Towards More Practical Linear Programming-based Techniques for Algorithmic Mechanism Design

R. Lavy and C. Swamy (FOCS 2005, J. ACM 2011) introduced a general method for obtaining truthful-in-expectation mechanisms from linear programming based approximation algorithms. Due to the use of the Ellipsoid method, a direct implementation of the method is unlikely to be efficient in practice. We propose to use the much simpler and usually faster multiplicative weights update method instead. The simplification comes at the cost of slightly weaker approximation and truthfulness guarantees

On the Number of Iterations for Dantzig-Wolfe Optimization and Packing-Covering Approximation Algorithms

We give a lower bound on the iteration complexity of a natural class of Lagrangean-relaxation algorithms for approximately solving packing/covering linear programs. We show that, given an input with $m$ random 0/1-constraints on $n$ variables, with high probability, any such algorithm requires $\Omega(\rho \log(m)/\epsilon^2)$ iterations to compute a $(1+\epsilon)$-approximate solution, where $\rho$ is the width of the input. The bound is tight for a range of the parameters $(m,n,\rho,\epsilon)$. The algorithms in the class include Dantzig-Wolfe decomposition, Benders' decomposition, Lagrangean relaxation as developed by Held and Karp [1971] for lower-bounding TSP, and many others (e.g. by Plotkin, Shmoys, and Tardos [1988] and Grigoriadis and Khachiyan [1996]). To prove the bound, we use a discrepancy argument to show an analogous lower bound on the support size of $(1+\epsilon)$-approximate mixed strategies for random two-player zero-sum 0/1-matrix games

Discarding IVF embryos: reporting on global practices

Purpose: To provide a global scale report on a representative sample of the clinical embryology community depicting the practice of discarding supernumerary IVF embryos. Methods: A web-based questionnaire titled “Anonymous questionnaire on embryo disposal practices” was designed in order to ensure anonymous participation of practicing clinical embryologists around the world. Results: During a data collection period of 8 months, 703 filled-in questionnaires from 65 countries were acquired. According to the data acquired, the majority of practitioners, dispose of embryos by placing them directly in a trash can strictly dedicated for embryo disposal for both fresh and frozen cycles (39% and 36.7% respectively). Moreover, 66.4% of practitioners discard the embryos separately—case by case—at different time points during the day. Over half of embryologists (54%) wait until day 6 to discard the surplus embryos, while 65.5% do not implement a specially allocated incubator space as a designated waiting area prior to disposal. The majority of 63.1% reported that this is a witnessed procedure. The vast majority of embryologists (93%) do not employ different protocols for different groups of patients. Nonetheless, 17.8% reported the request to perform a ceremony for these embryos. Assessing the embryologists’ perspective, 59.5% of participants stated that the embryology practice would benefit from a universally accepted and practiced protocol. Conclusion(s): This study uniquely provides insight into global embryo disposal practices and trends. Results highlight the divergence between reported practices, while indicating the significance on standardization of practice, with embryologists acknowledging the need for a universally accepted protocol implementation

Dual Mechanisms of LYN Kinase Dysregulation Drive Aggressive Behavior in Breast Cancer Cells

The SRC-family kinase LYN is highly expressed in triple-negative/basal-like breast cancer (TNBC) and in the cell of origin of these tumors, c-KIT-positive luminal progenitors. Here, we demonstrate LYN is a downstream effector of c-KIT in normal mammary cells and protective of apoptosis upon genotoxic stress. LYN activity is modulated by PIN1, a prolyl isomerase, and in BRCA1 mutant TNBC PIN1 upregulation activates LYN independently of c-KIT. Furthermore, the full-length LYN splice isoform (as opposed to the Δaa25-45 variant) drives migration and invasion of aggressive TNBC cells, while the ratio of splice variants is informative for breast cancer-specific survival across all breast cancers. Thus, dual mechanisms-uncoupling from upstream signals and splice isoform ratios-drive the activity of LYN in aggressive breast cancers

