cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Genomic basis for RNA alterations in cancer
Creators: name: Brazma, A.
name: Stegle, O.
name: Pedamallu, C.S.
name: Davidson, N.R.
name: PCAWG Consortium
name: Perry, M.D.
name: Zhang, Z.
name: Ouellette, B.F.F.
name: Wu, K.
name: He, Y.
name: Korbel, J.O.
name: Hoadley, K.A.
name: Liu, D.
name: Erkek, S.
name: Calabrese, C.
name: Soulette, C.M.
name: Nandi, T.
name: Waszak, S.M.
name: Zhang, J.
name: Yang, H.
name: Göke, J.
name: PCAWG Transcriptome Core Group
name: Fonseca, N.A.
name: Zhang, F.
name: Schwarz, R.F.
name: Hou, Y.
name: Liu, F.
name: Shiraishi, Y.
name: Rätsch, G.
name: Su, H.
name: Zhu, S.
name: Awadalla, P.
name: Bailey, P.
name: Meyerson, M.
name: Demircioglu, D.
name: Greger, L.
name: Xiang, Q.
name: Siebert, R.
name: Li, S.
name: Brooks, A.N.
name: Creighton, C.J.
name: Pan-Hammarström, Q.
name: Kilpinen, H.
name: PCAWG Transcriptome Working Group
name: Tan, P.
name: Markowski, J.
name: Kahles, A.
name: Huska, M.R.
name: Stark, S.G.
name: Lehmann, K.-V.
name: Urban, L.
name: Marin, M.G.
name: Yung, C.
Publisher: name: Nature Research
Year: 2020

description: Transcript alterations often result from somatic changes in cancer genomes1. Various forms of RNA alterations have been described in cancer, including overexpression2, altered splicing3 and gene fusions4; however, it is difficult to attribute these to underlying genomic changes owing to heterogeneity among patients and tumour types, and the relatively small cohorts of patients for whom samples have been analysed by both transcriptome and whole-genome sequencing. Here we present, to our knowledge, the most comprehensive catalogue of cancer-associated gene alterations to date, obtained by characterizing tumour transcriptomes from 1,188 donors of the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA)5. Using matched whole-genome sequencing data, we associated several categories of RNA alterations with germline and somatic DNA alterations, and identified probable genetic mechanisms. Somatic copy-number alterations were the major drivers of variations in total gene and allele-specific expression. We identified 649 associations of somatic single-nucleotide variants with gene expression in cis, of which 68.4% involved associations with flanking non-coding regions of the gene. We found 1,900 splicing alterations associated with somatic mutations, including the formation of exons within introns in proximity to Alu elements. In addition, 82% of gene fusions were associated with structural variants, including 75 of a new class, termed ‘bridged’ fusions, in which a third genomic location bridges two genes. We observed transcriptomic alteration signatures that differ between cancer types and have associations with variations in DNA mutational signatures. This compendium of RNA alterations in the genomic context provides a rich resource for identifying genes and mechanisms that are functionally implicated in cancer.
The Mumyōshō of Kamo no Chōmei and its significance in Japanese literature
Creators: name: Katō, Hilda
Publisher: name: University of British Columbia
Year: 2011

description: The purpose of this study is to investigate the significance of Japanese theoretical writing on poetry of the Heian period (794 - 1192) (as manifested in the distinctive literary genre known as the karon) with special reference to the development of esthetic concepts in general and the influence of this kind of writing on the Japanese literature of later periods. An attempt is made to show through the presentation of one of the major works in this field, which is here translated into English, what factors were responsible for the distinctive characteristics of Japanese poetry. This kind of study has never been undertaken in English and no source material is available in translation; I therefore thought it best to make a start in this field with a complete translation of the Mumyōshō by Kamo no Chōmei, one of the most important Japanese theoretical works on poetry. By presenting the full text I wish to draw attention to the problems of poetic taste and criticism, as the Japanese of the Heian period saw them. Going back to the sources which Kamo no Chōmei used in his writing, I have tried to give an account (admittedly very incomplete) of poetical thought in Japan up to his time. I have analyzed some of the most influential ideas of the Mumyōshō and presented them in summary. This study has made it clear to me that much further research is necessary to show the genius of Kamo no Chōmei in its proper perspective and to demonstrate the importance of the karon of the Heian period for the development of Japanese literature in general.
Crisaborole loaded nanoemulgel for the mitigation of atopic dermatitis in mice model
Creators: name: Kataria, Shubham
name: Roy, Supriya
name: Chaurasia, Mohini
name: Awasthi, Himani
name: Fatima, Zeeshan
name: Prasad, Rammani
name: Srivastava, Dipti
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Biochemistry
Space Science
Medicine
Pharmacology
Chemical Sciences not elsewhere classified
Developmental Biology
Cancer

