POTs: Protective Optimization Technologies

Algorithmic fairness aims to address the economic, moral, social, and political impact that digital systems have on populations through solutions that can be applied by service providers. Fairness frameworks do so, in part, by mapping these problems to a narrow definition and assuming the service providers can be trusted to deploy countermeasures. Not surprisingly, these decisions limit fairness frameworks' ability to capture a variety of harms caused by systems. We characterize fairness limitations using concepts from requirements engineering and from social sciences. We show that the focus on algorithms' inputs and outputs misses harms that arise from systems interacting with the world; that the focus on bias and discrimination omits broader harms on populations and their environments; and that relying on service providers excludes scenarios where they are not cooperative or intentionally adversarial. We propose Protective Optimization Technologies (POTs). POTs provide means for affected parties to address the negative impacts of systems in the environment, expanding avenues for political contestation. POTs intervene from outside the system, do not require service providers to cooperate, and can serve to correct, shift, or expose harms that systems impose on populations and their environments. We illustrate the potential and limitations of POTs in two case studies: countering road congestion caused by traffic-beating applications, and recalibrating credit scoring for loan applicants.Comment: Appears in Conference on Fairness, Accountability, and Transparency (FAT* 2020). Bogdan Kulynych and Rebekah Overdorf contributed equally to this work. Version v1/v2 by Seda G\"urses, Rebekah Overdorf, and Ero Balsa was presented at HotPETS 2018 and at PiMLAI 201

Real-Time Nuisance Fault Detection in Photovoltaic Generation Systems Using a Fine Tree Classifier

Nuisance faults are caused by weather events, which result in solar farms being disconnected from the electricity grid. This results in long stretches of downtime for troubleshooting as data are mined manually for possible fault causes, and consequently, cost thousands of dollars in lost revenue and maintenance. This paper proposes a novel fault detection technique to identify nuisance faults in solar farms. To initialize the design process, a weather model and solar farm model are designed to generate both training and testing data. Through an iterative design process, a fine tree model with a classification accuracy of 96.7% is developed. The proposed model is successfully implemented and tested in real-time through a server and web interface. The testbed is capable of streaming in data from a separate source, which emulates a supervisory control and data acquisition (SCADA) or weather station, then classifies the data in real-time and displays the output on another computer (which imitates an operator control room)

Bioluminescent avian pathogenic Escherichia coli for monitoring colibacillosis in experimentally infected chickens

Avian pathogenic Escherichia coli (APEC) are responsible for significant economic losses in the poultry industry. In this study, a model for investigating the pathogenesis of APEC infections was established. APEC strain CH2 (O78) was marked with the luciferase operon (luxCDABE) using a Tn7 transposon and tissues of experimentally infected chickens were analysed for a correlation between the bioluminescent signal and the number of bacteria. Transposition of the lux operon into the chromosome of the APEC isolate did not affect sensitivity to lytic bacteriophages and there was no effect on virulence in an intratracheal infection model in 1-day-old chicks, although results with a subcutaneous infection model were inconclusive. A correlation between the number of bacteria and the luminescent signal was found in liquid medium, as well as in homogenised heart, liver, spleen and lung of 4-week-old experimentally infected chickens. This study showed that lux could be used for identification of the infecting strain after experimental infection with APEC in poultry.publisher: Elsevier articletitle: Bioluminescent avian pathogenic Escherichia coli for monitoring colibacillosis in experimentally infected chickens journaltitle: The Veterinary Journal articlelink: http://dx.doi.org/10.1016/j.tvjl.2016.07.011 content_type: article copyright: © 2016 Elsevier Ltd. All rights reserved.status: publishe

Détérioration des matériaux cimentaires dans les ouvrages de nitrification des stations d’épuration

En assainissement, la nitrification est une étape de traitement biologique qui permet, par l’intermédiaire de bactéries nitrifiantes, de transformer les ions ammonium en ions nitrate. Les ouvrages dans lesquels se déroule la nitrification sont construits avec des matériaux cimentaires qui subissent des dégradations de plus en plus visibles ces dernières années. Dans la littérature, il n’existe qu’une seule étude réalisée par une équipe suisse qui s’est intéressée à la détérioration du béton dans les ouvrages de nitrification. Il est reporté dans ces travaux que les dégradations observées sur les ouvrages ont une origine biologique et résultent de l’acidité générée par l’activité biologique nitrifiante à l’interface paroi en béton/biofilm. Néanmoins, d’autres paramètres qui ne sont pas pris en compte peuvent être responsables de la dégradation du béton, ce qui signifie qu’une étude plus détaillée des mécanismes de dégradation est nécessaire pour bien qualifier et quantifier les dégradations dans les ouvrages de traitement biologique. En effet, les dégradations peuvent avoir une origine chimique, une origine mécanique ou une origine biologique. Cet article bibliographique a ainsi pour objectif de décrire et d’analyser les différents paramètres chimiques, biologiques et mécaniques susceptibles d’avoir une influence sur la dégradation du béton dans les ouvrages de nitrification

Trust and Biomedical Research Engagement of Minority and Under-Represented Communities in Mississippi, USA

Trust is critical to the development and maintenance of effective research collaborations and community engagement. The purpose of this study was to assess the current attitudes and level of trust pertaining to health research among residents of Central Mississippi, the priority health region for the Research Centers in Minority Institutions (RCMI) Center for Health Disparities Research (RCHDR) at Jackson State University. The cross-sectional study was conducted from November 2021 to April 2022. The data were analyzed using descriptive statistics carried out by SPSS statistical software. A total of 146 participants responded to the survey. The participants were predominately African American (99%) and female (75%). Historical research studies, the researchers’ qualities, and potential benefits from participation were factors affecting the level of trust in the research process. Ninety percent (n = 131) expressed that it was important to be involved in the research process, and 98.5% (n = 144) agreed that discussing the research findings with the participants was important for establishing trust in the research process. While trust in the research process does not guarantee participation, trust is a precursor for those who decide to engage in health disparities research. Key findings will be integrated into the RCHDR research agenda to foster further development and implementation of innovative community-based participatory research toward the control and/or prevention of diseases that disproportionately affect minority and under-represented populations in Mississippi

