Targeted sequencing for comprehensive genetic characterization of a recombinant CHO cell line

Next generation sequencing has revolutionized genomics, catalyzing an era of personally-tailored therapeutics with enhanced efficacy and safety profiles. This technology also holds great promise for bioprocess and cell line development. The combination of Targeted Locus Amplification (TLA) and next generation sequencing is an emerging approach for the characterization of transgene integration and genetic stability for recombinant cell lines. TLA [de Vree et al., Nature Biotechnology 32, 1019-1025 (2014)] is based on the crosslinking of physically proximal sequences and enables the targeted complete amplification and sequencing of transgenes and their integration sites with greatly increased sequence coverage and depth. Information about integration regions, Single Nucleotide Variants (SNVs), and structural changes in the transgene sequences can be tracked across different clones, over the course of multiple cell line generations and processes. TLA sequencing was successfully applied for the comprehensive genetic characterization of a recombinant monoclonal antibody-expressing CHO cell line. A single transgene integration region with three genome-transgene breakpoints was identified within the host genome. Evidence of genetic rearrangements including vector amplification, duplication, and inversion was found by mapping genome-transgene breakpoints and specific patterns of transgene vector-vector concatamers. A copy number \u3e20 transgene insertions was calculated, and PCR on both genomic DNA and cDNA verified a subset of vector fusions. Transgene sequencing to a median coverage of 2,388 reads per base pair also determined a limited number of homozygous and heterozygous SNVs. To further investigate the cell line’s genetic “fingerprint,” ~30 research cell bank sub-clones were examined after shake flask and bioreactor expansion. A highly specific and conserved transgene vector signature was identified, signifying stability. The targeted sequencing approach applied here can efficiently provide extensive genetic sequence and linkage insight for complex transgene integration regions of recombinant cell lines, enabling improved strategies for constructing and ensuring high producing and stable cell line platforms

International Commercial Arbitration – Enforcement of Arbitral Awards Revisited

International commercial arbitration is becoming increasingly convoluted, and hence requires a certain degree of uniformity in order to achieve true international applicability. As a result of this complexity, after arbitration proceedings finish both the national courts of the seat of arbitration and the national courts of enforcing jurisdiction are caught in the dilemma of how to interact with each other, as well as with the arbitral awards produced by arbitral tribunals. This article assesses this phenomenon critically in order to weight current developments in arbitration against the normative structure of arbitration as they were originally intended

Persons with Dementia and Their Capacity for Helping: An Exploratory Study

This observational study explored helping behaviors (HBs) among persons with dementia (PWD) in a communal dining space of a memory care facility. HBs were observed regularly and related to assistance with another resident, staff, and stuffed animal. PWD, even in the moderate stages of the disease, have the capacity to help others

Bat Monitoring, Fort Leonard Wood, Missouri: Sound and Seismic Effects

The U.S. Army Maneuver Support Center of Excellence and U.S. Army Garrison Fort Leonard Wood (Installation) has prepared a Biological Assessment (BA) to evaluate effects of the construction and operation of a Mine Clearing Line Charge (MICLIC) range on threatened and endangered species at the Installation. A pilot monitoring plan will describe the process in which field data are to be gathered and timelines in which field data are processed and/or reported. The data collected during this pilot monitoring survey will be used to validate the noise and seismic estimations, as described in the BA, for MICLIC detonations and ensure that thresholds of sound and vibration have not been surpassed. If field data results surpass thresholds, the USFWS will be consulted and appropriate coordination will be conducted. Dr. Kevin Mickus, geophysicist and Distinguished Professor in the Department of Geography, Geology, and Planning at Missouri State University (MSU), was the lead scientist on the pilot monitoring survey to assess the noise and sound effects during MICLIC testing. He was assisted in the field by Paul Wilkerson, an undergraduate student in geology. The seismic and sound data were collected at King Cave which is the closest of the seven caves to the MICLIC Range

Ecological effects and environmental fate of solid rocket exhaust

Specific target processes were classified as to the chemical, chemical-physical, and biological reactions and toxic effects of solid rocket emissions within selected ecosystems at Kennedy Space Center. Exposure of Citris seedlings, English peas, and bush beans to SRM exhaust under laboratory conditions demonstrated reduced growth rates, but at very high concentrations. Field studies of natural plant populations in three diverse ecosystems failed to reveal any structural damage at the concentration levels tested. Background information on elemental composition of selected woody plants from two terrestrial ecosystems is reported. LD sub 50 for a native mouse (peromysous gossypinus) exposed to SRM exhaust was determined to be 50 ppm/g body weight. Results strongly indicate that other components of the SRM exhaust act synergically to enhance the toxic effects of HCl gas when inhaled. A brief summary is given regarding the work on SRM exhaust and its possible impact on hatchability of incubating bird eggs

Grounded and Well-rounded: A Methodological Approach to the Study of Cross-modal and Cross-lingual Grounding

Grounding has been argued to be a crucial component towards the development of more complete and truly semantically competent artificial intelligence systems. Literature has divided into two camps: While some argue that grounding allows for qualitatively different generalizations, others believe it can be compensated by mono-modal data quantity. Limited empirical evidence has emerged for or against either position, which we argue is due to the methodological challenges that come with studying grounding and its effects on NLP systems. In this paper, we establish a methodological framework for studying what the effects are - if any - of providing models with richer input sources than text-only. The crux of it lies in the construction of comparable samples of populations of models trained on different input modalities, so that we can tease apart the qualitative effects of different input sources from quantifiable model performances. Experiments using this framework reveal qualitative differences in model behavior between cross-modally grounded, cross-lingually grounded, and ungrounded models, which we measure both at a global dataset level as well as for specific word representations, depending on how concrete their semantics is.Comment: accepted to Findings of EMNLP 202

Distributional Effects of Gender Contrasts Across Categories

This paper proposes a methodology for comparing grammatical contrasts across categories with the tools of distributional semantics. After outlining why such a comparison is relevant to current theoretical work on gender and other morphosyntactic features, we present intrinsic and extrinsic predictability as instruments for analyzing semantic contrasts between pairs of words. We then apply our method to a dataset of gender pairs of French nouns and adjectives. We find that, while the distributional effect of gender is overall less predictable for nouns than for adjectives, it is heavily influenced by semantic properties of the adjectives

How to Dissect a Muppet : The Structure of Transformer Embedding Spaces

Pretrained embeddings based on the Transformer architecture have taken the NLP community by storm. We show that they can mathematically be reframed as a sum of vector factors and showcase how to use this reframing to study the impact of each component. We provide evidence that multi-head attentions and feed-forwards are not equally useful in all downstream applications, as well as a quantitative overview of the effects of finetuning on the overall embedding space. This approach allows us to draw connections to a wide range of previous studies, from vector space anisotropy to attention weights.Peer reviewe

Mark my Word: A Sequence-to-Sequence Approach to Definition Modeling

International audienceDefining words in a textual context is a useful task both for practical purposes and for gaining insight into distributed word representations. Building on the distribu-tional hypothesis, we argue here that the most natural formalization of definition modeling is to treat it as a sequence-to-sequence task, rather than a word-to-sequence task: given an input sequence with a highlighted word, generate a con-textually appropriate definition for it. We implement this approach in a Transformer-based sequence-to-sequence model. Our proposal allows to train contextualization and definition generation in an end-to-end fashion, which is a conceptual improvement over earlier works. We achieve state-of-the-art results both in contextual and non-contextual definition modeling