Digital Commons Network^™

Transdisciplinarity: A Review Of Its Origins, Development, And Current Issues, Jay H. Bernstein

Publications and Research

Transdisciplinarity originated in a critique of the standard configuration of knowledge in disciplines in the curriculum, including moral and ethical concerns. Pronouncements about it were first voiced between the climax of government-supported science and higher education and the long retrenchment that began in the 1970s. Early work focused on questions of epistemology and the planning of future universities and educational programs. After a lull, transdisciplinarity re-emerged in the 1990s as an urgent issue relating to the solution of new, highly complex, global concerns, beginning with climate change and sustainability and extending into many areas concerning science, technology, social problems and …

The Interaction Between Fluid Wall Shear Stress And Solid Circumferential Strain Affects Endothelial Gene Expression, Ronny Amaya, Alexis Pierides, John M. Tarbell

Publications and Research

Endothelial cells lining the walls of blood vessels are exposed simultaneously to wall shear stress (WSS) and circumferential stress (CS) that can be characterized by the temporal phase angle between WSS and CS (stress phase angle – SPA). Regions of the circulation with highly asynchronous hemodynamics (SPA close to -180°) such as coronary arteries are associated with the development of pathological conditions such as atherosclerosis and intimal hyperplasia whereas more synchronous regions (SPA closer to 0°) are spared of disease. The present study evaluates endothelial cell gene expression of 42 atherosclerosis-related genes under asynchronous hemodynamics (SPA=-180 °) and synchronous hemodynamics …

Cyclometalated Iminophosphorane Gold(Iii) And Platinum(Ii) Complexes. A Highly Permeable Cationic Platinum(Ii) Compound With Promising Anticancer Properties, Malgorzata Frik, Jacob Fernández-Gallardo, Oscar Gonzalo, Víctor Mangas-Sanjuan, Marta González-Alvarez, Alfonso Serrano Del Valle, Chunhua Hu, Isabel González-Alvarez, Marival Bermejo, Isabel Marzo, María Contel

Publications and Research

New organometallic gold(III) and platinum(II) complexes containing iminophosphorane ligands are described. Most of them are more cytotoxic to a number of human cancer cell lines than cisplatin. Cationic Pt(II) derivatives 4 and 5, which differ only in the anion, Hg2Cl62– or PF6– respectively, display almost identical IC50 values in the sub-micromolar range (25–335-fold more active than cisplatin on these cell lines). The gold compounds induced mainly caspase-independent cell death, as previously reported for related cycloaurated compounds containing IM ligands. Cycloplatinated compounds 3, 4, and 5 can also activate alternative caspase-independent mechanisms of death. However, at short incubation times cell death …

Mechanotransduction: Use The Force(S), Ewa K. Paluch, Celeste M. Nelson, Nicolas Biais, Ben Fabry, Jens Moeller, Beth L. Pruitt, Carina Wollnik, Galina Kudryasheva, Florian Rehfeldt, Walter Federle

Publications and Research

Mechanotransduction - how cells sense physical forces and translate them into biochemical and biological responses - is a vibrant and rapidly-progressing field, and is important for a broad range of biological phenomena. This forum explores the role of mechanotransduction in a variety of cellular activities and highlights intriguing questions that deserve further attention.

Rationale, Design And Respondent Characteristics Of The 2013–2014 New York City Health And Nutrition Examination Survey (Nyc Hanes 2013–2014), Lorna E. Thorpe, Carolyn Greene, Amy Freeman, Elisabeth Snell, Jesica S. Rodriguez-Lopez, Martin Frankel, Amado Punsalang Jr., Claudia Chernov, Elizabeth Lurie, Mark Friedman, Ram Koppaka, Sharon E. Perlman

Publications and Research

Purpose. Capacity to monitor non-communicable diseases (NCDs) at state or local levels is limited. Emerging approaches include using biomeasures and electronic health record (EHR) data. In 2004, New York City (NYC) performed a population-based health study on adult residents using biomeasures (NYC Health and Nutrition Examination Study, or NYC HANES), modeled after NHANES. A second NYC HANES was launched in 2013 to examine change over time, evaluate municipal policies, and validate a proposed EHR-based surveillance system. We describe the rationale and methods of NYC HANES 2013–2014.

