Critical testing and parameters for consideration when manufacturing and evaluating tumor–associated antigen-specific T cells

The past year has seen remarkable translation of cellular and gene therapies, with U.S. Food and Drug Administration (FDA) approval of three chimeric antigen receptor (CAR) T-cell products, multiple gene therapy products, and the initiation of countless other pivotal clinical trials. What makes these new drugs most remarkable is their path to commercialization: they have unique requirements compared with traditional pharmaceutical drugs and require different potency assays, critical quality attributes and parameters, pharmacological and toxicological data, and in vivo efficacy testing. What's more, each biologic requires its own unique set of tests and parameters. Here we describe the unique tests associated with ex vivo–expanded tumor-associated antigen T cells (TAA-T). These tests include functional assays to determine potency, specificity, and identity; tests for pathogenic contaminants, such as bacteria and fungus as well as other contaminants such as Mycoplasma and endotoxin; tests for product characterization, tests to evaluate T-cell persistence and product efficacy; and finally, recommendations for critical quality attributes and parameters associated with the expansion of TAA-Ts.     

SENSORY ANALYSIS OF FIBER FORMULATED GROUND PORK PATTIES1

Pure cellulose (Solka-Floc), microcrystalline cellulose (Avicel), and a soluble gum (Nutriloid Fiberplus) were added to ground pork (25%± 2% fat) at 3.5% and 7.0% based on total dietary fiber content of each ingredient. Cooked samples of all treatments and a control were presented to a professional sensory panel and evaluated for the following six attributes: resistance to bite, juiciness, off flavor, pork flavor intensity, graininess/flouriness, and cohesiveness. Products containing Nutriloid Fiberplus at 3.5% and 7.0% had the least resistance to bite (softest), but no differences were detected between the two levels of these products. The Avicel and Solka-Floc products were similar to the control products for resistance to bite. Products containing Nutriloid Fiberplus carried a significant off-flavor, whereas products containing Avicel at 3.5% maintained a flavor similar to that of the control products. Products with Solka-Floc or Nutriloid Fiberplus had distinct graininess/flouriness attributes. Solka-Floc products and Nutriloid products were more cohesive (p < 0.05) than control products. Avicel products at 3.5% were not significantly different than control products for all attributes evaluated.     

Tools to study molecular mechanisms of Aspergillus pathogenicity

The unique nature of Aspergillus fungi represents a challenge for scrutinizing the attributes that render these saprophytic microorganisms pathogenic or allergenic under certain environmental circumstances. Recent publication of the genomic sequence from an isolate of the major pathogen Aspergillus fumigatus denotes enormous progress in aiming at cellular features and gene products that contribute to its pathogenicity. Latest developments to study virulence-related characteristics comprise profiling techniques, conditional gene inactivation and precise manipulation of the genome by means of gene targeting. Advances in assessing the virulence potential of particular mutant strains in alternative test systems complement these approaches.     

Java editor for biological pathways

SUMMARY: A visual Java-based tool for drawing and annotating biological pathways was developed. This tool integrates the possibilities of charting elements with different attributes (size, color, labels), drawing connections between elements in distinct characteristics (color, structure, width, arrows), as well as adding links to molecular biology databases, promoter sequences, information on the function of the genes or gene products, and references. It is easy to use and system independent. The result of the editing process is a PNG (portable network graphics) file for the images and XML (extended markup language) file for the appropriate links.     

基于景感生态学促进生态产品价值实现的方法

建立健全生态产品价值实现机制,迫切需要创新研究思路,突破思维束缚,深挖生态产品价值内涵。从景感生态学原理阐释生态产品属性,梳理生态产品供给特点,分析生态产品消费特征,进而理顺生态系统服务、生态产品、消费者感知与享用转化完整链条。研究发现,景感生态学关键原理与生态产品特征密切对接,景感生态方法能够显化生态产品普及和消费路径,景感指数能够有效度量生态产品数量、质量和溢价。研究认为,基于景感生态学的理论与方法将有助于引导人民群众认识生态产品的科学价值内涵、多样化表现形式,尤其是助力文化服务类生态产品价值转化。根据分析结果提出当前的生态产品价值转化工作具体建议：(1)在生态产品信息调查过程中,要注重与生态产品载体密切相关的光、热、水、土、地磁、放射性和地形地貌等环境信息获取,在基础测绘、自然资源调查基础上追加生态服务关键属性;(2)在制定生态产品目录清单中,应指明该类生态服务形式和对人的感官直接刺激的服务作用,并具体到对人们的视觉、嗅觉、听觉、味觉、光觉、触觉,以及身心健康的整体影响;(3)生态产品供给过程中要注重对人的心理感知,包括宗教、文化、愿景、隐喻、安全等属性的综合考量,保障自然属性与...     

