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Fundamental Awareness: A Framework For Integrating Science, Philosophy And Metaphysics, Neil D. Theise, Menas Kafatos

Mathematics, Physics, and Computer Science Faculty Articles and Research

The ontologic framework of Fundamental Awareness proposed here assumes that non-dual Awareness is foundational to the universe, not arising from the interactions or structures of higher level phenomena. The framework allows comparison and integration of views from the three investigative domains concerned with understanding the nature of consciousness: science, philosophy, and metaphysics. In this framework, Awareness is the underlying reality, not reducible to anything else. Awareness and existence are the same. As such, the universe is non-material, self-organizing throughout, a holarchy of complementary, process driven, recursive interactions. The universe is both its own first observer and subject. Considering the world …

Non-Canonical Roles Of Trnas And Trna Mimics In Bacterial Cell Biology, Assaf Katz, Sara Elgamal, Andrei Rajkovic, Michael Ibba

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Transfer RNAs (tRNAs) are the macromolecules that transfer activated amino acids from aminoacyl‐tRNA synthetases to the ribosome, where they are used for the mRNA guided synthesis of proteins. Transfer RNAs are ancient molecules, perhaps even predating the existence of the translation machinery. Albeit old, these molecules are tremendously conserved, a characteristic that is well illustrated by the fact that some bacterial tRNAs are efficient and specific substrates of eukaryotic aminoacyl‐tRNA synthetases and ribosomes. Considering their ancient origin and high structural conservation, it is not surprising that tRNAs have been hijacked during evolution for functions outside of translation. These roles beyond …

Rheumatoid Arthritis: Seeking An Answer, Cell By Cell, Jeff Hansen

Browse All News

No abstract provided.

Long-Term High Fat Diet Has A Profound Effect On Body Weight, Hormone Levels, And Estrous Cycle In Mice, Tandra R. Chakraborty, Laxminarasimha Donthireddy, Debasis Adhikary, Sanjoy Chakraborty

Publications and Research

Background: Obesity causes several health complications along with disruption of the reproductive system. The aim of the current study was to determine how long-term intake of very high fat diet (VHFD) changes the hormonal milieu, affecting the cellular morphology and reproductive cycle in female mice.

Material/Methods: Mice were fed on normal diet (ND) and VHFD for 2 weeks, 12 weeks, and 25–27 weeks. We assessed changes in body weight, food consumption, energy intake, cellular and tissue morphology, hormonal levels (leptin, insulin, and estradiol), and vaginal smears were performed at various time points to determine the length and cellularity at each …

Reflections On Skipping Stones To Diving Deep: The Process Of Immersion As A Practice, Judith Liu Dr

Engaging Pedagogies in Catholic Higher Education (EPiCHE)

Reflecting upon over 30 years of teaching courses with a community service-learning and engagement component, this article is a personal piece that explores the author’s journey through voluntarism, community service-learning and civic engagement, and how that path has led to embracing immersion as a critical pedagogical practice for community engagement.

Binomial Nomenclature, Emily Thomas

The Anthology

A poem

Spatial Synaptic Growth And Removal For Learning Individual Receptive Field Structures, Michael Teichmann, Fred H. Hamker

MODVIS Workshop

One challenge in creating neural models of the visual system is the appropriate definition of the connectivity. The modeler constrains the results with its definition. Unfortunately, there is often just insufficient information about connection sizes available, e.g. for deeper layer or different neuron types like interneurons. Hence, a mechanism refining the connection structure based on the learnings would be appreciated.