Methods. NYC HANES was a population-based, cross-sectional survey of NYC adults using three-stage cluster …

Lesion-Specific Immune Response In Granulomas Of Patients With Pulmonary Tuberculosis: A Pilot Study, Selvakumar Subbian, Liana Tsenova, Mi-Jeong Kim, Helen C. Wainwright, Annalie Visser, Nirmalya Bandyopadhyay, Joel S. Bader, Petros C. Karakousis, Gabriele B. Murrmann, Linda-Gail Bekker, David G. Russell, Gilla Kaplan

Publications and Research

The formation and maintenance of granulomas is central to the host response to Mycobacterium tuberculosis (Mtb) infection. It is widely accepted that the lungs of patients with tuberculosis (TB) usually contain multiple infection foci, and that the granulomas evolve and differentiate independently, resulting in considerable heterogeneity. Although gene expression profiles of human blood cells have been proposed as biomarkers of Mtb infection and/or active disease, the immune profiles of discrete lesion types has not been studied extensively. Using histology, immunopathology and genome-wide transcriptome analysis, we explored the immunological profile of human lung TB granulomas. We show that although the different …

Foregrounding The Research Log In Information Literacy Instruction, Louise R. Fluk

Publications and Research

Updating an earlier study, this article reviews the literature of information literacy (IL) instruction since 2008 for empirical evidence of the value of research logs or research journals for effective pedagogy, assessment, and prevention of plagiarism in IL instruction at the college level. The review reveals a mismatch between the acknowledged theoretical and practical value of research log assignments and the mixed advocacy for them in the literature. The article further analyzes the literature for the drawbacks of research log assignments and points toward ways of mitigating these drawbacks.

Monitoring The Progression Of Spontaneous Articular Cartilage Healing With Infrared Spectroscopy, Megan P. O'Brien, Madhuri Penmatsa, Uday Palukuru, Paul West, Xu Yang, Mathias P. G. Bostrom, Theresa Freeman, Nancy Pleshko

Publications and Research

Objective. Evaluation of early compositional changes in healing articular cartilage is critical for understanding tissue repair and for therapeutic decision-making. Fourier transform infrared imaging spectroscopy (FT-IRIS) can be used to assess the molecular composition of harvested repair tissue. Furthermore, use of an infrared fiber-optic probe (IFOP) has the potential for translation to a clinical setting to provide molecular information in situ. In the current study, we determined the feasibility of IFOP assessment of cartilage repair tissue in a rabbit model, and assessed correlations with gold-standard histology.

Design. Bilateral osteochondral defects were generated in mature white New Zealand rabbits, and …

Use Of Rna Sequencing To Evaluate Rheumatic Disease Patients, Eugenia Giannopoulou, Olivier Elemento, Lionel B. Ivashkiv

Publications and Research

Studying the factors that control gene expression is of substantial importance for rheumatic diseases with poorly understood etiopathogenesis. In the past, gene expression microarrays have been used to measure transcript abundance on a genome-wide scale in a particular cell, tissue or organ. Microarray analysis has led to gene signatures that differentiate rheumatic diseases, and stages of a disease, as well as response to treatments. Nowadays, however, with the advent of next-generation sequencing methods, massive parallel sequencing of RNA tends to be the technology of choice for gene expression profiling, due to several advantages over microarrays, as well as for the …

Inhibition Of Cell Differentiation In Bacillus Subtilis By Pseudomonas Protegens, Matthew J. Powers, Edgardo Sanabria-Valentín, Albert A. Bowers, Elizabeth A. Shanka

Publications and Research

Interspecies interactions have been described for numerous bacterial systems, leading to the identification of chemical compounds that impact bacterial physiology and differentiation for processes such as biofilm formation. Here, we identified soil microbes that inhibit biofilm formation and sporulation in the common soil bacterium Bacillus subtilis. We did so by creating a reporter strain that fluoresces when the transcription of a biofilm-specific gene is repressed. Using this reporter in a coculture screen, we identified Pseudomonas putida and Pseudomonas protegens as bacteria that secrete compounds that inhibit biofilm gene expression in B. subtilis. The active compound produced by P. protegens was …

Touching Brains, Jason Tougaw

Publications and Research

No abstract provided.

