Reassessing hierarchical correspondences between brain and deep networks through direct interface

Functional correspondences between deep convolutional neural networks (DCNNs) and the mammalian visual system support a hierarchical account in which successive stages of processing contain ever higher-level information. However, these correspondences between brain and model activity involve shared, not task-relevant, variance. We propose a stricter account of correspondence: If a DCNN layer corresponds to a brain region, then replacing model activity with brain activity should successfully drive the DCNN’s object recognition decision. Using this approach on three datasets, we found that all regions along the ventral visual stream best corresponded with later model layers, indicating that all stages of processing contained higher-level information about object category. Time course analyses suggest that long-range recurrent connections transmit object class information from late to early visual areas

Designing a microbial cultivation platform for continuous biopharmaceutical production

The existing biopharmaceutical manufacturing paradigm is poorly suited to produce biologic drugs on demand at a point-of-care. Generally, commercial-scale (~2,000 - 10,000 L) manufacturing using fed-batch cultivation and fixed stainless-steel infrastructure is concentrated in developed nations and results in process cycle times on the order of weeks to months.1,2 Coupled with the complex logistical challenges associated with continuous “plant-to-patient” cold-chains, the geographically biased nature of therapeutic protein production today can limit access to biologic drugs in developing areas of the world.3 There is an opportunity to create technologies capable of rapidly generating biopharmaceuticals in situ in emergency situations, in remote healthcare settings, and in the battlefield. A platform that incorporates a modular suite of bioreactor, purification, and in-line analytics technologies has the potential to bridge this gap if developed in parallel with appropriately engineered stains of a flexible expression host. This poster will describe a multifaceted approach towards the development of a fully automated bench-scale perfusion process for the cultivation of Pichia pastoris and expression of therapeutically relevant heterologous proteins. We demonstrate the application of computational fluid dynamics (CFD) simulations to the optimization of the cultivation environment within our bench-top bioreactors. We further show that Pichia pastoris is amenable to secreting a variety of recombinant proteins spanning a range of preexisting drug classes (e.g. hormones, cytokines, monoclonal antibodies, vaccine antigens). Among these therapeutic proteins are molecules that require proper co-/post-translational processing for bioactivity. We envision that the development of P. pastoris strains with the capability to perform these critical processing steps in vivo will mitigate the need to chemically modify proteins post-expression and reduce the number of unit operations required in a typical upstream process

A perfusion-capable microfluidic bioreactor for assessing microbial heterologous protein production

We present an integrated microfluidic bioreactor for fully continuous perfusion cultivation of suspended microbial cell cultures. This system allowed continuous and stable heterologous protein expression by sustaining the cultivation of Pichia pastoris over 11 days. This technical capability also allowed testing the impact of perfusion conditions on protein expression. This advance should enable small-scale models for process optimization in continuous biomanufacturing.United States. Defense Advanced Research Projects Agency (N66001-13-C-4025)National Cancer Institute (U.S.) (P30-CA14051)United States. National Institutes of Health (2T32GM008334-26

Automated pipeline for rapid production and screening of HIV-specific monoclonal antibodies using pichia pastoris

Monoclonal antibodies (mAbs) that bind and neutralize human pathogens have great therapeutic potential. Advances in automated screening and liquid handling have resulted in the ability to discover antigen-specific antibodies either directly from human blood or from various combinatorial libraries (phage, bacteria or yeast). There remain, however, bottlenecks in the cloning, expression and evaluation of such lead antibodies identified in primary screens that hinder high-throughput screening. As such, ‘hit-to-lead identification’ remains both expensive and time-consuming. By combining the advantages of overlap extension PCR (OE-PCR) and a genetically stable yet easily manipulatable microbial expression host Pichia pastoris, we have developed an automated pipeline for the rapid production and screening of full-length antigenspecific mAbs. Here, we demonstrate the speed, feasibility and cost-effectiveness of our approach by generating several broadly neutralizing antibodies against human immunodeficiency virus (HIV).Bill & Melinda Gates FoundationUnited States. Defense Advanced Research Projects AgencySpace and Naval Warfare Systems Center San Diego (U.S.) (Contract N66001-13-C-4025)W. M. Keck FoundationNational Institute of Allergy and Infectious Diseases (U.S.) (U19AI090970).National Cancer Institute (U.S.) (David H. Koch Institute for Integrative Cancer Research at MIT. Support (Core) Grant P30-CA14051

Assessing Function and Endurance in Adults with Spinal and Bulbar Muscular Atrophy: Validity of the Adult Myopathy Assessment Tool

Purpose. The adult myopathy assessment tool (AMAT) is a performance-based battery comprised of functional and endurance subscales that can be completed in approximately 30 minutes without the use of specialized equipment. The purpose of this study was to determine the construct validity and internal consistency of the AMAT with a sample of adults with spinal and bulbar muscular atrophy (SBMA). Methods. AMAT validity was assessed in 56-male participants with genetically confirmed SBMA (mean age, 53 ± 10 years). The participants completed the AMAT and assessments for disease status, strength, and functional status. Results. Lower AMAT scores were associated with longer disease duration (r = -0.29; P \u3c 0.03) and lower serum androgen levels (r = 0.49-0.59; P \u3c 0.001). The AMAT was significantly correlated with strength and functional status (r = 0.82-0.88; P \u3c 0.001). The domains of the AMAT exhibited good internal consistency (Cronbach\u27s α  = 0.77-0.89; P \u3c 0.001). Conclusions. The AMAT is a standardized, performance-based tool that may be used to assess functional limitations and muscle endurance. The AMAT has good internal consistency, and the construct validity of the AMAT is supported by its significant associations with hormonal, strength, and functional characteristics of adults with SBMA. This trial is registered with Clinicaltrials.gov identifier NCT00303446