Such mechanism can be found in the human brain by structural plasticity. That is, the formation and removal of synapses. For our model, we exploit that synaptic connections are likely to be formed in the proximity of other synapses and …

A Geometric Approach To Sparse Coding Yields Insight Into Nonlinear Responses, Kedarnath Vilankar, James Golden, David Field

MODVIS Workshop

In artificial and biological networks, it is a common accepted practice to describe a neurons (biological or artificial) response properties by a two-dimensional feature map (receptive field). However, real neurons have nonlinear response properties which are not represented by their receptive fields. The efficient coding mechanisms such as sparse coding network or ICA, learn the response properties of V1 neurons from natural images using neural networks. These networks learn the receptive fields which are similar to the receptive fields of V1 neurons. These networks also produces some of the nonlinearities (such as end-stopping and non-classical surround effect), which are exhibited …

The Use Of Swine Small Intestine Submucosa As A Dermal Suture Material, Paige Black, Charlotte Greene

Research Day

The purpose of this preliminary study is to determine if swine small intestine submucosa (SIS) can be used to create a suture that will perform comparably to commerciallyThe purpose of this preliminary study is to determine if swine small intestine submucosa (SIS) can be used to create a suture that will perform comparably to commercially available chromic gut sutures when placed into a wound in rat dermis. This study is part of an ongoing collaboration that has explored SIS as a biologic scaffold in various tissues and surgical procedures.In this study, eight Sprague-dawley rats were divided into two groups, each …

Identification Of Proteins Involved In Airway Remodeling In Human Lung Fibroblasts, Kyla Geary

Research Day

Asthma is an inflammatory disease associated with chronic perturbation of homeostatic mechanisms, leading to alterations in the structure of the airway walls, termed airway remodeling (AR). Lung fibrosis is characterized by increased deposition of extracellular matrix (ECM) proteins, especially collagens, and enhanced proliferation and activation of fibroblasts, and, ultimately, distortion of normal lung architecture and loss of respiratory function. L-arginine is a key precursor of nitric oxide and proline, an amino acid enriched in collagen. We hypothesized that L-arginine metabolism is altered in AR, ultimately affecting collagen synthesis. In this study we have analyzed the expression of key regulatory enzymes …

Reducing Posterior Capsule Opacification By Eliminating Myo/Nog Cells Through Targeted Drug Delivery Using 3dna Nanocarriers And The G8 Antibody., Jacquelyn Gerhart, Ms, Liliana Werner, Md, Marvin Greenbaum, Md, Nick Mamalis, Md, Bob Getts, Phd, Mindy George-Weinstein, Phd

Research Day

No abstract provided.

Investigating The Role Of Mitochondrial Fission In Cardiac Myocyte Hypoxia/Re-Oxygenation-Induced Cell Death, Amina Pratt, Erin Heine, Qian Chen, Robert Barsotti

Research Day

Currently there is no effective pharmacological intervention to attenuate myocardialischemia reperfusion (IR) injury. Understanding the mechanisms that govern IR injury would benefit myocardial infarction, coronary bypass and organ transplantpatients. Recent studies suggest that cardiac mitochondria undergo excessive fragmentation during IR, a process that is called fission. Increased mitochondrial fission may lead to increased cell death during IR. Mitochondrial fission has been shown to be mediated by association of dynamin related protein-1(Drp1), a GTPasethat translocates from the cytosol to interact with outer mitochondrial membrane proteins, fission protein 1 and mitochondrial fission factor, to induce fission. We hypothesize that attenuating mitochondrial fission …

Myringoplasty: Comparing Fresh Porcine Submucosa With Rice Paper Patch, Suraj Malhan, Charlotte Greene

Research Day

Objective: To evaluate and compare the efficacy of freshly prepared porcine small intestine submucosa (SIS) with rice paper patch in the repair of large chronic tympanic membrane perforations. Materials and methods: Chronic tympanic membrane perforations were bilaterally produced in five adult chinchillas using a 3mm aural speculum and a myringoplasty knife for a total of 10 perforations. Each chinchilla was post-operatively monitored for five weeks to assess whether perforations spontaneously closed or became infected prior to surgical repair with myringoplasty. The left and right ear of each chinchilla was repaired with a rice paper patch onlay and freshly prepared porcine …

Modelling Short-Latency Disparity-Vergence Eye Movements Under Dichoptic Unbalanced Stimulation, Agostino Gibaldi, Guido Maiello, Peter J. Bex, Silvio P. Sabatini

