Dendrimers : a themed issue in honor of Professor Donald A. Tomalia on the occasion of his 80th birthday / / edited by Ashok Kakkar

• Record Nr.: UNINA9910598003603321
• Pubbl/distr/stampa: Basel, Switzerland : , : MDPI - Multidisciplinary Digital Publishing Institute, , [2018]; ©2018
• Descrizione fisica: 1 online resource (292 pages)
• Disciplina: 668.9
• Soggetti: Dendrimers
• Lingua di pubblicazione: Inglese
• Formato: Materiale a stampa
• Livello bibliografico: Monografia
• Nota di contenuto: About the Special Issue Editor -- Preface to "Dendrimers" -- Donald A. Tomalia / A Serendipitous Journey Leading to My Love of Dendritic Patterns and Chemistry, Reprinted from: Molecules 2018, 23, 824, doi:10.3390/molecules23040824 -- Anne-Marie Caminade and Jean-Pierre Majoral / Which Dendrimer to Attain the Desired Properties? Focus on Phosphorhydrazone Dendrimers, Reprinted from: Molecules 2018, 23, 622, doi:10.3390/molecules23030622 -- In-Yup Jeon, Hyuk-Jun Noh and Jong-Beom Baek / Hyperbranched Macromolecules: From Synthesis to Applications, Reprinted from: Molecules 2018, 23, 657, doi:10.3390/molecules23030657 -- Didier Astruc, Christophe Deraedt, Rodrigue Djeda, Catia Ornelas, Xiang Liu, Amalia Rapakousiou, Jaime Ruiz, Yanlan Wang and Qi Wang / Dentromers, a Family of Super Dendrimers with Specific Properties and Applications, Reprinted from: Molecules 2018, 23, 966, doi:10.3390/molecules23040966 -- Burcu Sumer Bolu, Rana Sanyal and Amitav Sanyal / Drug Delivery Systems from Self-Assembly of Dendron-Polymer Conjugates, Reprinted from: Molecules 2018, 23, 1570, doi:10.3390/molecules23071570 -- Elizabeth Ladd, Amir Sheikhi, Na Li, Theo G.M. van de Ven and Ashok Kakkar / Design and Synthesis of Dendrimers with Facile Surface Group Functionalization, and an Evaluation of Their Bactericidal Efficacy, Reprinted from: Molecules 2017, 22, 868, doi:10.3390/molecules22060868 -- Takane Imaoka, Noriko Bukeo and Kimihisa ; Yamamoto / Epitaxially Grown Ultra-Flat Self-Assembling Monolayers with Dendrimers, Reprinted from: Molecules 2018, 23, 485, doi:10.3390/molecules23020485 -- Matteo Savastano, Carla Bazzicalupi, Claudia Giorgi, Paola Gratteri and Antonio Bianchi / Cation, Anion and Ion-Pair Complexes with a G-3 Poly(ethylene imine) Dendrimer in Aqueous Solution, Reprinted from: Molecules 2017, 22, 816, doi:10.3390/molecules22050816 -- Marisol Gouveia, Jo˜ao Figueira, Manuel G. Jardim, Rita Castro, Helena Tomás, Kari Rissanen and Jo˜ao Rodrigues / Poly(alkylidenimine) Dendrimers Functionalized with the Organometallic Moiety [Ru(?5-C5H5)(PPh3)2]+ as Promising Drugs Against Cisplatin-Resistant Cancer Cells and Human Mesenchymal Stem Cells, Reprinted from: Molecules 2018, 23, 1471, doi:10.3390/molecules23061471 -- Yossef Alnasser, Siva P. Kambhampati, Elizabeth Nance, Labchan Rajbhandari, Shiva Shrestha, Arun Venkatesan, Rangaramanujam M. Kannan and Sujatha Kannan / Preferential and Increased Uptake of Hydroxyl-Terminated PAMAM Dendrimers by Activated Microglia in Rabbit Brain Mixed Glial Culture, Reprinted from: Molecules 2018, 23, 1025, doi:10.3390/molecules23051025 -- Noemi Molina, Angela