The Algorithmic Black Box: Exploring the Impact of Spotify and TikTok on User Behavior

This master’s thesis takes us on a journey through the assumption of algorithms and data via a quantitative approach. This guides us through the complexities of Spotify and TikTok’s algorithm and data, illuminating the key concepts and ideas that are essential for understanding this fascinating and an important topic. As we read, we are struck by two important research questions: • RQ1: Can Spotify and TikTok users discover new music and content with the guidance of algorithms? • RQ2: Does the algorithm affect the user behavior’s data positively or negatively within these platforms? This study is based on the following hypotheses; users will have the ability to discover new music and sound easily on both platforms determined by the algorithm. Additionally, the user’s data within behavior will be more or less affected by the algorithm positively and negatively. The research will be conducted through quantitative methods utilizing a survey. In this case, Google Survey will be used for data collection from respondents and will explore user interactions with the recommendation algorithm on Spotify and TikTok, as well as examine consumer behavior and the perceived effects of the algorithms on personal data. Additionally, the study will consider the influence of the COVID-19 pandemic on platform usage

Cell fate decisions emerge as phages cooperate or compete inside their host

The system of the bacterium Escherichia coli and its virus, bacteriophage lambda, is paradigmatic for gene regulation in cell-fate development, yet insight about its mechanisms and complexities are limited due to insufficient resolution of study. Here we develop a 4-colour fluorescence reporter system at the single-virus level, combined with computational models to unravel both the interactions between phages and how individual phages determine cellular fates. We find that phages cooperate during lysogenization, compete among each other during lysis, and that confusion between the two pathways occasionally occurs. Additionally, we observe that phage DNAs have fluctuating cellular arrival times and vie for resources to replicate, enabling the interplay during different developmental paths, where each phage genome may make an individual decision. These varied strategies could separate the selection for replication-optimizing beneficial mutations during lysis from sequence diversification during lysogeny, allowing rapid adaptation of phage populations for various environments

Bacteriophage Lambda Integrates Microenvironments, Individuality, and Interactions to Formulate Subcellular Decisions

Decision-making influences the development of life over multiple levels. Understanding the core mechanisms of this complex process could yield new insights into the treatment of diseases and the evolution of lifeforms. To study the universal subject of decision-making, we investigate the simple bacteriophage lambda model to distill complicated decision-making into fundamental biological questions. Lambda is a virus that infects E. coli, choosing between alternative modes of propagation, lysis or lysogeny, as its decision. Despite a history of research spanning decades, the underlying mechanisms of lambda decision-making are unclear. Using fluorescence microscopy for quantitative, high-resolution study, we explore an established paradigm with a new perspective to discover the inner workings of cellular decision-making. In our studies, we find that phages within single cells behave analogous to advanced organisms within their niches. For lambda, we find that their viral DNA molecules compete with each other inside the cell over replication resources. This allows phages to dominate each other, particularly during lysis, when DNA replication is important. Conversely, cooperation is prevalent during lysogeny, allowing viruses to benefit each other during a different path of development. These behaviors play a role in evolutionary fitness, where both strategic domination and cooperation may minimize the chances of extinction. We then study the spatial organization of phage development in the cell. We build tools to specifically characterize the coordinates of lambda DNA replication, resource sequestration, transcription, and virion assembly. We find that lambda manipulates its environment by hoarding resources and confining replicated viral genomes spatially. We observe that phage transcripts are localized nearby the phage genomes, and that virion assembly transpires in the same location, resembling a phage factory. Through our analysis, we find that multiple factories arise in cells and may be quantitatively distinct, suggesting this to be the origin of viral individuality. Indeed, we observe that different transcription programs, corresponding to different fates, occur in single cells, corroborating our hypothesis that individual phages can vote for decisions within cells. Finally, we incorporate our quantitative data and new models into computational simulations of this biological process to work towards a more complete quantitative understanding of decision-making

Coupling of DNA Replication and Negative Feedback Controls Gene Expression for Cell-Fate Decisions