A Nearly Linear-Time PTAS for Explicit Fractional Packing and Covering Linear Programs

We give an approximation algorithm for packing and covering linear programs (linear programs with non-negative coefficients). Given a constraint matrix with n non-zeros, r rows, and c columns, the algorithm computes feasible primal and dual solutions whose costs are within a factor of 1+eps of the optimal cost in time O((r+c)log(n)/eps^2 + n).Comment: corrected version of FOCS 2007 paper: 10.1109/FOCS.2007.62. Accepted to Algorithmica, 201

Pharmacological levels of withaferin A (Withania somnifera) trigger clinically relevant anticancer effects specific to triple negative breast cancer cells

Withaferin A (WA) isolated from Withania somnifera (Ashwagandha) has recently become an attractive phytochemical under investigation in various preclinical studies for treatment of different cancer types. In the present study, a comparative pathway-based transcriptome analysis was applied in epithelial-like MCF-7 and triple negative mesenchymal MDA-MB-231 breast cancer cells exposed to different concentrations of WA which can be detected systemically in in vivo experiments. Whereas WA treatment demonstrated attenuation of multiple cancer hallmarks, the withanolide analogue Withanone (WN) did not exert any of the described effects at comparable concentrations. Pathway enrichment analysis revealed that WA targets specific cancer processes related to cell death, cell cycle and proliferation, which could be functionally validated by flow cytometry and real-time cell proliferation assays. WA also strongly decreased MDA-MB-231 invasion as determined by single-cell collagen invasion assay. This was further supported by decreased gene expression of extracellular matrix-degrading proteases (uPA, PLAT, ADAM8), cell adhesion molecules (integrins, laminins), pro-inflammatory mediators of the metastasis-promoting tumor microenvironment (TNFSF12, IL6, ANGPTL2, CSF1R) and concomitant increased expression of the validated breast cancer metastasis suppressor gene (BRMS1). In line with the transcriptional changes, nanomolar concentrations of WA significantly decreased protein levels and corresponding activity of uPA in MDA-MB-231 cell supernatant, further supporting its anti-metastatic properties. Finally, hierarchical clustering analysis of 84 chromatin writer-reader-eraser enzymes revealed that WA treatment of invasive mesenchymal MDA-MB-231 cells reprogrammed their transcription levels more similarly towards the pattern observed in non-invasive MCF-7 cells. In conclusion, taking into account that sub-cytotoxic concentrations of WA target multiple metastatic effectors in therapy-resistant triple negative breast cancer, WA-based therapeutic strategies targeting the uPA pathway hold promise for further (pre)clinical development to defeat aggressive metastatic breast cancer

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates

Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.ensembl.org). The two resources collectively present genome annotation through a consistent set of interfaces spanning the tree of life presenting genome sequence, annotation, variation, transcriptomic data and comparative analysis. Here we present our largest increase in plant, metazoan and fungal genomes since the project’s inception creating one of the world’s most comprehensive genomic resources and describe our efforts to reduce genome redundancy in our Bacteria portal. We also detail our new efforts in gene annotation, our emerging support for pangenome analysis and efforts to accelerate data dissemination through the Ensembl Rapid Release resource. We also present our new AlphaFold visualisation. Finally, we present details of our future plans including updates on our integration with Ensembl, and how we plan to improve our support for the microbial research community. Software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license). Data updates are synchronised with Ensembl’s release cycle