Chemorheology of photopolymerizable acrylates using a modified Boltzmann sigmoidal model

Experiments were conducted to evaluate the influence of ambient photoconversion on rheology for a range of photopolymerizable urethane dimethacrylate (UDMA) resins containing varying amounts of three comonomers including 1,6 hexane diol-dimethacrylate (HDDMA), an alkoxylated cyclohexane dimethanol diacrylate monomer (CD-582), and hydroxyethyl methacrylate (HEMA). Experiments were performed both as a function of composition and time-dependent dose varying the intensity using a photorheometer. A semilog-based sigmoidal model allowed the determination of four physical model parameters to define the relationship between reaction kinetics and its dynamic influence on viscosity. We have observed induction times and viscosity changes associated with the model that shows a trend in reaction kinetics in the following order from most to least reactive: UDMA > CD582 > HDDMA > HEMA. With increasing amounts of reactive diluent included in the formulation, the kinetics of reaction was more sluggish. The value of this sigmoidal model is that it could help define formulation and process conditions most likely to control crosslinking to maximize dimensional stability or other thermophysical properties. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 46: 2319–2325, 2008Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/61230/1/21563_ftp.pd

Assessing function and endurance in adults with spinal and bulbar muscular atrophy: validity of the adult myopathy assessment tool.

Purpose. The adult myopathy assessment tool (AMAT) is a performance-based battery comprised of functional and endurance subscales that can be completed in approximately 30 minutes without the use of specialized equipment. The purpose of this study was to determine the construct validity and internal consistency of the AMAT with a sample of adults with spinal and bulbar muscular atrophy (SBMA). Methods. AMAT validity was assessed in 56-male participants with genetically confirmed SBMA (mean age, 53 ± 10 years). The participants completed the AMAT and assessments for disease status, strength, and functional status. Results. Lower AMAT scores were associated with longer disease duration (r = -0.29; P \u3c 0.03) and lower serum androgen levels (r = 0.49-0.59; P \u3c 0.001). The AMAT was significantly correlated with strength and functional status (r = 0.82-0.88; P \u3c 0.001). The domains of the AMAT exhibited good internal consistency (Cronbach\u27s α  = 0.77-0.89; P \u3c 0.001). Conclusions. The AMAT is a standardized, performance-based tool that may be used to assess functional limitations and muscle endurance. The AMAT has good internal consistency, and the construct validity of the AMAT is supported by its significant associations with hormonal, strength, and functional characteristics of adults with SBMA. This trial is registered with Clinicaltrials.gov identifier NCT00303446

Widespread FRA1-Dependent Control of Mesenchymal Transdifferentiation Programs in Colorectal Cancer Cells

Tumor invasion and metastasis involves complex remodeling of gene expression programs governing epithelial homeostasis. Mutational activation of the RAS-ERK is a frequent occurrence in many cancers and has been shown to drive overexpression of the AP-1 family transcription factor FRA1, a potent regulator of migration and invasion in a variety of tumor cell types. However, the nature of FRA1 transcriptional targets and the molecular pathways through which they promote tumor progression remain poorly understood. We found that FRA1 was strongly expressed in tumor cells at the invasive front of human colorectal cancers (CRCs), and that its depletion suppressed mesenchymal-like features in CRC cells in vitro. Genome-wide analysis of FRA1 chromatin occupancy and transcriptional regulation identified epithelial-mesenchymal transition (EMT)-related genes as a major class of direct FRA1 targets in CRC cells. Expression of the pro-mesenchymal subset of these genes predicted adverse outcomes in CRC patients, and involved FRA-1-dependent regulation and cooperation with TGFβ signaling pathway. Our findings reveal an unexpectedly widespread and direct role for FRA1 in control of epithelial-mesenchymal plasticity in CRC cells, and suggest that FRA1 plays an important role in mediating cross talk between oncogenic RAS-ERK and TGFβ signaling networks during tumor progression.This work was supported by project grants 1026228 and 1044168 (to A.S.D.) and Senior Research Fellowships (to R.D.H., R.B.P. and J.M.M.) from the National Health and Medical Research Council of Australia

Perfluorodecalin enhances in vivo confocal microscopy resolution of Arabidopsis thaliana mesophyll.

*Air spaces in the leaf mesophyll generate deleterious optical effects that compromise confocal microscopy. *Leaves were mounted in the nontoxic, nonfluorescent perfluorocarbon, perfluorodecalin (PFD), and optical enhancement and physiological effect were assessed using confocal microscopy and chlorophyll fluorescence. *Mounting leaves of Arabidopsis thaliana in PFD significantly improved the optical qualities of the leaf, thereby enabling high-resolution laser scanning confocal imaging over twofold deeper into the mesophyll, compared with using water. Incubation in PFD had less physiological impact on the mounted specimen than water. *We conclude that the application of PFD as a mounting medium substantially increases confocal image resolution of living mesophyll and vascular bundle cells, with minimal physiological impact