Excerpts from Witness’s Testimony

Excerpts from Witness’s Testimony (New York v Taylor) including “Eyes Like the Eyes of a Man, and a Mouth Speaking Pompous Words” by Dr. Daniel Yochai Introduction by Dr. Yehuda Mendelsoh

Worst-case Performance of Popular Approximate Nearest Neighbor Search Implementations: Guarantees and Limitations

Graph-based approaches to nearest neighbor search are popular and powerful tools for handling large datasets in practice, but they have limited theoretical guarantees. We study the worst-case performance of recent graph-based approximate nearest neighbor search algorithms, such as HNSW, NSG and DiskANN. For DiskANN, we show that its "slow preprocessing" version provably supports approximate nearest neighbor search query with constant approximation ratio and poly-logarithmic query time, on data sets with bounded "intrinsic" dimension. For the other data structure variants studied, including DiskANN with "fast preprocessing", HNSW and NSG, we present a family of instances on which the empirical query time required to achieve a "reasonable" accuracy is linear in instance size. For example, for DiskANN, we show that the query procedure can take at least $0.1 n$ steps on instances of size $n$ before it encounters any of the $5$ nearest neighbors of the query.Comment: Accepted by NeurIPS 202

Method for measurement of bacillithiol redox potential changes using the Brx-roGFP2 redox biosensor in Staphylococcus aureus

Recent advances in the design of genetically encoded redox biosensors, such as redox-sensitive GFP (roGFP) have facilitated the real-time imaging of the intracellular redox potential in eukaryotic cells at high sensitivity and at spatiotemporal resolution. To increase the specificity of roGFP2 for the interaction with the glutathione (GSH)/ glutathione disulfide (GSSG) redox couple, roGFP2 has been fused to glutaredoxin (Grx) to construct the Grx-roGFP2 biosensor. We have previously designed the related Brx-roGFP2 redox biosensor for dynamic measurement of the bacillithiol redox potential (E-BSH) in the human pathogen Staphylococcus aureus. Here, we describe the detailed method for measurements of the oxidation degree (OxD) of the Brx-roGFP2 biosensor in S. aureus using the microplate reader. In particularly, we provide details for determination of the E-BSH changes during the growth and after oxidative stress. For future biosensor applications at the single cell level, we recommend the design of genome-encoded roGFP2 biosensors enabling stable expression and fluorescence in bacteria. Brx-roGFP2 is specific for measurements of the bacillithiol redox potential in Staphylococcus aureus cells Control samples for fully reduced and oxidized states of Brx-roGFP2 are required for calibration during OxD measurements Easy to measure fluorescence excitation intensities at the 405 and 488 nm excitation maxima using microplate reader

Embeddings and Labeling Schemes for A*

A* is a classic and popular method for graphs search and path finding. It assumes the existence of a heuristic function h(u,t) that estimates the shortest distance from any input node u to the destination t. Traditionally, heuristics have been handcrafted by domain experts. However, over the last few years, there has been a growing interest in learning heuristic functions. Such learned heuristics estimate the distance between given nodes based on "features" of those nodes. In this paper we formalize and initiate the study of such feature-based heuristics. In particular, we consider heuristics induced by norm embeddings and distance labeling schemes, and provide lower bounds for the tradeoffs between the number of dimensions or bits used to represent each graph node, and the running time of the A* algorithm. We also show that, under natural assumptions, our lower bounds are almost optimal

De infraestructura vial a espacio urbano. Transformación de Via Flaminia en un nuevo eje cultural de Roma

