Digital Commons Network^™

Factors Influencing Lysis Time Stochasticity In Bacteriophage L, John J. Dennehy, Ing-Nang Wang

Publications and Research

Background Despite identical genotypes and seemingly uniform environments, stochastic gene expression and other dynamic intracellular processes can produce considerable phenotypic diversity within clonal microbes. One trait that provides a good model to explore the molecular basis of stochastic variation is the timing of host lysis by bacteriophage (phage).

Results Individual lysis events of thermally-inducible l lysogens were observed using a temperature-controlled perfusion chamber mounted on an inverted microscope. Both mean lysis time (MLT) and its associated standard deviation (SD) were estimated. Using the SD as a measure of lysis time stochasticity, we showed that lysogenic cells in controlled environments varied …

Bone Morphogenetic Protein Inhibition Promotes Neurological Recovery After Intraventricular Hemorrhage, Krishna Dummula, Govindaiah Vinukonda, Philip Chu, Yiping Xing, Furong Hu, Sabrina Mailk, Anna Csiszar, Caroline Chua, Peter Mouton, Robert J. Kayton, Joshua C. Brumberg, Rashmi Bansal, Praveen Ballabh

Publications and Research

Intraventricular hemorrhage (IVH) results in neural cell death and white matter injury in premature infants. No therapeutic strategy is currently available against this disorder. Bone morphogenetic protein (BMP) signaling suppresses oligodendrocyte development through basic-helix-loop-helix (bHLH) transcription factors and promotes astrocytosis. Therefore, we hypothesized that IVH in premature newborns initiates degeneration and maturation arrest of oligodendrocyte lineage and that BMP inhibition alleviates hypomyelination, gliosis, and motor impairment in the survivors of IVH. To test the hypotheses, a rabbit model of IVH was used in which premature rabbit pups (E29) are treated with intraperitoneal glycerol at 2 hours of age to induce …

Dynamic Biclustering Of Microarray Data By Multi-Objective Immune Optimization, Junwan Liu, Zhoujun Li, Xiaohua Hu, Yiming Chen, Ek Park

Publications and Research

Abstract Background Newly microarray technologies yield large-scale datasets. The microarray datasets are usually presented in 2D matrices, where rows represent genes and columns represent experimental conditions. Systematic analysis of those datasets provides the increasing amount of information, which is urgently needed in the post-genomic era. Biclustering, which is a technique developed to allow simultaneous clustering of rows and columns of a dataset, might be useful to extract more accurate information from those datasets. Biclustering requires the optimization of two conflicting objectives (residue and volume), and a multi-objective artificial immune system capable of performing a multi-population search. As a heuristic search …

Computational Insight With Monte Carlo Simulations, Boyan Kostadinov

Publications and Research

We introduce Monte Carlo simulations for estimating areas by playing a game of "darts". We also introduce simulations of random walks. We use compact, vectorized programming, based on the R language, for all computer simulations and visualizations, aimed at high school students. This presentation is based on the Invited, prime time lecture given at the summer camp for gifted high school students at City College of New York, July 13, 2011.

Fathers' Time Investments In Children: Do Sons Get More?, Kristin Mammen

Publications and Research

Evidence suggests that, from birth, fathers treat sons differently than daughters in the U.S., as well as in developing countries. Fathers' time investments in children are one channel through which differential treatment by gender may affect children's outcomes. This paper uses data from the 2003 American Time Use Survey to explore three questions about paternal time in married two-parent families: Does the gender composition of his children affect the amount of time a father spends with them? If so, does the gender of the individual child have an additional effect? And is a girl advantaged or disadvantaged by the presence …

Mechanical Intervention For Maintenance Of Cartilage And Bone, Hui B. Sun, Luis Cardoso, Hiroki Yokota