description: The present work aims to formulate nanoemulgel of crisaborole (CB) and evaluate its effectiveness against 2,4-Di-nitrochlorobenzene induced (DNCB) atopic dermatitis (AD) in mice. AD is a chronic inflammation of the skin affecting the quality of life. CB is a topical PDE4 inhibitor marketed as a 2% ointment. It, however, possesses poor aqueous solubility. An o/w nanoemulsion shall exhibit an enhanced therapeutic effect owing to the increased solubility of CB and an augmented skin penetration. The addition of a gelling agent to form a nanoemulgel further provides ease of application to the patients. Nanoemulsion was prepared by aqueous titration method using caproyl PGMC, cremophore EL and propylene glycol as the oil, surfactant, and cosurfactant respectively. The formulations were characterized by their size, zeta potential and polydispersity index (PDI). 1% Carbopol 934 was used as the gelling agent to formulate nanoemulgel comprising of optimized nanoemulsion (NE 9). Ex vivo skin permeation of the CB nanoemulgel was compared with the CB ointment. Its therapeutic effect was evaluated in Balb/c mice. NE 9 comprised of 7.49% oil, 37.45% Smix (1:3) and water 55.06%. Its particle size, PDI and zeta potential were 15.45 ± 5.265 nm, 0.098 and −17.9 ± 8.00 mV respectively. The nanoemulgel exhibited a 3-fold higher permeation flux as compared to the ointment. In vivo studies demonstrated that the nanoemulgel provided better therapeutic effect than the ointment. We can thereby conclude that nanoemulgel formulation can be a successful drug delivery strategy for enhancing the therapeutic effect of CB.
Androgen Receptor mRNA Expression in Urothelial Carcinoma of the Bladder: A Retrospective Analysis of Two Independent Cohorts
Creators: name: Breyer, J.
name: Hartmann, A.
name: Sikic, D.
name: Erben, P.
name: Lerner, S.P.
name: Otto, W.
name: Bolenz, C.
name: Keck, B.
name: Wach, S.
name: Hoadley, K.A.
name: Wirtz, R.M.
name: Eckstein, M.
name: Dyrskjøt, L.
Publisher: name: Neoplasia Press, Inc.
Year: 2019

description: INTRODUCTION: Gender-specific differences have led to the androgen receptor (AR) being considered a possible factor in the pathophysiology of urothelial carcinoma of the bladder (UCB), but the exact role remains unclear. MATERIALS AND METHODS: The association of AR mRNA expression with clinicopathological features was retrospectively analyzed in two previously described cohorts. The first cohort consisted of 41 patients with all stages of UCB treated at Aarhus University Hospital, Denmark. The second cohort consisted of 323 patients with muscle-invasive bladder cancer (MIBC) accumulated by the Cancer Genome Atlas (TCGA) Research Network. RESULTS: AR mRNA expression is significantly higher in non-muscle-invasive bladder cancer (NMIBC) when compared to MIBC (P =.0004), with no relevant changes within the different stages of MIBC. AR mRNA expression was significantly associated with TCGA molecular subtypes (P <.0001). In the total cohort, there was no association between AR expression and gender (P =.23). When analyzed separately, females showed a significantly worse disease-free (P =.03) and overall survival (P =.02) when expressing AR mRNA above median level, while the same was not observed for men. Multivariable Cox's regression analyses revealed AR mRNA expression to be an independent prognostic marker for disease-free survival in women (P =.007). CONCLUSIONS: AR mRNA expression is significantly higher in NMIBC than in MIBC, while high AR mRNA expression is associated with worse survival in females with MIBC. Further studies need to investigate the gender-specific role of AR in UCB.
An experimental investigation of subjective organization in college students and traumatically brain injured individuals
Creators: name: Nickerson, Sherry D.
Publisher: name: Maryland Shared Open Access Repository
Year: 2014

description: Part-whole or whole-whole overlapping list learning paradigms have been used extensively to study verbal learning and memory for many years. This study compared three theories (organizational theory, frequency theory and list discrimination theory) of overlapping list learning. The first experiments compared the transfer effects with 141 college students using both verbal and non-verbal stimuli. A second experiment assessed transfer effects with TBI survivors who learned verbal stimuli. Experiment 1 replicated the often reported negative transfer phenomenon with overlapping word lists and then compared these results with those obtained when the overlapping lists were symbols. Results indicated negative transfer of performance for the old words relative to new words; new words were recalled better than old words on the second list. However, positive transfer occurred when symbols were used; old symbols were recalled better than new symbols on the second list. The difference between these findings indicates that verbal and visual information may be processed differently in the brain and that subjective organization may occur only with verbal information. Experiment 2 replicated previous research that showed a positive transfer using 60 brain injured individuals in an overlapping word list manipulation. The positive transfer resulted from an inability to subjectively organize information after a traumatic brain injury. The results of both experiments either supported or were consistent with Tulving's (1969) organizational theory.
description: (M.A.) -- Towson University, 2014.
Deep Learning for Protein-Ligand Docking: Are We There Yet?
Creators: name: Morehead, Alex
Publisher: name: Zenodo
Year: 2024
Subjects: Deep Learning
Protein-Ligand Docking

description: Included are preprocessed datasets and benchmark method predictions accompanying the benchmarking manuscript "Deep Learning for Protein-Ligand Docking: Are We There Yet?" [1]. In particular, the preprocessed Astex Diverse and PoseBusters Benchmark datasets as well as the publicly available CASP15 targets referenced in the manuscript are available for download. Also available are baseline method predictions from a variety of deep learning and conventional docking methods (e.g., DiffDock-L, Vina) for each of these benchmarking datasets. Note that the "holo_aligned" predicted protein structures provided for the Astex Diverse and PoseBusters Benchmark datasets have been pre-aligned to the corresponding ground-truth (holo) protein structures. Similarly, the "predicted_structures" predicted protein structures provided for the CASP15 dataset have been pre-aligned to the corresponding ground-truth (holo) protein structures.

