Digital Commons Network^™

Candidatus Syngnamydia Venezia, A Novel Member Of The Phylum Chlamydiae From The Broad Nosed Pipefish, Syngnathustyphle Typhle, Alexander Fehr, Elisabeth Walther, Heike Schmidt-Posthaus, Lisbeth Nufer, Anthony B. Wilson, Miroslav Svercel, Denis Richter, Helmut Segner, Andreas Pospischil, Lloyd Vaughan

Publications and Research

Chlamydia are obligate intracellular bacteria and important pathogens of humans and animals. Chlamydia-related bacteria are also major fish pathogens, infecting epithelial cells of the gills and skin to cause the disease epitheliocystis. Given the wide distribution, ancient origins and spectacular diversity of bony fishes, this group offers a rich resource for the identification and isolation of novel Chlamydia. The broad-nosed pipefish (Syngnathus typhle) is a widely distributed and genetically diverse temperate fish species, susceptible to epitheliocystis across much of its range. We describe here a new bacterial species, Candidatus Syngnamydia venezia; epitheliocystis agent of S. typhle and close relative to …

Transcriptome Deep-Sequencing And Clustering Of Expressed Isoforms From Favia Corals, Shaadi F. Pooyaei Mehr, Rob Desalle, Hung-Teh Kao, Apurva Narechania, Zhou Han, Dan Tchernov, Vincent A. Pieribone, David F. Gruber

Publications and Research

Background: Genomic and transcriptomic sequence data are essential tools for tackling ecological problems. Using an approach that combines next-generation sequencing, de novo transcriptome assembly, gene annotation and synthetic gene construction, we identify and cluster the protein families from Favia corals from the northern Red Sea.

Results: We obtained 80 million 75 bp paired-end cDNA reads from two Favia adult samples collected at 65 m (Fav1, Fav2) on the Illumina GA platform, and generated two de novo assemblies using ABySS and CAP3. After removing redundancy and filtering out low quality reads, our transcriptome datasets contained 58,268 (Fav1) and 62,469 (Fav2) contigs …

Ready For Success: A Profile Of Youthbuild Mentoring Participants, Kathleen A. Tomberg

Publications and Research

The YouthBuild USA National Mentoring Alliance program (“YouthBuild Mentoring”) seeks to engage students with responsible, supportive, committed adult volunteers to help young people achieve success in education, employment, and social relationships. By matching students with adult mentors for a minimum of 15 months, YouthBuild Mentoring helps these youth form strong emotional bonds and continuing relationships that will ideally last for years beyond the end of the program. YouthBuild USA partnered with the Research and Evaluation Center of John Jay College of Criminal Justice to assess the attitudes of YouthBuild Mentoring participants on a variety of topics, including self-image, self-efficacy, perceptions …

Associations Between The Legal Context Of Hiv, Perceived Social Capital, And Hiv Antiretroviral Adherence In North America, J Craig Phillips, Allison Webel, Carol Dawson Rose, Inge B. Corless, Kathleen M. Sullivan, Joachim Voss, Dean Wantland, Kathleen Nokes, John Brion, Wei-Ti Chen, Scholastika Iipinge, Lucille Sanzero Eller, Lynda Tyer-Viola, Marta Rivero-Méndez, Patrice K. Nicholas, Mallory O. Johnson, Mary Maryland, Jeanne Kemppainen, Carmen J. Portillo, Puangtip Chaiphibalsarisdi

Publications and Research

Background Human rights approaches to manage HIV and efforts to decriminalize HIV exposure/transmission globally offer hope to persons living with HIV (PLWH). However, among vulnerable populations of PLWH, substantial human rights and structural challenges (disadvantage and injustice that results from everyday practices of a well-intentioned liberal society) must be addressed. These challenges span all ecosocial context levels and in North America (Canada and the United States) can include prosecution for HIV nondisclosure and HIV exposure/transmission. Our aims were to: 1) Determine if there were associations between the social structural factor of criminalization of HIV exposure/transmission, the individual factor of perceived …