The street is the outside space that shapes our daily life. Its study means to understand the most important public space of the city. The research project described herein attempts to understand how the street becomes an urban space -a livable space-, its importance as a social realm and the design elements that make it a successful space in the city. The scope of the research goes from a general overview of the street to the study of the specific case represented by Via Flaminia, one of the most important historical axes of Rome. The approach to the research is divided into two parts; first a theoretical, historical and referential investigation; and a second part that includes a focused analysis of Via Flaminia and concludes with the application of this analysis to the design of an urban and an architectural project for this chosen street. The proposed project seeks to solve the limited permeability of the street and attempts to provide continuity to its image. It explores the repurposing the existing building typologies with new social, cultural and recreational functions. One of the main goals is to transform this street into a revitalized cultural node of the city, to transform Via Flaminia from a road infrastructure to a quality urban space of the City of Rome, seeking that it becomes the new cultural axis of the city. The architectural project focuses on a critical point of the street, developing a Cultural and Educational Center.La calle es el espacio exterior que configura la vida cotidiana. Su estudio significa entender el espacio público más importante de la ciudad. El proyecto de investigación aquí descrito intenta comprender cómo la calle se convierte en un espacio urbano -un espacio habitable-, su importancia como ámbito social y en los elementos de diseño que lo convierten en un área exitosa en la ciudad. El alcance va desde una visión general de la calle hasta el estudio del caso específico representado por Vía Flaminia, uno de los ejes históricos más importantes de Roma. Primeramente, la investigación es teórica, histórica y referencial; y segundo incluye un análisis enfocado de Via Flaminia, concluyendo con la aplicación de éste análisis al diseño de un proyecto urbano y arquitectónico. El plan maestro propuesto busca resolver la permeabilidad limitada de la calle, e intenta dar continuidad a su imagen. Explora la reutilización de las tipologías de edificios existentes con nuevas funciones sociales, culturales y recreativas. Uno de los objetivos principales de este master plan es convertir esta calle en un nodo cultural revitalizado de la ciudad para transformar Via Flaminia de una infraestructura vial a un espacio urbano de calidad en la Ciudad de Roma, buscando que se convierta en un nuevo eje cultural. El proyecto arquitectónico se centra en un punto crítico, abordando la conexión de la ciudad con la naturaleza circundante, planteando el desarrollo de un Centro Cultural y Educacional

La lénition romane : l’héritage martinétien et sa modélisation formelle

La lénition, tant sur le plan synchronique que sur le plan diachronique (Martinet, 1955 ; Bichakjian, 1977 ; Gurevich, 2004), montre une nette tendance à maintenir des contrastes. Dans cet article, nous allons passer en revue et critiquer des approches qui postulent des contraintes du type *NoMerge ou *Neut, des approches basées sur des contraintes localement conjointes ainsi qu’une analyse basée sur le marquage comparatif. Ensuite, nous allons illustrer comment les données synchroniques romanes peuvent être analysées dans la théorie de l’Optimalité avec des chaînes de candidats et nous montrons que les données romanes en question ne permettent pas à la phonologie de se passer des contraintes de marquage.Both diachronically and synchronically, lenition shows a clear non-neutralizing tendency (Martinet, 1955 ; Bichakjian, 1977 ; Gurevich, 2004). In this article, we will critically review approaches based on constraints of the type *NoMerge or *Neut, approaches based on local constraint conjunction and a recent analysis based on comparative markedness. After that, we will illustrate how the romance facts can be analyzed with OT-CC and argue that markedness constraints are a crucial ingredient of phonological theory

The Catalase KatA Contributes to Microaerophilic H2O2 Priming to Acquire an Improved Oxidative Stress Resistance in Staphylococcus aureus

Staphylococcus aureus has to cope with oxidative stress during infections. In this study, S. aureus was found to be resistant to 100 mM H2O2 during aerobic growth. While KatA was essential for this high aerobic H2O2 resistance, the peroxiredoxin AhpC contributed to detoxification of 0.4 mM H2O2 in the absence of KatA. In addition, the peroxiredoxins AhpC, Tpx and Bcp were found to be required for detoxification of cumene hydroperoxide (CHP). The high H2O2 tolerance of aerobic S. aureus cells was associated with priming by endogenous H2O2 levels, which was supported by an oxidative shift of the bacillithiol redox potential to −291 mV compared to −310 mV in microaerophilic cells. In contrast, S. aureus could be primed by sub-lethal doses of 100 µM H2O2 during microaerophilic growth to acquire an improved resistance towards the otherwise lethal triggering stimulus of 10 mM H2O2. This microaerophilic priming was dependent on increased KatA activity, whereas aerobic cells showed constitutive high KatA activity. Thus, KatA contributes to the high H2O2 resistance of aerobic cells and to microaerophilic H2O2 priming in order to survive the subsequent lethal triggering doses of H2O2, allowing the adaptation of S. aureus under infections to different oxygen environments