Digital Commons Network^™

A Note On Graphs With Prescribed Orbit Structure, Abbe Mowshowitz, Matthias Dehmer, Frank Emmert-Streib

Publications and Research

No abstract provided.

Hiv Prevention Via Mobile Messaging For Men Who Have Sex With Men (M-Cubed): Protocol For A Randomized Controlled Trial, Patrick Sean Sullivan, Ryan J. Zahn, Sarah Wiatrek, Cristian J. Chandler, Sabina Hirshfield, Rob Stephenson, Jose A. Bauermeister, Mary Ann Chiasson, Martin J. Downing, Deborah J. Gelaude, Aaron J. Siegler, Keith Horvath, Erin Rogers, Ana Alas, Evelyn J. Olansky, Heather Saul, Eli S. Rosenberg, Gordon Mansergh

Publications and Research

Background:

Men who have sex with men (MSM) continue to be the predominately impacted risk group in the United States HIV epidemic and are a priority group for risk reduction in national strategic goals for HIV prevention. Modeling studies have demonstrated that a comprehensive package of status-tailored HIV prevention and care interventions have the potential to substantially reduce new infections among MSM. However, uptake of basic prevention services, including HIV testing, sexually transmitted infection (STI) testing, condom distribution, condom-compatible lubricant distribution, and preexposure prophylaxis (PrEP), is suboptimal. Further, stronger public health strategies are needed to promote engagement in HIV care …

Residential Household Yard Care Practices Along Urban-Exurban Gradients In Six Climatically-Diverse U.S. Metropolitan Areas, Dexter H. Locke, Colin Polsky, J. Morgan Grove, Peter M. Groffman, Kristen C. Nelson, Kelli L. Larson, Jeannine Cavender-Bares, James B. Heffernan, Rinku Roy Chowdhury, Sarah E. Hobbie, Neil D. Bettez, Sharon J. Hall, Christopher Neill, Laura Ogden, Jarlath O'Neil-Dunne

Publications and Research

Residential land is expanding in the United States, and lawn now covers more area than the country’s leading irrigated crop by area. Given that lawns are widespread across diverse climatic regions and there is rising concern about the environmental impacts associated with their management, there is a clear need to understand the geographic variation, drivers, and outcomes of common yard care practices. We hypothesized that 1) income, age, and the number of neighbors known by name will be positively associated with the odds of having irrigated, fertilized, or applied pesticides in the last year, 2) irrigation, fertilization, and pesticide application …

Scythes, Sickles And Other Blades: Defining The Diversity Of Pectoral Fin Morphotypes In Pachycormiformes, Jeff J. Liston, Anthony E. Maltese, Paul H. Lambers, Dominique Delsate, William E.H. Harcourt-Smith, Anneke H. Van Heteren

Publications and Research

The traditional terminology of ‘scythe’ or ‘sickle’ shaped is observed to be flawed as an effective descriptor for pectoral fin shape in pachycormids. The diversity of pachycormid pectoral fin shapes is assessed across the 14 recognised genera that preserve complete pectoral fins, and improved terms are defined to more effectively describe their form, supported by anatomical observation and aspect ratio analysis of individual fins, and corroborated by landmark analysis. Three clear and distinct pectoral fin structural morphotypes emerge (falceform, gladiform, falcataform), reflecting a diversity of pachycormid lifestyles throughout the Mesozoic, from agile pursuit predator to slow-cruising suspension feeder.

“We Cannot Imagine”: Us Preservice Teachers’ Othering Of Trans And Gender Creative Student Experiences, Elizabeth E. Blair, Sherry L. Deckman

Publications and Research

Research suggests that teachers are not meeting the needs of trans and gender creative students. Thus, we ask: How do US preservice teachers (PSTs) discursively construct the experiences of trans and gender creative students? How are these constructions informed by and reinscribe broader gender normativities in educational contexts? We analyzed 549 PST authored, online discussion posts from an educational foundations course, finding PSTs lacked familiarity with and engaged in rhetorical distancing from trans and gender creative student experiences suggesting barriers to empathy that may obstruct teacher-student relationships and promotion of equity, which teacher education is called to address.