Habitual Chocolate Consumption May Increase Body Weight In A Dose-Response Manner, James A. Greenberg, Brian Buijsse

Publications and Research

Objective Habitual chocolate intake was recently found to be associated with lower body weight in three cross-sectional epidemiological studies. Our objective was to assess whether these cross-sectional results hold up in a more rigorous prospective analysis. Methods We used data from the Atherosclerosis Risk in Communities cohort. Usual dietary intake was assessed by questionnaire at baseline (1987–98), and after six years. Participants reported usual chocolate intake as the frequency of eating a 1-oz (∼28 g) serving. Body weight and height were measured at the two visits. Missing data were replaced by multiple imputation. Linear mixed-effects models were used to evaluate …

Exposure To Advertisement Calls Of Reproductive Competitors Activates Vocal-Acoustic And Catecholaminergic Neurons In The Plainfin Midshipman Fish, Porichthys Notatus, Christopher L. Petersen, Miky Timothy, D. Spencer Kim, Ashwin A. Bhandiwad, Robert A. Mohr, Joseph A. Sisneros, Paul M. Forlano

Publications and Research

While the neural circuitry and physiology of the auditory system is well studied among vertebrates, far less is known about how the auditory system interacts with other neural substrates to mediate behavioral responses to social acoustic signals. One species that has been the subject of intensive neuroethological investigation with regard to the production and perception of social acoustic signals is the plainfin midshipman fish, Porichthys notatus, in part because acoustic communication is essential to their reproductive behavior. Nesting male midshipman vocally court females by producing a long duration advertisement call. Females localize males by their advertisement call, spawn and deposit …

Effortless Awareness: Using Real Time Neurofeedback To Investigate Correlates Of Posterior Cingulate Cortex Activity In Meditators' Self-Report, Kathleen A. Garrison, Juan F. Santoyo, Jake H. Davis, Thomas A. Thomhill Iv, Catherine E. Kerr, Judson A. Brewer

Publications and Research

Neurophenomenological studies seek to utilize first-person self-report to elucidate cognitive processes related to physiological data. Grounded theory offers an approach to the qualitative analysis of self-report, whereby theoretical constructs are derived from empirical data. Here we used grounded theory methodology (GTM) to assess how the first-person experience of meditation relates to neural activity in a core region of the default mode network—the posterior cingulate cortex (PCC). We analyzed first-person data consisting of meditators' accounts of their subjective experience during runs of a real time fMRI neurofeedback study of meditation, and third-person data consisting of corresponding feedback graphs of PCC activity …

Functional Connectivity In The First Year Of Life In Infants At-Risk For Autism: A Preliminary Near-Infrared Spectroscopy Study, Brandon Keehn, Jennifer B. Wagner, Helen Tager-Flusberg, Charles A. Nelson

Publications and Research

Background: Autism spectrum disorder (ASD) has been called a “developmental disconnection syndrome,” however the majority of the research examining connectivity in ASD has been conducted exclusively with older children and adults. Yet, prior ASD research suggests that perturbations in neurodevelopmental trajectories begin as early as the first year of life. Prospective longitudinal studies of infants at risk for ASD may provide a window into the emergence of these aberrant patterns of connectivity. The current study employed functional connectivity near-infrared spectroscopy (NIRS) in order to examine the development of intra- and inter-hemispheric functional connectivity in high- and low-risk infants across the …

Gender And Resistance: Afro-Brazilian Women's Anti-Naming As Recovery From Trauma In Conceição Evaristo' "Eu-Mulher" And Ponciá Vicencio, Sarah S. Ohmer

Publications and Research

No abstract provided.

Standards In Research And Academia: The Role Of Standards In Teaching Professional Skills At The City University Of New York, Angelo Lampousis

Publications and Research

Standards Developing Organizations (SDOs) are pairing up with academia to continue to break the barriers to standards education at the undergraduate level. In addition, SDOs are working with the research facilities of academic institutions in a public-private partnership to maintain standards technological relevancy and to find new opportunities to provide standardization to industry and government. This session provides several examples of relationships between SDOs, government, academic institutions, and SES, and describes the advances made from these relationships.