Publications and Research

Mechanical loading provides indispensible stimuli for growth and development of the articular cartilage and bone. Interestingly, depending on loading conditions loads applied to the joint can be beneficial as well as harmful to skeletal maintenance and remodeling. Moderate loads to the synovial joint, for instance, suppress the expression levels of matrix metallproteinases (MMPs), while loads above a threshold tend to increase their destructive activities. This report focuses on two recently developed loading modalities from animal studies, joint motion and joint loading. Their unique characteristics and potential usages for maintenance of the articular cartilage and stimulation of bone remodeling are reviewed. …

Transcription And Translation Of Human F11r Gene Are Required For An Initial Step Of Atherogenesis Induced By Inflammatory Cytokines, Bani M. Azari, Jonathan D. Marmur, Moro O. Salifu, Yigal H. Ehrlich, Elizabeth Kornecki, Anna Babinska

Publications and Research

Background - The F11 Receptor (F11R; aka JAM-A, JAM-1) is a cell adhesion protein present constitutively on the membrane surface of circulating platelets and within tight junctions of endothelial cells (ECs). Previous reports demonstrated that exposure of ECs to pro-inflammatory cytokines causes insertion of F11R molecules into the luminal surface of ECs, ensuing with homologous interactions between F11R molecules of platelets and ECs, and a resultant adhesion of platelets to the inflamed ECs. The main new finding of the present report is that the first step in this chain of events is the de-novo transcription and translation of F11R molecules, …

Weight-Related Behavior Among Adolescents: The Role Of Peer Effects, Mir M. Ali, Aliaksandr Amialchuk, Frank W. Heiland

Publications and Research

Purpose To investigate whether social interactions in friendship networks influence the following weight-related behaviors of adolescents: exercising regularly, playing an active sport, hours of TV/Video viewing, sleeping six or fewer hours, eating breakfast on weekdays, frequency of eating at fast food restaurants, eating five servings of fruits/vegetables daily, and consuming calorie-dense snacks.

Method Data from a nationally representative sample of adolescents are used to examine the association between peer and individual weight-related behaviors. Evidence from multivariate regression analysis controlling for an extensive list of individual- and family-level factors as well as school-level unobserved heterogeneity is obtained. Results We find a …

Smoking Cessation And Relapse Among Pregnant African-American Smokers In Washington, Dc, Ayman El-Mohandes, M. Nabil El-Khorazaty, Michele Kieley, Marie G. Gantz

Publications and Research

Smoking is the single most preventable cause of perinatal morbidity. This study examines smoking behaviors during pregnancy in a high risk population of African Americans. The study also examines risk factors associated with smoking behaviors and cessation in response to a cognitive behavioral therapy (CBT) intervention. This study is a secondary analysis of data from a randomized controlled trial addressing multiple risks during pregnancy. Five hundred African-American Washington, DC residents who reported smoking in the 6 months preceding pregnancy were randomized to a CBT intervention. Psycho-social and behavioral data were collected. Self-reported smoking and salivary cotinine levels were measured prenatally …

Automated Auction Mechanism Design With Competing Markets, Jinzhong Niu

Publications and Research

Resource allocation is a major issue in multiple areas of computer science. Despite the wide range of resource types across these areas, for example real commodities in e-commerce and computing resources in distributed computing, auctions are commonly used in solving the optimization problems involved in these areas, since well designed auctions achieve desirable economic outcomes.

Auctions are markets with strict regulations governing the information available to traders in the market and the possible actions they can take. Auction mechanism design aims to manipulate the rules of an auction in order to achieve specific goals. Economists traditionally use mathematical methods, mainly …

Conformational-Dependent And Independent Rna Binding To The Fragile X Mental Retardation Protein, Xin Yan, Robert B. Denman

Publications and Research

The interaction between the fragile X mental retardation protein (FMRP) and BC1 RNA has been the subject of controversy. We probed the parameters of RNA binding to FMRP in several ways. Nondenaturing agarose gel analysis showed that BC1 RNA transcripts produced by in vitro transcription contain a population of conformers, which can be modulated by preannealing. Accordingly, FMRP differentially binds to the annealed and unannealed conformer populations. Using partial RNase digestion, we demonstrate that annealed BC1 RNA contains a unique conformer that FMRP likely binds. We further demonstrate that this interaction is 100-fold weaker than that the binding of eEF-1A …

