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Interactive Kinds, Muhammad Ali Khalidi

Publications and Research

This paper examines the phenomenon of 'interactive kinds' first identified by Ian Hacking. An interactive kind is one that is created or significantly modified once a concept of it has been formulated and acted upon in certain ways. Interactive kinds may also 'loop back' to influence our concepts and classifications. According to Hacking, interactive kinds are found exclusively in the human domain. After providing a general account of interactive kinds and outlining their philosophical significance, I argue that they are not confined to the human realm, but that they can also occur elsewhere. Hence, I conclude by arguing that interactive …

Induction Of Neuro-Protective/Regenerative Genes In Stem Cells Infiltrating Post-Ischemic Brain Tissue, Gokhan Yilmaz, J Steven Alexander, Cigdem Erkuran Yilmaz, D Neil Granger

Publications and Research

Background- Although the therapeutic potential of bone marrow-derived stromal stem cells (BMSC) has been demonstrated in different experimental models of ischemic stroke, it remains unclear how stem cells (SC) induce neuroprotection following stroke. In this study, we describe a novel method for isolating BMSC that infiltrate postischemic brain tissue and use this method to identify the genes that are persistently activated or depressed in BMSC that infiltrate brain tissue following ischemic stroke. Methods- Ischemic strokes were induced in C57BL/6 mice by middle cerebral artery occlusion for 1 h, followed by reperfusion. BMSC were isolated from H-2 Kb-tsA58 (immortomouse™) mice, and …

Estimated Birth Weight And Adult Cardiovascular Risk Factors In A Developing Southern Chinese Population: A Cross Sectional Study, C. Mary Schooling, C. Q. Jiang, T. H. Lam, B. J. Cowling, S. L. Yeung, W. S. Zhang, K. K. Cheng, G. M. Leung

Publications and Research

Background: Birth weight is negatively associated with cardiovascular diseases and diabetes, but the associations are less well-established in developing populations where birth weight is often unavailable. We studied the association of birth weight and cardiovascular risk, using birth rank as an instrumental variable, in Southern China.

Methods: We used published data on birth weight by birth rank from an appropriate population and baseline data from the Guangzhou Biobank Cohort Study phases 2 & 3 (2005-8) to examine the adjusted associations, using instrumental variable analysis, of birth weight with clinically measured cardiovascular risk factors and the metabolic syndrome in older …

The Dunaliella Salina Organelle Genomes: Large Sequences, Inflated With Intronic And Intergenic Dna, David Roy Smith, Robert W. Lee, John C. Cushman, Jon K. Magnuson, Duc Tran, Jürgen Ew Polle

Publications and Research

Background Dunaliella salina Teodoresco, a unicellular, halophilic green alga belonging to the Chlorophyceae, is among the most industrially important microalgae. This is because D. salina can produce massive amounts of β-carotene, which can be collected for commercial purposes, and because of its potential as a feedstock for biofuels production. Although the biochemistry and physiology of D. salina have been studied in great detail, virtually nothing is known about the genomes it carries, especially those within its mitochondrion and plastid. This study presents the complete mitochondrial and plastid genome sequences of D. salina and compares them with those of the model …

Interactions Of Host Proteins With The Murine Leukemia Virus Integrase, Barbara Studamire, Stephen P. Goff

Publications and Research

Retroviral infections cause a variety of cancers in animals and a number of diverse diseases in humans such as leukemia and acquired immune deficiency syndrome. Productive and efficient proviral integration is critical for retroviral function and is the key step in establishing a stable and productive infection, as well as the mechanism by which host genes are activated in leukemogenesis. Host factors are widely anticipated to be involved in all stages of the retroviral life cycle, and the identification of integrase interacting factors has the potential to increase our understanding of mechanisms by which the incoming virus might appropriate cellular …

Hsp110 Chaperones Control Client Fate Determination In The Hsp70–Hsp90 Chaperone System, Atin K. Mandal, Patrick A. Gibney, Nadinath B. Nillegoda, Maria A. Theodoraki, Avrom J. Caplan, Kevin A. Morano

Publications and Research

The Hsp110 family of protein chaperones was known to promote maturation of Hsp90 client proteins. The yeast Hsp110 ortholog Sse1 is now shown to influence the decision to fold or degrade substrates of the Hsp70–Hsp90 chaperone system when maturation is compromised.