Reflections On The 2013 Gsc-Gsa ‘Roof Of The World’ China Meeting And Chengdu, Nazrul I. Khandaker

Publications and Research

The recently concluded First Joint Scientific Meeting of Geological Society of China (GSC) and Geological Society of America (GSA) proceeded efficiently in the modern setting of the Jinjiang Hotel, Chengdu, Sichuan Province, China. GSA’s International Section played a key role bringing this meeting to the overseas communities. The meeting, titled ‘Roof of the World’, ended on 19^th June, 2013, followed by several field trips that lasted from three to six days. The meeting was designed to promote and bolster the academic communication between the GSC and GSA, and covered a wide range of topics presented through 15 technical sessions …

Tectonosedimentologic Significance Of The Upper Cretaceous Foreland Basin Siliciclastics: Western Interior, Usa, Nazrul I. Khandaker

Publications and Research

The Upper Cretaceous Frontier Formation exposed along the western margin of the western interior foreland basin is composed of clastic sediments that were deposited during the initial late Cretaceous transgressive-regressive phases of the Western Interior Seaway across Wyoming (Figure 1). Current study is aimed at providing attendees with the best practices associated with tectonic, lithofacies and sedimentologic interpretation of foreland basin sequences and emphasizing the need for utilizing field, structural, geochemical, and compositional data for reconstructing a viable scenario connected with foreland basin sedimentary packages. An attempt will be made to compare documented sedimentological findings with foreland basins located in …

The 2012 Economic Burden Of Intimate Partner Violence (Ipv) In Ecuador: Setting The Agenda For Future Research And Violence Prevention Policies, Maria-Isabel Roldos, Phaedra Corso

Publications and Research

Introduction: Intimate partner violence (IPV) is a widespread social structural problem that affects a great proportion of Ecuadorian women. IPV is a sexually, psychologically, or physically coercive act against an adult or adolescent woman by a current or former intimate partner. Not-for-profit groups in Ecuador report that 70% of women experience 1 of the forms of IPV sometime during their lifetime, but population-based surveys suggest that 41% of Ecuadorian women are exposed to emotional violence, 31% physical violence, and 12% sexual violence by their spouse or partner over their lifetime. Despite the high prevalence, the response of the Ecuadorian government …

Remote Sensing Of Soil Moisture In Vineyards Using Airborne And Ground-Based Thermal Inertia Data, Aiman Soliman, Richard J. Heck, Alexander Brenning, Ralph Brown, Stephen Miller

Publications and Research

Thermal remote sensing of soil moisture in vineyards is a challenge. The grass-covered soil, in addition to a standing grape canopy, create complex patterns of heating and cooling and increase the surface temperature variability between vine rows. In this study, we evaluate the strength of relationships between soil moisture, mechanical resistance and thermal inertia calculated from the drop of surface temperature during a clear sky night over a vineyard in the Niagara region. We utilized data from two sensors, an airborne thermal camera (height ≈ 500 m a.g.l.) and a handheld thermal gun (height ≈ 1 m a.g.l.), to explore …

The Discrimination Power Of Structural Superindices, Matthias Dehmer, Abbe Mowshowitz

Publications and Research

In this paper, we evaluate the discrimination power of structural superindices. Superindices for graphs represent measures composed of other structural indices. In particular, we compare the discrimination power of the superindices with those of individual graph descriptors. In addition, we perform a statistical analysis to generalize our findings to large graphs.

What Should Science Reference Librarians Do With Books Classified As Science That Aren't Science: Revisiting The Well-Known Worlds In Collision By Immanuel Velikovsky As A Case Study., Philip Barnett Ph.D.