Martin-Serrano, Tahia D. Fernandez, Amene Tesfaye, Francisco Najera, Mar´ia J. Torres, Cristobalina Mayorga, Yolanda Vida, Maria I. Montanez ˜and Ezequiel Perez-Inestrosa / Dendrimeric Antigens for Drug Allergy Diagnosis: A New Approach for Basophil Activation Tests, Reprinted from: Molecules 2018, 23, 997, doi:10.3390/molecules23050997 -- Lisa Christadore, Mark W. Grinstaff and Scott E. Schaus / Fluorescent Dendritic Micro-Hydrogels: Synthesis, Analysis and Use in Single-Cell Detection, Reprinted from: Molecules 2018, 23, 936, doi:10.3390/molecules23040936 -- Feng Gao, Ivan Djordjevic, Oleksandr Pokholenko, Haobo Zhang, Junying Zhang and Terry W.J. Steele / On-Demand Bioadhesive Dendrimers with Reduced Cytotoxicity , Reprinted from: Molecules 2018, 23, 796, doi:10.3390/molecules23040796 -- Abhay Singh Chauhan / Dendrimers for Drug Delivery, Reprinted from: Molecules 2018, 23, 938, doi:10.3390/molecules23040938 -- Mohiuddin Quadir, Susanne Fehse, Gerhard Multhaup and Rainer Haag / Hyperbranched Polyglycerol Derivatives as Prospective Copper Nanotransporter Candidates, Reprinted from: Molecules 2018, 23, 1281, doi:10.3390/molecules23061281 -- Celia Sehad, Tze Chieh Shiao, Lamyaa M. Sallam, Abdelkrim Azzouz and Ren´e Roy / Effect of Dendrimer Generation and Aglyconic Linkers on the Binding Properties of Mannosylated Dendrimers Prepared by a Combined Convergent and Onion Peel Approach, Reprinted from: Molecules 2018, 23, 1890, doi:10.3390/molecules23081890 -- Patrik Stenstr ¨om, Dario Manzanares, Yuning Zhang, Valentin Ce ˜na and Michael Malkoch / Evaluation of Amino-Functional Polyester Dendrimers Based on Bis-MPA as Nonviral Vectors for siRNA Delivery, Reprinted from: Molecules 2018, 23, 2028, doi:10.3390/molecules23082028 -- Renan Vinicius de Araujo, Soraya da Silva Santos, Elizabeth Igne Ferreira and Jeanine Giarolla / New Advances in General Biomedical Applications of PAMAM Dendrimers, Reprinted from: Molecules 2018, 23, 2849, doi:10.3390/molecules23112849.
• Sommario/riassunto: Dendrimers have firmly established their space in the macromolecular field since their first discovery in 1978. These monodispersed and hyperbranched macromolecules present unique properties with demonstrated potential in varied scientific disciplines. Dr. Donald A Tomalia is one of the pioneers in this area whose name is synonym for polyamidoamine (PAMAM) dendrimers, one of the most extensively investigated macromolecular architectures. In this monograph, his colleagues and friends celebrate Don's achievements and contributions ; to the field, on the occasion of his 80th birthday in 2018, which also coincides with the 40th anniversary of the first report on dendrimers. It provides the reader with excellent reviews on different aspects of dendritic architectures, followed by research articles that explore the state-of-the-art in synthesis, properties and varied applications, including in biology. Collectively, it provides scientists just beginning their careers, as well as firmly established ones, with the pulse of the field and inspiration to continue to explore these intriguing macromolecules.