Exploratory Analysis Of Protein Translation Regulatory Networks Using Hierarchical Random Graphs, Daniel D. Wu, Xiaohua Hu, Ek Park, Xiaofeng Wang, Jiali Feng, Xindong Wu

Publications and Research

Abstract Background Protein translation is a vital cellular process for any living organism. The availability of interaction databases provides an opportunity for researchers to exploit the immense amount of data in silico such as studying biological networks. There has been an extensive effort using computational methods in deciphering the transcriptional regulatory networks. However, research on translation regulatory networks has caught little attention in the bioinformatics and computational biology community. Results In this paper, we present an exploratory analysis of yeast protein translation regulatory networks using hierarchical random graphs. We derive a protein translation regulatory network from a protein-protein interaction dataset. …

Smap-Ws: A Parallel Web Service For Structural Proteome-Wide Ligand-Binding Site Comparison, Jingyuan Ren, Lei Xie, Wilfred W. Li, Philip E. Bourne

Publications and Research

The proteome-wide characterization and analysis of protein ligand-binding sites and their interactions with ligands can provide pivotal information in understanding the structure, function and evolution of proteins and for designing safe and efficient therapeutics. The SMAP web service (SMAP-WS) meets this need through parallel computations designed for 3D ligand-binding site comparison and similarity searching on a structural proteome scale. SMAP-WS implements a shape descriptor (the Geometric Potential) that characterizes both local and global topological properties of the protein structure and which can be used to predict the likely ligand-binding pocket [Xie,L. and Bourne,P.E. (2007) A robust and efficient algorithm for …

Excitability Changes In The Sciatic Nerve And Triceps Surae Muscle After Spinal Cord Injury In Mice, Zaghloul Ahmed, Robert Freedland, Andrzej Wieraszko

Publications and Research

Background From the onset to the chronic phase of spinal cord injury (SCI), peripheral axons and muscles are subjected to abnormal states of activity. This starts with very intense spasms during the first instant of SCI, through a no activity flaccidity phase, to a chronic hyperactivity phase. It remains unclear how the nature of this sequence may affect the peripheral axons and muscles. Methods We set out to investigate the changes in excitability of the sciatic nerve and to characterize the properties of muscle contractility after contusive injury of the mouse thoracic spinal cord. Results The following changes were observed …

Exercise As An Intervention For The Age-Related Decline In Neural Metabolic Support, Brenda J. Anderson, Shayri J. Greenwood, Daniel Mccloskey

Publications and Research

To identify interventions for brain aging, we must first identify the processes in which we hope to intervene. Brain aging is a period of decreasing functional capacity and increasing vulnerability, which reflect a reduction in morphological organization and perhaps degeneration. Since life is ultimately dependent upon the ability to maintain cellular organization through metabolism, this review explores evidence for a decline in neural metabolic support during aging, which includes a reduction in whole brain cerebral blood flow, and cellular metabolic capacity. Capillary density may also decrease with age, although the results are less clear. Exercise may be a highly effective …

Tyrannobdella Rex N. Gen. N. Sp. And The Evolutionary Origins Of Mucosal Leech Infestations, Anna J. Phillips, Renzo Arauco-Brown, Alejandro Oceguera-Figueroa, Gloria P. Gomez, María Beltrán, Yi-Te Lai, Mark E. Siddall

Publications and Research

Background: Leeches have gained a fearsome reputation by feeding externally on blood, often from human hosts. Orificial hirudiniasis is a condition in which a leech enters a body orifice, most often the nasopharyngeal region, but there are many cases of leeches infesting the eyes, urethra, vagina, or rectum. Several leech species particularly in Africa and Asia are well known for their propensity to afflict humans. Because there has not previously been any data suggesting a close relationship for such geographically disparate species, this unnerving tendency to be invasive has been regarded only as a loathsome oddity and not a unifying …

Dynamics On Multiple Timescales In The Rna-Directed Rna Polymerase From The Cystovirus Φ6, Zhen Ren, Hsin Wang, Ranajeet Ghose

Publications and Research

The de novoinitiating RNA-directed RNA polymerase (RdRP), P2, forms the central machinery in the infection cycle of the bacteriophage ϕ6 by performing the dual tasks of replication and transcription of the double-stranded RNA genome in the host cell. By measurement and quantitative analysis of multiple-quantum spin-relaxation data for the δ1 positions of Ile residues that are distributed over the 3D-fold of P2, we find that the enzyme is dynamic both on the fast (ps–ns) and slow (µs–ms) timescales. The characteristics of several motional modes including those that coincide with the catalytic timescale (500–800/s) are altered in the presence of …

The Lethal Giant Larvae Tumour Suppressor Mutation Requires Dmyc Oncoprotein To Promote Clonal Malignancy, Francesca Froldi, Marcello Ziosi, Flavio Garoia, Andrea Pession, Nicola A. Grzeschik, Paola Bellosta, Dennis Strand, Helena E. Richardson, Annalisa Pession, Daniela Grifoni