Science And Charity: Rival Catholic Visions For Humanitarian Practice At The End Of French Rule In Cameroon, Charlotte Walker-Said

Publications and Research

This paper explores the conflict between local expressions of Christian charity and new theories of scientific humanitarianism in the final years of French rule in Africa. Compassionate phenomena inspired by Catholic social organizing had transformed everyday life throughout French Cameroon’s cities and villages in the interwar and postwar years, and yet, in 1950, poverty, crime, poor public health, and social tensions remained prevalent. Seeking a more deeply transformative approach to social rehabilitation, ecclesiastical leaders in the Catholic Church in Europe and French foreign missionary societies in Africa partnered with international medical and scientific organizations in order to invigorate charity with …

Familiarity With And Preferences For Oral And Long-Acting Injectable Hiv Pre-Exposure Prophylaxis (Prep) In A National Sample Of Gay And Bisexual Men In The U.S., Jeffrey T. Parsons, H. Jonathan Rendina, Thomas H.F. Whitfield, Christian Grov

Publications and Research

Objectives: We sought to determine preferences for oral versus long-acting injectable (LAI) PrEP among gay and bisexual men (GBM).

Methods: We surveyed a national U.S. sample of 1,071 GBM about forms of PrEP.

Results: Overall, 46.0% preferred LAI, 14.3% oral, 21.7% whichever was most effective, 10.1% had no preference, and 7.8% would not take PrEP. There were no differences in PrEP preferences by race/ethnicity, income, region of residence, or relationship status. Those unwilling to take PrEP were significantly older than those who preferred LAI PrEP and those who would take either. Those who preferred the most effective …

Interferon-Γ Regulates Cellular Metabolism And Mrna Translation To Potentiate Macrophage Activation, Xiaodi Su, Yingpu Yu, Yi Zhong, Eugenia Giannopoulou, Xiaoyu Hu, Hui Liu, Justin R. Cross, Gunnar Rätsch, Charles M. Rice, Lionel B. Ivashkiv

Publications and Research

Interferon-γ (IFN-γ) primes macrophages for enhanced inflammatory activation by Toll-like receptors (TLRs) and microbial killing, but little is known about the regulation of cell metabolism or mRNA translation during priming. We found that IFN-γ regulates human macrophage metabolism and translation by targeting the kinases mTORC1 and MNK that both converge on the selective regulator of translation initiation eIF4E. Physiological downregulation of mTORC1 by IFN-γ was associated with autophagy and translational suppression of repressors of inflammation such as HES1. Genome-wide ribosome profiling in TLR2-stimulated macrophages revealed that IFN-γ selectively modulates the macrophage translatome to promote inflammation, further reprogram metabolic pathways, and …

Sacrificial Amphiphiles: Eco-Friendly Chemical Herders As Oil Spill Mitigation Chemicals, Deeksha Gupta, Bivas Sarker, Keith Thadikaran, Vijay John, Charles Maldarelli, George John

Publications and Research

Crude oil spills are a major threat to marine biota and the environment. When light crude oil spills on water, it forms a thin layer that is difficult to clean by any methods of oil spill response. Under these circumstances, a special type of amphiphile termed as “chemical herder” is sprayed onto the water surrounding the spilled oil. The amphiphile forms a monomolecular layer on the water surface, reducing the air–sea surface tension and causing the oil slick to retract into a thick mass that can be burnt in situ. The current best-known chemical herders are chemically stable and nonbiodegradable, …