Fluid Shear Stress Regulates The Invasive Potential Of Glioma Cells Via Modulation Of Migratory Activity And Matrix Metalloproteinase Expression, Henry Qazi, Zhong-Dong Shi, John M. Tarbell

Publications and Research

Background Glioma cells are exposed to elevated interstitial fluid flow during the onset of angiogenesis, at the tumor periphery while invading normal parenchyma, within white matter tracts, and during vascular normalization therapy. Glioma cell lines that have been exposed to fluid flow forces in vivo have much lower invasive potentials than in vitro cell motility assays without flow would indicate. Methodology/Principal Findings A 3D Modified Boyden chamber (Darcy flow through collagen/cell suspension) model was designed to mimic the fluid dynamic microenvironment to study the effects of fluid shear stress on the migratory activity of glioma cells. Novel methods for gel …

Investigating The Distance Limit Of A Metal Nanoparticle Based Spectroscopic Ruler, Subhasish Chatterjee, Jong Bum Lee, Nikesh V. Valappil, Dan Luo, Vinod M. Menon

Publications and Research

Conventional Förster resonance energy transfer (FRET) processes involving a pair of fluorophore and organic quencher are restricted to an upper distance limit of ~10 nm. The application of a metal nanoparticle as a quencher can overcome the distance barrier of the traditional FRET technique. However, no standard distance dependence of this resonance energy transfer (RET) process has been firmly established. We have investigated the nonradiative energy transfer process between an organic donor (fluorescein) and gold nanoparticle quencher connected by double stranded (ds) DNA. The quenching efficiency of the gold nanoparticle as a function of distance between the donor and acceptor …

Electrode Positioning And Montage In Transcranial Direct Current Stimulation, Alexandre F. Dasilva, Magdalena Sarah Volz, Marom Bikson, Felipe Fregni

Publications and Research

Transcranial direct current stimulation (tDCS) is a technique that has been intensively investigated in the past decade as this method offers a non-invasive and safe alternative to change cortical excitability2. The effects of one session of tDCS can last for several minutes, and its effects depend on polarity of stimulation, such as that cathodal stimulation induces a decrease in cortical excitability, and anodal stimulation induces an increase in cortical excitability that may last beyond the duration of stimulation6. These effects have been explored in cognitive neuroscience and also clinically in a variety of neuropsychiatric disorders – especially when applied over …

Mathematical Model Of The Dynamics Of Psychotherapy, Larry S. Liebovitch, Paul R. Peluso, Michael D. Norman, Jessica Su, John M. Gottman

Publications and Research

The success of psychotherapy depends on the nature of the therapeutic relationship between a therapist and a client. We use dynamical systems theory to model the dynamics of the emotional interaction between a therapist and client. We determine how the therapeutic endpoint and the dynamics of getting there depend on the parameters of the model. Previously Gottman et al. used a very similar approach (physical-sciences paradigm) for modeling and making predictions about husband–wife relationships. Given that this novel approach shed light on the dyadic interaction between couples, we have applied it to the study of the relationship between therapist and …

A Transcriptional Analysis Of Carotenoid, Chlorophyll And Plastidial Isoprenoid Biosynthesis Genes During Development And Osmotic Stress Responses In Arabidopsis Thaliana, Stuart Meier, Oren Tzfadia, Ratnakar Vallabhaneni, Chris Gehring, Eleanore T. Wurtzel

Publications and Research

Background The carotenoids are pure isoprenoids that are essential components of the photosynthetic apparatus and are coordinately synthesized with chlorophylls in chloroplasts. However, little is known about the mechanisms that regulate carotenoid biosynthesis or the mechanisms that coordinate this synthesis with that of chlorophylls and other plastidial synthesized isoprenoid-derived compounds, including quinones, gibberellic acid and abscisic acid. Here, a comprehensive transcriptional analysis of individual carotenoid and isoprenoid-related biosynthesis pathway genes was performed in order to elucidate the role of transcriptional regulation in the coordinated synthesis of these compounds and to identify regulatory components that may mediate this process in Arabidopsis …