Publications and Research

Background Neoplastic overgrowth depends on the cooperation of several mutations ultimately leading to major rearrangements in cellular behaviour. Precancerous cells are often removed by cell death from normal tissues in the early steps of the tumourigenic process, but the molecules responsible for such a fundamental safeguard process remain in part elusive. With the aim to investigate the molecular crosstalk occurring between precancerous and normal cells in vivo, we took advantage of the clonal analysis methods that are available in Drosophila for studying the phenotypes due to lethal giant larvae (lgl) neoplastic mutation induced in different backgrounds and tissues. Results We …

An Intervention To Reduce Environmental Tobacco Smoke Exposure Improves Pregnancy Outcomes, Ayman El-Mohandes, Michele Kiely, Susan M. Blake, Marie G. Gantz, M. Nabil El-Khorazaty

Publications and Research

Objective—We tested the efficacy of a cognitive-behavioral intervention in reducing environmental tobacco smoke exposure (ETSE) and improving pregnancy outcomes among African-American women.

Methods—We recruited 1,044 women to a randomized controlled trial during 2001-2004 in Washington, DC. Data on 691 women with self-reported ETSE were analyzed. A subset of 520 ETSE women and salivary cotinine levels (SCLs)/ml was also analyzed. Individually tailored counseling sessions adapted from evidence-based interventions for ETSE and other risks, were delivered to the intervention group. The usual care group received routine prenatal care as determined by their provider. Logistic regression models were used to predict …

Going No Place?: Foreground Nostalgia And Psychological Spaces In Wharton's The House Of Mirth, Sean Scanlan

Publications and Research

This essay argues that the power of Edith Wharton's The House of Mirth comes not from Lily Bart's function as a mere symptom of historical and economic pressures, but from the complex narrative and psychological process by which she negotiates a sequence of homes and their repeated collapse. Informing this process is nostalgia, a feeling that frames Lily Bart's step-by-step fall from riches to rags. Reading Lily via cognitive and family systems approaches suggests that Lily's rootlessness is predicated on a subtle transformation from her reliance upon simple “background” (aesthetic and monetary) nostalgia to a more complex and overwhelming “foreground” …

Laetoli Footprints Preserve Earliest Direct Evidence Of Human-Like Bipedal Biomechanics, David A. Raichlen, Adam D. Gordon, William E. H. Harcourt-Smith, Adam D. Foster, Wm. Randall Haas

Publications and Research

Background Debates over the evolution of hominin bipedalism, a defining human characteristic, revolve around whether early bipeds walked more like humans, with energetically efficient extended hind limbs, or more like apes with flexed hind limbs. The 3.6 million year old hominin footprints at Laetoli, Tanzania represent the earliest direct evidence of hominin bipedalism. Determining the kinematics of Laetoli hominins will allow us to understand whether selection acted to decrease energy costs of bipedalism by 3.6 Ma. Methodology/Principal Findings Using an experimental design, we show that the Laetoli hominins walked with weight transfer most similar to the economical extended limb bipedalism …

Tredd—A Database For Tandem Repeats Over The Edit Distance, Dina Sokol, Firat Atagun

Publications and Research

A ‘tandem repeat’ in DNA is a sequence of two or more contiguous, approximate copies of a pattern of nucleotides. Tandem repeats are common in the genomes of both eukaryotic and prokaryotic organisms. They are significant markers for human identity testing, disease diagnosis, sequence homology and population studies. In this article, we describe a new database, TRedD, which contains the tandem repeats found in the human genome. The database is publicly available online, and the software for locating the repeats is also freely available. The definition of tandem repeats used by TRedD is a new and innovative definition based upon …

Campaigns To Change Health Damaging Corporate Practices, Nicholas Freudenberg

Publications and Research

When corporations claim the same citizenship rights as human citizens, they exercise an undue influence on health policy and democratic processes. Surprisingly, the same basic repertoire of tactics has been found to be employed by corporations to effect this influence, regardless of the specific industry at work. In this book, authors from around the world reveal the range of tactics used across the corporate world that ultimately favor the bottom line over the greater good.