Hyperpolarized Relaxometry Based Nuclear T1 Noise Spectroscopy In Diamond, A. Ajoy, B. Safvati, R. Nazaryan, J. T. Oon, B. Han, P. Raghavan, R. Nirodi, A. Aguilar, K. Liu, X. Cai, X. Lv, E. Druga, C. Ramanathan, J. A. Reimer, C. A. Meriles, D. Suter, A. Pines

Publications and Research

The origins of spin lifetimes in quantum systems is a matter of importance in several areas of quantum information. Spectrally mapping spin relaxation processes provides insight into their origin and motivates methods to mitigate them. In this paper, we map nuclear relaxation in a prototypical system of ¹³C nuclei in diamond coupled to Nitrogen Vacancy (NV) centers over a wide field range (1 mT-7 T). Nuclear hyperpolarization through optically pumped NV electrons allows signal measurement savings exceeding million-fold over conventional methods. Through a systematic study with varying substitutional electron (P1 center) and ¹³C concentrations, we identify the operational …

Rasp 4: Ancestral State Reconstruction Tool For Multiple Genes And Characters, Yan Yu, Christopher Blair, Xingjin He

Publications and Research

With the continual progress of sequencing techniques, genome-scale data are increasingly used in phylogenetic studies. With more data from throughout the genome, the relationship between genes and different kinds of characters is receiving more attention. Here, we present version 4 of RASP, a software to reconstruct ancestral states through phylogenetic trees. RASP can apply generalized statistical ancestral reconstruction methods to phylogenies, explore the phylogenetic signal of characters to particular trees, calculate distances between trees, and cluster trees into groups. RASP 4 has an improved graphic user interface and is freely available from http://mnh.scu.edu.cn/soft/blog/RASP (program) and https://github.com/sculab/RASP (source code).

How To Create And Maintain An Effective Information Architecture And Navigation System For Science Gateway Websites, Noreen Y. Whysel, Omni Marketing Interactive

Publications and Research

Whether you have an existing Science Gateway website or are creating your first one, this hands-on tutorial will show you, step by step, how to create and update gateway websites so that their content is easier to find and easier to use.

As a Science Gateway provides its web-based tools and resources, it is essential that these sites utilize specific usability tests and other research methods to ensure positive and productive experiences with the sites. Successful information architecture (IA), intuitive site navigation, and clear user interfaces (UIs) all rely on knowing where various users expect to find needed information.

Since …

The Concurrent Decline Of Soil Lead And Children’S Blood Lead In New Orleans, Howard W. Mielke, Christopher R. Gonzales, Eric T. Powell, Mark A. S. Laidlow, Kenneth J. Berry, Paul W. Mielke Jr., Sara Perl Egendorf

Publications and Research

Lead (Pb) is extremely toxic and a major cause of chronic diseases worldwide. Pb is associated with health disparities, particularly within low-income populations. In biological systems, Pb mimics calcium and, among other effects, interrupts cell signaling. Furthermore, Pb exposure results in epigenetic changes that affect multigenerational gene expression. Exposure to Pb has decreased through primary prevention, including removal of Pb solder from canned food, regulating lead-based paint, and especially eliminating Pb additives in gasoline. While researchers observe a continuous decline in children’s blood lead (BPb), reservoirs of exposure persist in topsoil, which stores the legacy dust from leaded gasoline and …

Venom Diversity And Evolution In The Most Divergent Cone Snail Genus Profundiconus, Guilia Fassio, Maria Vittoria Modica, Lou Mary, Paul Zaharias, Alexander E. Fedosov, Juliette Gorson, Yuri I. Kantor, Mandë E. Holford, Nicolas Puillandre

Publications and Research

Profundiconus is the most divergent cone snail genus and its unique phylogenetic position, sister to the rest of the family Conidae, makes it a key taxon for examining venom evolution and diversity. Venom gland and foot transcriptomes of Profundiconus cf. vaubani and Profundiconus neocaledonicus were de novo assembled, annotated, and analyzed for differential expression. One hundred and thirty-seven venom components were identified from P. cf. vaubani and 82 from P. neocaledonicus, with only four shared by both species. The majority of the transcript diversity was composed of putative peptides, including conotoxins, profunditoxins, turripeptides, insulin, and prohormone-4. However, there were also …