Summary: Cellular decision-making arises from the expression of genes along a regulatory cascade, which leads to a choice between distinct phenotypic states. DNA dosage variations, often introduced by replication, can significantly affect gene expression to ultimately bias decision outcomes. The bacteriophage lambda system has long served as a paradigm for cell-fate determination, yet the effect of DNA replication remains largely unknown. Here, through single-cell studies and mathematical modeling we show that DNA replication drastically boosts cI expression to allow lysogenic commitment by providing more templates. Conversely, expression of CII, the upstream regulator of cI, is surprisingly robust to DNA replication due to the negative autoregulation of the Cro repressor. Our study exemplifies how living organisms can not only utilize DNA replication for gene expression control but also implement mechanisms such as negative feedback to allow the expression of certain genes to be robust to dosage changes resulting from DNA replication. : Gene Network; Microbial Genomics; Bioinformatics; Mathematical Biosciences Subject Areas: Gene Network, Microbial Genomics, Bioinformatics, Mathematical Bioscience

Prophylactic Administration of a Bacteriophage Cocktail Is Safe and Effective in Reducing Salmonella enterica Serovar Typhimurium Burden in Vivo

International audienceNontyphoidal Salmonella bacteria are the causative agent of salmonellosis, which accounts for the majority of foodborne illness of bacterial etiology in humans. Here, we demonstrate the safety and efficacy of the prophylactic administration of a bacteriophage preparation termed FOP (foodborne outbreak pill), which contains lytic phages targeting Salmonella (SalmoFresh phage cocktail), Shiga toxin-producing Escherichia coli (STEC), and Listeria monocytogenes, for lowering Salmonella burdens in OMM12 gnotobiotic mice. Prophylactic administration of FOP significantly reduced the levels of Salmonella in feces and in intestinal sections compared to the levels in controls. Moreover, the overall symptoms of the disease were also considerably lessened. Dose-dependent administration of FOP showed that phage amplification reached similarly high levels in less than 48 h independent of dose. In addition, 16S rRNA gene analysis showed that FOP did not alter the intestinal microbiota of healthy OMM12 mice and reduced microbiota perturbations induced by Salmonella. FOP maintained its full potency against Salmonella in comparison to that of SalmoFresh, its Salmonella-targeting component phages alone. Altogether, the data support that preventive administration of FOP may offer a safe and effective approach for reducing the risk of foodborne infections caused by Salmonella and, potentially, other foodborne bacteria (namely, STEC and L. monocytogenes) targeted by the FOP preparation

A Bacteriophage Cocktail Significantly Reduces Listeria monocytogenes without Deleterious Impact on the Commensal Gut Microbiota under Simulated Gastrointestinal Conditions

In this study, we examined the effect of a bacteriophage cocktail (tentatively designated as the Foodborne Outbreak Pill (FOP)) on the levels of Listeria monocytogenes in simulated small intestine, large intestine, and Caco-2 model systems. We found that FOP survival during simulated passage of the upper gastrointestinal was dependent on stomach pH, and that FOP robustly inhibited L. monocytogenes levels with effectiveness comparable to antibiotic treatment (ampicillin) under simulated ilium and colon conditions. The FOP did not inhibit the commensal bacteria, whereas ampicillin treatment led to dysbiosis-like conditions. The FOP was also more effective than an antibiotic in protecting Caco-2 cells from adhesion and invasion by L. monocytogenes (5-log reduction vs. 1-log reduction) while not triggering an inflammatory response. Our data suggested that the FOP may provide a robust protection against L. monocytogenes should the bacterium enter the human gastrointestinal tract (e.g., by consumption of contaminated food), without deleterious impact on the commensal bacteria

Towards an Operational SAR-Based Rice Monitoring System in Asia: Examples from 13 Demonstration Sites across Asia in the RIICE Project