The Bottom Line or Public Health deconstructs some of the most ubiquitous tactics at play, including public relations, political influence, legal maneuvering, and financial power, …

Yeast Cell Adhesion Molecules Have Functional Amyloid-Forming Sequences, Caleen B. Ramsook, Cho Tan, Melissa C. Garcia, Raymond Fung, Gregory Soybelman, Ryan Henry, Anna Litewka, Shanique O’Meally, Henry N. Otoo, Roy A. Khalaf, Anne M. Dranginis, Nand K. Gaur, Stephen A. Klotz, Jason M. Rauceo, Chong K. Jue, Peter N. Lipke

Publications and Research

The occurrence of highly conserved amyloid-forming sequences in Candida albicans Als proteins (H. N. Otoo et al., Eukaryot. Cell 7:776–782, 2008) led us to search for similar sequences in other adhesins from C. albicans and Saccharomyces cerevisiae. The beta-aggregation predictor TANGO found highly beta-aggregation-prone sequences in almost all yeast adhesins. These sequences had an unusual amino acid composition: 77% of their residues were beta-aggregation aliphatic amino acids Ile, Thr, and Val, which is more than 4-fold greater than their prevalence in the S. cerevisiae proteome. High beta-aggregation potential peptides from S. cerevisiae Flo1p and C. albicans Eap1p rapidly formed insoluble …

Structure And Function Of Glycosylated Tandem Repeats From Candida Albicans Als Adhesins, Aaron T. Frank, Caleen B. Ramsook, Henry N. Otoo, Cho Tan, Gregory Soybelman, Jason M. Rauceo, Nand K. Gaur, Stephen A. Klotz, Peter N. Lipke

Publications and Research

Tandem repeat (TR) regions are common in yeast adhesins, but their structures are unknown, and their activities are poorly understood. TR regions in Candida albicans Als proteins are conserved glycosylated 36-residue sequences with cell-cell aggregation activity (J. M. Rauceo, R. De Armond, H. Otoo, P. C. Kahn, S. A. Klotz, N. K. Gaur, and P. N. Lipke, Eukaryot. Cell 5:1664–1673, 2006). Ab initio modeling with either Rosetta or LINUS generated consistent structures of three-stranded antiparallel beta-sheet domains, whereas randomly shuffled sequences with the same composition generated various structures with consistently higher energies. O- and N-glycosylation patterns showed that each TR …

The Correlation Between Rates Of Cancer And Autism: An Exploratory Ecological Investigation, Hung-Teh Kao, Stephen L. Buka, Karl T. Kelsey, David F. Gruber, Barbara Porton

Publications and Research

Background: Autism is associated with high rates of genomic aberrations, including chromosomal rearrangements and de novo copy-number variations. These observations are reminiscent of cancer, a disease where genomic rearrangements also play a role. We undertook a correlative epidemiological study to explore the possibility that shared risk factors might exist for autism and specific types of cancer.

Methodology/Principal Findings: To determine if significant correlations exist between the prevalence of autism and the incidence of cancer, we obtained and analyzed state-wide data reported by age and gender throughout the United States. Autism data were obtained from the U.S. Department of Education via …

Dkk1 Mediated Inhibition Of Wnt Signaling In Postnatal Mice Leads To Loss Of Tec Progenitors And Thymic Degeneration, Masako Osada, Logan Jardine, Ruth Misir, Thomas Andl, Sarah E. Millar, Mark Pezzano

Publications and Research

Background Thymic epithelial cell (TEC) microenvironments are essential for the recruitment of T cell precursors from the bone marrow, as well as the subsequent expansion and selection of thymocytes resulting in a mature self-tolerant T cell repertoire. The molecular mechanisms, which control both the initial development and subsequent maintenance of these critical microenvironments, are poorly defined. Wnt signaling has been shown to be important to the development of several epithelial tissues and organs. Regulation of Wnt signaling has also been shown to impact both early thymocyte and thymic epithelial development. However, early blocks in thymic organogenesis or death of the …

Identification And Quantitation Of 3,4-Methylenedioxy-N-Methylamphetamine (Mdma, Ecstasy) In Human Urine By 1h Nmr Spectroscopy. Application To Five Cases Of Intoxication, Jonathan Liu, John Decatur, Gloria Proni, Elise Champeil

Publications and Research

Identification of 3,4-methylenedioxy-N-methylamphetamine (MDMA, ecstasy) in five cases of intoxication using nuclear magnetic resonance (NMR) spectroscopy of human urine is reported. A new water suppression technique PURGE (Presaturation Utilizing Relaxation Gradients and Echoes) was used. A calibration curve was obtained using spiked samples. The method gave a linear response (correlation coefficient of 0.992) over the range 0.01–1 mg/mL. Subsequently, quantitation of the amount of MDMA present in the samples was performed. The benefit and reliability of NMR investigations of human urine for cases of intoxication with MDMA are discussed.

