LIVE AUDIENCE ENGAGEMENT SYSTEM

A live fan engagement system enables video creators to engage with viewers while the viewers are watching a video. The system sets up online group viewing sessions for creator and viewers. When the creator and viewers join these sessions, the system initiates playback of a desired media and concurrently starts a chat session. Further, the system determines whether the creator or the viewers have a second screen device available during the session. If the second screen device is present for any of the viewers or the creator, the media is played on one of the screens and the chat session is initiated on the other screen. Alternatively, in the absence of a second screen device, the media and the chat session are initiated on the same screen. The system further allows recording of these group viewing sessions including media and text from the chat session

Automated Design of Dynamic Programming Schemes for RNA Folding with Pseudoknots

Despite being a textbook application of dynamic programming (DP) and routine task in RNA structure analysis, RNA secondary structure prediction remains challenging whenever pseudoknots come into play. To circumvent the NP-hardness of energy minimization in realistic energy models, specialized algorithms have been proposed for restricted conformation classes that capture the most frequently observed configurations. While these methods rely on hand-crafted DP schemes, we generalize and fully automatize the design of DP pseudoknot prediction algorithms. We formalize the problem of designing DP algorithms for an (infinite) class of conformations, modeled by (a finite number of) fatgraphs, and automatically build DP schemes minimizing their algorithmic complexity. We propose an algorithm for the problem, based on the tree-decomposition of a well-chosen representative structure, which we simplify and reinterpret as a DP scheme. The algorithm is fixed-parameter tractable for the tree-width tw of the fatgraph, and its output represents a ?(n^{tw+1}) algorithm for predicting the MFE folding of an RNA of length n. Our general framework supports general energy models, partition function computations, recursive substructures and partial folding, and could pave the way for algebraic dynamic programming beyond the context-free case

Language, the Parent of Thought: Speculating with Hegel

We speculate with Hegel about language, critiquing interpretations of Hegel's views on language given by Jim Vernon, John McCumber, Stephen Houlgate, and Michael N. Forster, as well as defending Sophisticated Radical Whorfianism from the objections of Maria Francisca Reines and Jesse Prinz.  Prior to discussing Forster, we explicate Hegel's views on mechanical memory.  We conclude by discussing why, although thought grows up, it does not move out

Scalable downstream purification of recombinant adeno-associated viral vectors

Scalable manufacturing technologies are essential for ensuring modern medicines can be produced to meet the needs of clinical trials, process development, and commercial manufacture. Recent advances in in vivo gene therapies have resulted in multiple regulatory approvals of rAAV vectors for gene transfer in humans. These vectors can be produced using transient transfection of mammalian cells, baculovirus infection of insect cells or produced via engineered stable producer cells. These production methods are performed in single-use bioreactors and utilize other scalable technologies as used in commercial monoclonal antibody manufacture. In this work, we evaluated the use of existing single-use filtration and separation technologies for downstream purification of an rAAV5 viral vector. rAAV5 vector was produced by transient transfection of HEK293 cells in the Pall iCELLis® Nano bioreactor. Bioreactor harvest lysis material was clarified using direct flow filtration with both depth and sterilizing grade filters. The product was concentrated 10x using 100kD OmegaTM flat-sheet tangential flow-filtration (TFF) before primary purification using affinity chromatography. The rAAV5 vector was then polished using Mustang® Q membrane chromatography to enrich for full capsids. A second TFF step was performed to concentrate and buffer exchange with flat sheet TFF with the same 100KD Omega membrane. Final sterile filtration was performed using Supor® EKV validated sterilizing grade filters. All downstream unit operations resulted in acceptable performance. Feasibility of a complete downstream process was established with a theoretical whole process yield of ~25%. This process results in a very low contaminant profile as host cell protein (HCP) and host cell DNA were reduced to near and below the assays’ limits of quantitation during purification. Of particular interest, Mustang Q polishing resulted in retention of only ~10% of total capsids, while recovering ~50% of full capsids enriching the ratio of full capsids to empty capsids by 4.5 fold

Anxiety and depression following cumulative low-level exposure to organophosphate pesticides

Previous research suggests that individuals with a prior history of pesticide poisoning are at increased risk of psychiatric disorder (Freire and Koifman, 2013), but findings regarding the impact of cumulative low-level exposure are inconsistent. The aim of the current study was to investigate whether sheep farmers with a history of low-level exposure to organophosphate pesticides (1) report a higher level of psychological distress on subjective symptom questionnaires, compared to unexposed controls (2) also meet internationally agreed diagnostic criteria for a psychiatric disorder more often than unexposed controls. 127 sheep farmers were evaluated and compared to 78 unexposed controls, matched in terms of gender, education, level of intelligence, working status and area of residence. Both self-report measures and structured clinical interviews were used to assess mental health. The exposed cohort reported significantly higher rates of anxiety and depression when self-report questionnaires were used to evaluate mood, even when stressful life events, demographic and physical health factors were taken into account. However, when diagnostic interviews were used to assess mood, this pattern only held true for anxiety

Novel Insights into the Bovine Polled Phenotype and Horn Ontogenesis in Bovidae

Despite massive research efforts, the molecular etiology of bovine polledness and the developmental pathways involved in horn ontogenesis are still poorly understood. In a recent article, we provided evidence for the existence of at least two different alleles at the Polled locus and identified candidate mutations for each of them. None of these mutations was located in known coding or regulatory regions, thus adding to the complexity of understanding the molecular basis of polledness. We confirm previous results here and exhaustively identify the causative mutation for the Celtic allele (PC) and four candidate mutations for the Friesian allele (PF). We describe a previously unreported eyelash-and-eyelid phenotype associated with regular polledness, and present unique histological and gene expression data on bovine horn bud differentiation in fetuses affected by three different horn defect syndromes, as well as in wild-type controls. We propose the ectopic expression of a lincRNA in PC/p horn buds as a probable cause of horn bud agenesis. In addition, we provide evidence for an involvement of OLIG2, FOXL2 and RXFP2 in horn bud differentiation, and draw a first link between bovine, ovine and caprine Polled loci. Our results represent a first and important step in understanding the genetic pathways and key process involved in horn bud differentiation in Bovidae