Childhood Meat Eating And Inflammatory Markers: The Guangzhou Biobank Cohort Study, Mary Schooling, Chao Q. Jiang, Tai H. Lam, W. S. Zhang, Kar Keung Cheng, Gabriel M. Leung

Publications and Research

Background
We hypothesized that socio-economic development could, via nutritionally driven levels of pubertal sex-steroids, promote a pro-inflammatory state among men but not women in developing countries. We tested this hypothesis, using recalled childhood meat eating as a proxy for childhood nutrition, in southern China.

Methods
We used multivariable linear regression in the Guangzhou Biobank Cohort Study phase 3 (2006-8) to examine the adjusted associations of recalled childhood meat eating, <1/week (n = 5,023), about once per week (n = 3,592) and almost daily (n = 1,252), with white blood cell count and its differentials among older (≥50 years) men (n = 2,498) and women (n = 7,369).

Results
Adjusted for age, childhood socio-economic position, education and smoking, childhood meat eating had sex-specific associations with white blood cell count and lymphocyte count, but not granulocyte count. Men with childhood …

Parental Death During Childhood And Adult Cardiovascular Risk In A Developing Country: The Guangzhou Biobank Cohort Study, C. Mary Schooling, Chaoqiang Jiang, Tai Hing Lam, Weisen Zhang, Kar Keung Cheng, Gabriel M. Leung

Publications and Research

Background In observational studies from western countries childhood emotional adversity is usually associated with adult cardiovascular disease. These findings are open to contextual biases making evidence from other settings valuable. We examined the association of a potential marker of childhood emotional adversity with cardiovascular disease risk factors in a developing country. Methods We used multivariable regression in cross-sectional analysis of older (≥50 years) men (n = 7,885) and women (n = 20,886) from the Guangzhou Biobank Cohort Study (2003–8) to examine the adjusted association of early life (<18 years) parental death (none, one or two deaths) with blood pressure, fasting glucose, LDL-cholesterol, HDL-cholesterol, triglycerides, body mass index (BMI), waist-hip ratio (WHR) and white blood cell count (WBC). We used seated height and delayed 10-word recall to assess content validity of parental death as a measure of childhood emotional adversity. We also examined whether associations varied by sex. Results Early life parental death was associated with shorter age- and sex-adjusted seated height. It was also associated with lower 10-word recall score adjusted for age, sex, socio-economic position, leg length and lifestyle. Similarly, adjusted early life parental death was not associated with blood pressure, fasting glucose, LDL-cholesterol or HDL-cholesterol but was associated with lower BMI (−0.40, 95% confidence interval (CI) −0.62 to −0.19 for 2 compared with no early life parental deaths) and triglycerides. Associations varied by sex for WHR and WBC. Among men only, early life parental death was associated with lower WHR (−0.008, 95% CI −0.015 to −0.001) and WBC (−0.35 109/L, 95% CI −0.56 to −0.13). Conclusions In a non-western population from a developing country, childhood emotional adversity was negatively associated with some cardiovascular risk factors, particularly among men. Our study suggests that some of the observed associations in western populations may be socially rather than biologically based or may be population specific.

Understanding Depressive Symptoms Among High-Risk Pregnant African American Women, Kristine M. Molina, Michele Kiely

Publications and Research

Much has been written about depression and its risk factors, particularly among women. However, a growing body of literature on prenatal depression has begun to emerge, given that depression during pregnancy presents a major public health concern, since it is found to be a common experience among childbearing aged women (Gaynes et al., 2005; Marcus, 2009). In fact, the onset of depressive symptoms is most likely to occur between 20 to 40 years of age, the range when most women become pregnant (Marcus & Heringhausen, 2009). Further, prior studies have found rates of depression among pregnant women to range from …