Athens by Sound

Architecture is not only that which is built. Architecture is made up of different aspects, both material and immaterial. The atmosphere, the sounds, the smells, the possibility of interaction between human bodies: these all constitute characteristics of space, characteristics that are assuming an increasing importance within architectural research worldwide. Within this field of thought about “Architecture Beyond Building”, we focus on one particular non-material spatial phenomenon that lies ‘beyond the built’: sound. We have created, thus, an interactive sonic map of Athens, which presents, in an unexpected way, fragments of the atmosphere of the city. What would a non-visual map look like? What would it feel like if you wandered within a forest of headphones, playing sounds from different places in Athens? How would it feel if you found yourself in a ‘map’ that only appeared when you walked in it? What would it be like if the map only appeared when you invited one more person to be with you? The Greek pavilion addresses these questions through an atmospheric interactive ‘game’, presenting fragments of sounds and visual sequences of Athens. The visitor recreates the space around him through his own presence and movement. The map appears only where he walks, and/or when he invites one more person to sit next to him. The bodies of the visitors react with one another and with the space itself, creating a dynamic, changing field. This walk in the pavilion takes you “out there”, through invisible Athens. The pavilion brings forth the aspects of architecture that are ‘beyond the material’: the ‘beyond the built’, the almost unreachable, elusive aspects of space, such as sound, non-visual senses, atmosphere. It challenges, thus, the limits of architecture, the limits of what can be mapped and re-located and what cannot. An edited collection by A. Karandinou, C. Achtypi, S. Giamarelos, including texts by: Ιntothepill, Katie Lloyd Thomas, Martin Parker, Panayiotis Tournikiotis, Mark Wigley, Dorian Wiszniewski, Leslie Kavanaugh, Stephen Cairns, Jonathan Hill, Vassilis Ganiatsas, Anastasios Kotsiopoulos, Constance Classen, Stavros Stavrides, Ole Bouman, William Mitchell, Richard Coyne, Neil Spiller, Kas Oosterhuis, Nora Schueler, Zissis Kotionis, Stelarc, Andreas Angelidakis, Aristide Antonas, Slavoj Žižek, Nikolaos Laskaris, Argyris Rokas, Andreas Kourkoulas, John Peponis, Yorgos Ioannou, Yorgos Tzirtzilakis, Konstantinos Vita, Dionyssis Kapsalis, United Visual Artists, Platon Rivellis, and Dimitris Filippidis. Contributors to the Greek National Participation to the 11th International Architecture Exhibition La Biennale di Venezia "Out there. Architecture beyond building" (2008) Organised by: Hellenic Ministry of Culture [yppo.gr] General Directorate of Modern Culture Directorate of Visual Arts Department for the Promotion of Contemporary Art Curators: Anastasia Karandinou Christina Achtypi Stylianos Giamarelos Video works by Intothepill net [intothepill.net] Artists: Yiannis Grigoriadis Yiannis Isidorou Lina Theodorou Sound Recording / Sound Design Dimitris Miyakis [movement.gr] Vangelis Lympouridis Exhibition Graphics / Catalogue Design Company [company-london.com] Design and Implementation of interactive environment 2monochannels [2monochannels.com] Audiovisual and interactive systems design / acoustic design / construction supervision Iraklis Lampropoulos Giorgos Lampropoulos Software programming Vassilis Boukis Electronic subsystem design Michail Kritsotakis Electrical Design Giorgos Satolias Interconnection of interactive elements Vangelis Lympouridis [inter-axions.com] Dimitris Miyakis Light design L+DG lighting architects [lightingdg.com] Thomas Gravanis Christina Frangeti Construction Gavrilos Michalis [gavrilos.gr] Digital printing Polichromo [polichromo.com] Translations Rachel Howard Nikos Masourides Catalogue photographs Intothepill – Internet video platform Catalogue published by futura publications Marketing communication Chryssa Vrouzi Communication associate Katerina Stamidi Photographer Cathy Cunliffe [cathycunliffeΑΤgmail.com] For their financial and material support for the Greek participation at the 11th International Exhibition of Architecture, La Biennale di Venezia, we express our deepest thanks to the sponsors: Alexander S. Onassis Public Benefit Foundation [onassis.gr] Akzonobel [akzonobel.com] Carteco - Architectural Materials & Design [carteco.gr] L+DG Lighting Architects [lightingdg.com] Plaisio [plaisio.gr] Polichromo Advertising Applications [polichromo.com] iGuzzini illuminazione [iguzzini.com] Diathlasis Architectural Lighting [diathlasis.gr