DNA Physical Properties and Nucleosome Positions Are Major Determinants of HIV-1 Integrase Selectivity

International audienceRetroviral integrases (INs) catalyse the integration of the reverse transcribed viral DNA into the host cell genome. This process is selective, and chromatin has been proposed to be a major factor regulating this step in the viral life cycle. However, the precise underlying mechanisms are still under investigation. We have developed a new in vitro integration assay using physiologically-relevant, reconstituted genomic acceptor chromatin and high-throughput determination of nucleosome positions and integration sites, in parallel. A quantitative analysis of the resulting data reveals a chromatin-dependent redistribution of the integration sites and establishes a link between integration sites and nucleosome positions. The co-activator LEDGF/ p75 enhanced integration but did not modify the integration sites under these conditions. We also conducted an in cellulo genome-wide comparative study of nucleosome positions and human immunodeficiency virus type-1 (HIV-1) integration sites identified experimentally in vivo. These studies confirm a preferential integration in nucleosome-covered regions. Using a DNA mechanical energy model, we show that the physical properties of DNA probed by IN binding are important in determining IN selectivity. These novel in vitro and in vivo approaches confirm that IN has a preference for integration into a nucleosome, and suggest the existence of two levels of IN selectivity. The first depends on the physical properties of the target DNA and notably, the energy required to fit DNA into the IN catalytic pocket. The second depends on the DNA deformation associated with DNA wrapping around a nucleosome. Taken together , these results indicate that HIV-1 IN is a shape-readout DNA binding protein

Schematic diagram of the experimental strategy on the selected sequences.

<p>A) Nucleosome positioning. To obtain nucleosome positions, naked DNA control, or <i>in vitro</i> assembled PN templates were digested with the Miccrococal nuclease (MNase) at a concentration optimal for obtaining a discrete mononucleosome band, and the bands were cut and extracted from an agarose gel and deep sequenced using Illumina technology. B) Integration site mapping. To obtain integration sites on the same DNA or polynucleosome templates, <i>in vitro</i> integration assays were performed with SupF viral donor and purified recombinant IN enzyme, or IN co-purified with LEDGF/p75. Integration products were deproteinized by proteinase K treatment, then used as templates for a PCR with primers specific to the U3 and U5 viral DNA ends, and primers common to the 5’ or 3’ ends of the DNA fragment. PCR products were pooled and deep sequenced using Illumina technology. Top strand integrations give a forward read PCR product and bottom strand integrations give a reverse read.</p

Nucleosome positions along four selected sequences.

<p>A) Predicted [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0129427#pone.0129427.ref066" target="_blank">66</a>] (blue line) or experimentally derived [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0129427#pone.0129427.ref052" target="_blank">52</a>] (magenta line) nucleosome occupancies (log2 values) around four HIV integration sites identified in infected cells: CL529183, CL529481 and CL528939 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0129427#pone.0129427.ref011" target="_blank">11</a>] and DX598014 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0129427#pone.0129427.ref013" target="_blank">13</a>]. Analysis are presented along 2 000 bp windows centred at these sites. B) PNs were assembled <i>in vitro</i> on 1.2 kb DNA fragments corresponding to the four selected sequences and centred on the position of <i>in vivo</i> identified integration site. Nucleosome positions were either predicted (upper panels) or mapped by MNase seq (middle and lower panels). Upper panels: heat maps of predicted nucleosome occupancies P(s) (defined in Materials and Methods). These occupancies were calculated along the studied sequences (positions on X axis) as a function of the chemical potential μ (Y axis) using an algorithm described in [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0129427#pone.0129427.ref061" target="_blank">61</a>]. On these maps, dark blue corresponds to low probability and red to high probability. Middle panels: MNase digestion products of PNs assembled at one histone/DNA ratio (0.74 μg/1 μg) are represented by black points along the four sequences, according to their centre (X axis) and size (Y axis). To clarify this representation, only one tenth of the total MNase seq products are plotted. Lower panels: Nucleosome occupancies calculated from the MNase digestion products of PN assembled at two histone/DNA ratios (0.74 μg/1 μg, black solid line; 1 μg/1 μg, black dot line) (nucleosome occupancy values at a given site correspond to the total number of paired-end reads of MNase digestion products that covers this site, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0129427#sec002" target="_blank">Materials and Methods</a> for more details). On the same panel is represented the nucleosome occupancy calculated from MNase-seq of cellular chromatin [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0129427#pone.0129427.ref052" target="_blank">52</a>] (magenta line).</p

Autocorrelations between integration sites identified on three selected sequences (CL528939, CL529481 and CL529183).

<p>Autocorrelations were calculated between integration sites identified on three selected sequences and corresponding to different conditions of integration. A) IN-LEDGF/p75 on DNA, B) IN-LEDGF/p75 on PN assembled at histone/DNA ratio (0.74 μg/1 μg), C) IN-LEDGF/p75 on PN assembled at histone/DNA ratio (1.3 μg/1 μg) and D) IN on PN assembled at histone/DNA ratio (1.3 μg/1 μg). For each panel, autocorrelations were calculated between integration sites of the same strand (+/+ red and-/- blue) or complementary strands (+/- green).</p