Publications and Research

Students browsing the science sections in their library may naturally assume that all of the books are scientifically valid and accurate. Science collections may also contain books that may not now be accurate, either because they are out-of-date, or never belonged there. While out-of-date knowledge can sometimes be beneficial, invalid books can only mislead. The well-known book Worlds in Collision by Immanuel Velikovsky is a case study on how librarians can handle such books. For these books, an explanatory note can be placed on the book's online catalog entry or even in the book. The book can also be weeded …

Secondary Organic Aerosols Over Oceans Via Oxidation Of Isoprene And Monoterpenes From Arctic To Antarctic, Qi-Hou Hu, Zhou-Qing Xie, Xin-Ming Wang, Hui Kang, Quan-Fu He, Pengfei Zhang

Publications and Research

Isoprene and monoterpenes are important precursors of secondary organic aerosols (SOA) in continents. However, their contributions to aerosols over oceans are still inconclusive. Here we analyzed SOA tracers from isoprene and monoterpenes in aerosol samples collected over oceans during the Chinese Arctic and Antarctic Research Expeditions. Combined with literature reports elsewhere, we found that the dominant tracers are the oxidation products of isoprene. The concentrations of tracers varied considerably. The mean average values were approximately one order of magnitude higher in the Northern Hemisphere than in the Southern Hemisphere. High values were generally observed in coastal regions. This phenomenon was …

30 Days In The Life: Daily Nutrient Balancing In A Wild Chacma Baboon, Caley A. Johnson, David Raubenheimer, Jessica M. Rothman, David Clarke, Larissa Swedell

Publications and Research

For most animals, the ability to regulate intake of specific nutrients is vital to fitness. Recent studies have demonstrated nutrient regulation in nonhuman primates over periods of one observation day, though studies of humans indicate that such regulation extends to longer time frames. Little is known about longer-term regulation in nonhuman primates, however, due to the challenges of multiple-day focal follows. Here we present the first detailed study of nutrient intake across multiple days in a wild nonhuman primate. We conducted 30 consecutive all day follows on one female chacma baboon (Papio hamadryas ursinus) in the Cape Peninsula of South …

Tethered Domains And Flexible Regions In Trnase Zl, The Long Form Of Trnase Z, Christopher Wilson, Daryl Ramai, Dmitri Serjanov, Neema Lama, Louis Levinger, Emmanuel J. Chang

Publications and Research

tRNase Z, a member of the metallo-β-lactamase family, endonucleolytically removes the pre-tRNA 3′ trailer in a step central to tRNA maturation. The short form (tRNase ZS) is the only one found in bacteria and archaebacteria and is also present in some eukaryotes. The homologous long form (tRNase ZL), exclusively found in eukaryotes, consists of related amino- and carboxy-domains, suggesting that tRNase ZL arose from a tandem duplication of tRNase ZS followed by interdependent divergence of the domains. X-ray crystallographic structures of tRNase ZS reveal a flexible arm (FA) extruded from the body of tRNase Z remote from the active site …

Technique And Considerations In The Use Of 4x1 Ring High-Definition Transcranial Direct Current Stimulation (Hd-Tdcs), Mauricio F. Villamar, Magdalena Sarah Volz, Marom Bikson, Abhishek Datta, Alexandre F. Dasilva, Felipe Fregni

Publications and Research

High-definition transcranial direct current stimulation (HD-tDCS) has recently been developed as a noninvasive brain stimulation approach that increases the accuracy of current delivery to the brain by using arrays of smaller "high-definition" electrodes, instead of the larger pad-electrodes of conventional tDCS. Targeting is achieved by energizing electrodes placed in predetermined configurations. One of these is the 4x1-ring configuration. In this approach, a center ring electrode (anode or cathode) overlying the target cortical region is surrounded by four return electrodes, which help circumscribe the area of stimulation. Delivery of 4x1-ring HD-tDCS is capable of inducing significant neurophysiological and clinical effects in …