From The Human To The Planetary: Speculative Futures Of Care, Miriam Ticktin

Publications and Research

This is largely a theoretical, speculative essay that takes on the question of what ‘care’ looks like at a moment when climate change is increasingly taking center stage in public and political discussions. Starting with two new practices, namely, humanitarian care for nonhumans and One Health collaborations, I seek to determine what forms of political care can incorporate the well-being of future generations and future iterations of the earth. After an exploration of One Health as an approach to planetary care, I ask what its parts enable us to think, despite its limitations; I focus on the new human-nonhuman assemblages …

The United Nations Declaration On The Rights Of Peasants And Other People Working In Rural Areas, Marc Edelman, Priscilla Claeys

Publications and Research

In December 2018, the United Nations adopted the Declaration on the Rights of Peasants and Other People Working in Rural Areas. UNDROP is the product of 17 years of struggle by La Via Campesina, other transnational agrarian movements and allies that included NGOs, states, UN mandate holders, and academics. It recognises the dignity of rural populations, their contributions to global food production, and their ‘special relationship’ to land, water and nature, as well as their vulnerabilities to eviction, hazardous working conditions and political repression. It reiterates rights protected in other instruments and sets new standards for individual and collective rights …

Invertebrate Retinal Progenitors As Regenerative Models In A Microfluidic System, Caroline D. Pena, Stephanie Zhang, Robert Majeska, Tadmiri Venkatesh, Maribel Vazquez

Publications and Research

Regenerative retinal therapies have introduced progenitor cells to replace dysfunctional or injured neurons and regain visual function. While contemporary cell replacement therapies have delivered retinal progenitor cells (RPCs) within customized biomaterials to promote viability and enable transplantation, outcomes have been severely limited by the misdirected and/or insuffcient migration of transplanted cells. RPCs must achieve appropriate spatial and functional positioning in host retina, collectively, to restore vision, whereas movement of clustered cells differs substantially from the single cell migration studied in classical chemotaxis models. Defining how RPCs interact with each other, neighboring cell types and surrounding extracellular matrixes are critical to …

Specific Effects Of Antitumor Active Norspermidine On The Structure And Function Of Dna, Takashi Nishio, Yuko Yoshikawa, Chwen-Yang Shew, Naoki Umezawa, Tsunehiko Higuchi, Kenichi Yoshikawa

Publications and Research

We compared the effects of trivalent polyamines, spermidine (SPD) and norspermidine (NSPD), a chemical homologue of SPD, on the structure of DNA and gene expression. The chemical structures of SPD and NSPD are different only with the number of methylene groups between amine groups,[N-3-N-4-N] and [N-3-N-3-N], respectively. SPD plays vital roles in cell function and survival, including in mammals. On the other hand, NSPD has antitumor activity and is found in some species of plants, bacteria and algae, but not in humans. We found that both polyamines exhibit biphasic effect; enhancement and inhibition on in vitro gene expression, where SPD …

Treatment Patterns And Economic Burden Of Sickle-Cell Disease Patients Prescribed Hydroxyurea: A Retrospective Claims-Based Study, Nirmish Shah, Menaka Bhor, Lin Xie, Rashid Halloway, Steve Arcona, Jincy Paulose, Huseyin Yuce

Publications and Research

Background: This study aimed to evaluate sickle-cell disease (SCD) treatment patterns and economic burden among patients prescribed hydroxyurea (HU) in the US, through claims data.

Methods: SCD patients with pharmacy claims for HU were selected from the Medicaid Analytic Extracts (MAX) from January 1, 2009 - December 31, 2013. The first HU prescription during the identification period was defined as the index date and patients were required to have had continuous medical and pharmacy benefits for ≥6 months baseline and 12 months follow-up periods. Patient demographics, clinical characteristics, treatment patterns, health care utilization, and costs were examined, and variables were …

Nuclear Tau, P53 And Pin1 Regulate Parn-Mediated Deadenylation And Gene Expression, Jorge Baquero, Sophia Varriano, Martha Ordonez, Pawel Kuczaj, Michael R. Murphy, Gamage Aruggoda, Devon Lundine, Viktoriya Morozova, Ali Elhadi Makki, Alejandra Del C. Alonso, Frida E. Kleiman