What You Gotta Know To Play Good In The Iterated Prisoner’S Dilemma, Ethan Akin

Publications and Research

For the iterated Prisoner’s Dilemma there exist good strategies which solve the problem when we restrict attention to the long term average payoff. When used by both players, these assure the cooperative payoff for each of them. Neither player can benefit by moving unilaterally to any other strategy, i.e., these provide Nash equilibria. In addition, if a player uses instead an alternative which decreases the opponent’s payoff below the cooperative level, then his own payoff is decreased as well. Thus, if we limit attention to the long term payoff, these strategies effectively stabilize cooperative behavior. The existence of such strategies …

Cell Type Specificity Of Tissue Plasminogen Activator In The Mouse Barrel Cortex, Philip Chu, Eric Chen, Adesh Bajnath, Joshua C. Brumberg

Publications and Research

It has been suggested that tissue-type plasminogen activator (tPA), a serine protease, plays a key role in regulating the extracellular matrix core proteins, thereby impacting the structural plasticity in the cerebral cortex. Much is known about its role in regulating plasticity in the visual cortex. However, its permissive role has not been demonstrated to generalize to other cerebral cortical areas. By utilizing a combination of immunofluorescent histochemistry and confocal microscopy, we demonstrate that endogenous tPA is indeed present in the somatosensory cortex, and its expression is experience-dependent. Chronic sensory deprivation induced by whisker trimming from birth for one month leads …

Core And Shell Song Systems Unique To The Parrot Brain, Mukta Chakraborty, Solveig Walloe, Signe Nedergaard, Emma E. Fridel, Torben Dabelsteen, Bente Pakkenberg, Mads F. Bertelsen, Gerry M. Dorrestein, Steven E. Brauth, Sarah E. Durand, Erich D. Jarvis

Publications and Research

The ability to imitate complex sounds is rare, and among birds has been found only in parrots, songbirds, and hummingbirds. Parrots exhibit the most advanced vocal mimicry among non-human animals. A few studies have noted differences in connectivity, brain position and shape in the vocal learning systems of parrots relative to songbirds and hummingbirds. However, only one parrot species, the budgerigar, has been examined and no differences in the presence of song system structures were found with other avian vocal learners. Motivated by questions of whether there are important differences in the vocal systems of parrots relative to other vocal …

Assessing The Carcinogenic Potential Of Low-Dose Exposures To Chemical Mixtures In The Environment: The Challenge Ahead, William H. Goodson, Leroy Lowe, David O. Carpenter, Michael Gilbertson, Abdul Manaf Ali, Adela Lopez De Cerain Salsamendi, Ahmed Lasfar, Amancio Carnero, Amaya Azqueta, Amedeo Amedei, Amelia K. Charles, Andrew R. Collins, Andrew Ward, Anna C. Salzberg, Annamaria Colacci, Ann-Karin Olsen, Arthur Berg, Barry J. Barclay, Binhua P. Zhou, Carmen Blanco-Aparicio, Debasish Roy

Publications and Research

Summary Low-dose exposures to common environmental chemicals that are deemed safe individually may be combining to instigate carcinogenesis, thereby contributing to the incidence of cancer. This risk may be overlooked by current regulatory practices and needs to be vigorously investigated.

Independent Demographic Responses To Climate Change Among Temperate And Tropical Milksnakes (Colubridae: Genus Lampropeltis), Sara Ruane, Omar Torres-Carvajal, Frank T. Burbrink

Publications and Research

The effects of Late Quaternary climate change have been examined for many temperate New World taxa, but the impact of Pleistocene glacial cycles on Neotropical taxa is less well understood, specifically with respect to changes in population demography. Here, we examine historical demographic trends for six species of milksnake with representatives in both the temperate and tropical Americas to determine if species share responses to climate change as a taxon or by area (i.e., temperate versus tropical environments). Using a multilocus dataset, we test for the demographic signature of population expansion and decline using non-genealogical summary statistics, as well as …

Attenuated Neural Processing Of Risk In Young Adults At Risk For Stimulant Dependence, Martina Reske, Jennifer L. Stewart, Taru M. Flagan, Martin P. Paulus