Targeting The Endocannabinoid System For Neuroprotection: A 19f-Nmr Study Of A Selective Faah Inhibitor Binding With An Anandamide Carrier Protein, Hsa, Jianqin Zhuang, De-Ping Yang, Xiaoyu Tian, Spyros P. Nikas, Rishi Sharma, Jason Jianxin Guo, Alexandros Makriyannis

Publications and Research

Fatty acid amide hydrolase (FAAH), the enzyme involved in the inactivation of the endocannabinoid anandamide (AEA), is being considered as a therapeutic target for analgesia and neuroprotection. We have developed a brain permeable FAAH inhibitor, AM5206, which has served as a valuable pharmacological tool to explore neuroprotective effects of this class of compounds. In the present work, we characterized the interactions of AM5206 with a representative AEA carrier protein, human serum albumin (HSA), using 19F nuclear magnetic resonance (NMR) spectroscopy. Our data showed that as a drug carrier, albumin can significantly enhance the solubility of AM5206 in aqueous environment. Through …

Long-Term Effects Of Weak Electrical Stimulation On Active Neuronal Networks, Davide Reato, Marom Bikson, Lucas C. Parra

Publications and Research

No abstract provided.

Stochastic Dea With A Perfect Object And Its Application To Analysis Of Environmental Efficiency, Alexander Vaninsky

Publications and Research

The paper introduces stochastic DEA with a Perfect Object (SDEA PO). The Perfect Object (PO) is a virtual Decision Making Unit (DMU) that has the smallest inputs and greatest outputs. Including the PO in a collection of actual objects yields an explicit formula of the efficiency index. Given the distributions of DEA inputs and outputs, this formula allows us to derive the probability distribution of the efficiency score, to find its mathematical expectation, and to deliver common (group–related) and partial (object-related) efficiency components. We apply this approach to a prospective analysis of environmental efficiency of the major national and regional …

Rapid Staining Method To Detect And Identify Downy Mildew (Peronospora Belbahrii) In Basil1, Adolfina R. Koroch, Thomas S. Villani, Robert M. Pyne, James E. Simon

Publications and Research

• Premise of the study: Demand for fresh-market sweet basil continues to increase, but in 2009 a new pathogen emerged, threatening commercial field/greenhouse production and leading to high crop losses. This study describes a simple and effective staining method for rapid microscopic detection of basil downy mildew (Peronospora belbahrii) from leaves of basil (Ocimum basilicum). • Methods and Results: Fresh leaf sections infected with P. belbahrii were placed on a microscope slide, cleared with Visikol™, and stained with iodine solution followed by one drop of 70% sulfuric acid. Cell walls of the pathogen were stained with a distinct coloration, providing …

An Integrative Framework For Bayesian Variable Selection With Informative Priors For Identifying Genes And Pathways, Bin Peng, Dianwen Zhu, Bradley P. Ander, Xiaoshuai Zhang, Fuzhong Xue, Frank R. Sharp, Xiaowei Yang

Publications and Research

The discovery of genetic or genomic markers plays a central role in the development of personalized medicine. A notable challenge exists when dealing with the high dimensionality of the data sets, as thousands of genes or millions of genetic variants are collected on a relatively small number of subjects. Traditional gene-wise selection methods using univariate analyses face difficulty to incorporate correlational, structural, or functional structures amongst the molecular measures. For microarray gene expression data, we first summarize solutions in dealing with ‘large p, small n’ problems, and then propose an integrative Bayesian variable selection (iBVS) framework for simultaneously identifying causal …

Evolution And Allometry Of Calcaneal Elongation In Living And Extinct Primates, Doug M. Boyer, Erik R. Seiffert, Justin T. Gladman, Jonathan I. Bloch

Publications and Research

Specialized acrobatic leaping has been recognized as a key adaptive trait tied to the origin and subsequent radiation of euprimates based on its observed frequency in extant primates and inferred frequency in extinct early euprimates. Hypothesized skeletal correlates include elongated tarsal elements, which would be expected to aid leaping by allowing for increased rates and durations of propulsive acceleration at takeoff. Alternatively, authors of a recent study argued that pronounced distal calcaneal elongation of euprimates (compared to other mammalian taxa) was related primarily to specialized pedal grasping. Testing for correlations between calcaneal elongation and leaping versus grasping is complicated by …