Rice is the most important food security crop in Asia. Information on its seasonal extent forms part of the national accounting of many Asian countries. Synthetic Aperture Radar (SAR) imagery is highly suitable for detecting lowland rice, especially in tropical and subtropical regions, where pervasive cloud cover in the rainy seasons precludes the use of optical imagery. Here, we present a simple, robust, rule-based classification for mapping rice area with regularly acquired, multi-temporal, X-band, HH-polarized SAR imagery and site-specific parameters for classification. The rules for rice detection are based on the well-studied temporal signature of rice from SAR backscatter and its relationship with crop stages. We also present a procedure for estimating the parameters based on “temporal feature descriptors” that concisely characterize the key information in the rice signatures in monitored field locations within each site. We demonstrate the robustness of the approach on a very large dataset. A total of 127 images across 13 footprints in six countries in Asia were obtained between October 2012, and April 2014, covering 4.78 m ha. More than 1900 in-season site visits were conducted across 228 monitoring locations in the footprints for classification purposes, and more than 1300 field observations were made for accuracy assessment. Some 1.6 m ha of rice were mapped with classification accuracies from 85% to 95% based on the parameters that were closely related to the observed temporal feature descriptors derived for each site. The 13 sites capture much of the diversity in water management, crop establishment and maturity in South and Southeast Asia. The study demonstrates the feasibility of rice detection at the national scale using multi-temporal SAR imagery with robust classification methods and parameters that are based on the knowledge of the temporal dynamics of the rice crop. We highlight the need for the development of an open-access library of temporal signatures, further investigation into temporal feature descriptors and better ancillary data to reduce the risk of misclassification with surfaces that have temporal backscatter dynamics similar to those of rice. We conclude with observations on the need to define appropriate SAR acquisition plans to support policies and decisions related to food security

Genome-wide association study identifies five new susceptibility loci for primary angle closure glaucoma.

Primary angle closure glaucoma (PACG) is a major cause of blindness worldwide. We conducted a genome-wide association study (GWAS) followed by replication in a combined total of 10,503 PACG cases and 29,567 controls drawn from 24 countries across Asia, Australia, Europe, North America, and South America. We observed significant evidence of disease association at five new genetic loci upon meta-analysis of all patient collections. These loci are at EPDR1 rs3816415 (odds ratio (OR) = 1.24, P = 5.94 × 10(-15)), CHAT rs1258267 (OR = 1.22, P = 2.85 × 10(-16)), GLIS3 rs736893 (OR = 1.18, P = 1.43 × 10(-14)), FERMT2 rs7494379 (OR = 1.14, P = 3.43 × 10(-11)), and DPM2-FAM102A rs3739821 (OR = 1.15, P = 8.32 × 10(-12)). We also confirmed significant association at three previously described loci (P < 5 × 10(-8) for each sentinel SNP at PLEKHA7, COL11A1, and PCMTD1-ST18), providing new insights into the biology of PACG

Genome-wide association study identifies five new susceptibility loci for primary angle closure glaucoma.

Primary angle closure glaucoma (PACG) is a major cause of blindness worldwide. We conducted a genome-wide association study (GWAS) followed by replication in a combined total of 10,503 PACG cases and 29,567 controls drawn from 24 countries across Asia, Australia, Europe, North America, and South America. We observed significant evidence of disease association at five new genetic loci upon meta-analysis of all patient collections. These loci are at EPDR1 rs3816415 (odds ratio (OR) = 1.24, P = 5.94 × 10(-15)), CHAT rs1258267 (OR = 1.22, P = 2.85 × 10(-16)), GLIS3 rs736893 (OR = 1.18, P = 1.43 × 10(-14)), FERMT2 rs7494379 (OR = 1.14, P = 3.43 × 10(-11)), and DPM2-FAM102A rs3739821 (OR = 1.15, P = 8.32 × 10(-12)). We also confirmed significant association at three previously described loci (P < 5 × 10(-8) for each sentinel SNP at PLEKHA7, COL11A1, and PCMTD1-ST18), providing new insights into the biology of PACG