Fine-mapping identifies multiple prostate cancer risk loci at 5p15, one of which associates with TERT expression

Associations between single nucleotide polymorphisms (SNPs) at 5p15 and multiple cancer types have been reported. We have previously shown evidence for a strong association between prostate cancer (PrCa) risk and rs2242652 at 5p15, intronic in the telomerase reverse transcriptase (TERT) gene that encodes TERT. To comprehensively evaluate the association between genetic variation across this region and PrCa, we performed a fine-mapping analysis by genotyping 134 SNPs using a custom Illumina iSelect array or Sequenom MassArray iPlex, followed by imputation of 1094 SNPs in 22 301 PrCa cases and 22 320 controls in The PRACTICAL consortium. Multiple stepwise logistic regression analysis identified four signals in the promoter or intronic regions of TERT that independently associated with PrCa risk. Gene expression analysis of normal prostate tissue showed evidence that SNPs within one of these regions also associated with TERT expression, providing a potential mechanism for predisposition to disease

The Substitutions L50F, E166A, and L167F in SARS-CoV-2 3CLpro Are Selected by a Protease Inhibitor In Vitro and Confer Resistance To Nirmatrelvir.

The SARS-CoV-2 main protease (3CLpro) has an indispensable role in the viral life cycle and is a therapeutic target for the treatment of COVID-19. The potential of 3CLpro-inhibitors to select for drug-resistant variants needs to be established. Therefore, SARS-CoV-2 was passaged in vitro in the presence of increasing concentrations of ALG-097161, a probe compound designed in the context of a 3CLpro drug discovery program. We identified a combination of amino acid substitutions in 3CLpro (L50F E166A L167F) that is associated with a >20× increase in 50% effective concentration (EC50) values for ALG-097161, nirmatrelvir (PF-07321332), PF-00835231, and ensitrelvir. While two of the single substitutions (E166A and L167F) provide low-level resistance to the inhibitors in a biochemical assay, the triple mutant results in the highest levels of resistance (6× to 72×). All substitutions are associated with a significant loss of enzymatic 3CLpro activity, suggesting a reduction in viral fitness. Structural biology analysis indicates that the different substitutions reduce the number of inhibitor/enzyme interactions while the binding of the substrate is maintained. These observations will be important for the interpretation of resistance development to 3CLpro inhibitors in the clinical setting. IMPORTANCE Paxlovid is the first oral antiviral approved for treatment of SARS-CoV-2 infection. Antiviral treatments are often associated with the development of drug-resistant viruses. In order to guide the use of novel antivirals, it is essential to understand the risk of resistance development and to characterize the associated changes in the viral genes and proteins. In this work, we describe for the first time a pathway that allows SARS-CoV-2 to develop resistance against Paxlovid in vitro. The characteristics of in vitro antiviral resistance development may be predictive for the clinical situation. Therefore, our work will be important for the management of COVID-19 with Paxlovid and next-generation SARS-CoV-2 3CLpro inhibitors

Prediagnostic plasma metabolomics and the risk of amyotrophic lateral sclerosis

Objective: To identify prediagnostic plasma metabolomic biomarkers associated with amyotrophic lateral sclerosis (ALS). Methods: We conducted a global metabolomic study using a nested case-control study design within 5 prospective cohorts and identified 275 individuals who developed ALS during follow-up. We profiled plasma metabolites using liquid chromatography–mass spectrometry and identified 404 known metabolites. We used conditional logistic regression to evaluate the associations between metabolites and ALS risk. Further, we used machine learning analyses to determine whether the prediagnostic metabolomic profile could discriminate ALS cases from controls. Results: A total of 31 out of 404 identified metabolites were associated with ALS risk (p < 0.05). We observed inverse associations (n = 27) with plasma levels of diacylglycerides and triacylglycerides, urate, purine nucleosides, and some organic acids and derivatives, while we found positive associations for a cholesteryl ester, 2 phosphatidylcholines, and a sphingomyelin. The number of significant associations increased to 67 (63 inverse) in analyses restricted to cases with blood samples collected within 5 years of onset. None of these associations remained significant after multiple comparison adjustment. Further, we were not able to reliably distinguish individuals who became cases from controls based on their metabolomic profile using partial least squares discriminant analysis, elastic net regression, random forest, support vector machine, or weighted correlation network analyses. Conclusions: Although the metabolomic profile in blood samples collected years before ALS diagnosis did not reliably separate presymptomatic ALS cases from controls, our results suggest that ALS is preceded by a broad, but poorly defined, metabolic dysregulation years before the disease onset

A large scale hearing loss screen reveals an extensive unexplored genetic landscape for auditory dysfunction

The developmental and physiological complexity of the auditory system is likely reflected in the underlying set of genes involved in auditory function. In humans, over 150 non-syndromic loci have been identified, and there are more than 400 human genetic syndromes with a hearing loss component. Over 100 non-syndromic hearing loss genes have been identified in mouse and human, but we remain ignorant of the full extent of the genetic landscape involved in auditory dysfunction. As part of the International Mouse Phenotyping Consortium, we undertook a hearing loss screen in a cohort of 3006 mouse knockout strains. In total, we identify 67 candidate hearing loss genes. We detect known hearing loss genes, but the vast majority, 52, of the candidate genes were novel. Our analysis reveals a large and unexplored genetic landscape involved with auditory function