Care In Specialist Medical And Mental Health Unit Compared With Standard Care For Older People With Cognitive Impairment Admitted To General Hospital: Randomised Controlled Trial (Nihr Team Trial), Sarah E. Goldberg, Lucy E. Bradshaw, Fiona C. Kearney, Catherine Russell, Kathy H. Whittamore, Pippa E R Foster, Jil Mamza, John R F Gladman, Rob G. Jones, Sarah A. Lewis, Davina Porock, Rowan H. Harwood

Publications and Research

Objective To develop and evaluate a best practice model of general hospital acute medical care for older people with cognitive impairment.

Design Randomised controlled trial, adapted to take account of constraints imposed by a busy acute medical admission system.

Setting Large acute general hospital in the United Kingdom.

Participants 600 patients aged over 65 admitted for acute medical care, identified as “confused” on admission.

Interventions Participants were randomised to a specialist medical and mental health unit, designed to deliver best practice care for people with delirium or dementia, or to standard care (acute geriatric or general medical wards). Features of …

Neurophysiological Processing Of Emotion And Parenting Interact To Predict Inhibited Behavior: An Affective-Motivational Framework, Ellen M. Kessel, Rebecca F. Huselid, Jennifer M. Decicco, Tracy A. Dennis

Publications and Research

Although inhibited behavior problems are prevalent in childhood, relatively little is known about the intrinsic and extrinsic factors that predict a child's ability to regulate inhibited behavior during fear- and anxiety-provoking tasks. Inhibited behavior may be linked to both disruptions in avoidance-related processing of aversive stimuli and in approach-related processing of appetitive stimuli, but previous findings are contradictory and rarely integrate consideration of the socialization context. The current exploratory study used a novel combination of neurophysiological and observation-based methods to examine whether a neurophysiological measure sensitive to approach- and avoidance-oriented emotional processing, the late positive potential (LPP), interacted with observed …

The Association Between A Medical History Of Depression And Gestational Diabetes In A Large Multi-Ethnic Cohort In The United States, Katherine Bowers, S. Katherine Laughon, Sungduk Kim, Sunni L. Mumford, Jennifer Brite, Michele Kiely, Cuilin Zhang

Publications and Research

Background: Both major depression and gestational diabetes mellitus (GDM) are prevalent among women of reproductive age. Our objective was to determine whether a medical history of depression is related to subsequent development of GDM.

Methods: The Consortium on Safe Labor was a US retrospective cohort study of 228 562 births between 2002 and 2008. Exclusion criteria for the present analysis included multiple gestation pregnancies (n = 5059), pre-existing diabetes (n = 12 771), deliveries(n = 395), site GDM prevalence (

Results: The final analytic population included 121 260 women contributing 128 295 pregnancies, of which 5606 were affected by GDM. …

A Randomized Clinical Trial Of Trans-Dermal Nicotine Replacement In Pregnant African-American Smokers, Ayman El-Mohandes, Richard Windsor, Sylvia Tan, David C. Perry, Marie G. Gantz, Michele Kiely

Publications and Research

We compared acceptability, adherence and efficacy of trans-dermal nicotine patches and cognitive behavioral therapy (Group 1) to cognitive behavioral therapy alone (Group 2) in minority pregnant smokers. This is a randomized controlled trial. 52 women were recruited during pregnancy with a mean gestational age 18.5 ± 5.0 weeks and followed through delivery. Randomization was by site and initial cotinine levels. Interventionists and interviewers were blinded to group assignment. Two different nicotine replacement therapy dosing regiments were administered according to the baseline salivary cotinine level. A process evaluation model summarized patient adherence. The main outcome measure was self-report of cessation since …