Transplantation Of Adult Mouse Ips Cell-Derived Photoreceptor Precursors Restores Retinal Structure And Function In Degenerative Mice, Budd A. Tucker, In-Hyun Park, Sara D. Qi, Henry J. Klassen, Caihui Jiang, Jing Yao, Stephen Redenti, George Q. Daley, Michael J. Young

Publications and Research

This study was designed to determine whether adult mouse induced pluripotent stem cells (iPSCs), could be used to produce retinal precursors and subsequently photoreceptor cells for retinal transplantation to restore retinal function in degenerative hosts. iPSCs were generated using adult dsRed mouse dermal fibroblasts via retroviral induction of the transcription factors Oct4, Sox2, KLF4 and c-Myc. As with normal mouse ES cells, adult dsRed iPSCs expressed the pluripotency genes SSEA1, Oct4, Sox2, KLF4, c-Myc and Nanog. Following transplantation into the eye of immunecompromised retinal degenerative mice these cells proceeded to form teratomas containing tissue comprising all three germ layers. At …

Drug Discovery Using Chemical Systems Biology: Weak Inhibition Of Multiple Kinases May Contribute To The Anti-Cancer Effect Of Nelfinavir, Li Xie, Thomas Evangelidis, Lei Xie, Philip E. Bourne

Publications and Research

Nelfinavir is a potent HIV-protease inhibitor with pleiotropic effects in cancer cells. Experimental studies connect its anti-cancer effects to the suppression of the Akt signaling pathway, but the actual molecular targets remain unknown. Using a structural proteome-wide off-target pipeline, which integrates molecular dynamics simulation and MM/GBSA free energy calculations with ligand binding site comparison and biological network analysis, we identified putative human off-targets of Nelfinavir and analyzed the impact on the associated biological processes. Our results suggest that Nelfinavir is able to inhibit multiple members of the protein kinase-like superfamily, which are involved in the regulation of cellular processes vital …

The Association Of Tree Pollen Concentration Peaks And Allergy Medication Sales In New York City: 2003–2008, Perry E. Sheffield, Kate R. Weinberger, Kazuhiko Ito, Thomas D. Matte, Robert W. Mathes, Guy S. Robinson, Patrick L. Kinney

Publications and Research

The impact of pollen exposure on population allergic illness is poorly characterized. We explore the association of tree pollen and over-the-counter daily allergy medication sales in the New York City metropolitan area. Dates of peak tree pollen (maple, oak, and birch) concentrations were identified from 2003 to 2008. Daily allergy medication sales reported to the city health department were analyzed as a function of the same-day and lagged tree pollen peak indicators, adjusting for season, year, temperature, and day of week. Significant associations were found between tree pollen peaks and allergy medication sales, with the strongest association at 2-day lag …

Fine Particulate Matter Constituents Associated With Cardiovascular Hospitalizations And Mortality In New York City, Kazuhiko Ito, Robert Mathes, Zev Ross, Arthur Nádas, George Thurston, Thomas Matte

Publications and Research

Background Recent time-series studies have indicated that both cardiovascular disease (CVD)mortality and hospitalizations are associated with particulate matter (PM). However, seasonal patterns of PM associations with these outcomes are not consistent, and PM components responsible for these associations have not been determined. We investigated this issue in New York City (NYC), where PM originates from regional and local combustion sources. Objective In this study, we examined the role of particulate matter with aerodynamic diameter ≤ 2.5 μm (PM2.5) and its key chemical components on both CVD hospitalizations and on mortality in NYC. Methods We analyzed daily deaths and emergency hospitalizations …

Dual Testing Algorithm Of Bed-Ceia And Axsym Avidity Index Assays Performs Best In Identifying Recent Hiv Infection In A Sample Of Rwandan Sex Workers, Sarah L. Braunstein, Denis Nash, Andrea A. Kim, Ken Ford, Lambert Mwambarangwe, Chantal M. Ingabire, Joseph Vyankandondera, Janneke H. H. M. Van De Wijgert

Publications and Research

Background

To assess the performance of BED-CEIA (BED) and AxSYM Avidity Index (Ax-AI) assays in estimating HIV incidence among female sex workers (FSW) in Kigali, Rwanda.