 

Paper Abstract:

The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein-ligand docking have recently been introduced, to date no prior works have systematically studied the behavior of docking methods within the practical context of (1) predicted (apo) protein structures, (2) multiple ligands concurrently binding to a given target protein, and (3) having no prior knowledge of binding pockets. To enable a deeper understanding of docking methods' real-world utility, we introduce PoseBench, the first comprehensive benchmark for practical protein-ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL docking methods for apo-to-holo protein-ligand docking and protein-ligand structure generation using both single and multi-ligand benchmark datasets, the latter of which we introduce for the first time to the DL community. Empirically, using PoseBench, we find that all recent DL docking methods but one fail to generalize to multi-ligand protein targets and also that template-based docking algorithms perform equally well or better for multi-ligand docking as recent single-ligand DL docking methods, suggesting areas of improvement for future work. Code, data, tutorials, and benchmark results are available at https://github.com/BioinfoMachineLearning/PoseBench.

 

References:

[1] Morehead A, Giri N, Liu J, Cheng J. Deep Learning for Protein-Ligand Docking: Are We There Yet? arXiv; 2024. Available from: http://arxiv.org/abs/2308.05777
Measurements incompatible in Quantum Theory cannot be measured jointly in any other local theory
Creators: name: Wolf, Michael M.
name: Perez-Garcia, David
name: Fernandez, Carlos
Publisher: name: arXiv
Year: 2009
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: It is well known that jointly measurable observables cannot lead to a violation of any Bell inequality - independent of the state and the measurements chosen at the other site. In this letter we prove the converse: every pair of incompatible quantum observables enables the violation of a Bell inequality and therefore must remain incompatible within any other no-signaling theory. While in the case of von Neumann measurements it is sufficient to use the same pair of observables at both sites, general measurements can require different choices. The main result is obtained by showing that for arbitrary dimension the CHSH inequality provides the Lagrangian dual of the characterization of joint measurability. This leads to a simple criterion for joint measurability beyond the known qubit case.
description: 4 pages
Pairwise Entanglement and Geometric Phase in $d=2,3$-Dimensional Free-Fermion Lattice Systems
Creators: name: Cui, H. T.
name: Zhang, Y. F.
Publisher: name: arXiv
Year: 2009
Subjects: subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: The pairwise entanglement, measured by concurrence and geometric phase in $d=2,3$-dimensional free-fermion lattice systems have been studied for the ground state in this paper. Their derivation with respect to the external parameter show the singularity closed to the phase transition points, and can be used to detect the phase transition in this model. Furthermore our studies show for the free-fermion model that both concurrence and geometric phase shows the intimate connection with the correlation functions. The possible relation between concurrence and geometric phase has been also discussed.
description: 7+pages, EPJD style
Multiple Criteria Analysis
Creators: name: Roumeliotis, Anargyros
Publisher: name: Zenodo
Year: 2024
Subjects: Multiple criteria analysis
Rural areas
Connectivity
Edge Processing

description: This technical article disucsses how operational research uses Multiple Criteria Decision Methods (MCDM) like TOPSIS and VIKOR to assess predetermined alternatives against conflicting criteria, ranking them based on factors like techno-economic and environmental considerations. In the XGAIN Knowledge Facilitation Tool (KFT), MADM is integrated to evaluate and rank technological solutions for rural user needs, factoring in different criteria and user preferences.

 

This work has been developed in the context of the XGain project (101060294). XGain fosters a sustainable, balanced, and inclusive development of rural, coastal and urban areas by facilitating access to relevant stakeholders to a comprehensive inventory of smart XG, last-mile connectivity and edge computing solutions, and of related assessment methods. Learn more at xgain-project.eu.
Bayesian changepoint models motivated by cyber-security applications
Creators: name: Hallgren, Karl
Publisher: name: Imperial College London
Year: 2022

description: Changepoint detection has an important role to play in the next generation of cyber security defenses. A cyber attack typically changes the behaviour of the target network. Therefore, to detect the presence of a network intrusion, it can be informative to monitor for changes in the high-volume data sources that are collected inside an enterprise computer network. However, most traditional changepoint detection methods are not adapted to characterise what cyber security analysts mean by a change, and consequently raise too many false alerts but also overlook weak signals that are suggestive of a real attack. This thesis will present three novel Bayesian changepoint models that address some challenges raised by cyber data: the first model combines evidence across a graph of time series to identify patterns of changepoints that are a priori more likely to correspond to an attack; the second model offers robustness to non-exchangeable data within segments so that normal dynamic phenomena observed in cyber data can be captured; and, the third model relaxes the standard assumption that changes are instantaneous, so that time intervals where cyber data may be subject to non-instantaneous changes can be identified.
Multiple Criteria Analysis for Ranking Alternatives
Creators: name: Roumeliotis, Anargyros
Publisher: name: Zenodo
Year: 2024
Subjects: Multiple criteria analysis
Rural areas
Connectivity
Edge Processing

description: This technical article disucsses how operational research uses Multiple Criteria Decision Methods (MCDM) like TOPSIS and VIKOR to assess predetermined alternatives against conflicting criteria, ranking them based on factors like techno-economic and environmental considerations. In the XGAIN Knowledge Facilitation Tool (KFT), MADM is integrated to evaluate and rank technological solutions for rural user needs, factoring in different criteria and user preferences.