Publications and Research

While nuclear tau plays a role in DNA damage response (DDR) and chromosome relaxation, the mechanisms behind these functions are not fully understood. Here, we show that tau forms complex(es) with factors involved in nuclear mRNA processing such as tumor suppressor p53 and poly(A)-specific ribonuclease (PARN) deadenylase. Tau induces PARN activity in different cellular models during DDR, and this activation is further increased by p53 and inhibited by tau phosphorylation at residues implicated in neurological disorders. Tau’s binding factor Pin1, a mitotic regulator overexpressed in cancer and depleted in Alzheimer’s disease (AD), also plays a role in the activation of …

Spatial Upscaling Of Forest Response To Drought, Wei Fang, Peipei Xu, Tao Zhao, Xiang Zhao, Hui Luo, George Hendrey, Chuixiang Yi

Publications and Research

We have integrated the observational capability of satellite remote sensing with plot-scale tree ring data to up-scale the evaluation of forest responses to drought. Satellite data, such as Normalized Difference Vegetation Index (NDVI), can provide a spatially continuous measure with limited temporal coverage, while tree Ring Width Index (RWI) provides accurate assessment with much longer time series local scales. Here, we explored the relationship between RWI and NDVI of three dominant species in the Southwestern United States (SWUS), and predicted RWI spatial distribution from 2001 to 2017 based on MODIS 1-km resolution NDVI data with stringent quality control. We detected …

An Amyloid Core Sequence In The Major Candida Albicans Adhesin Als1p Mediates Cell-Cell Adhesion, Vida Ho, Philippe Herman-Bausier, Christopher Shaw, Karen A. Conrad, Melissa C. Garcia-Sherman, Jeremy Draghi, Yves F. Dufrene, Peter N. Lipke, Jason M. Rauceo

Publications and Research

ABSTRACT The human fungal commensal Candida albicans can become a serious opportunistic pathogen in immunocompromised hosts. The C. albicans cell adhesion protein Als1p is a highly expressed member of a large family of paralogous adhesins. Als1p can mediate binding to epithelial and endothelial cells, is upregulated in infections, and is important for biofilm formation. Als1p includes an amyloidforming sequence at amino acids 325 to 331, identical to the sequence in the paralogs Als5p and Als3p. Therefore, we mutated Val326 to test whether this sequence is important for activity. Wild-type Als1p (Als1pWT) and Als1p with the V326N mutation (Als1pV326N) were expressed …

Cytotoxic Xanthones From Hypericum Stellatum, An Ethnomedicine In Southwest China, Yuanyuan Ji, Ruifei Zhang, Chen Zhang, Xingyu Li, Adam Negrin, Chaonan Yuan, Edward J. Kennelly, Chunlin Long

Publications and Research

Hypericum stellatum, a species endemic to China, is used to treat hepatitis by several ethnic groups in Guizhou Province. This research was inspired by the traditional medicinal usage of H. stellatum, and aims to explore the phytochemistry and bioactivity of H. stellatum to explain why local people in Guizhou widely apply H. stellatum for liver protection. In this study, two new prenylated xanthones, hypxanthones A (8) and B (9), together with seven known compounds, were isolated from the aerial parts of the plant. Spectroscopic data as well as experimental and calculated ECD spectra were used to establish the structures of …

Medical Dental Device: Biogeneric Implant Prototype, Ibeth Erazo, Aneeza Hussain, Renata Budny, Gaffar Gailani

Publications and Research

Teeth are lost due to tooth decay, injury, disease, or other causes. Today, dental implants extend the range of care to a variety of patients undergoing necessary prosthodontic rehabilitation. If the benefits of such treatments are to be maximized, then implants must be selected on logical basis and placed within the context of the full range of treatment modalities. However, modern dental implant systems are based on multiple components often leading to micro-movements which cause stress on the bone or bacterial infections, both of which compromise the success of osseointegration and consequently jeopardize the whole implant adaptation. Thus, a new …

Create A Revolution In Undergraduates' Understanding Of Science: Teach Through Close Analysis Of Scientific Literature, Sally G. Hoskins