SENSORY DIRECTIONALS FOR PIZZA: A DEEPER ANALYSIS

This paper presents a set of analyses on sensory directional attributes used to rate experimentally designed pizza products. Consumers may or may not know the 'optimal' sensory level of attributes for pizza, so that the usefulness of the sensory directional varies by attribute. Furthermore, the sensory magnitude of each sensory directional attribute varies, as shown by the slope (B) relating the two attributes (Sensory Magnitude = A + B (Directional Rating)). The study incorporated sensory directionals into evaluation of products varied according to an experimental design. The optimal product emerging from the design does not necessarily exhibit a sensory directional profile where all attributes are 'on target', nor does a product whose sensory attributes are all on 'target' exhibit the highest level of liking.     

Knowledge acquisition,consistency checking and concurrency control for Gene Ontology (GO)

MOTIVATION: A critical element of the computational infrastructure required for functional genomics is a shared language for communicating biological data and knowledge. The Gene Ontology (GO; http://www.geneontology.org) provides a taxonomy of concepts and their attributes for annotating gene products. As GO increases in size, its ongoing construction and maintenance becomes more challenging. In this paper, we assess the applicability of a Knowledge Base Management System (KBMS), Protégé-2000, to the maintenance and development of GO. RESULTS: We transferred GO to Protégé-2000 in order to evaluate its suitability for GO. The graphical user interface supported browsing and editing of GO. Tools for consistency checking identified minor inconsistencies in GO and opportunities to reduce redundancy in its representation. The Protégé Axiom Language proved useful for checking ontological consistency. The PROMPT tool allowed us to track changes to GO. Using Protégé-2000, we tested our ability to make changes and extensions to GO to refine the semantics of attributes and classify more concepts. AVAILABILITY: Gene Ontology in Protégé-2000 and the associated code are located at http://smi.stanford.edu/projects/helix/gokbms/. Protégé-2000 is available from http://protege.stanford.edu.     

A novel mitochondrial septin-like protein, ARTS, mediates apoptosis dependent on its P-loop motif

Here we describe a protein product of the human septin H5/PNUTL2/CDCrel2b gene, which we call ARTS (for apoptosis-related protein in the TGF-beta signalling pathway). ARTS is expressed in many cells and acts to enhance cell death induced by TGF-beta or, to a lesser extent, by other apoptotic agents. Unlike related septin gene products, ARTS is localized to mitochondria and translocates to the nucleus when apoptosis occurs. Mutation of the P-loop of ARTS abrogates its competence to activate caspase 3 and to induce apoptosis. Taken together, these observations expand the functional attributes of septins previously described as having roles in cytokinesis and cellular morphogenesis.     

SENSORY PROPERTIES AND CONSUMER PERCEPTION OF 'HOME-MADE'AND COMMERCIAL DAIRY ICE CREAM

Sensory properties and consumer perception of 2 'home-made'and 4 commercial dairy ice creams were examined. Conventional profiling by a trained panel found that most samples differed significantly in all attributes, but distinction of 'home-made'from commercial products was limited to few attributes. Principal component analysis separated the 'home-made'products from the commercial ones mainly on the basis of differences in appearance, aroma, creamy flavors and textural attributes. A consumer group (n=105) recorded preconception of 'home-made'ice cream acceptance, then received the product samples, in unlabeled condition, for assessment of degree of liking (DOL) and for identification as 'home-made'or commercial. Internal preference mapping of the DOL ratings showed that consumers were more closely grouped around samples which had higher intensities of certain attributes. Higher 'denseness', 'vanilla'aroma and 'buttery'flavor, were associated with more liking for commercial products. The 'home-made'high fat sample, although liked, tended to be grouped with commercial products. More marked textural attributes of 'ice crystals'and 'breakage'aided identification of the low-fat 'home-made'formulation, which was less liked overall. Overall, differences between the 'home-made'and commercial samples were small but consumer perception of the term 'home-made'was viewed favorably for dairy ice cream.     

基因本体论的蟾蜍bHLH转录因子功能富集分布

基因本体论是国际上标准的基因和蛋白质功能知识词汇.利用基因本体论的功能富集分布比较和分析了两种蟾蜍bHLH基因分子功能分布特点.结果发现,两种蟾蜍的bHLH基因均有显著富集分布的GO注释语句,其中转录调控活性( GO:0030528)、转录调控(GO:0045449)、DNA结合(GO:0003677)、RNA代谢过程调控(G0:0051252)、DNA依赖的转录调控(GO:0006355)、转录(G0:0006350)和转录因子活性(GO:0003700)等频率很高,表明这些GO注释是蟾蜍bHLH基因常见的功能;此外,蟾蜍bHLH基因在肌肉器官发育、神经管和眼发育等一些重要的发育或生理过程的基因表达调控中发挥着重要的作用.     