 

This work has been developed in the context of the XGain project (101060294). XGain fosters a sustainable, balanced, and inclusive development of rural, coastal and urban areas by facilitating access to relevant stakeholders to a comprehensive inventory of smart XG, last-mile connectivity and edge computing solutions, and of related assessment methods. Learn more at xgain-project.eu.
Additional file 5 of Assessment of mitochondrial genomes for heterobranch gastropod phylogenetics
Creators: name: Varney, Rebecca M.
name: Brenzinger, Bastian
name: Malaquias, Manuel António E.
name: Meyer, Christopher P.
name: Schrödl, Michael
name: Kocot, Kevin M.
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 5: Figure S4. Maximum likelihood phylogeny of heterobranch gastropods based on the full set of available heterobranch mitochondrial genomes (including long-branched taxa). The data set was partitioned by gene, trimmed with BMGE, and each partition was allowed to select its own optimal model via ModelFinder implemented in IQ-TREE 2. The analysis was run with the –GENESITE correction to facilitate resampling first within partition and then within sites. Bootstrap support values are presented at each node.
Deep Learning for Protein-Ligand Docking: Are We There Yet?
Creators: name: Morehead, Alex
name: Giri, Nabin
name: Liu, Jian
name: Cheng, Jianlin
Publisher: name: Zenodo
Year: 2024
Subjects: Deep Learning
Protein-Ligand Docking

description: Included are preprocessed datasets and benchmark method predictions accompanying the benchmarking manuscript "Deep Learning for Protein-Ligand Docking: Are We There Yet?" [1]. In particular, the preprocessed Astex Diverse, PoseBusters Benchmark, and DockGen datasets as well as the publicly available CASP15 targets referenced in the manuscript are available for download. Also available are baseline method predictions from a variety of deep learning and conventional docking methods (e.g., DiffDock-L, Vina) for each of these benchmarking datasets (including pocket-only baseline results for the PoseBusters Benchmark dataset). Note that the "holo_aligned" predicted protein structures provided for the Astex Diverse, PoseBusters Benchmark, and DockGen datasets have been pre-aligned to the corresponding ground-truth (holo) protein structures. Similarly, the "predicted_structures" predicted protein structures provided for the CASP15 dataset have been pre-aligned to the corresponding ground-truth (holo) protein structures.

 

Paper Abstract:

The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein-ligand docking have recently been introduced, to date no prior works have systematically studied the behavior of docking methods within the practical context of (1) predicted (apo) protein structures (e.g., for broad applicability); (2) multiple ligands concurrently binding to a given target protein (e.g., for enzyme design); and (3) having no prior knowledge of binding pockets (e.g., for pocket generalization). To enable a deeper understanding of docking methods' real-world utility, we introduce PoseBench, the first comprehensive benchmark for practical protein-ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL docking methods for apo-to-holo protein-ligand docking and protein-ligand structure generation using both single and multi-ligand benchmark datasets, the latter of which we introduce for the first time to the DL community. Empirically, using PoseBench, we find that all recent DL docking methods but one fail to generalize to multi-ligand protein targets and also that template-based docking algorithms perform equally well or better for multi-ligand docking as recent single-ligand DL docking methods, suggesting areas of improvement for future work. Code, data, tutorials, and benchmark results are available at https://github.com/BioinfoMachineLearning/PoseBench.

 

References:

[1] Morehead A, Giri N, Liu J, Cheng J. Deep Learning for Protein-Ligand Docking: Are We There Yet? arXiv; 2024. Available from: http://arxiv.org/abs/2308.05777
Galaxy Clusters as mirrors of the distant Universe. Implications for the kSZ and ISW effects
Creators: name: Hernandez-Monteagudo, Carlos
name: Sunyaev, Rashid A.
Publisher: name: arXiv
Year: 2009
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: It is well known that Thomson scattering of CMB photons in galaxy clusters introduces new anisotropies in the CMB radiation field, but however little attention is payed to the fraction of CMB photons that are scattered off the line of sight, causing a slight blurring of the CMB anisotropies present at the moment of scattering. In this work we study this {\it blurring} effect, and find that it has a non-negligible impact on estimations of the kinetic Sunyaev-Zel'dovich (kSZ) effect: it induces a 10% correction in 20-40% of the clusters/groups, and a 100% correction in $\sim 5$% of the clusters in an ideal (noiseless) experiment. We explore the possibility of using this blurring term to probe the CMB anisotropy field at different epochs in our Universe. In particular, we study the required precision in the removal of the kSZ that enables detecting the blurring term $-τ_T δT / T_0$ in galaxy cluster populations placed at different redshift shells. By mapping this term in those shells, we would provide a tomographic probe for the growth of the Integrated Sachs Wolfe effect (ISW) during the late evolutionary stages of the Universe. We find that the required precision of the cluster peculiar velocity removal is of the order of 100 -- 200 km s$^{-1}$ in the redshift range 0.2 -- 0.8, after assuming that all clusters more massive than 10$^{14}$ h$^{-1}$ M$_{\odot}$ are observable. These errors are comparable to the total expected linear line of sight velocity dispersion for clusters in WMAPV cosmogony, and correspond to a residual level of roughly 900 -- 1800 $τ_T μ$K per cluster, including all types of contaminants and systematics. Were this precision requirement achieved, then independent constraints on the intrinsic cosmological dipole would be simultaneously provided.
description: Notation clarified and typos and errors corrected in eqs.(2-4)
Acute spontaneous spinal subdural hematoma in the cervical spine
Creators: name: Takahashi, Hiroaki
Publisher: name: EURORAD
Year: 2015
Subjects: subject: Neuroradiology spine
subject: CT
subject: MR
subject: Computer Applications-General
subject: Haemorrhage

description: Clinical History Image Findings Discussion Find Diagnosis Differential Diagnosis
description: female, 84 years
description: Clinical History: An 84-year-old woman was admitted to the hospital with sudden onset neck pain, bilateral upper extremities paresthesia and bilateral lower limbs paraplegia. The symptoms occurred acutely when she was at rest. Deep tendon reflexes were increased at both lo... Final Diagnosis: Acute spontaneous spinal subdural hematoma
Deep Learning for Protein-Ligand Docking: Are We There Yet?
Creators: name: Morehead, Alex
name: Giri, Nabin
name: Liu, Jian
name: Cheng, Jianlin
Publisher: name: Zenodo
Year: 2024
Subjects: Deep Learning
Protein-Ligand Docking

description: Included are preprocessed datasets and benchmark method predictions accompanying the benchmarking manuscript "Deep Learning for Protein-Ligand Docking: Are We There Yet?" [1]. In particular, the preprocessed Astex Diverse, PoseBusters Benchmark, and DockGen datasets as well as the publicly available CASP15 targets referenced in the manuscript are available for download. Also available are baseline method predictions from a variety of deep learning and conventional docking methods (e.g., DiffDock-L, Vina) for each of these benchmarking datasets (including pocket-only baseline results for the PoseBusters Benchmark dataset). Note that the "holo_aligned" AlphaFold 3-predicted protein structures provided for the Astex Diverse, PoseBusters Benchmark, and DockGen datasets have been pre-aligned to the corresponding ground-truth (holo) protein structures. Similarly, the "predicted_structures" AlphaFold 3-predicted protein structures provided for the CASP15 dataset have been pre-aligned to the corresponding ground-truth (holo) protein structures.

 

Paper Abstract:

The effects of ligand binding on protein structures and their in vivo functions carry numerous implications for modern biomedical research and biotechnology development efforts such as drug discovery. Although several deep learning (DL) methods and benchmarks designed for protein-ligand docking have recently been introduced, to date no prior works have systematically studied the behavior of docking methods within the broadly applicable context of (1) using predicted (apo) protein structures for docking (e.g., for applicability to unknown structures); (2) docking multiple ligands concurrently to a given target protein (e.g., for enzyme design); and (3) having no prior knowledge of binding pockets (e.g., for unknown pocket generalization). To enable a deeper understanding of docking methods' real-world utility, we introduce PoseBench, the first comprehensive benchmark for broadly applicable protein-ligand docking. PoseBench enables researchers to rigorously and systematically evaluate DL docking methods for apo-to-holo protein-ligand docking and protein-ligand structure generation using both single and multi-ligand benchmark datasets, the latter of which we introduce for the first time to the DL community. Empirically, using PoseBench, we find that (1) DL methods consistently outperform conventional docking algorithms; (2) most recent DL docking methods fail to generalize to multi-ligand protein targets; and (3) training DL methods with physics-informed loss functions on diverse clusters of protein-ligand complexes is a promising direction for future work. Code, data, tutorials, and benchmark results are available at https://github.com/BioinfoMachineLearning/PoseBench.