Comparative genomics : 19th international conference, RECOMB-CG 2022, La Jolla, CA, USA, May 20-21, 2022, proceedings / / edited by Lingling Jin and Dannie Durand

• Record Nr.: UNISA996475771703316
• Pubbl/distr/stampa: Cham, Switzerland : , : Springer, , [2022]; ©2022
• ISBN: 3-031-06220-5
• Descrizione fisica: 1 online resource (344 pages)
• Collana: Lecture Notes in Computer Science ; ; v.13234
• Disciplina: 570.285
• Soggetti: Bioinformatics; Genomics
• Lingua di pubblicazione: Inglese
• Formato: Materiale a stampa
• Livello bibliografico: Monografia
• Nota di bibliografia: Includes bibliographical references and index.
• Nota di contenuto: Intro -- Preface -- Organization -- Contents -- Evolution -- On the Comparison of Bacteriophage Populations -- 1 Introduction -- 1.1 Recombinations and Mosaicism in Phage Genomes -- 1.2 Recombination Between Phage Populations -- 2 Methods -- 2.1 Basic Definitions and Properties -- 2.2 Minimum Covers -- 2.3 Lower Bounds -- 3 Experiments -- 3.1 Dataset Construction -- 3.2 Comparing Factories -- 3.3 Shared Evolution -- 3.4 Population Structure -- 4 Discussion and Conclusion -- References -- Syntenic Dimensions of Genomic Evolution -- 1 Introduction -- 2 The Construction and Biological Significance of Synteny Blocks -- 3 Review of Sequence ; Divergence -- 4 Fractionation and Gap Size -- 5 Spatial Evolution -- 6 Data Summary -- 7 Correlational Analysis -- 8 Discussion -- References -- Phylogenetics -- Fast and Accurate Branch Support Calculation for Distance-Based Phylogenetic Placements -- 1 Introduction -- 2 Approach -- 2.1 Background on APPLES-2 -- 2.2 Distance-Based Support Estimation: Goals and Background -- 2.3 Non-parametric Bootstrapping -- 2.4 Parametric Bootstrapping (Binomial and Poisson Models) -- 3 Experimental Study -- 3.1 Dataset -- 3.2 Measurements -- 4 Results and Discussion -- 4.1 Simulated Single-Gene RNASim Dataset: Full-Length Sequences -- 4.2 Simulated Single-Gene RNASim Dataset: Fragmentary Sequences -- 4.3 Multi-gene Web of Life (WoL) Dataset -- 4.4 Runtimes -- 5 Discussions -- References -- The Sackin Index of Simplex Networks -- 1 Introduction -- 2 Basic Concepts and Notation -- 2.1 Tree-Child Networks -- 2.2 Node Depth, Network Height and Sackin Index -- 3 The Expected Sackin Index of Random Simplex Networks -- 3.1 Enumerating Simplex Networks -- 3.2 The Total Depths of the Nodes in the Top Tree Component -- 3.3 The Expected Total C-Depth of Random Simplex Networks -- 3.4 Bounds on the Sackin Index for a Random Simplex Network.; 4 Conclusion -- References -- Phylogenetic Placement Problem: A Hyperbolic Embedding Approach -- 1 Introduction -- 2 Background on Hyperbolic Spaces -- 3 Problem Definition -- 4 H-DEPP -- 5 Experimental Setup -- 5.1 Datasets -- 5.2 Evaluation -- 6 Results and Discussions -- 6.1 Comparison of H-DEPP Alternatives -- 6.2 Comparison to Euclidean Embedding -- 6.3 Tree Updates -- 7 Conclusions and Future Work -- References -- Phylogenetic Network Dissimilarity Measures that Take Branch Lengths into Account -- 1 Introduction -- 2 Methods -- 2.1 Rooted Network Branch Score (rNBS) -- 2.2 Average Path Distance (APD) -- 3 Results and Discussion -- 3.1 Dissimilarity Under Various Network Perturbations -- 3.2 Analyzing Posterior Samples Using the Dissimilarity Measures -- 3.3 Runtime Comparison -- 4 