Publications and Research

The teaching of science to undergraduates aligns poorly with the practice of science, leading many students to conclude that research is boring and researchers themselves are antisocial geniuses. Creativity, a key driver of scientific progress, is underemphasized or ignored altogether in many classrooms, as teaching focuses on the complex integrated concepts and voluminous amounts of information typical of STEM curricula. Faculty, largely untrained in science education per se, teach largely as they were taught, through lectures based in textbooks. This situation could change, and students' understanding of research practice could be fostered relatively easily, if faculty began teaching classes focused …

Temporal Changes In Abundance–Occupancy Relationships Over 40 Years, Lisa L. Manne, Richard R. Veit

Publications and Research

1. Abundance–occupancy (A–O) relationships are widely documented for many organismal groups and regions, and have been used to gain an understanding of regional population and community trends. Monitoring changes in abundance and occupancy over time may be what is required to document changes in conservation status and needs for some species, communities, or areas.
2. We hypothesize that if there is a higher proportion of declining species in one group of species compared with another (e.g., migratory species vs. permanent residents), then a consequence of that difference will be vastly different abundance–occupancy relationships. If this difference persists through time, then the resulting …

Inclusion Of Enclosed Hydration Effects In The Binding Free Energy Estimation Of Dopamine D3 Receptor Complexes, Rajat Kumar Pal, Satishkumar Gadhiya, Steven Ramsey, Pierpaolo Cordone, Lauren Wickstrom, Wayne W. Harding, Tom Kurtzman, Emilio Gallicchio

Publications and Research

Confined hydration and conformational flexibility are some of the challenges encountered for the rational design of selective antagonists of G-protein coupled receptors.We present a set of C3-substituted (-) -stepholidine derivatives as potent binders of the dopamine D3 receptor.The compounds are characterized biochemically, as well as by computer modeling using a novel molecular dynamics-based alchemical binding free energy approach which incorporates the effect of the displacement of enclosed water molecules from the binding site.The free energy of displacement of specific hydration sites is obtained using the Hydration Site Analysis method with explicit solvation. This work underscores the critical role of confined …

Stretchable Piezoelectric Power Generators Based On Zno Thin Films On Elastic Substrates, Ioana Voiculescu, Fang Li, Glen Kowach, Nicolas Mistou, Russell Kastberg

Publications and Research

The paper describes a stretchable, microfabricated power generator that will be attached on the skin and will produce energy based on the movements of the human body. The device was fabricated on a polymeric, elastomeric, poly(dimethylsiloxane) (PDMS) sheet. It consists of a piezoelectric thin film of ZnO sandwiched between two stretchable gold electrodes. An innovative technique was used for the deposition of ZnO thin film on the gold electrode-coated polymeric substrate at low temperatures below 150C. This is the first attempt to use a uniform film of ZnO, for energy harvesting. The ZnO film had the thickness at the submicron …

Bright Green Biofluorescence In Sharks Derives From Bromo-Kynurenine Metabolism, Hyun Bong Park, Yick Chong Lam, Jean P. Gaffney, James C. Weaver, Sara Rose Krivoshik, Randy Hamchand, Vincent Pieribone, David F. Gruber, Jason M. Crawford

Publications and Research

Although in recent years there has been an increased awareness of the widespread nature of biofluorescence in the marine environment, the diversity of the molecules responsible for this luminescent phenotype has been mostly limited to green fluorescent proteins (GFPs), GFP-like proteins, and fluorescent fatty acid-binding proteins (FABPs). In the present study, we describe a previously undescribed group of brominated tryptophan-kynurenine small molecule metabolites responsible for the green biofluorescence in two species of sharks and provide their structural, antimicrobial, and spectral characterization. Multi-scale fluorescence microscopy studies guided the discovery of metabolites that were differentially produced in fluorescent versus non-fluorescent skin, as …

Repeated Transspinal Stimulation Decreases Soleus H-Reflex Excitability And Restores Spinal Inhibition In Human Spinal Cord Injury, Maria Knikou, Lynda M. Murray