A Novel Tcr Transgenic Model Reveals That Negative Selection Involves An Immediate, Bim-Dependent Pathway And A Delayed, Bim-Independent Pathway, Damian Kovalovsky, Mark Pezzano, Benjamin D. Ortiz, Derek B. Sant'angelo

Publications and Research

A complete understanding of negative selection has been elusive due to the rapid apoptosis and clearance of thymocytes in vivo. We report a TCR transgenic model in which expression of the TCR during differentiation occurs only after V(D)J-like recombination. TCR expression from this transgene closely mimics expression of the endogenous TCRα locus allowing for development that is similar to wild type thymocytes. This model allowed us to characterize the phenotypic changes that occurred after TCR-mediated signaling in self-reactive thymocytes prior to their deletion in a highly physiological setting. Self-reactive thymocytes were identified as being immature, activated and CD4loCD8lo. These cells …

Optimization And Analysis Of A Quantitative Real-Time Pcr-Based Technique To Determine Microrna Expression In Formalin-Fixed Paraffin-Embedded Samples, Rashmi S. Goswami, Levi Waldron, Jerry Machado, Nilva K. Cervigne, Wei Xu, Patricia Reis, Denis Bailey, Igor Jurisica, Michael R. Crump, Suzanne Kamel-Reid

Publications and Research

Background: MicroRNAs (miRs) are non-coding RNA molecules involved in post-transcriptional regulation, with diverse functions in tissue development, differentiation, cell proliferation and apoptosis. miRs may be less prone to degradation during formalin fixation, facilitating miR expression studies in formalin-fixed paraffin-embedded (FFPE) tissue.

Results: Our study demonstrates that the TaqMan Human MicroRNA Array v1.0 (Early Access) platform is suitable for miR expression analysis in FFPE tissue with a high reproducibility (correlation coefficients of 0.95 between duplicates, p < 0.00001) and outlines the optimal performance conditions of this platform using clinical FFPE samples. We also outline a method of data analysis looking at differences in miR abundance between FFPE and fresh-frozen samples. By dividing the profiled miR into abundance strata of high (Ct35), we show that reproducibility between technical replicates, equivalent dilutions, and FFPE vs. frozen samples is best in the high abundance stratum. We also demonstrate that the miR expression profiles of FFPE samples are comparable to those of fresh-frozen samples, with a correlation of up to 0.87 (p < 0.001), when examining all miRs, regardless of RNA extraction method used. Examining correlation coefficients between FFPE and fresh-frozen samples in terms of miR abundance reveals correlation coefficients of up to 0.32 (low abundance), 0.70 (medium abundance) and up to 0.97 (high abundance).

Conclusion: Our study thus demonstrates the utility, reproducibility, and optimization steps needed in miR expression studies using FFPE samples on a high-throughput quantitative PCR-based miR …

Family Structure, Parent-Child Conversation Time And Substance Use Among Chinese Adolescents, Kwok-Kei Mak, Sai-Yin Ho, G Neil Thomas, C Mary Schooling, Sarah M. Mcghee, Tai-Hing Lam

Publications and Research

Background: The family plays a vital role in shaping adolescent behaviours. The present study investigated the associations between family structure and substance use among Hong Kong Chinese adolescents.

Methods: A total of 32,961 Form 1 to 5 (grade 7-12 in the US) Hong Kong students participated in the Youth Smoking Survey in 2003-4. An anonymous questionnaire was used to obtain information about family structure, daily duration of parent-child conversation, smoking, alcohol drinking and drug use. Logistic regression was used to calculate the adjusted odds ratios (OR) for each substance use by family structure.

Results: Adjusting for sex, age, type of …

Archives & Records In Armed Conflict: International Law And The Current Debate Over Iraqi Records And Archives, Douglas Cox

Publications and Research

No abstract provided.

What The 2007 Tac Market Design Game Tells Us About Effective Auction Mechanisms, Jinzhong Niu, Kai Cai, Simon Parsons, Peter Mcburney, Enrico Gerding

Publications and Research

This paper analyzes the entrants to the 2007 TAC Market Design Game. We present a classification of the entries to the competition, and use this classification to compare these entries. The paper also attempts to relate market dynamics to the auction rules adopted by these entries and their adaptive strategies via a set of post-tournament experiments. Based on this analysis, the paper speculates about the design of effective auction mechanisms, both in the setting of this competition and in the more general case.

Sex Education And Rape, Michelle Anderson

Publications and Research

No abstract provided.

When Your Attorney Is Your Enemy: Preliminary Thoughts On Ensuring Effective Representation For Queer Youth, Sarah Valentine

Publications and Research

No abstract provided.