrelation using Vecchia's Gaussian approximation will accurately model burn severity. In all combinations of test and training sets explored, the results of our model showed the SL algorithm outperformed standard Linear Regression methods. After fitting and verifying the performance of the SL model, we use interpretable machine learning tools to determine the main drivers of severe burn damage, including greenness, elevation and fire weather variables. These findings provide actionable insights that enable communities to strategize interventions, such as early fire detection systems, pre-fire season vegetation clearing activities, and resource allocation during emergency responses. When implemented, this model has the potential to minimize the loss of human life, property, resources, and ecosystems in California.
description: 18 pages, 3 figures
BindingDB Entry 12142: BORONIC ACID COMPOUNDS, COMPOSITIONS AND METHODS
Creators: name: BindingDB
Publisher: name: BindingDB
Year: 2024
Subjects: Dipeptidyl peptidase 4, Presequence protease, mitochondrial, and Prolyl endopeptidase FAP, Trustees Of Tufts College, Affinity

description: Small molecule binding data for protein Dipeptidyl peptidase 4, Presequence protease, mitochondrial, and Prolyl endopeptidase FAP, Uniprot P27487, Q12884, and Q5JRX3
BindingDB Entry 12141: (R)-Glutarimide CRBN Ligands and Methods of Use
Creators: name: BindingDB
Publisher: name: BindingDB
Year: 2024
Subjects: DNA damage-binding protein 1/Protein Cereblon [40-442], Beigene Switzerland, Affinity

description: Small molecule binding data for protein DNA damage-binding protein 1/Protein Cereblon [40-442], Uniprot Q16531
[WHITE PAPER] The Periodic Flower - a re-interpretation of the Periodic Flower (2022)
Creators: name: Teia, Luis
Publisher: name: figshare
Year: 2022
Subjects: subject: 30199 Analytical Chemistry not elsewhere classified
subject: FOS: Chemical sciences
subject: 30799 Theoretical and Computational Chemistry not elsewhere classified
subject: 30699 Physical Chemistry not elsewhere classified

description: ABSTRACT The hypothesis of this paper is that contemporary knowledge in quantum mechanics (energy levels and orbital dispositions) should allow the construction of a more integrated and meaningful periodic representation of an atom (other than Mendeleev’s original). A novel approach that models electrons as triangles is presented. Triangles determine electron’s spin (up or down) and govern their fitting into (sub)shells. The result is the Spin-based Periodic Structure. Starting at the nucleus (Period/Group 0), it evolves energetically outwardly with guidance from the quantum numbers. The model favors spin over atomic number when organizing the elements, and as a result, the model collapses all available thermal and electrical conductivity data of the elements into one continuous peak for the transition metals, and one axis of instability for the entire structure.
III: The Heronbridge archaeological research project: an interim report on the 2002 and 2003 seasons of the Society's new fieldwork initiative
Creators: name: Mason, D J P
Publisher: name: Archaeology Data Service
Year: 2018

description: Journal of the Chester Archaeological Society, 78, 49-106
description: Report describing the results of fieldwork undertaken by the Chester Archaeological Society during 2002 and 2003 at the multi-period site of Heronbridge. The investigations focused on the part of the site lying between the modern road (ancient Watling Street) and the River Dee, which contained the eastern half of the Roman roadside settlement overlain by a large curvilinear enclosure defended by a rampart and ditch. it was shown that the defensive works did not continue along the river bank, but that the rampart was originally reinforced by a stone revetment. The earthwork is now thought to have been constructed at some time between c. AD 890 and c. AD 980. Investigation of the ancient river cliff at the north end of the site revealed a natural inlet which had been modified to function as a quay serving the Roman settlement, a ramped trackway from the north providing access. These works were provisionally dated to the early- to mid-second century. Around the middle of the third century, three graves were excavated in the rock close to the edge of the quay which was by this time disused. Two were for adults and the third for a child. Although the graves had been ransacked in antiquity, fragments of sculpture recovered from the fill on one and from silt nearby indicate that the two adult graves were covered by a substantial funerary monument.
Noise Dynamics in the Quantum Regime
Creators: name: Farley, Clovis
name: Pinsolle, Edouard
name: Reulet, Bertrand
Publisher: name: arXiv
Year: 2023
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: A time-dependent bias voltage on a tunnel junction generates a time-dependent modulation of its current fluctuations, and in particular of its variance. This translates into an excitation at frequency $\tilde{f}$ generating correlations between current fluctuating at any frequency $f$ and at frequency $\pm$ $\tilde{f} -f$. We report the measurement of such a correlation in the fully quantum regime, i.e. when both frequencies are much greater than $k_BT/h$ with $T$ the temperature. Such a correlator, usually referred to as the noise susceptibility, is involved in corrections to the measurements of higher-order moments and in the squeezing of noise.
description: 4 pages, 4 figures, to be published in the 2023 International Conference on Noise and Fluctuations (ICNF) proceedings