Digital Commons Network^™

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. …

Impact Of Resilience Enhancing Programs On Youth Surviving The Beslan School Siege, Stefan Vetter, Igor Dulaev, Mario Mueller, Robert R. Henley, William T. Gallo, Zalina Kanukova

Publications and Research

The objective of this study was to evaluate a resilience-enhancing program for youth (mean age = 13.32 years) from Beslan, North Ossetia, in the Russian Federation. The program, offered in the summer of 2006, combined recreation, sport, and psychosocial rehabilitation activities for 94 participants, 46 of who were taken hostage in the 2004 school tragedy and experienced those events first hand. Self-reported resilience, as measured by the CD-RISC, was compared within subjects at the study baseline and at two follow-up assessments: immediately after the program and 6 months later. We also compared changes in resilience levels across groups that differed …

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 …

Impact Of Insurance Status On Migraine Care In The United States, Andrew Wilper, Steffie Woolhandler, David U. Himmelstein, Rachel Nardin

Publications and Research

Objective
To determine whether insurance status is associated with differential outpatient treatment of migraine in the United States.

Methods
We analyzed 11 years of data from the National Ambulatory Medical Care Survey and National Hospital Ambulatory Medical Care Survey (1997–2007), which survey patient visits to doctors’ offices, hospital outpatient departments, and emergency departments (EDs) in the United States. We used logistic regression to determine whether insurance status was associated with the prescription of standard migraine therapy, defined as 1) a triptan or dihydroergotamine and 2) a prophylactic agent.

Results
We identified 6,814 individual patient visits for migraine, representing 68.6 million …

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 …

Positive Youth Justice: Framing Justice Interventions Using The Concepts Of Positive Youth Development, Jeffrey A. Butts, Gordon Bazemore, Aundra Saa Meroe

Publications and Research

Positive youth development could be an effective framework for designing general interventions for young offenders. Such a framework would encourage youth justice systems to focus on protective factors and risk factors, strengths, problems, and broader efforts to facilitate successful transitions to adulthood for justice-involved youth. The positive youth development approach supports youth in successfully transitioning from adolescence to early adulthood by encouraging young people to develop useful skills and competencies and build stronger connections with pro-social peers, families, and communities (Butts, Mayer, & Ruth, & Ruth, 2005). Young people engaged with trustworthy adults and peers to pursue meaningful activities and …

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” …

Using Podcasts For Assessing Information Research, Lauren Yannotta, Brian Lym, Shiao-Chuan Kung

Publications and Research

This paper reports on the use of podcast audio recordings to assess learning in a hybrid information research course. Evidence of learning that appeared in the audio recordings and how the project affected student learning were investigated. Findings suggest that student-created podcasts can be beneficial in that instructors can see what students learned from the podcast content; students can see evidence of own learning by looking at before and after podcasts; and that students see methods used by other students and reflect on own methods/knowledge.

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 …

Contribution Of Soil Moisture Feedback To Hydroclimatic Variability, Nir Krakauer, B. I. Cook, M. J. Puma

Publications and Research

While a variety of model experiments and analyses of observations have explored the impact of soil moisture variation on climate, it is not yet clear how large or detectable soil moisture feedback is across spatial and temporal scales. Here, we study the impact of dynamic versus climatological soil moisture in the GISS GCM ModelE (with prescribed sea-surface temperatures) on the variance and on the spatial and temporal correlation scale of hydrologically relevant climate variables (evaporation, precipitation, temperature, cloud cover) over the land surface. We also confirm that synoptic variations in soil moisture have a substantial impact on the mean climate …

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, …

Information Literacy And Social Power, Jonathan Cope

Publications and Research

An examination of information literacy literature using the perspective of social power research.

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 …

"Can't Anyone Be A Teacher Anyway?": Student Perceptions Of Academic Librarians As Teachers, Mark Aaron Polger, Karen Okamoto

Publications and Research

The study explores student perceptions of the academic librarian as teachers. A questionnaire was distributed to 500 students at two City University of New York colleges. Convenience and snowball sampling were employed to reach as many respondents as possible. Questionnaires were administered following a library instruction class and in the campus cafeteria. Contrary to results from previous studies, many respondents consider librarians to be teachers.