 

References:

[1] Morehead A, Giri N, Liu J, Cheng J. Deep Learning for Protein-Ligand Docking: Are We There Yet? arXiv; 2024. Available from: http://arxiv.org/abs/2308.05777
Understanding building and urban environment interactions: An integrated framework for building occupancy modelling
Creators: name: Hou, Huiqiao
Publisher: name: Imperial College London
Year: 2022

description: Improving building energy efficiency requires accurate modelling and a comprehensive understanding of how occupants use building space. This thesis focuses on modelling building occupancy to enhance the predictive accuracy of occupancy patterns and gain a better understanding of the causal reasons for occupancy behaviour. A conceptual framework is proposed to relax the restriction of isolated building analysis, which accounts for interactions between buildings, its occupants, and other urban systems, such as the effects of transport incidents on occupancy and circulation in buildings. This thesis also presents a counterpart mapping of the framework that elaborates the links between modelling of transport and building systems. To operationalise the proposed framework, a novel modelling approach which has not been used in the current context, called the hazard-based model, is applied to model occupancy from a single building up to a district area. The proposed framework is further adapted to integrate more readily with transport models, to ensure that arrivals and departures to and from the building are consistent with the situation of the surrounding transport systems. The proposed framework and occupancy models are calibrated and validated using Wi-Fi data and other variables, such as transport and weather parameters, harvested from the South Kensington campus of Imperial College London. In addition to calibrating the occupancy model, integrating a travel simulator produces synthetic arrivals into or around the campus, which are further distributed over campus buildings via an adapted technique and feed the occupancy simulations. The model estimation results reveal the causal reasons for or exogenous effects on individual occupancy states. The validation results confirm the ability of the proposed models to predict building occupancy accurately both on average and day by day across the future dataset. Finally, evaluating occupancy simulations for various hypothetical scenarios provides valuable suggestions for efficient building design and facility operation.
Additional file 9 of Assessment of mitochondrial genomes for heterobranch gastropod phylogenetics
Creators: name: Varney, Rebecca M.
name: Brenzinger, Bastian
name: Malaquias, Manuel António E.
name: Meyer, Christopher P.
name: Schrödl, Michael
name: Kocot, Kevin M.
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 9: Table S2. RogueNaRok leaf instability indices, run with the tree from Figure 1. Lsi_42_max represents the maximum leaf instability across four possible quartets, lsi_42_ent the entropy between the two most different quartets, and Lsi_42_dif the leaf stability differences between the two most common quartets.
The chromatin accessibility landscape of primary human cancers
Creators: name: Curtis, C.
name: Sheffield, N.C.
name: Shams, S.
name: Cho, S.W.
name: Greenleaf, W.J.
name: Satpathy, A.T.
name: Zhou, W.
name: Robertson, A.G.
name: Hoadley, K.A.
name: Berman, B.P.
name: Mumbach, M.R.
name: Felau, I.
name: Zenklusen, J.C.
name: Corces, M.R.
name: Silva, T.C.
name: Laird, P.W.
name: Castro, M.A.A.
name: Chang, H.Y.
name: Wong, C.K.
name: Louie, B.H.
name: Granja, J.M.
name: Staudt, L.M.
name: Groeneveld, C.
name: Seoane, J.A.
Publisher: name: American Association for the Advancement of Science
Year: 2018

description: We present the genome-wide chromatin accessibility profiles of 410 tumor samples spanning 23 cancer types from The Cancer Genome Atlas (TCGA).We identify 562,709 transposase-accessible DNA elements that substantially extend the compendium of known cis-regulatory elements. Integration of ATAC-seq (the assay for transposase-accessible chromatin using sequencing) with TCGA multi-omic data identifies a large number of putative distal enhancers that distinguish molecular subtypes of cancers, uncovers specific driving transcription factors via protein-DNA footprints, and nominates long-range gene-regulatory interactions in cancer. These data reveal genetic risk loci of cancer predisposition as active DNA regulatory elements in cancer, identify gene-regulatory interactions underlying cancer immune evasion, and pinpoint noncoding mutations that drive enhancer activation and may affect patient survival. These results suggest a systematic approach to understanding the noncoding genome in cancer to advance diagnosis and therapy.
The Semantics of Kalah Game
Creators: name: Musumbu, Kaninda
Publisher: name: arXiv
Year: 2009
Subjects: subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: The present work consisted in developing a plateau game. There are the traditional ones (monopoly, cluedo, ect.) but those which interest us leave less place at the chance (luck) than to the strategy such that the chess game. Kallah is an old African game, its rules are simple but the strategies to be used are very complex to implement. Of course, they are based on a strongly mathematical basis as in the film "Rain-Man" where one can see that gambling can be payed with strategies based on mathematical theories. The Artificial Intelligence gives the possibility "of thinking" to a machine and, therefore, allows it to make decisions. In our work, we use it to give the means to the computer choosing its best movement.
VIV and WIO using wake oscillator. Comparison on 2D response with experiments
Creators: name: Cebron, David
name: Gaurier, Benoît
name: Grégory, Germain
Publisher: name: arXiv
Year: 2010
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: Experimental results are used to validate a 2D phenomenological model of the near wake based on Van Der Pol wake oscillators, which is the first one which describes the 2D motion of a cylinder in its transversal plan. In the case of a single cylinder, experimental and numerical results are in relatively good agreement. Those first results show that the proposed model can be used as a simple computation tool in the prediction of 2D VIV effects.
Intratumor heterogeneity of the estrogen receptor and the long-term risk of fatal Breast cancer
Creators: name: Benz, C.C.
name: Datnow, B.
name: Fornander, T.
name: Hoadley, K.A.
name: Esserman, L.J.
name: Lindström, L.S.
name: Thompson, C.K.
name: Zhang, Y.
name: Yau, C.
name: Lin, F.
name: Hasteh, F.
name: Krings, G.
name: Bishop, J.W.
name: Czene, K.
name: Stål, O.
name: Borowsky, A.D.
name: Balassanian, R.
name: Carpenter, P.M.
name: Van't Veer, L.J.
name: Chen, Y.-Y.
name: Nordenskjöld, B.
Publisher: name: Oxford University Press
Year: 2018