Publications and Research

Objective Approximately 10% of young adults report non-medical use of stimulants (cocaine, amphetamine, methylphenidate), which puts them at risk for the development of dependence. This fMRI study investigates whether subjects at early stages of stimulant use show altered decision making processing. Methods 158 occasional stimulants users (OSU) and 50 comparison subjects (CS) performed a “risky gains” decision making task during which they could select safe options (cash in 20 cents) or gamble them for double or nothing in two consecutive gambles (win or lose 40 or 80 cents, “risky decisions”). The primary analysis focused on risky versus safe decisions. Three …

Canonical And Noncanonical Sites Determine Npt2a Binding Selectivity To Nherf1 Pdz1, Tatyana Mamonova, Qiangmin Zhang, Jahan Ali Khajeh, Zimei Bu, Alessandro Bisello, Peter A. Friedman

Publications and Research

Na+/H+ Exchanger Regulatory Factor-1 (NHERF1) is a scaffolding protein containing 2 PDZ domains that coordinates the assembly and trafficking of transmembrane receptors and ion channels. Most target proteins harboring a C-terminus recognition motif bind more-or-less equivalently to the either PDZ domain, which contain identical core-binding motifs. However some substrates such as the type II sodium-dependent phosphate co-transporter (NPT2A), uniquely bind only one PDZ domain. We sought to define the structural determinants responsible for the specificity of interaction between NHERF1 PDZ domains and NPT2A. By performing all-atom/explicit-solvent molecular dynamics (MD) simulations in combination with biological mutagenesis, fluorescent polarization (FP) binding assays, …

Behavioral And Cognitive Changes After Early Postnatal Lesions Of The Rat Mediodorsal Thalamus, Zakaria Ouhaz, Saadua B-M'Hamed, Anna S. Mitchell, Abdeslem Elidrissi, Mohamed Bennis

Publications and Research

Early insults to the thalamus result in functional and/or structural abnormalities in the cerebral cortex. However, differences in behavioral and cognitive changes after early insult are not well characterized. The present study assessed whether early postnatal damage to mediodorsal nucleus of the thalamus (MD), reciprocally interconnected with the prefrontal cortex, causes behavioral and cognitive alterations in young adult rats. Rat pups at postnatal day 4 received bilateral electrolytic lesion of MD, or aMD Sham lesion or were anesthetized controls; on recovery they were returned to their mothers until weaning. Seven weeks later, all rats were tested with the following behavioral …

Predicting And Exploring Network Components Involved In Pathogenesis In The Malaria Parasite Via Novel Subnetwork Alignments, Hong Cai, Timothy G. Lilburn, Changjin Hong, Jianying Gu, Rui Kuang, Yufeng Wang

Publications and Research

Background Malaria is a major health threat, affecting over 40% of the world's population. The latest report released by the World Health Organization estimated about 207 million cases of malaria infection, and about 627,000 deaths in 2012 alone. During the past decade, new therapeutic targets have been identified and are at various stages of characterization, thanks to the emerging omics-based technologies. However, the mechanism of malaria pathogenesis remains largely unknown. In this paper, we employ a novel neighborhood subnetwork alignment approach to identify network components that are potentially involved in pathogenesis. Results Our module-based subnetwork alignment approach identified 24 functional …

Destabilisation Of Dimeric 14-3-3 Proteins As A Novel Approach To Anti-Cancer Therapeutics, Joanna M. Woodcock, Carl Coolen, Katy L. Goodwin, Dong Jae Baek, Robert Bittman, Michael S. Samuel, Stuart M. Pitson, Angel F. Lopez

Publications and Research

14-3-3 proteins play a pivotal role in controlling cell proliferation and survival, two commonly dysregulated hallmarks of cancers. 14-3-3 protein expression is enhanced in many human cancers and correlates with more aggressive tumors and poor prognosis, suggesting a role for 14-3-3 proteins in tumorigenesis and/or progression. We showed previously that the dimeric state of 14-3-3 proteins is regulated by the lipid sphingosine, a physiological inducer of apoptosis. As the functions of 14-3-3 proteins are dependent on their dimeric state, this sphingosine-mediated 14-3-3 regulation provides a possible means to target dimeric 14-3-3 for therapeutic effect. However, sphingosine mimics are needed that …