Conclusions and Future Work -- References -- Homology and Reconciliation -- The Complexity of Finding Common Partitions of Genomes with Predefined Block Sizes -- 1 Introduction -- 2 Preliminary Notions -- 3 The Exact F-Strip Recovery Problem with Fixed F -- 4 GSR-F in Polynomial Time for Fixed F and Alphabet -- 5 Fixed Alphabet with Unbounded F is NP-Hard -- 6 Conclusion -- References -- Reconciliation with Segmental Duplication, Transfer, Loss and Gain -- 1 Introduction -- 2 Preliminary Definitions -- 3 Evolutionary Histories for Syntenies -- 4 Most Parsimonious Super-Reconciliations -- 5 A Two-Steps Method -- 6 A Dynamic Programming Algorithm for DTL Super-Reconciliation -- 7 Application to CRISPR-Associated (Cas) Gene Syntenies -- 7.1 Cas Gene Syntenies -- 7.2 Dataset -- 8 Results -- 8.1 DTL Super-Reconciliation Settings -- 8.2 An Evolutionary Scenario -- 9 Conclusion -- A Additional Content for Sect. 4 (``Most Parsimonious Super-Reconciliations'') -- B Additional Content for Sect. 6 (``A Dynamic Programming Algorithm for DTL Super- Reconciliation'').; References -- Quantifying Hierarchical Conflicts in Homology Statements -- 1 Introduction -- 2 Methodological Foundations -- 2.1 Overlapping Homology Statements and the Block Graph -- 2.2 Homology Witnesses and Block Hierarchies -- 2.3 Relating Block Hierarchy to Stars in the Block Graph -- 3 Algorithms -- 3.1 NP-Hardness of MDDS -- 3.2 A Heuristic for MDDS -- 4 Quantifying Hierarchical Conficts -- 4.1 Discordance Ratio and Distinction from Jaccard Index -- 4.2 Mycobacterium Tuberculosis Clinical Isolates -- 4.3 Alignathon -- 5 Discussion and Conclusions -- A NP-Hardness of MDDS -- B Collections of Block that are not Clean -- C Segmental ; Duplications -- References -- On Partial Gene Transfer and Its Impact on Gene Tree Reconstruction -- 1 Introduction -- 2 Materials and Methods -- 2.1 Simulated Datasets -- 2.2 Biological Datasets -- 2.3 Gene Tree Construction and Comparison -- 2.4 Using PhyML-Multi to Detect PGTs -- 3 Trippd: Tri-Partition Based PGT Detection -- 4 Results -- 4.1 Impact of PGT on Gene Tree Reconstruction Accuracy -- 4.2 PGT Detection Accuracy -- 4.3 Application to Biological Datasets -- 5 Discussion and Conclusion -- References -- Genome Rearrangements -- Sorting by k-Cuts on Signed Permutations -- 1 Introduction -- 2 Basic Definitions -- 3 Breakpoints and Strips -- 3.1 SKCBR is NP-Hard for k 5 -- 4 An Approximation Algorithm for SKCBR -- 5 Cycle Graph and Complement Cycle Graph -- 6 Increasing the Number of Cycles in G() with 4-Cuts -- 7 A 1.5-Approximation Algorithm for SKCBR When k=4 -- 8 Conclusion -- References -- A New Approach for the Reversal Distance with Indels and Moves in Intergenic Regions -- 1 Introduction -- 2 Background -- 2.1 Weighted Breakpoint Graph -- 3 Results -- 3.1 Complexity Analysis -- 3.2 Lower Bounds -- 3.3 Reversal and Move Operations -- 3.4 Reversal, Move, and Indel Operations -- 4 Conclusion.; References -- .26em plus .1em minus .1emChromothripsis Rearrangements Are Informed by 3D-Genome Organization -- 1 Introduction -- 2 Materials and Methods -- 2.1 Hi-C Data -- 2.2 SVs Data -- 2.3 Chromothripsis Rearrangements Data -- 2.4 Breakpoints Pairwise Distances Analysis -- 2.5 Statistical Analysis -- 3 Results and Discussion -- 4 Conclusions -- References -- Metagenomics -- Using Computational