description: Background: Breast cancer patients with estrogen receptor (ER)–positive disease have a continuous long-term risk for fatal Breast cancer, but the biological factors influencing this risk are unknown. We aimed to determine whether high intratumor heterogeneity of ER predicts an increased long-term risk (25 years) of fatal Breast cancer. Methods: The STO-3 trial enrolled 1780 postmenopausal lymph node–negative Breast cancer patients randomly assigned to receive adjuvant tamoxifen vs not. The fraction of cancer cells for each ER intensity level was scored by Breast cancer pathologists, and intratumor heterogeneity of ER was calculated using Rao’s quadratic entropy and categorized into high and low heterogeneity using a predefined cutoff at the second tertile (67%). Long-term Breast cancer-specific survival analyses by in-tra-tumor heterogeneity of ER were performed using Kaplan-Meier and multivariable Cox proportional hazard modeling adjusting for patient and tumor characteristics. Results: A statistically significant difference in long-term survival by high vs low intratumor heterogeneity of ER was seen for all ER-positive patients (P < .001) and for patients with luminal A subtype tumors (P ¼ .01). In multivariable analyses, patients with high intratumor heterogeneity of ER had a twofold increased long-term risk as compared with patients with low intratumor heterogeneity (ER-positive: hazard ratio [HR] ¼ 1.98, 95% confidence interval [CI] ¼ 1.31 to 3.00; luminal A subtype tumors: HR ¼ 2.43, 95% CI ¼ 1.18 to 4.99). Conclusions: Patients with high intratumor heterogeneity of ER had an increased long-term risk of fatal Breast cancer. Interestingly, a similar long-term risk increase was seen in patients with luminal A subtype tumors. Our findings suggest that intratumor heterogeneity of ER is an independent long-term prognosticator with potential to change clinical management, especially for patients with luminal A tumors.
Monitoring peace in Solomon Islands
Creators: name: Hegarty, David
Publisher: name: Canberra, ACT: State, Society and Governance in Melanesia (SSGM) Program, The Australian National University
Year: 2001
Subjects: Solomon Islands
peace agreement
Townsville Peace Agreement
Peace Monitoring Council
International Peace Monitoring Team

description: The ethnic conflict which erupted in the small South Pacific nation of Solomon Islands in late 1998 resulted in the loss of over 100 lives, the displacement of 30,000 people, the overthrow of an elected government, and severe damage to the country’s economy and polity. Actual fighting took place only in and around the capital, Honiara, and in other parts of Guadalcanal between militant groups from Guadalcanal and from the neighbouring island of Malaita. Fighting was initiated by Guadalcanalese youth who believed that immigrant Malaitans had taken their land without proper compensation, were denying them job opportunities, and had been disrespectful of their culture. But the conflict impacted on Solomon Islands as a whole such that the country is now on the verge of bankruptcy, its government is unable to deliver services and relies on cash handouts as a proxy for governing, the police force is compromised and divided, the lack of reintegration of militarised and disaffected gangs of youth continues to threaten community relations already traumatised by the conflict, and most Provinces which make up the Solomons are demanding either separate statehood or independence.
Additional file 11 of Assessment of mitochondrial genomes for heterobranch gastropod phylogenetics
Creators: name: Varney, Rebecca M.
name: Brenzinger, Bastian
name: Malaquias, Manuel António E.
name: Meyer, Christopher P.
name: Schrödl, Michael
name: Kocot, Kevin M.
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 11: Table S3. Mitochondrial gene orders in all taxa from the present study, including outgroups, with < and > indicating directionality and orange boxes indicating possible locations of gene rearrangements.
Quantifying Rational Belief
Creators: name: Caticha, Ariel
Publisher: name: arXiv
Year: 2009
Subjects: subject: Data Analysis, Statistics and Probability (physics.data-an)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: Some criticisms that have been raised against the Cox approach to probability theory are addressed. Should we use a single real number to measure a degree of rational belief? Can beliefs be compared? Are the Cox axioms obvious? Are there counterexamples to Cox? Rather than justifying Cox's choice of axioms we follow a different path and derive the sum and product rules of probability theory as the unique (up to regraduations) consistent representations of the Boolean AND and OR operations.
description: Presented at MaxEnt 2009, the 29th International Workshop on Bayesian Inference and Maximum Entropy Methods in Science and Engineering (July 5-10, 2009, Oxford, Mississippi, USA.) In version 2 one mistake and a few typos have been corrected
Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation
Creators: name: Stuart, J.M.
name: Huelsken, J.
name: Czerwińska, P.
name: Kamińska, B.
name: Mishra, L.
name: Godwin, A.K.
name: Mazurek, S.
name: Noushmehr, H.
name: Wiznerowicz, M.
name: Lazar, A.J.
name: Sokolov, A.
name: The Cancer Genome Atlas Research Network
name: Krasnitz, A.
name: Laird, P.W.
name: Gentles, A.J.
name: Hoadley, K.A.
name: Burzykowski, T.
name: Omberg, L.
name: Gevaert, O.
name: Malta, T.M.
name: Weinstein, J.N.
name: Heyn, H.
name: Colaprico, A.
name: Poisson, L.
Publisher: name: Cell Press
Year: 2018