MODVIS Workshop

Vergence eye movements align the optical axes of our two eyes onto an object of interest, thus facilitating the binocular summation of the images projected onto the left and the right retinae into a single percept. Both the computational substrate and the functional behaviour of binocular vergence eye movements have been the topic of in depth investigation. Here, we attempt to bring together what is known about computation and function of vergence mechanism. To this aim, we evaluated of a biologically inspired model of horizontal and vertical vergence control, based on a network of V1 simple and complex cells. The …

Investigating How Calcium Diffusion Affects Metabolic Oscillations And Synchronization Of Pancreatic Beta Cells, George Eskandar, Jennifer Houser, Ellen Prochaska, Jessica Wojtkiewicz, Teresa Lebair, Bradford E. Peercy, Margaret Watts, Arthur Sherman

Spora: A Journal of Biomathematics

Diabetes is a disease characterized by improper concentrations of blood glucose due to irregular insulin production or sensitivity. Coupled in islets of Langerhans within the pancreas, β-cells are responsible for the production and regulation of insulin based on changes in glucose levels. Using the Dual Oscillator Model (DOM), we will examine how calcium handling between individual pancreatic β-cells affects the synchronization of metabolic oscillations within electrically coupled islets. Calcium permeability was implemented into the DOM, and numerical solutions of the system were obtained via MATLAB using a modified ordinary differential equation solver for stiff systems and the Automatic Differentiation for …

Learning Object Representations For Modeling Attention In Real World Scenes, Alex Schwarz, Frederik Beuth, Fred H. Hamker

MODVIS Workshop

Models of visual attention have been rarely used in real world tasks as they have been typically developed for psychophysical setups using simple stimuli. Thus, the question remains how objects must be represented to allow such models an operation in real world scenarios. We have previously presented an attention model capable of operating on real-world scenes (Beuth, F., and Hamker, F. H. 2015, NCNC, which is a successor of Hamker, F. H., 2005, Cerebral Cortex), and show here how its object representations have been learned. We have used a learning rule based on temporal continuity (Földiák, P., 1991, Neural Computation) …

Zombie Apocalypse: Using The Unreal As A Pedagogical Tool, Crystal A. Evans, Lorin Mayo

Jesuit Higher Education: A Journal

The following paper opens with a first person account illustrating how “the Unreal” was used in a classroom setting as a class management tool by one of the authors. This method had the benefit of resetting a classroom environment that had become hostile by creating a fun atmosphere that encouraged lively debate. Next, a faux journal article is provided to the students as a way to introduce this method. Finally, sample discussion questions are provided for classroom debate followed by a conclusion.

Interpretable High-Dimensional Inference Via Score Maximization With An Application In Neuroimaging, Simon N. Vandekar, Philip T. Reiss, Russell T. Shinohara

UPenn Biostatistics Working Papers

In the fields of neuroimaging and genetics a key goal is testing the association of a single outcome with a very high-dimensional imaging or genetic variable. Oftentimes summary measures of the high-dimensional variable are created to sequentially test and localize the association with the outcome. In some cases, the results for summary measures are significant, but subsequent tests used to localize differences are underpowered and do not identify regions associated with the outcome. We propose a generalization of Rao's score test based on maximizing the score statistic in a linear subspace of the parameter space. If the test rejects the …

Genomics Reveals Historic And Contemporary Transmission Dynamics Of A Bacterial Disease Among Wildlife And Livestock, Pauline L. Kamath, Jeffrey T. Foster, Kevin P. Drees, Gordon Luikart, Christine Quance, Neil J. Anderson, P. Ryan Clarke, Eric K. Cole, Mark L. Drew, William H. Edwards, Jack C. Rhyan, John J. Treanor, Rick L. Wallen, Patrick J. White, Suelee Robbe-Austerman, Paul C. Cross

New Hampshire Agricultural Experiment Station Publications

Whole-genome sequencing has provided fundamental insights into infectious disease epidemiology, but has rarely been used for examining transmission dynamics of a bacterial pathogen in wildlife. In the Greater Yellowstone Ecosystem (GYE), outbreaks of brucellosis have increased in cattle along with rising seroprevalence in elk. Here we use a genomic approach to examine Brucella abortus evolution, cross-species transmission and spatial spread in the GYE. We find that brucellosis was introduced into wildlife in this region at least five times. The diffusion rate varies among Brucella lineages (∼3 to 8 km per year) and over time. We also estimate 12 host transitions …