Publications and Research

Transcutaneous spinal cord or transspinal stimulation over the thoracolumbar enlargement, the spinal location of motoneurons innervating leg muscles, modulates neural circuits engaged in the control of movement. The extent to which daily sessions (e.g. repeated) of transspinal stimulation affects soleus H-reflex excitability in individuals with chronic spinal cord injury (SCI) remains largely unknown. In this study, we established the effects of repeated cathodal transspinal stimulation on soleus H-reflex excitability and spinal inhibition in individuals with and without chronic SCI. Ten SCI and 10 healthy control subjects received monophasic transspinal stimuli of 1-ms duration at 0.2 Hz at subthreshold and suprathreshold …

The Huntingtin Inclusion Is A Dynamic Phase-Separated Compartment, Fahmida Aktar, Chakkapong Burudpakdee, Mercedes Polanco, Sen Pei, Theresa C. Swayne, Peter N. Lipke, Lesley Emtage

Publications and Research

Inclusions of disordered protein are a characteristic feature of most neurodegenerative diseases, including Huntington’s disease. Huntington’s disease is caused by expansion of a polyglutamine tract in the huntingtin protein; mutant huntingtin protein (mHtt) is unstable and accumulates in large intracellular inclusions both in affected individuals and when expressed in eukaryotic cells. Using mHtt-GFP expressed in Saccharomyces cerevisiae, we find that mHtt-GFP inclusions are dynamic, mobile, gel-like structures that concentrate mHtt together with the disaggregase Hsp104. Although inclusions may associate with the vacuolar membrane, the association is reversible and we find that inclusions of mHtt in S. cerevisiae are not taken …

Integrating Ligand-Receptor Interactions And In Vitro Evolution For Streamlined Discovery Of Artificial Nucleic Acid Ligands, Hasan E. Zumrut, Sana Batool, Kimon V. Argyropoulos, Nicole Williams, Roksana Azad, Prabodhika R. Mallikaratchy

Publications and Research

To discover DNA ligands against a predetermined receptor protein complex, we introduce a comprehensive version of ligand-guided selection (LIGS). LIGS is, itself, a variant of systematic evolution of ligands by exponential enrichment (SELEX). Herein, we have optimized LIGS to identify higher affinity aptamers with high specificity. In addition, we demonstrate the expandability of LIGS by performing specific aptamer elution at 25C, utilizing multiple monoclonal antibodies (mAbs) against cultured cells and primary cells obtained from human donors expressing the same receptor. Eluted LIGS libraries obtained through Illumina high-throughput (HT) DNA sequencing were analyzed by bioinformatics tools to discover five DNA aptamers …

Normal And Pathological Tau Uptake Mediated By M1/M3 Muscarinic Receptors Promotes Opposite Neuronal Changes, Viktoriya Morozova, Leah S. Cohen, Ali El-Hadi Makki, Alison Shur, Guillermo Pilar, Abdeslem El Idrissi, Alejandra D. Alonso

Publications and Research

The microtubule associated protein tau is mainly found in the cell’s cytosol but recently it was also shown in the extracellular space. In neurodegenerative diseases, like Alzheimer’s disease (AD), pathological tau spreads from neuron to neuron enhancing neurodegeneration. Here, we show that HEK293 cells and neurons in culture uptake extracellular normal and pathological Tau. Muscarinic receptor antagonists atropine and pirenzepine block 80% this uptake. CHO cells do not express these receptors therefore cannot uptake tau, unless transfected with M1 and/or M3 receptor. These results strongly suggest that muscarinic receptors mediate this process. Uptake of normal tau in neurons enhances neuronal …

Contemporary Stories Of Female Development And The Outer Limits Of Maternal Sexuality In Susan Choi’S My Education And Amy Sohn’S Prospect Park West, Christa Baiada

Publications and Research

While liberal sexuality has been integrated into contemporary discursive understandings of female possibilities, barriers remain to representing mothers as sexual beings. This essay explores maternal representations in Choi’s My Education (2013) and Sohn’s Prospect Park West (2009) that challenge cultural ideals of good motherhood and invite scrutiny of normative paths and goals of female development. These 21^st-century American novels confront and even embrace active maternal sexuality but retreat at the boundary of the maternal/sexual breast to allow protagonists in contemporary alterations of female stories of development to achieve maturity through acceptance of the ideal of good motherhood .Each …