Synthetic Biology Tools to Modulate Gene Expression Within a Microbiome -- 1 Introduction -- 2 Methods -- 2.1 Translation Efficiency Modeling -- 2.2 Transcription Optimization -- 2.3 Editing Restriction Site Presence -- 2.4 Data Curation for In-SilicoAnalysis -- 2.5 In-vitro Methods -- 3 Results -- 3.1 Editing Restriction Site Presence -- 3.2 Translation Efficiency Modeling -- 3.3 Transcription Optimization -- 3.4 In-vitro Results -- 4 Discussion -- 4.1 Future Plans -- 4.2 Applications -- References -- Metagenomics Binning of Long Reads Using Read-Overlap Graphs -- 1 Introduction -- 2 Methods -- 2.1 Step 1: Constructing Read-Overlap Graph -- 2.2 Step 2: Obtaining Read Features -- 2.3 Step 3: Performing Probabilistic Sampling -- 2.4 Step 4: Detecting Clusters for Sampled Reads -- 2.5 Step 5: Binning Remaining Reads by Inductive Learning -- 3 Experimental Setup -- 3.1 Simulated Datasets -- 3.2 Real Datasets -- 3.3 Baselines and Evaluation Criteria -- 4 Results and Discussion -- 4.1 Binning Results -- 4.2 Assembly Results -- 5 Implementation -- 6 Conclusion -- A Dataset Information -- B Interpretation of AMBER Per-bin F1-Score -- References -- A Mixed Integer Linear Programming Algorithm for Plasmid Binning -- 1 Introduction -- 2 Hybrid Approach for Plasmid Binning Using Mixed Integer Linear Programming -- 2.1 Input: Contigs and the Assembly Graph -- 2.2 PlasBin Workflow -- 2.3 MILP Formulation -- 3 Experimental Results.; 3.1 Performance Comparison of Plasmid Binning Tools -- 3.2 Comparison of PlasBin and HyAsP -- 3.3 Computational Footprint -- 4 Discussion -- References -- Genomic Sequencing -- Benchmarking Penalized Regression Methods in Machine Learning for Single Cell RNA Sequencing Data -- 1 Introduction -- 2 Methods -- 2.1 Penalized Regression -- 2.2 Clustering -- 2.3 K-Fold Cross-validation -- 2.4 ROC AUC -- 3 Research Design and Data -- 3.1 Experimental Data -- 3.2 Research Design -- 4 Results -- 5 Discussion -- 6 Conclusion and Future Work -- References -- Deciphering the Tissue-Specific Regulatory Role of Intronless Genes Across Cancers -- 1 Introduction -- 2 Results -- 2.1 Functional Assignment and Gene Expression of IGs ; in Normal Tissue -- 2.2 IGs Tend to Have a More Induced Gene Expression Pattern When Compared to MEGs -- 2.3 Upregulated IGs Across Cancer Types Encode for Highly Conserved HDAC Deacetylate Histones Involved in Negative Gene Regulation -- 2.4 IG Downregulation Is Conserved in Breast and Colon Cancers and Is Involved in Signaling and Cell-Specific Functions -- 2.5 Cancer-Specific Differentially Expressed IGs -- 2.6 Proteins Encoded by Cancer-Specific Deregulated IGs Interact with Distinct Groups of Proteins in PPI Networks -- 2.7 DE-IGs Participate in the Genetic ``rewiring'' of Cancer Cells -- 3 Discussion -- 4 Materials and Methods -- 4.1 Data Extraction and Curation for IG, and MEG Datasets -- 4.2 Gene Expression Profiles in Healthy Tissue Tissue -- 4.3 Bipartite Network and Quantification of Shared and Unique DE-IGs -- 4.4 Data Source and Differential Expression Analysis Across Cancer -- 4.5 Upregulation Significant Differences of IGs and MEGs Among Cancers -- 4.6 Functional Enrichment Analysis of Differentially Expressed IGs -- 4.7 DE-IGs PPI Network Construction and Protein Complex Identification -- 4.8 BRCA Network Deconvolution.; References.