Spartan Daily, May 11, 2016, San Jose State University, School Of Journalism And Mass Communications

Spartan Daily, 2016

Volume 146, Issue 41

Tunable Depletion Potentials Driven By Shape Variation Of Surfactant Micelles, M. D. Gratale, T. Still, C. Matyas, Z. S. Davidson, S. Lobel, Peter J. Collings, A. G. Yodh

Physics & Astronomy Faculty Works

Depletion interaction potentials between micron-sized colloidal particles are induced by nanometer-scale surfactant micelles composed of hexaethylene glycol monododecyl ether (C12E6), and they are measured by video microscopy. The strength and range of the depletion interaction is revealed to arise from variations in shape anisotropy of the surfactant micelles. This shape anisotropy increases with increasing sample temperature. By fitting the colloidal interaction potentials to theoretical models, we extract micelle length and shape anisotropy as a function of temperature. This work introduces shape anisotropy tuning as a means to control interparticle interactions in colloidal suspensions, and it shows how the interparticle depletion …

Rapid Development Of A Perfusion Process With High Productivity, Sen Xu, Linda Hoshan, Balrina Gupta, Hao Chen

Cell Culture Engineering XV

Continuous process improvement is required during a biologics process life cycle to increase process yield and reduce cost. In this poster, we will present a case study in late stage process development where everything was changed but the product quality. The following major changes were made when developing the new process:

• Production cell line – subclone of the original clone used.
• Media – from hydrolysate-containing feeds to fully chemically-defined feeds.
• Feeding strategy – from fixed volume/fixed schedule feeding to daily on-demand feeding.

Media components were optimized through spent media analysis and mechanistic understanding to accommodate the new feeding strategy. High-throughput …

Bioanalytical Comparability Of Biotechnology Products Subject To Changes In Their Manufacturing Process, Jose Menezes, Maria Campos, Pedro Felizardo

Cell Culture Engineering XV

Over lifecycle, from development through all industrialization stages and then over manufacturing history across multiple sites, a biotechnology product must show very high levels of quality consistency, as that is a pre-requisite for safety and efficacy to patients (cf. ICH Q5E, 2004).

Bioanalytical similarity has acquired over the last years another meaning with the introduction of biosimilars: products that in principle cannot be identical to their reference products as processes used and other design options are not exactly identical, leading for example to minor differences in clinically inactive components. However, biosimilars must be proven to be pharmacologically identical to their …

Poly-Pathway Model Approach: Simulation Of Multiple Metabolic States, Erika Hagrot, Hildur Oddsdottir, Anders Forsgren, Veronique Chotteau

Cell Culture Engineering XV

Animal cell lines have a complex and flexible metabolism and can display varied metabolic behavior depending on the culture conditions. A model that simulate and predict these variations would be a precious tool in the development of media, feeds or processes. However, in order to function as a predictive tool such a model has to describe the multiple metabolic states that can occur for a variety of conditions. This leads to the challenge of identifying a flexible model structure of relevant metabolic pathways and kinetics. To address this challenge, we have introduced the poly-pathway model approach aiming at capturing …

Systems Analysis Of Cho Cell Metabolism For Enhanced Fed-Batch Process Performance: Identification Of Novel Growth Inhibitors And Their Control, Bhanu Chandra, Jaitahree Kale, Anamaria Ovalle, Gregory Hiller

Cell Culture Engineering XV

Over the past decade, process development efforts have led to attaining titers close to 3-4g/L on a routine basis in CHO fed-batch cultures. However, with the advent of biosimilars and the ever expanding therapeutic portfolio of innovator drugs, there is a growing need for enhancing the throughput of fed-batch cultures in order to meet the product requirements with the limited manufacturing capacity. The classical hurdle for higher productivities in fed-batch cultures is the sub-optimal metabolism of mammalian cells that causes accumulation of byproducts, including lactate and ammonia, resulting in growth inhibition. With a robust CHO expression system, our group has …