description: Cancer progression involves the gradual loss of a differentiated phenotype and acquisition of progenitor and stem-cell-like features. Here, we provide novel stemness indices for assessing the degree of oncogenic dedifferentiation. We used an innovative one-class logistic regression (OCLR) machine-learning algorithm to extract transcriptomic and epigenetic feature sets derived from non-transformed pluripotent stem cells and their differentiated progeny. Using OCLR, we were able to identify previously undiscovered biological mechanisms associated with the dedifferentiated oncogenic state. Analyses of the tumor microenvironment revealed unanticipated correlation of cancer stemness with immune checkpoint expression and infiltrating immune cells. We found that the dedifferentiated oncogenic phenotype was generally most prominent in metastatic tumors. Application of our stemness indices to single-cell data revealed patterns of intra-tumor molecular heterogeneity. Finally, the indices allowed for the identification of novel targets and possible targeted therapies aimed at tumor differentiation. Stemness features extracted from transcriptomic and epigenetic data from TCGA tumors reveal novel biological and clinical insight, as well as potential drug targets for anti-cancer therapies.
An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics
Creators: name: Benz, C.C.
name: Hoadley, K.A.
name: Thorsson, V.
name: Lazar, A.J.
name: Levine, D.A.
name: Lee, A.V.
name: Cherniack, A.D.
name: Wolf, D.M.
name: Poisson, L.M.
name: Omberg, L.
name: Liu, J.
name: Lichtenberg, T.
name: The Cancer Genome Atlas Research Network
name: Kovatich, A.J.
name: Hu, H.
name: Shriver, C.D.
Publisher: name: Cell Press
Year: 2018

description: For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types.
Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer
Creators: name: Stuart, J.M.
name: Hinoue, T.
name: Malta, T.M.
name: Yau, C.
name: Wong, C.K.
name: Thorsson, V.
name: Benz, C.C.
name: Lazar, A.J.
name: Noushmehr, H.
name: Cherniack, A.D.
name: Akbani, R.
name: Taylor, A.M.
name: Robertson, A.G.
name: Bowlby, R.
name: Shen, R.
name: The Cancer Genome Atlas Network
name: Lawrence, M.S.
name: Drill, E.
name: Wiznerowicz, M.
name: Schneider, B.G.
name: Sanchez-Vega, F.
name: Hoadley, K.A.
name: Laird, P.W.
name: Wolf, D.M.
Publisher: name: Cell Press
Year: 2018

description: We conducted comprehensive integrative molecular analyses of the complete set of tumors in The Cancer Genome Atlas (TCGA), consisting of approximately 10,000 specimens and representing 33 types of cancer. We performed molecular clustering using data on chromosome-arm-level aneuploidy, DNA hypermethylation, mRNA, and miRNA expression levels and reverse-phase protein arrays, of which all, except for aneuploidy, revealed clustering primarily organized by histology, tissue type, or anatomic origin. The influence of cell type was evident in DNA-methylation-based clustering, even after excluding sites with known preexisting tissue-type-specific methylation. Integrative clustering further emphasized the dominant role of cell-of-origin patterns. Molecular similarities among histologically or anatomically related cancer types provide a basis for focused pan-cancer analyses, such as pan-gastrointestinal, pan-gynecological, pan-kidney, and pan-squamous cancers, and those related by stemness features, which in turn may inform strategies for future therapeutic development. Comprehensive, integrated molecular analysis identifies molecular relationships across a large diverse set of human cancers, suggesting future directions for exploring clinical actionability in cancer treatment.
Intrinsic-extrinsic motivation and its effects upon feedback at mid-management levels
Creators: name: MacGillivray, James
Publisher: name: University of British Columbia
Year: 2011

description: This study was an attempt to determine the relationship between two broad motive patterns or sets and preference for one or the other of two specific types of information which an executive might expect to receive from his superior. An Intrinsic-Extrinsic motive dichotomy was utilized, while information preferences were divided into Job-related and Career-related information. Data were gathered from ninety-one mid-management executives by means of a paired-comparison questionnaire and a special ranking scale devised for this study. The data were then analyzed on the basis of four clearly defined Motivation-Information groups: (l) Intrinsic — Job-related (2) Intrinsic — Career-related (3) Extrinsic — Job-related and (4) Extrinsic — Career-related. Analysis of the results confirmed the following three hypotheses: (I) Intrinsically motivated executives will prefer job-related information over career-related information. (II) Extrinsically motivated executives view information generally (i.e.: either job-related or career-related) as more important than do intrinsically motivated executives. (Ill) There were a significantly larger number of intrinsically than extrinsically motivated executives. The fourth hypothesis, that: (IV) Extrinsically motivated executives will prefer career-related information over job-related information was rejected.