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 …

Decaffeinated Coffee And Glucose Metabolism In Young Men, James A. Greenberg, David R. Owen, Allan Geliebter

Publications and Research

OBJECTIVE The epidemiological association between coffee drinking and decreased risk of type 2 diabetes is strong. However, caffeinated coffee acutely impairs glucose metabolism. We assessed acute effects of decaffeinated coffee on glucose and insulin levels. RESEARCH DESIGN AND METHODS This was a randomized, cross-over, placebo-controlled trial of the effects of decaffeinated coffee, caffeinated coffee, and caffeine on glucose, insulin, and glucose-dependent insulinotropic polypeptide (GIP) levels during a 2-h oral glucose tolerance test (OGTT) in 11 young men. RESULTS Within the first hour of the OGTT, glucose and insulin were higher for decaffeinated coffee than for placebo (P < 0.05). During the whole OGTT, decaffeinated coffee yielded higher insulin than placebo and lower glucose and a higher insulin sensitivity index than caffeine. Changes in GIP could not explain any beverage effects on glucose and insulin. CONCLUSIONS Some types of decaffeinated coffee may acutely impair glucose metabolism but less than caffeine.

The Career Progression Of Women In State Government Agencies, Maria J. D'Agostino, Helisse Levine

Publications and Research

Purpose – The purpose of this paper is to empirically examine the impact of the utilization of organizational practices on the career progression of women to executive positions in state-level government organizations in the USA.

Design/methodology/approach – The design included an online survey instrument sent to a purposive sample of 600 female administrative agency executives in 50 states. A standard multilinear regression model tests the predictive power of three composite explanatory utilization variables on the dependent variable, career progression of women to upper level management. The composite predictor variables are: utilization of work/family practices; utilization of diversity practices; and utilization …

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 …

An Integrated Intervention To Reduce Intimate Partner Violence In Pregnancy: A Randomized Trial, Michele Kiely, Ayman El-Mohandes, M. Nabil El-Khorazaty, Marie G. Gantz

Publications and Research

OBJECTIVE: We estimated the efficacy of a psycho-behavioral intervention in reducing intimate partner violence (IPV) recurrence during pregnancy and postpartum, and in improving birth outcomes in African-American women

METHODS: We conducted a randomized controlled trial in which 1,044 women were recruited. Individually-tailored counseling sessions were adapted from evidence-based interventions for IPV and other risks. Logistic regression was used to model IPV victimization recurrence, to predict minor, severe, physical and sexual IPV.

RESULTS: Women randomized to the intervention were less likely to have recurrent episodes of IPV victimization (OR=0.48, 95%CI=0.29-0.80). Women with minor IPV were significantly less likely to experience further …

Re-Thinking Library Jargon: Maintaining Consistency And Using Plain Language, Mark Aaron Polger

Publications and Research

No abstract provided.

Information Takeout & Delivery And The Itrain: Different Outreach Methods To Garner More Users, Mark Aaron Polger

Publications and Research

No abstract provided.

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.

Analysis Of Large Scale Spatial Variability Of Soil Moisture Using A Geostatistical Method, Tarendra Lakhankar, Andrew S. Jones, Cynthia L. Combs, Manajit Sengupta, Thomas H. Vonder Haar, Reza Khanbilvardi

Publications and Research

Spatial and temporal soil moisture dynamics are critically needed to improve the parameterization for hydrological and meteorological modeling processes. This study evaluates the statistical spatial structure of large-scale observed and simulated estimates of soil moisture under pre- and post-precipitation event conditions. This large scale variability is a crucial in calibration and validation of large-scale satellite based data assimilation systems. Spatial analysis using geostatistical approaches was used to validate modeled soil moisture by the Agriculture Meteorological (AGRMET) model using in situ measurements of soil moisture from a state-wide environmental monitoring network (Oklahoma Mesonet). The results show that AGRMET data produces larger …

From Ideal To Practice And Back Again: Beginning Teachers Teaching For Social Justice, Ruchi Agarwal, Shira Epstein, Rachel Oppenheim, Celia Oyler, Debbie Sonu

Publications and Research

The five authors of this article designed a multicase study to follow recent graduates of an elementary preservice teacher education program into their beginning teaching placements and explore the ways in which they enacted social justice curricula. The authors highlight the stories of three beginning teachers, honoring the plurality of their conceptions of social justice teaching and the resiliency they exhibited in translating social justice ideals into viable pedagogy. They also discuss the struggles the teachers faced when enacting social justice curricula and the tenuous connection they perceived between their conceptions and their practices. The authors emphasize that such struggles …