Factors Affecting The Sialylation Of Fc- Fusion Protein In Recombinant Cho Cell Culture, Gyun Min Lee

Cell Culture Engineering XV

Over the past decade, product titers from recombinant CHO cells have increased significantly. However, not only the product titer but also the product quality is important for therapeutic efficacy. When sodium butyrate (NaBu) was added to a culture of CHO cells producing Fc-fusion protein, it increased Fc-fusion protein titer, but it decreased sialylation of the Fc-fusion protein. Analysis of N-glycosylation-related genes revealed that altered expression patterns in st3gal3, neu 1, and neu3, which have roles in the sialic acid biosynthesis pathway, correlated with reduced sialic acid content of the Fc-fusion protein by NaBu. St3gal3, sialic transferase, was down-regulated and, nue1 …

Challenges Of Scale Down Model For Disposable Bioreactors: Case Studies On Growth & Product Quality Impacts, Jincai Li, Guangming Zhang, Huilin Zhu, Weichang Zhou

Cell Culture Engineering XV

Despite wide-spread use of disposable bioreactors, there is a lack of well-established scale-down model for larger scale SUBs. Here we report a case of NS0 cell culture process transfer from 2000L stainless steel bioreactor (SST) to 2000L disposable bioreactor (SUB). Initial attempts in trying to grow the NS0 cells in the small scale 2D bags yielded non-satisfactory results, as growth was impacted by bag material type as well as by suppliers of the same bag material type. However, 3D bags of 50L and above proved to be supportive of the NS0 cell line growth.

Even for cell lines that do …

Advances In Bioreactor Scale-Down Modeling Using Process Analytical Technology, Liying Yang, Jimmy Liu, Benjamin D'Alessio

Cell Culture Engineering XV

A bioreactor scale-down model is an essential element in process development and commercialization. In this poster presentation, key strategies in bioreactor scale-down model development and characterization will be discussed. A 4-Liter bioreactor scale-down model was developed to emulate a 15,000-Liter commercial scale bioreactor. Mass transfer characterization studies were conducted for the 15,000-Liter bioreactor, from which the results were summarized and utilized to guide scale-down model development / characterization. Case studies are shown where scale-down model representativeness is enhanced by implementing PAT. Specifically, automated dissolved carbon dioxide (pCO₂) control was implemented during scale-down model development in order to establish …

Characterization Of Tap Ambr250 Disposable Bioreactors As A Reliable Scale-Down Model For Biologics Process Development, Ping Xu, Colleen Clark, Todd Ryder, Charo Scott

Cell Culture Engineering XV

In recent years, biologic drugs such as antibodies, biosimilars and fusion proteins have continued to enter into the pharmaceutical pipeline. To shorten cell culture process development and accelerate clinical trials and regulatory filing, the disposable Advanced Microscale Bioreactors (Ambr 250) has burgeoned to be a useful tool due to the advantages of highly automated control and short turnaround. However, the traditional early stage upstream process development is normally conducted in 3L or 5L bioreactors. The usage of Ambr 250 instead of 5L bioreactors in the development has many benefits, but also brings necessity to establish a scale-down model of Ambr …

Scale-Up In The Single Use Age: Does Geometry Matter?, Colin Jaques, Anthony Beaney

Cell Culture Engineering XV

Singe use bioreactors (SUBs) are becoming standard work horses in the biopharmaceutical industry. These SUBs are supplied by vendors as off the shelf designs limiting the cell culture engineer’s ability to match the geometry of the SUB to the geometry of their existing stirred tank reactor (STR) capacity. The first generation of SUBs departed from conventional stirred tank bioreactor (STR) geometry in terms of impeller number, and orientation and sparger hole diameter. Moreover, one marked feature of SUB bioreactors was that they could be operated at lower volumes than conventional STRs, bringing considerable operational flexibility. This practice, however, further negated …