Transcriptome Sequencing And Annotation Of The Polychaete Hermodice Carunculata (Annelida, Amphinomidae), Shaadi Mehr, Aida Verdes, Rob Desalle, John S. Sparks, Vincent A. Pieribone, David F. Gruber

Publications and Research

Background: The amphinomid polychaete Hermodice carunculata is a cosmopolitan and ecologically important omnivore in coral reef ecosystems, preying on a diverse suite of reef organisms and potentially acting as a vector for coral disease. While amphinomids are a key group for determining the root of the Annelida, their phylogenetic position has been difficult to resolve, and their publically available genomic data was scarce.

Results: We performed deep transcriptome sequencing (Illumina HiSeq) and profiling on Hermodice carunculata collected in the Western Atlantic Ocean. We focused this study on 58,454 predicted Open Reading Frames (ORFs) of genes longer than 200 amino acids …

New Insights Into The Evolution Of The Human Diet From Faecal Biomarker Analysis In Wild Chimpanzee And Gorilla Faeces, Ainara Sistiaga, Richard Wrangham, Jessica M. Rothman, Roger E. Summons

Publications and Research

Our understanding of early human diets is based on reconstructed biomechanics of hominin jaws, bone and teeth isotopic data, tooth wear patterns, lithic, taphonomic and zooarchaeological data, which do not provide information about the relative amounts of different types of foods that contributed most to early human diets. Faecal biomarkers are proving to be a valuable tool in identifying relative proportions of plant and animal tissues in Palaeolithic diets. A limiting factor in the application of the faecal biomarker approach is the striking absence of data related to the occurrence of faecal biomarkers in non-human primate faeces. In this study …

The Energetic Value Of Land-Based Foods In Western Hudson Bayand Their Potential To Alleviate Energy Deficits Of Starving Adult Male Polar Bears, Linda J. Gormezano, Robert F. Rockwell

Publications and Research

Climate change is predicted to expand the ice-free season in western Hudson Bay and when it grows to 180 days, 28–48% of adult male polar bears are projected to starve unless nutritional deficits can be offset by foods consumed on land. We updated a dynamic energy budget model developed by Molnar et al. to allow influx of additional energy from novel terrestrial foods (lesser snow geese, eggs, caribou) that polar bears currently consume as part of a mixed diet while on land. We calculated the units of each prey, alone and in combination, needed to alleviate these lethal energy deficits …

The Nutritional Geometry Of Resource Scarcity: Effects Of Lean Seasons And Habitat Disturbance On Nutrient Intakes And Balancing In Wild Sifakas, Mitchell T. Irwin, Jean-Luc Raharison, David R. Raubenheimer, Colin A. Chapman, Jessica M. Rothman

Publications and Research

Animals experience spatial and temporal variation in food and nutrient supply, which may cause deviations from optimal nutrient intakes in both absolute amounts (meeting nutrient requirements) and proportions (nutrient balancing). Recent research has used the geometric framework for nutrition to obtain an improved understanding of how animals respond to these nutritional constraints, among them free-ranging primates including spider monkeys and gorillas. We used this framework to examine macronutrient intakes and nutrient balancing in sifakas (Propithecus diadema) at Tsinjoarivo, Madagascar, in order to quantify how these vary across seasons and across habitats with varying degrees of anthropogenic disturbance. Groups in intact …

Evolutionary Dynamics Of Rhomboid Proteases In Streptomycetes, Peter A. Novick, Naydu M. Carmona, Monica Trujillo

Publications and Research

Background Proteolytic enzymes are ubiquitous and active in a myriad of biochemical pathways. One type, the rhomboids are intramembrane serine proteases that release their products extracellularly. These proteases are present in all forms of life and their function is not fully understood, although some evidence suggests they participate in cell signaling. Streptomycetes are prolific soil bacteria with diverse physiological and metabolic properties that respond to signals from other cells and from the environment. In the present study, we investigate the evolutionary dynamics of rhomboids in Streptomycetes, as this can shed light into the possible involvement of rhomboids in the complex …