Variability of intended copies for etanercept (Enbrel®): Data on multiple batches of seven products

Fusion protein and monoclonal antibody-based tumor necrosis factor (TNF) inhibitors represent established treatment options for a range of inflammatory diseases. Regulatory authorities have outlined the structural characterization and clinical assessments necessary to establish biosimilarity of a new biotherapeutic product with the innovator biologic drug. Biologic products that would not meet the minimum World Health Organization's standard for evaluation of similar biotherapeutic products are available in some countries; in some cases relevant data to assess biosimilarity and appropriate regulatory approval pathways are lacking.

Batches of seven intended copy (IC) products for etanercept (Enbrel®) were subjected to a subset of test methods used in the routine release and heightened characterization of Enbrel®, to determine key attributes of identity, quality, purity, strength, and activity. While a number of quality attributes of the IC lots tested met the release specifications for Enbrel®, none fell within these limits across all methods performed, and there were no IC lots that satisfied the criteria typically applied by the innovator to support comparability with Enbrel®. Although the consequences of these differences are largely unknown, the potential for unanticipated clinical outcomes should not be overlooked.     

PRODUCT OPTIMIZATION AND THE ACCEPTOR SET SIZE

The acceptability of a product, measured by the acceptor set size (percentage of consumers rating the product acceptable), is a function of the perception of its attributes. The attributes are themselves a function of the inputs to the product (such as ingredients, processing or storage variables). These assumptions lead to the following model:
Acceptor set size = F (attribute₁, attribute₂, …, attribute_n)
Attribute j = f (input₁, input₂, …, input_m)
If we assume that these functions are differentiable, we can estimate the partial derivatives of the acceptor set size, with respect to the input variables. The gradient vector obtained indicates the fastest way to maximize the acceptor set size. The gradient search method, using the acceptor set size as an objective measure, can be applied in a variety of situations: to improve existing products, to maximize the acceptability of new products, and to study the relationship between shelf-life and acceptability.     

Quality attributes of recombinant therapeutic proteins: an assessment of impact on safety and efficacy as part of a quality by design development approach

Quality by Design (QbD) is a new approach to the development of recombinant therapeutic protein products that promotes a better understanding of the product and its manufacturing process. The first step in the QbD approach consists in identifying the critical quality attributes (CQA), i.e., those quality attributes of the product that have an impact on its clinical efficacy or safety. CQAs are identified through a science-based risk assessment taking into consideration a combination of clinical and nonclinical data obtained with the molecule or other similar molecules or platform products, as well as the published literature. The purpose of this article is to perform a comprehensive review of the published literature, supporting an assessment of the impact on safety and efficacy of the quality attributes commonly encountered in recombinant therapeutic proteins, more specifically those produced in mammalian cell expression systems. Quality attributes generally observed in biopharmaceutical proteins including product-related impurities and substances, process-related impurities, product attributes, and contaminants are evaluated one by one for their impact on biological activity, pharmacokinetics and pharmacodynamics, immunogenicity, and overall safety/toxicity.     

Attribute clustering for grouping, selection, and classification of gene expression data

This paper presents an attribute clustering method which is able to group genes based on their interdependence so as to mine meaningful patterns from the gene expression data. It can be used for gene grouping, selection, and classification. The partitioning of a relational table into attribute subgroups allows a small number of attributes within or across the groups to be selected for analysis. By clustering attributes, the search dimension of a data mining algorithm is reduced. The reduction of search dimension is especially important to data mining in gene expression data because such data typically consist of a huge number of genes (attributes) and a small number of gene expression profiles (tuples). Most data mining algorithms are typically developed and optimized to scale to the number of tuples instead of the number of attributes. The situation becomes even worse when the number of attributes overwhelms the number of tuples, in which case, the likelihood of reporting patterns that are actually irrelevant due to chances becomes rather high. It is for the aforementioned reasons that gene grouping and selection are important preprocessing steps for many data mining algorithms to be effective when applied to gene expression data. This paper defines the problem of attribute clustering and introduces a methodology to solving it. Our proposed method groups interdependent attributes into clusters by optimizing a criterion function derived from an information measure that reflects the interdependence between attributes. By applying our algorithm to gene expression data, meaningful clusters of genes are discovered. The grouping of genes based on attribute interdependence within group helps to capture different aspects of gene association patterns in each group. Significant genes selected from each group then contain useful information for gene expression classification and identification. To evaluate the performance of the proposed approach, we applied it to two well-known gene expression data sets and compared our results with those obtained by other methods. Our experiments show that the proposed method is able to find the meaningful clusters of genes. By selecting a subset of genes which have high multiple-interdependence with others within clusters, significant classification information can be obtained. Thus, a small pool of selected genes can be used to build classifiers with very high classification rate. From the pool, gene expressions of different categories can be identified.