Methodology and Findings

Eight hundred FSW of unknown HIV status were HIV tested; HIV-positive women had BED and Ax-AI testing at baseline and ≥12 months later to estimate assay false-recent rates (FRR). STARHS-based HIV incidence was estimated using the McWalter/Welte formula, and adjusted with locally derived FRR and CD4 results. HIV incidence and local assay window periods were estimated from a prospective cohort of FSW. At baseline, 190 HIV-positive women were BED and Ax-AI …

Experimental Tuberculosis In The Wistar Rat: A Model For Protective Immunity And Control Of Infection, Amit Singhal, El Moukhtar Aliouat, Maxime Herve, Vanessa Mathys, Mehdi Kiass, Colette Creusy, Baptiste Delaire, Liana Tsenova, Laurence Fleurisse, Julie Bertout, Luis Camacho, Damian Foo, Hui Chien Tay, Jie Yee Siew, Warda Boukhouchi, Marta Romano, Barun Mathema, Veronique Dartois, Gilla Kaplan, Pablo Bifani

Publications and Research

Background: Despite the availability of many animal models for tuberculosis (TB) research, there still exists a need for better understanding of the quiescent stage of disease observed in many humans. Here, we explored the use of the Wistar rat model for the study of protective immunity and control of Mycobacterium tuberculosis (Mtb) infection.

Methodology/Principal Findings: The kinetics of bacillary growth, evaluated by the colony stimulating assay (CFU) and the extent of lung pathology in Mtb infected Wistar rats were dependent on the virulence of the strains and the size of the infecting inoculums. Bacillary growth control was associated with induction …

A Model Of A Mapk•Substrate Complex In An Active Conformation: A Computational And Experimental Approach, Sunbae Lee, Mangalika Warthaka, Chunli Yan, Tamer S. Kaoud, Andrea Piserchio, Ranajeet Ghose, Pengyu Ren, Kevin N. Dalby

Publications and Research

The mechanisms by which MAP kinases recognize and phosphorylate substrates are not completely understood. Efforts to understand the mechanisms have been compromised by the lack of MAPK-substrate structures. While MAPK-substrate docking is well established as a viable mechanism for bringing MAPKs and substrates into close proximity the molecular details of how such docking promotes phosphorylation is an unresolved issue. In the present study computer modeling approaches, with restraints derived from experimentally known interactions, were used to predict how the N-terminus of Ets-1 associates with ERK2. Interestingly, the N-terminus does not contain a consensus-docking site ((R/K)2-3-X2-6-ΦA-X-ΦB, where Φ is aliphatic hydrophobic) …

Review Of The Book Vibrant Matter: A Political Ecology Of Things, Karen Weingarten

Publications and Research

No abstract provided.

Bad Girls And Biopolitics: Abortion, Popular Fiction, And Population Control, Karen Weingarten

Publications and Research

No abstract provided.

Faculty Of 1000 And Vivo: Invisible Colleges And Team Science, John Carey

Publications and Research

Within the traditional model of scholarly communications, "invisible colleges" facilitate a process of social diffusion that fuels the growth of scientific specialties. This diffusion of ideas operates not through published journal articles but rather through informal communications between researchers. In recent years, researchers have availed themselves of collaborative Web 2.0 forums such as blogs, wikis, and social networking sites to meet their need for increasingly sophisticated vehicles of informal communication. Examinations of the database Faculty of 1000 and the semantic web application VIVO help to illustrate how invisible colleges have migrated to a networked environment where they can play an …

Bitten By The Science Bug (Nycsef 2011), Maribel Vazquez

Publications and Research

The invited keynote address to the participants of the final round of the 2011 New York City Science and Engineering Fair (NYCSeF) at the American Museum of Natural History (AMNH).